SMTL ID : 5hwu.1

Crystal Structure of DR2231_E46A mutant in complex with dUMPNPP and Manganese

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: E.41, E.44, E.73, D.76 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.41, A:E.44, A:E.73, A:D.76, H2O.1, H2O.2 MN.4: 6 residues within 4Å: Chain B: E.41, E.44, E.73, D.76 Ligands: DUP.3, MN.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.41, B:E.44, B:E.73, B:D.76, H2O.4 MN.5: 4 residues within 4Å: Chain B: H.72, D.76 Ligands: DUP.3, MN.4 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.72, B:D.76, H2O.4, H2O.5

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: E.41, D.76, Y.79, V.80 Chain B: V.99, N.103 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.41, B:N.103

1 x DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE(Non-covalent)

DUP.3: 15 residues within 4Å: Chain A: V.99, N.103, K.106, K.116, Q.117, K.119, W.123 Chain B: F.11, E.41, H.72, D.76, Y.79, V.80 Ligands: MN.4, MN.5 16 PLIP interactions: 10 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:K.116, A:Q.117, B:V.80 Hydrogen bonds: A:N.103, A:K.106, A:K.116, A:K.116, A:Q.117, A:K.119, A:K.119 Salt bridges: A:K.119, B:H.72 Water bridges: B:R.34, B:R.34, B:R.34, B:R.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mota, C.S. et al., Deinococcus radiodurans DR2231 is a two-metal-ion mechanism hydrolase with exclusive activity on dUTP. FEBS J. (2016)

Release Date

2016-10-26

Peptides

DR2231: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DR2231

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