Browser

select function

select ligand

clear

→ advanced search

PyDISH No: 05333

PDB: 3d1i,
chainID: B, resSeq: 1005
heme type: C

distortion

Protein data

function: oxidoreductase
experiment: X-RAY DIFFRACTION
resolution: 1.8 Å

axial ligand #1: HIS

chainID: B,
resSeq: 231,
Coordination distance[Å]: 1.974
molecule: Eight-heme nitrite reductase
Organism: Thioalkalivibrio nitratireducens

axial ligand #2: HIS

chainID: B,
resSeq: 398,
Coordination distance[Å]: 1.946
molecule: same as ligand #1

List of other hemes in pdb:3d1i

ID of heme	Distortion	Axial ligands on heme		Function & structure
3d1i-A-1004	`sad. +0.60 ruf. -0.39 dom. +0.08 bre. -0.04`	LYS	chainID: A, resSeq: 188, molecule: Eight-heme nitrite reductase	oxidoreductase oligomeric count: 6 pocket vol.: 414.0 Å³ d(Fe-oop): 0.019 Å
3d1i-A-1004	`sad. +0.60 ruf. -0.39 dom. +0.08 bre. -0.04`	NO2	chainID: A, resSeq: 528, molecule: NITRITE ION
3d1i-A-1005	`sad. +1.11 ruf. -0.34 dom. -0.01 bre. +0.06`	HIS	chainID: A, resSeq: 231, molecule: Eight-heme nitrite reductase	oxidoreductase oligomeric count: 6 pocket vol.: 469.0 Å³ d(Fe-oop): 0.017 Å
3d1i-A-1005	`sad. +1.11 ruf. -0.34 dom. -0.01 bre. +0.06`	HIS	chainID: A, resSeq: 398, molecule: Eight-heme nitrite reductase
3d1i-A-1006	`sad. -0.18 ruf. -0.79 dom. +0.20 bre. -0.01`	HIS	chainID: A, resSeq: 119, molecule: Eight-heme nitrite reductase	oxidoreductase oligomeric count: 6 pocket vol.: 403.0 Å³ d(Fe-oop): 0.001 Å
3d1i-A-1006	`sad. -0.18 ruf. -0.79 dom. +0.20 bre. -0.01`	HIS	chainID: A, resSeq: 300, molecule: Eight-heme nitrite reductase
3d1i-A-1007	`sad. +0.74 ruf. -0.66 dom. -0.12 bre. +0.07`	HIS	chainID: A, resSeq: 383, molecule: Eight-heme nitrite reductase	oxidoreductase oligomeric count: 6 pocket vol.: 443.0 Å³ d(Fe-oop): 0.026 Å
3d1i-A-1007	`sad. +0.74 ruf. -0.66 dom. -0.12 bre. +0.07`	HIS	chainID: A, resSeq: 491, molecule: Eight-heme nitrite reductase
3d1i-A-1008	`sad. -0.34 ruf. -0.82 dom. +0.17 bre. +0.17`	HIS	chainID: A, resSeq: 372, molecule: Eight-heme nitrite reductase	oxidoreductase oligomeric count: 6 pocket vol.: 547.0 Å³ d(Fe-oop): 0.072 Å
3d1i-A-1008	`sad. -0.34 ruf. -0.82 dom. +0.17 bre. +0.17`	HIS	chainID: A, resSeq: 415, molecule: Eight-heme nitrite reductase
3d1i-A-1002	`sad. -0.12 ruf. -0.50 dom. +0.00 bre. -0.06`	HIS	chainID: A, resSeq: 39, molecule: Eight-heme nitrite reductase	oxidoreductase oligomeric count: 6 pocket vol.: 359.0 Å³ d(Fe-oop): 0.027 Å
3d1i-A-1002	`sad. -0.12 ruf. -0.50 dom. +0.00 bre. -0.06`	HIS	chainID: A, resSeq: 234, molecule: Eight-heme nitrite reductase
3d1i-A-1003	`sad. +0.45 ruf. -0.48 dom. +0.01 bre. +0.06`	HIS	chainID: A, resSeq: 30, molecule: Eight-heme nitrite reductase	oxidoreductase oligomeric count: 6 pocket vol.: 498.0 Å³ d(Fe-oop): 0.047 Å
3d1i-A-1003	`sad. +0.45 ruf. -0.48 dom. +0.01 bre. +0.06`	HIS	chainID: A, resSeq: 70, molecule: Eight-heme nitrite reductase
3d1i-A-1001	`sad. +0.07 ruf. -0.34 dom. -0.02 bre. -0.12`	HIS	chainID: A, resSeq: 18, molecule: Eight-heme nitrite reductase	oxidoreductase oligomeric count: 6 pocket vol.: 406.0 Å³ d(Fe-oop): 0.031 Å
3d1i-A-1001	`sad. +0.07 ruf. -0.34 dom. -0.02 bre. -0.12`	HIS	chainID: A, resSeq: 44, molecule: Eight-heme nitrite reductase
3d1i-B-1004	`sad. +0.55 ruf. -0.44 dom. +0.14 bre. -0.07`	LYS	chainID: B, resSeq: 188, molecule: Eight-heme nitrite reductase	oxidoreductase oligomeric count: 6 pocket vol.: 404.0 Å³ d(Fe-oop): 0.022 Å
3d1i-B-1004	`sad. +0.55 ruf. -0.44 dom. +0.14 bre. -0.07`	NO2	chainID: B, resSeq: 528, molecule: NITRITE ION
3d1i-B-1006	`sad. -0.21 ruf. -0.84 dom. +0.23 bre. +0.06`	HIS	chainID: B, resSeq: 119, molecule: Eight-heme nitrite reductase	oxidoreductase oligomeric count: 6 pocket vol.: 411.0 Å³ d(Fe-oop): 0.008 Å
3d1i-B-1006	`sad. -0.21 ruf. -0.84 dom. +0.23 bre. +0.06`	HIS	chainID: B, resSeq: 300, molecule: Eight-heme nitrite reductase
3d1i-B-1007	`sad. +0.79 ruf. -0.68 dom. -0.14 bre. +0.07`	HIS	chainID: B, resSeq: 383, molecule: Eight-heme nitrite reductase	oxidoreductase oligomeric count: 6 pocket vol.: 432.0 Å³ d(Fe-oop): 0.026 Å
3d1i-B-1007	`sad. +0.79 ruf. -0.68 dom. -0.14 bre. +0.07`	HIS	chainID: B, resSeq: 491, molecule: Eight-heme nitrite reductase
3d1i-B-1008	`sad. -0.34 ruf. -0.80 dom. +0.18 bre. +0.12`	HIS	chainID: B, resSeq: 372, molecule: Eight-heme nitrite reductase	oxidoreductase oligomeric count: 6 pocket vol.: 547.0 Å³ d(Fe-oop): 0.040 Å
3d1i-B-1008	`sad. -0.34 ruf. -0.80 dom. +0.18 bre. +0.12`	HIS	chainID: B, resSeq: 415, molecule: Eight-heme nitrite reductase
3d1i-B-1002	`sad. -0.08 ruf. -0.39 dom. -0.01 bre. -0.08`	HIS	chainID: B, resSeq: 39, molecule: Eight-heme nitrite reductase	oxidoreductase oligomeric count: 6 pocket vol.: 352.0 Å³ d(Fe-oop): 0.048 Å
3d1i-B-1002	`sad. -0.08 ruf. -0.39 dom. -0.01 bre. -0.08`	HIS	chainID: B, resSeq: 234, molecule: Eight-heme nitrite reductase
3d1i-B-1003	`sad. +0.33 ruf. -0.50 dom. +0.01 bre. +0.06`	HIS	chainID: B, resSeq: 30, molecule: Eight-heme nitrite reductase	oxidoreductase oligomeric count: 6 pocket vol.: 498.0 Å³ d(Fe-oop): 0.026 Å
3d1i-B-1003	`sad. +0.33 ruf. -0.50 dom. +0.01 bre. +0.06`	HIS	chainID: B, resSeq: 70, molecule: Eight-heme nitrite reductase
3d1i-B-1001	`sad. -0.15 ruf. -0.39 dom. -0.05 bre. -0.11`	HIS	chainID: B, resSeq: 18, molecule: Eight-heme nitrite reductase	oxidoreductase oligomeric count: 6 pocket vol.: 409.0 Å³ d(Fe-oop): 0.045 Å
3d1i-B-1001	`sad. -0.15 ruf. -0.39 dom. -0.05 bre. -0.11`	HIS	chainID: B, resSeq: 44, molecule: Eight-heme nitrite reductase