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PyDISH No: 14537

PDB: 6ymx,
chainID: D, resSeq: 401
heme type: B

distortion

Protein data

function: translocase
experiment: ELECTRON MICROSCOPY
resolution: 3.17 Å

axial ligand #1: HIS

chainID: D,
resSeq: 105,
Coordination distance[Å]: 2.68
molecule: Cytochrome c1, heme protein, mitochondrial
EC number: 7.1.1.8
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

axial ligand #2: MET

chainID: D,
resSeq: 225,
Coordination distance[Å]: 2.973
molecule: same as ligand #1

List of other hemes in pdb:6ymx

ID of heme	Distortion	Axial ligands on heme		Function & structure
6ymx-a-602	`sad. -0.02 ruf. -0.04 dom. +0.30 bre. +0.02`	HIS	chainID: a, resSeq: 62, molecule: Cytochrome c oxidase subunit 1	oxidoreductase oligomeric count: 32 pocket vol.: 641.0 Å³ d(Fe-oop): 0.111 Å
6ymx-a-602	`sad. -0.02 ruf. -0.04 dom. +0.30 bre. +0.02`	HIS	chainID: a, resSeq: 378, molecule: Cytochrome c oxidase subunit 1
6ymx-a-603	`sad. -0.04 ruf. -0.34 dom. +0.33 bre. +0.02`	HIS	chainID: a, resSeq: 376, molecule: Cytochrome c oxidase subunit 1	oxidoreductase oligomeric count: 32 pocket vol.: 773.0 Å³ d(Fe-oop): 0.123 Å
6ymx-a-603	`sad. -0.04 ruf. -0.34 dom. +0.33 bre. +0.02`	Not assigned.
6ymx-C-402	`sad. +0.15 ruf. -0.32 dom. -0.01 bre. +0.09`	HIS	chainID: C, resSeq: 82, molecule: Cytochrome b	translocase oligomeric count: 32 pocket vol.: 441.0 Å³ d(Fe-oop): 0.061 Å
6ymx-C-402	`sad. +0.15 ruf. -0.32 dom. -0.01 bre. +0.09`	HIS	chainID: C, resSeq: 183, molecule: Cytochrome b
6ymx-C-403	`sad. -0.40 ruf. -0.57 dom. +0.42 bre. +0.15`	HIS	chainID: C, resSeq: 96, molecule: Cytochrome b	translocase oligomeric count: 32 pocket vol.: 456.0 Å³ d(Fe-oop): 0.069 Å
6ymx-C-403	`sad. -0.40 ruf. -0.57 dom. +0.42 bre. +0.15`	HIS	chainID: C, resSeq: 197, molecule: Cytochrome b
6ymx-N-401	`sad. -0.12 ruf. +0.18 dom. -0.10 bre. +0.05`	HIS	chainID: N, resSeq: 82, molecule: Cytochrome b	translocase oligomeric count: 32 pocket vol.: 457.0 Å³ d(Fe-oop): 0.094 Å
6ymx-N-401	`sad. -0.12 ruf. +0.18 dom. -0.10 bre. +0.05`	HIS	chainID: N, resSeq: 183, molecule: Cytochrome b
6ymx-N-402	`sad. -0.44 ruf. -0.63 dom. +0.16 bre. +0.16`	HIS	chainID: N, resSeq: 96, molecule: Cytochrome b	translocase oligomeric count: 32 pocket vol.: 433.0 Å³ d(Fe-oop): 0.142 Å
6ymx-N-402	`sad. -0.44 ruf. -0.63 dom. +0.16 bre. +0.16`	HIS	chainID: N, resSeq: 197, molecule: Cytochrome b
6ymx-O-402	`sad. +0.07 ruf. -0.81 dom. -0.16 bre. +0.10`	HIS	chainID: O, resSeq: 105, molecule: Cytochrome c1, heme protein, mitochondrial	translocase oligomeric count: 32 pocket vol.: 510.0 Å³ d(Fe-oop): 0.279 Å
6ymx-O-402	`sad. +0.07 ruf. -0.81 dom. -0.16 bre. +0.10`	MET	chainID: O, resSeq: 225, molecule: Cytochrome c1, heme protein, mitochondrial