SMTL ID : 2yfc.2 (1 other biounit)

STRUCTURAL AND FUNCTIONAL INSIGHTS OF DR2231 PROTEIN, THE MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE FROM DEINOCOCCUS RADIODURANS, COMPLEXED WITH Mn and dUMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

1 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)

UMP.1: 18 residues within 4Å: Chain A: V.111, N.115, K.118, K.128, Q.129, K.131 Chain B: L.20, F.23, L.45, R.46, L.49, E.52, E.53, D.88, Y.91, V.92 Ligands: MN.5, MN.6 20 PLIP interactions: 8 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:Y.91, B:V.92, A:K.128, A:Q.129 Hydrogen bonds: B:D.88, A:N.115, A:K.118, A:Q.129 Water bridges: B:H.24, B:R.46, B:R.46, B:R.46, B:E.53, A:K.131, A:K.131, A:K.131, A:K.131 Salt bridges: A:K.118, A:K.128, A:K.131

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

MN.2: 4 residues within 4Å: Chain A: E.53, E.56, E.85, D.88 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.53, A:E.56, A:E.85, A:D.88, H2O.3 MN.5: 6 residues within 4Å: Chain B: E.53, E.56, E.85, D.88 Ligands: UMP.1, MN.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.53, B:E.56, B:E.85, B:D.88, H2O.6 MN.6: 6 residues within 4Å: Chain A: K.128 Chain B: E.52, E.53, E.56 Ligands: UMP.1, MN.5 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.52, B:E.53, B:E.56, H2O.6, H2O.6

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: A.138, D.139, V.140, R.141, G.142 Chain B: A.80, P.81, H.84 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.140, A:R.141, B:H.84 GOL.4: 6 residues within 4Å: Chain A: P.14, E.18, R.19, H.21, E.22, R.25 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goncalves, A.M.D. et al., Structural and Functional Insights Into Dr2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase from Deinococcus Radiodurans. J.Biol.Chem. (2011)

Release Date

2011-07-06

Peptides

MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE

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