SMTL ID : 4wud.1

N-terminal 43 kDa fragment of the E. coli DNA gyrase B subunit grown from no salt condition

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 26 residues within 4Å: Chain A: E.41, N.45, E.49, D.72, G.76, I.77, I.93, A.99, G.100, G.101, K.102, Y.108, G.113, L.114, H.115, G.116, V.117, G.118, V.119, S.120, T.164, Q.334, K.336 Chain B: Y.4, I.9 Ligands: MG.2 24 PLIP interactions: 23 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.45, A:D.72, A:G.101, A:K.102, A:K.102, A:Y.108, A:L.114, A:H.115, A:G.116, A:V.117, A:V.117, A:G.118, A:V.119, A:S.120, A:T.164, A:Q.334, A:K.336, A:K.336, B:Y.4 Water bridges: A:E.41, A:G.100, A:G.100, A:K.102 pi-Cation interactions: A:K.102 ANP.5: 26 residues within 4Å: Chain A: Y.4, I.9 Chain B: E.41, N.45, E.49, D.72, G.76, I.77, I.93, A.99, G.100, G.101, K.102, Y.108, G.113, L.114, H.115, G.116, V.117, G.118, V.119, S.120, T.164, Q.334, K.336 Ligands: MG.6 24 PLIP interactions: 23 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.45, B:E.49, B:D.72, B:G.101, B:K.102, B:K.102, B:L.114, B:H.115, B:G.116, B:V.117, B:V.117, B:G.118, B:V.119, B:S.120, B:Q.334, B:K.336, B:K.336, A:Y.4 Water bridges: B:D.72, B:D.72, B:K.102, B:T.164, B:T.164 pi-Cation interactions: B:K.102

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: N.45, K.102 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: N.45, K.102 Ligands: ANP.5 No protein-ligand interaction detected (PLIP)

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 2 residues within 4Å: Chain A: K.102, D.104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.102 NA.7: 2 residues within 4Å: Chain B: K.102, D.104 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.104

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 6 residues within 4Å: Chain A: P.78, T.79, G.80, R.135 Chain B: D.5, S.6 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain A: D.5, S.6 Chain B: P.78, T.79, G.80, R.135 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hearnshaw, S.J. et al., The role of monovalent cations in the ATPase reaction of DNA gyrase. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-04-08

Peptides

DNA gyrase subunit B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DNA gyrase subunit B

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