PDBsum entry 4l38

Oxidoreductase

PDB id: 4l38

Contents

Protein chains

520 a.a.

Ligands

HEC ×16

NO2 ×2

MPD ×2

GOL ×5

SO4 ×2

NO2-NO2 ×2

Metals

_CA ×4

Waters ×1295

PDB id:

4l38

Name:

Oxidoreductase

Title:

Nitrite complex of tvnir, low dose data set

Structure:

Eight-heme nitrite reductase. Chain: a, b. Fragment: unp residues 33-551. Ec: 1.7.2.2

Source:

Thioalkalivibrio nitratireducens. Organism_taxid: 1255043. Strain: dsm 14787 / uniqem 213 / alen2

Resolution:

1.80Å R-factor: 0.154 R-free: 0.170

Authors:

A.A.Trofimov,K.M.Polyakov,V.A.Lazarenko,A.N.Popov,T.V.Tikhonova, A.V.Tikhonov,V.O.Popov

Key ref:

A.A.Trofimov et al. Investigation of the X-Ray-Induced nitrite reduction catalysed by cytochrome c nitrite reductase from the bacterium thioalkalivibrio nitratireducens. To be published, . PubMed id: 25945574

Date:

05-Jun-13 Release date: 16-Jul-14

Protein chains

L0DSL2  (NIR_THIND) -  Cytochrome c-552 from Thioalkalivibrio nitratireducens (strain DSM 14787 / UNIQEM 213 / ALEN2)

Seq: 553 a.a.

Struc: 520 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.7.2.2 - nitrite reductase (cytochrome; ammonia-forming).
• Reaction: 6 Fe(III)-[cytochrome c] + NH4⁺ + 2 H2O = 6 Fe(II)-[cytochrome c] + nitrite + 8 H⁺

6 × Fe(III)-[cytochrome c] + NH4(+) + 2 × H2O = 6 × Fe(II)-[cytochrome c] + nitrite (Bound ligand (Het Group name = NO2) corresponds exactly) + 8 × H(+)

• Cofactor: Ca(2+); Heme

Ca(2+) Heme (Bound ligand (Het Group name = HEC) matches with 95.45% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site