Structure of PDB 3hb3 Chain A Binding Site BS04

Receptor Information

>3hb3 Chain A (length=529) Species: 266 (Paracoccus denitrificans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

GFFTRWFMSTNHKDIGILYLFTAGIVGLISVCFTVYMRMELQHPGVQYMC
LEGARLIADASAECTPNGHLWNVMITYHGVLMMFFVVIPALFGGFGNYFM
PLHIGAPDMAFPRLNNLSYWMYVCGVALGVASLLAPGGNDQMGSGVGWVL
YPPLSTTEAGYSMDLAIFAVHVSGASSILGAINIITTFLNMRAPGMTLFK
VPLFAWSVFITAWLILLSLPVLAGAITMLLMDRNFGTQFFDPAGGGDPVL
YQHILWFFGHPEVYIIILPGFGIISHVISTFAKKPIFGYLPMVLAMAAIG
ILGFVVWAHHMYTAGMSLTQQAYFMLATMTIAVPTGIKVFSWIATMWGGS
IEFKTPMLWAFGFLFLFTVGGVTGVVLSQAPLDRVYHDTYYVVAHFHYVM
SLGAVFGIFAGVYYWIGKMSGRQYPEWAGQLHFWMMFIGSNLIFFPQHFL
GRQGMPRRYIDYPVEFAYWNNISSIGAYISFASFLFFIGIVFYTLFAGKR
VNVPNYWNEHADTLEWTLPSPPPEHTFET

Ligand information

Ligand ID

InChI

InChI=1S/Mn/q+2

InChIKey

WAEMQWOKJMHJLA-UHFFFAOYSA-N

SMILES

Software	SMILES
ACDLabs 10.04 OpenEye OEToolkits 1.5.0	[Mn+2]
CACTVS 3.341	[Mn++]

Formula

Name

MANGANESE (II) ION

PDB chain

3hb3 Chain A Residue 562 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

Global view

Local view

Structure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

PDB	3hb3 High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase: New insights into the active site and the proton transfer pathways
Resolution	2.25 Å
Binding residue (original residue number in PDB)	H403 D404
Binding residue (residue number reindexed from 1)	H387 D388
Annotation score	1

Enzymatic activity

Catalytic site (original residue number in PDB)	Y35 I45 F49 M53 I91 H94 N113 D124 N131 S134 Y138 W164 S192 S193 G196 T203 H276 E278 Y280 S291 P307 H325 H326 T351 K354 H411 F412 H413 R473 R474
Catalytic site (residue number reindexed from 1)	Y19 I29 F33 M37 I75 H78 N97 D108 N115 S118 Y122 W148 S176 S177 G180 T187 H260 E262 Y264 S275 P291 H309 H310 T335 K338 H395 F396 H397 R457 R458
Enzyme Commision number	7.1.1.9: cytochrome-c oxidase.

Gene Ontology

	Molecular Function
GO:0004129	cytochrome-c oxidase activity
GO:0020037	heme binding
GO:0046872	metal ion binding

	Biological Process
GO:0006119	oxidative phosphorylation
GO:0009060	aerobic respiration
GO:0015990	electron transport coupled proton transport
GO:0022904	respiratory electron transport chain
GO:1902600	proton transmembrane transport

	Cellular Component
GO:0005886	plasma membrane
GO:0016020	membrane
GO:0045277	respiratory chain complex IV

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:3hb3, PDBe:3hb3, PDBj:3hb3
PDBsum	3hb3
PubMed	19374884
UniProt	P98002\|COX1B_PARDE Cytochrome c oxidase subunit 1-beta (Gene Name=ctaDII)

[Back to BioLiP]