SMTL ID : 1hk8.1

STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DGTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

4 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.1: 18 residues within 4Å: Chain A: I.99, E.100, T.101, P.102, K.103, V.107, A.110, I.111, Q.114, K.146 Chain B: K.169, D.173, Q.176, A.177, Y.180, E.181, T.184 Ligands: MN.4 19 PLIP interactions: 7 interactions with chain A, 12 interactions with chain B Hydrogen bonds: A:E.100, A:K.103, A:S.104, B:D.173, B:Q.176 Water bridges: A:K.103, A:K.146, A:K.146, B:K.169, B:K.169, B:D.173, B:D.173, B:E.181, B:E.181 Salt bridges: A:K.146, B:K.169, B:K.169, B:E.181 Hydrophobic interactions: B:Y.180 DGT.2: 8 residues within 4Å: Chain A: H.64, H.66, D.67, A.445, E.446, N.447, L.448, R.451 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:H.64, A:D.67, A:N.447, A:N.447, A:L.448 Water bridges: A:H.64, A:V.65, A:A.445, A:E.446 Salt bridges: A:H.64, A:H.66 DGT.5: 18 residues within 4Å: Chain A: K.169, D.173, Q.176, A.177, Y.180, E.181, T.184 Chain B: I.99, E.100, T.101, P.102, K.103, V.107, A.110, I.111, Q.114, K.146 Ligands: MN.8 19 PLIP interactions: 8 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:E.100, B:K.103, B:S.104, A:D.173, A:Q.176, A:T.184 Water bridges: B:K.103, B:S.104, B:K.146, B:K.146, A:K.169, A:K.169, A:E.181, A:E.181 Salt bridges: B:K.146, A:K.169, A:K.169, A:E.181 Hydrophobic interactions: A:Y.180 DGT.6: 8 residues within 4Å: Chain B: H.64, H.66, D.67, A.445, E.446, N.447, L.448, R.451 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:H.64, B:D.67, B:N.447, B:N.447, B:L.448 Water bridges: B:H.64, B:V.65, B:H.66, B:H.66, B:D.67, B:A.445, B:E.446 Salt bridges: B:H.64, B:H.66

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.543, C.546, C.561, C.564 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.543, A:C.546, A:C.561, A:C.564 ZN.7: 4 residues within 4Å: Chain B: C.543, C.546, C.561, C.564 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.543, B:C.546, B:C.561, B:C.564

2 x MN: MANGANESE (II) ION(Non-functional Binders)

MN.4: 1 residues within 4Å: Ligands: DGT.1 No protein-ligand interaction detected (PLIP) MN.8: 1 residues within 4Å: Ligands: DGT.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Logan, D.T. et al., A Metal-Binding Site in the Catalytic Subunit of Anaerobic Ribonucleotide Reductase. Proc.Natl.Acad.Sci.USA (2003)

Release Date

2003-03-27

Peptides

ANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE REDUCTASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE REDUCTASE

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