Structure of PDB 3ehb Chain A Binding Site BS05

Receptor Information

>3ehb 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
PLHIGAPDMAFPRLDNLSYWMYVCGVALGVASLLAPGGNDQMGSGVGWVL
YPPLSTTEAGYSMDLAIFAVHVSGASSILGAINIITTFLNMRAPGMTLFK
VPLFAWSVFITAWLILLSLPVLAGAITMLLMDRNFGTQFFDPAGGGDPVL
YQHILWFFGHPEVYIIILPGFGIISHVISTFAKKPIFGYLPMVLAMAAIG
ILGFVVWAHHMYTAGMSLTQQAYFMLATMTIAVPTGIKVFSWIATMWGGS
IEFKTPMLWAFGFLFLFTVGGVTGVVLSQAPLDRVYHDTYYVVAHFHYVM
SLGAVFGIFAGVYYWIGKMSGRQYPEWAGQLHFWMMFIGSNLIFFPQHFL
GRQGMPRRYIDYPVEFAYWNNISSIGAYISFASFLFFIGIVFYTLFAGKR
VNVPNYWNEHADTLEWTLPSPPPEHTFET

Ligand information

Ligand ID

InChI

InChI=1S/Ca/q+2

InChIKey

BHPQYMZQTOCNFJ-UHFFFAOYSA-N

SMILES

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

Formula

Name

CALCIUM ION

PDB chain

3ehb Chain A Residue 563 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	3ehb A d-pathway mutation decouples the paracoccusdenitrificans cytochrome C oxidase by altering the side-chain orientation of a distant conserved glutamate
Resolution	2.32 Å
Binding residue (original residue number in PDB)	E56 H59 G61 Q63
Binding residue (residue number reindexed from 1)	E40 H43 G45 Q47
Annotation score	1

Enzymatic activity

Catalytic site (original residue number in PDB)	Y35 I45 F49 M53 I91 H94 N113 D124 D131 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 D115 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

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:3ehb, PDBe:3ehb, PDBj:3ehb
PDBsum	3ehb
PubMed	18930738
UniProt	P98002\|COX1B_PARDE Cytochrome c oxidase subunit 1-beta (Gene Name=ctaDII)

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