SMTL ID : 6iph.1

Binary Complex of Human DNA Polymerase Mu with MndATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: H.203, D.204, D.206 Ligands: MN.2, DTP.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.204, A:D.206, H2O.7 MN.2: 5 residues within 4Å: Chain A: D.204, D.206, D.280 Ligands: MN.1, DTP.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.204, A:D.206, A:D.280, H2O.8

1 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.3: 16 residues within 4Å: Chain A: G.193, G.194, R.197, K.199, G.202, H.203, D.204, D.206, F.263, D.280, G.295, W.296, G.298, K.300 Ligands: MN.1, MN.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.194, A:H.203, A:D.204, A:D.280 Water bridges: A:R.197, A:R.197, A:R.197, A:R.197, A:K.199, A:K.199 Salt bridges: A:R.197, A:K.199, A:K.199, A:H.203, A:H.203 pi-Stacking: A:W.296

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

SO4.4: 4 residues within 4Å: Chain A: G.121, V.122, K.123, T.124 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.121, A:G.121, A:K.123, A:T.124 Water bridges: A:T.124, A:T.124 SO4.5: 4 residues within 4Å: Chain A: S.46, E.47, G.48, R.49 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.47, A:G.48, A:R.49 SO4.6: 2 residues within 4Å: Chain A: T.147, Q.148 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.148, A:Q.148 Water bridges: A:Q.149 SO4.7: 4 residues within 4Å: Chain A: T.188, T.190, T.210, F.289 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.188, A:T.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, Y.K. et al., Human DNA Polymerase mu Can Use a Noncanonical Mechanism for Multiple Mn2+-Mediated Functions. J.Am.Chem.Soc. (2019)

Release Date

2019-05-29

Peptides

DNA-directed DNA/RNA polymerase mu: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA-directed DNA/RNA polymerase mu

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