Structure of PDB 3sxq Chain B Binding Site BS04

Receptor Information

>3sxq Chain B (length=517) Species: 108010 (Thioalkalivibrio paradoxus)

LKPVDALQCYDCHTQIEDMHVVGKHATVNCVHCHDATEHVETASARRMGE
RPVTHTSPEACASCHTAQFNSFASVRHESHPREEKANPRSRSPKFDTLIG
AHGFSLEHAEPRSHAFMLVDHFIVDRAYGGRFQYKSWQNVTDGLGAVRGA
WTVIEDMDPTTSDQRRFLAQTATAANPVCLNCKTQDHILDWAYMGDEHDA
AKWARTSKVVDFARDLHHPVNCYMCHDPHSTEPRVVRDALIHAVVDQGLG
TYPYDEAKSEHVTLTPVTFQRGGEDFRKIGLLNVADSNLMCGQCHVEYNC
NPGFQQSDGAPVGMDDRRTNHFFWANVFDYAEAAKEIDFFDFTHVTTGAP
LPKLQHPELETFWGSTHERNGVTCADCHMPRVKLENGKEYTMHSPRTPRD
MMNRACLNCHDGWTEAEAEYAIDYIKNYTHGKIMKAEFWLARMIDLFPVA
KRAGVSEDVLNEVRALHYDAHLHWEWWTAENSVGFHNPDQARESLMKSIT
KSKEGVGKLDAAIDAAV

Ligand information

• Ligand ID: HEC
• InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,9-12H2,1-6H3,(H,39,40)(H,41,42);/q-4;+4/b21-7?,22-8?,26-13-,29-14-,30-15-,31-16-;
• InChIKey: HXQIYSLZKNYNMH-LJNAALQVSA-N
• SMILES:
  ACDLabs 10.04: O=C(O)CCC1=C(C2=CC6=C(C(=C/C)\C5=CC4=C(C(\C3=Cc7c(c(c8C=C1N2[Fe](N34)(N56)n78)CCC(=O)O)C)=C/C)C)C)C
  OpenEye OEToolkits 1.5.0: CC=C1C(=C2C=C3C(=CC)C(=C4N3[Fe]56N2C1=Cc7n5c(c(c7C)CCC(=O)O)C=C8N6C(=C4)C(=C8CCC(=O)O)C)C)C
  CACTVS 3.341: C\C=C1/C(=C2C=C3N4C(=Cc5n6c(C=C7N8C(=C(C)\C7=C/C)C=C1N2[Fe@@]468)c(C)c5CCC(O)=O)C(=C3C)CCC(O)=O)C
  CACTVS 3.341: CC=C1C(=C2C=C3N4C(=Cc5n6c(C=C7N8C(=C(C)C7=CC)C=C1N2[Fe]468)c(C)c5CCC(O)=O)C(=C3C)CCC(O)=O)C
• Formula: C34 H34 Fe N4 O4
• Name: HEME C
• PDB chain: 3sxq Chain B Residue 1007

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3sxq Comparative structural and functional analysis of two octaheme nitrite reductases from closely related Thioalkalivibrio species.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): H300 E363 F367 H372 T378 C379 C382 H383 T402 R404 I427 K431 N486 S487 F490 H491
• Binding residue (residue number reindexed from 1): H295 E358 F362 H367 T373 C374 C377 H378 T397 R399 I422 K426 N481 S482 F485 H486
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 1.7.2.2: nitrite reductase (cytochrome; ammonia-forming).

Gene Ontology

Molecular Function

• GO:0016491 oxidoreductase activity
• GO:0020037 heme binding
• GO:0042279 nitrite reductase (cytochrome, ammonia-forming) activity
• GO:0046872 metal ion binding

Biological Process

• GO:0019645 anaerobic electron transport chain

Cellular Component

• GO:0030288 outer membrane-bounded periplasmic space
• GO:0042597 periplasmic space

External links

• PDB: RCSB:3sxq, PDBe:3sxq, PDBj:3sxq
• PDBsum: 3sxq
• PubMed: 22935005
• UniProt: E7EDQ7