SMTL ID : 1ei1.1

DIMERIZATION OF E. COLI DNA GYRASE B PROVIDES A STRUCTURAL MECHANISM FOR ACTIVATING THE ATPASE CATALYTIC CENTER

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 7 residues within 4Å: Chain A: P.78, T.79, G.80, R.135 Chain B: S.4, D.5, S.6 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.79, A:G.80, B:D.5, B:S.6 Salt bridges: A:R.135 SO4.2: 3 residues within 4Å: Chain A: D.5, S.6 Chain B: G.80 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:G.80, B:E.136 Hydrogen bonds: A:S.6, A:S.6 SO4.5: 5 residues within 4Å: Chain B: R.290, T.291, A.294, K.298, A.357 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.290, B:R.290 Salt bridges: B:R.290, B:K.298

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

ANP.3: 25 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: I.9 Ligands: GOL.4 20 PLIP interactions: 20 interactions with chain A 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:H.115, A:G.116, A:V.117, A:G.118, A:V.119, A:S.120, A:T.164, A:Q.334, A:K.336 Water bridges: A:G.76, A:G.100 pi-Cation interactions: A:K.102 ANP.6: 25 residues within 4Å: Chain A: 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: GOL.7 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:N.45, B:E.49, B:D.72, B:G.101, B:K.102, B:L.114, B:H.115, B:G.116, B:V.117, B:G.118, B:V.119, B:S.120, B:Q.334, B:Q.334, B:K.336 Water bridges: B:D.72, B:D.72, B:G.100, B:T.164, B:Q.334 pi-Cation interactions: B:K.102

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 12 residues within 4Å: Chain A: E.49, R.75, G.76, P.78, G.101, S.107, Y.108, R.135 Chain B: S.4, S.8, I.9 Ligands: ANP.3 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.75, A:S.107, A:Y.108, A:R.135, B:S.8 GOL.7: 12 residues within 4Å: Chain A: S.4, S.8, I.9 Chain B: E.49, R.75, G.76, P.78, G.101, S.107, Y.108, R.135 Ligands: ANP.6 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.107, B:R.135, A:S.4, A:S.8, A:S.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brino, L. et al., Dimerization of Escherichia coli DNA-gyrase B provides a structural mechanism for activating the ATPase catalytic center. J.Biol.Chem. (2000)

Release Date

2000-03-31

Peptides

DNA GYRASE B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA GYRASE B