[ { "distances": [], "labels": [ { "i_atom": 1240, "text": "heme" } ], "user_id": "117908387177518174476", "version": 2, "show": { "peptide": true, "trace": false, "sidechain": false, "all_atom": false, "water": false, "sphere": false, "ligands": true, "hydrogen": false, "transparent": false, "ribbon": true }, "lock": true, "view_id": "view:z5dpfp", "selected": [], "camera": { "up": [ 16.65189795504742, 30.401206876192365, 0.706173197073111 ], "slab": { "z_front": -23.523016759776546, "z_back": 27.396983240223452, "zoom": 32.406336890588385 }, "pos": [ 16.729999999994085, 30.480000000003347, 1.6999999999996858 ], "in": [ 16.335088270340503, 29.567119397741568, 1.803410501382209 ] }, "pdb_id": "1mbo", "selected_traces": [], "grid": { "bCutoff": null, "isElem": {} }, "i_atom": 1236, "text": "This cavity is designed to bind a heme molecule.", "creator": "other", "order": 12 }, { "distances": [], "labels": [ { "i_atom": 153, "text": "kink in alpha-helix" } ], "user_id": "117908387177518174476", "version": 2, "show": { "peptide": true, "trace": false, "sidechain": false, "all_atom": false, "water": false, "sphere": false, "ligands": false, "hydrogen": false, "transparent": false, "ribbon": true }, "lock": true, "view_id": "view:cc8izq", "selected": [], "camera": { "up": [ 25.38460083250035, 21.24022005054768, 9.314346199129451 ], "slab": { "z_front": -2, "z_back": 12.23039246467818, "zoom": 69.28452731387182 }, "pos": [ 26.259999999998318, 21.37000000000411, 9.7799999999976 ], "in": [ 26.442510387563498, 20.389275062291787, 9.710224968790408 ] }, "pdb_id": "1mbo", "selected_traces": [], "grid": { "bCutoff": null, "isElem": {} }, "i_atom": 166, "text": "The first alpha-helix is long with a large kink in the helix.", "creator": "other", "order": 19 }, { "distances": [], "labels": [], "user_id": null, "version": 2, "show": { "peptide": true, "trace": true, "sidechain": false, "all_atom": false, "water": false, "sphere": false, "ligands": true, "hydrogen": false, "transparent": false, "ribbon": true }, "lock": false, "view_id": "view:inbcuc", "selected": [], "camera": { "up": [ 15.962254052400253, 20.260144123030614, 4.095847362625918 ], "slab": { "z_front": -25.459999084472656, "z_back": 25.459999084472656, "zoom": 89.1099967956539 }, "pos": [ 15.513836110654749, 20.896995673697237, 4.723016759148301 ], "in": [ 16.236137412234207, 20.741870299749216, 5.396972950672725 ] }, "pdb_id": "1mbo", "selected_traces": [], "grid": { "isChanged": false, "bCutoff": 0.5, "isElem": {} }, "i_atom": -1, "text": "The structure of the myogolbin provides a a cavity in the middle of the protein.", "creator": "public", "order": 13 }, { "distances": [], "labels": [], "user_id": null, "version": 2, "show": { "peptide": true, "trace": true, "sidechain": false, "all_atom": false, "water": false, "sphere": false, "ligands": true, "hydrogen": false, "transparent": false, "ribbon": true }, "lock": false, "view_id": "view:v9d8nz", "selected": [], "camera": { "up": [ 15.513836110654749, 19.896995673697237, 4.723016759148301 ], "slab": { "z_front": -25.459999084472656, "z_back": 25.459999084472656, "zoom": 87.01813983913033 }, "pos": [ 15.513836110654749, 20.896995673697237, 4.723016759148301 ], "in": [ 15.513836110654749, 20.896995673697237, 5.723016759148301 ] }, "pdb_id": "1mbo", "selected_traces": [], "grid": { "isChanged": false, "bCutoff": 0.5, "isElem": {} }, "i_atom": -1, "text": "Myoglobin is a long single chain polymer of amino acids that fold up into five a-helices", "creator": "public", "order": 10 }, { "distances": [], "labels": [], "user_id": "117645193347562248846", "version": 2, "show": { "peptide": true, "trace": true, "sidechain": false, "all_atom": false, "water": false, "sphere": false, "ligands": true, "hydrogen": false, "transparent": false, "ribbon": true }, "lock": true, "view_id": "view:ovy4hn", "selected": [], "camera": { "up": [ 15.513836110654749, 19.896995673697237, 4.723016759148301 ], "slab": { "z_front": -25.459999084472656, "z_back": 25.459999084472656, "zoom": 89.1099967956543 }, "pos": [ 15.513836110654749, 20.896995673697237, 4.723016759148301 ], "in": [ 15.513836110654749, 20.896995673697237, 5.723016759148301 ] }, "pdb_id": "1mbo", "selected_traces": [], "grid": { "isChanged": false, "bCutoff": 0.5, "isElem": {} }, "i_atom": -1, "text": "Click edit to change this text.", "creator": "other", "order": 8 }, { "distances": [], "labels": [ { "i_atom": 1233, "text": "heme" } ], "user_id": null, "version": 2, "show": { "peptide": true, "trace": false, "sidechain": false, "all_atom": false, "water": false, "sphere": false, "ligands": true, "hydrogen": false, "transparent": false, "ribbon": true }, "lock": false, "view_id": "view:ivn7z4", "selected": [], "camera": { "up": [ 15.406719302241672, 27.861180022537074, -0.43495141509887425 ], "slab": { "z_front": -2.3794392523364434, "z_back": 13.627697536108753, "zoom": 73.21182399733594 }, "pos": [ 15.360000000002508, 27.949999999999722, 0.5599999999972702 ], "in": [ 14.41946231879145, 28.281583486049204, 0.48623508963063167 ] }, "pdb_id": "1mbo", "selected_traces": [], "grid": { "bCutoff": null, "isElem": {} }, "i_atom": 1274, "text": "Click edit to change this text.", "creator": "public", "order": 23 }, { "distances": [], "labels": [], "user_id": null, "version": 2, "show": { "peptide": true, "trace": true, "sidechain": false, "all_atom": false, "water": false, "sphere": false, "ligands": true, "hydrogen": false, "transparent": false, "ribbon": true }, "lock": false, "view_id": "view:2r19rc", "selected": [], "camera": { "up": [ 15.513836110654749, 19.896995673697237, 4.723016759148301 ], "slab": { "z_front": -25.459999084472656, "z_back": 25.459999084472656, "zoom": 55.73680653492341 }, "pos": [ 15.513836110654749, 20.896995673697237, 4.723016759148301 ], "in": [ 15.513836110654749, 20.896995673697237, 5.723016759148301 ] }, "pdb_id": "1mbo", "selected_traces": [], "grid": { "isChanged": false, "bCutoff": 0.5, "isElem": {} }, "i_atom": -1, "text": "Click edit to change this text.", "creator": "public", "order": 24 }, { "distances": [], "labels": [ { "i_atom": 1, "text": "N-terminal" }, { "i_atom": 1223, "text": "C-terminal" } ], "user_id": "117908387177518174476", "version": 2, "show": { "peptide": true, "trace": false, "sidechain": false, "all_atom": false, "water": false, "sphere": false, "ligands": false, "hydrogen": false, "transparent": false, "ribbon": true }, "lock": true, "view_id": "view:eagu1g", "selected": [], "camera": { "up": [ 14.761473352983558, 12.95507735443775, 0.19369917775702478 ], "slab": { "z_front": -23.523016759776546, "z_back": 27.396983240223452, "zoom": 120.35486387217624 }, "pos": [ 13.860000000000673, 13.029999999999806, 0.619999999998524 ], "in": [ 14.144988425426066, 13.874028586744313, 1.0743097424998547 ] }, "pdb_id": "1mbo", "selected_traces": [], "grid": { "bCutoff": null, "isElem": {} }, "i_atom": 873, "text": "Myoglobin is a long single chain polymer of amino-acids that folds up into five α-helices.", "creator": "other", "order": 9 }, { "distances": [], "labels": [ { "i_atom": 1274, "text": "Iron atom" }, { "i_atom": 1275, "text": "O1 of oxygen molecule" }, { "i_atom": 1276, "text": "O2 of oxygen molecule" } ], "user_id": "117908387177518174476", "version": 2, "show": { "peptide": true, "trace": false, "sidechain": false, "all_atom": false, "water": false, "sphere": false, "ligands": true, "hydrogen": false, "transparent": false, "ribbon": true }, "lock": true, "view_id": "view:l74skx", "selected": [], "camera": { "up": [ 16.824599703395478, 27.080705061072702, -0.27762624816544346 ], "slab": { "z_front": -2, "z_back": 5.58086661002549, "zoom": 14.86804454178133 }, "pos": [ 17.050000000004935, 27.259999999998165, 0.6799999999940791 ], "in": [ 16.15280442554322, 26.915043079460567, 0.9557622601739835 ] }, "pdb_id": "1mbo", "selected_traces": [], "grid": { "bCutoff": null, "isElem": {} }, "i_atom": 1275, "text": "The iron atom, in turn, has a high affinity for oxygen molecules.", "creator": "other", "order": 18 }, { "lock": false, "distances": [], "selected": [], "user_id": null, "version": 2, "creator": "public", "text": "STRUCTURE AND REFINEMENT OF OXYMYOGLOBIN AT 1.6 ANGSTROMS RESOLUTION ", "view_id": "view:000000", "labels": [], "pdb_id": "1mbo", "camera": { "up": [ 15.359999656677246, 26.950000762939453, 0.5600000023841858 ], "slab": { "z_front": -25.46, "z_back": 25.46, "zoom": 50.92 }, "pos": [ 15.359999656677246, 27.950000762939453, 0.5600000023841858 ], "in": [ 15.359999656677246, 27.950000762939453, 1.5600000023841858 ] }, "i_atom": 1274, "show": { "peptide": true, "trace": false, "sidechain": false, "all_atom": false, "water": false, "hydrogen": false, "ligands": true, "ribbon": true }, "res_id": "A:155", "order": 1 }, { "distances": [], "labels": [], "user_id": "117908387177518174476", "version": 2, "show": { "peptide": true, "trace": false, "sidechain": false, "all_atom": false, "water": false, "sphere": false, "ligands": true, "hydrogen": false, "transparent": false, "ribbon": true }, "lock": true, "view_id": "view:e9mx4p", "selected": [ 154, 155, 341, 42, 63, 67, 92 ], "camera": { "up": [ 16.501362135372435, 26.98427451475052, -0.3975675760496816 ], "slab": { "z_front": -7.753908948194662, "z_back": 5.58086661002549, "zoom": 29.280544867879286 }, "pos": [ 17.410000000001787, 26.58999999999918, -0.2600000000028232 ], "in": [ 17.00123423615934, 25.682855200046887, -0.16000568901555362 ] }, "pdb_id": "1mbo", "selected_traces": [], "grid": { "bCutoff": null, "isElem": {} }, "i_atom": 1276, "text": "The surrounding residues around the oxygen is crucial for oxygen molecule binding.", "creator": "other", "order": 15 }, { "distances": [], "labels": [], "user_id": "106949578407835494908", "version": 2, "show": { "peptide": true, "trace": false, "sidechain": false, "all_atom": false, "water": false, "sphere": false, "ligands": true, "hydrogen": false, "transparent": false, "ribbon": true }, "lock": true, "view_id": "view:n7cal0", "selected": [], "camera": { "up": [ 17.80261419747432, 27.320988325630708, 1.335631217908581 ], "slab": { "z_front": -2, "z_back": 5.58086661002549, "zoom": 14.86804454178136 }, "pos": [ 17.050000000004935, 27.259999999998165, 0.6799999999940791 ], "in": [ 17.452627052044996, 26.429506158467138, 0.29506956972833753 ] }, "pdb_id": "1mbo", "selected_traces": [], "grid": { "bCutoff": null, "isElem": {} }, "i_atom": 1275, "text": "Click edit to change this text.", "creator": "other", "order": 25 }, { "distances": [], "labels": [ { "i_atom": 1274, "text": "Iron atom" } ], "user_id": "117908387177518174476", "version": 2, "show": { "peptide": true, "trace": false, "sidechain": false, "all_atom": false, "water": false, "sphere": false, "ligands": true, "hydrogen": false, "transparent": false, "ribbon": true }, "lock": true, "view_id": "view:77smzs", "selected": [], "camera": { "up": [ 15.31524611040343, 27.4737644253482, -0.3181780951480112 ], "slab": { "z_front": -2.3794392523364434, "z_back": 13.627697536108753, "zoom": 36.264826756986935 }, "pos": [ 15.359999999976905, 27.95000000001393, 0.5599999999960467 ], "in": [ 14.365440765250709, 27.888464655689724, 0.6440555174814825 ] }, "pdb_id": "1mbo", "selected_traces": [], "grid": { "bCutoff": null, "isElem": {} }, "i_atom": 1274, "text": "Specifically, the heme group traps an iron atom in its centre.\n", "creator": "other", "order": 16 }, { "distances": [], "labels": [ { "i_atom": 1233, "text": "heme" } ], "user_id": "117908387177518174476", "version": 2, "show": { "peptide": true, "trace": false, "sidechain": false, "all_atom": false, "water": false, "sphere": false, "ligands": true, "hydrogen": false, "transparent": false, "ribbon": true }, "lock": true, "view_id": "view:ekemch", "selected": [], "camera": { "up": [ 15.406719302241672, 27.861180022537074, -0.43495141509887425 ], "slab": { "z_front": -2.3794392523364434, "z_back": 13.627697536108753, "zoom": 73.21182399733587 }, "pos": [ 15.360000000002508, 27.949999999999722, 0.5599999999972702 ], "in": [ 14.41946231879145, 28.281583486049204, 0.48623508963063156 ] }, "pdb_id": "1mbo", "selected_traces": [], "grid": { "bCutoff": null, "isElem": {} }, "i_atom": 1274, "text": "The heme group is the molecule responsible for binding oxygen to the molecule.", "creator": "other", "order": 17 }, { "distances": [], "labels": [ { "i_atom": 525, "text": "blocking histidine" } ], "user_id": "117908387177518174476", "version": 2, "show": { "peptide": true, "trace": false, "sidechain": false, "all_atom": false, "water": false, "sphere": false, "ligands": true, "hydrogen": false, "transparent": false, "ribbon": true }, "lock": true, "view_id": "view:4vbozk", "selected": [ 154, 155, 341, 42, 63, 67, 92 ], "camera": { "up": [ 20.383243209498293, 28.031169367579384, -0.06794444260717364 ], "slab": { "z_front": -7.753908948194662, "z_back": 5.58086661002549, "zoom": 18.564351701805727 }, "pos": [ 21.16000000000296, 27.419999999998726, -0.22000000000626052 ], "in": [ 20.709588659445995, 26.712172377861318, 0.3241596104362823 ] }, "pdb_id": "1mbo", "selected_traces": [], "grid": { "bCutoff": null, "isElem": {} }, "i_atom": 525, "text": "A crucial histidine makes contact with the oxygen molecule.", "creator": "other", "order": 20 }, { "distances": [], "labels": [ { "i_atom": 527, "text": "blocks potential carbon monoxide binding" } ], "user_id": "117908387177518174476", "version": 2, "show": { "peptide": true, "trace": false, "sidechain": false, "all_atom": false, "water": false, "sphere": false, "ligands": true, "hydrogen": false, "transparent": false, "ribbon": true }, "lock": true, "view_id": "view:1mg5ap", "selected": [ 154, 155, 341, 42, 63, 67, 92 ], "camera": { "up": [ 20.124179198711857, 28.83979151500971, 0.050216399016241677 ], "slab": { "z_front": -2, "z_back": 4.55642072213501, "zoom": 18.564351701805748 }, "pos": [ 19.8500000000011, 27.880000000000567, -0.010000000002429177 ], "in": [ 19.787737884292653, 27.835231838168752, 0.987055284640157 ] }, "pdb_id": "1mbo", "selected_traces": [], "grid": { "bCutoff": null, "isElem": {} }, "i_atom": 527, "text": "The histidine sits right on top of the oxygen atom. The reason is that carbon monoxide (C=O) also likes to bind to the iron atom. But this is prevented by the blocking histidine which sits exactly where the C of the carbon monoxide would like to sit. Therefore myoglobin binds oxygen molecules over carbon monoxide molecules.", "creator": "other", "order": 22 }, { "distances": [], "labels": [ { "i_atom": 831, "text": "bottom of cavity" } ], "user_id": "117908387177518174476", "version": 2, "show": { "peptide": true, "trace": false, "sidechain": false, "all_atom": false, "water": false, "sphere": false, "ligands": false, "hydrogen": false, "transparent": false, "ribbon": true }, "lock": true, "view_id": "view:coun7l", "selected": [], "camera": { "up": [ 19.228697779635795, 26.212721086500764, 4.194530378819982 ], "slab": { "z_front": -23.523016759776546, "z_back": 27.396983240223452, "zoom": 69.28452731387468 }, "pos": [ 19.179999999998742, 26.050000000001305, 5.179999999999071 ], "in": [ 18.61162633704652, 25.24319664220601, 5.018693704050929 ] }, "pdb_id": "1mbo", "selected_traces": [], "grid": { "bCutoff": null, "isElem": {} }, "i_atom": 547, "text": "The structure of the myoglobin provides a cavity in the middle of the protein.", "creator": "other", "order": 11 } ]