SMTL ID : 4u9b.1

Crystal structure of an H-NOX protein from S. oneidensis in the Fe(II)NO ligation state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 31 residues within 4Å: Chain A: M.1, K.2, I.4, I.5, F.74, L.77, H.81, V.84, V.85, L.94, V.95, I.98, I.102, V.106, Y.110, P.113, S.114, L.115, P.116, I.118, L.130, Y.132, S.134, R.136, L.138, C.141, A.142, L.145, L.146, A.149 Ligands: NO.2 25 PLIP interactions: 24 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:I.5, A:H.81, A:V.85, A:L.94, A:I.98, A:I.102, A:I.102, A:V.106, A:Y.110, A:L.115, A:P.116, A:Y.132, A:L.138, A:A.142, A:L.145, A:L.145, A:L.146 Hydrogen bonds: A:K.2, A:S.114, A:Y.132, A:S.134 Water bridges: A:M.1, A:M.1 Salt bridges: A:R.136 Metal complexes: NO.2

1 x NO: NITRIC OXIDE(Non-covalent)

NO.2: 6 residues within 4Å: Chain A: I.98, I.102, L.115, P.116, I.118 Ligands: HEM.1 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: C.139, H.161, C.164, M.165, H.166, C.172 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.139, A:H.161, A:C.164, A:C.172

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 3 residues within 4Å: Chain A: H.99, H.117, N.119 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.119, A:N.119 Water bridges: A:I.118, A:I.118 Salt bridges: A:H.99, A:H.117

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: N.107, K.108, L.109, Y.110, H.111 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.111 Water bridges: A:L.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Herzik, M.A. et al., Structural insights into the role of iron-histidine bond cleavage in nitric oxide-induced activation of H-NOX gas sensor proteins. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-10-01

Peptides

NO-binding heme-dependent sensor protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NO-binding heme-dependent sensor protein