SMTL ID : 4awn.1

Structure of recombinant human DNase I (rhDNaseI) in complex with Magnesium and Phosphate.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: N.18, L.21, Q.244, L.245, A.248 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.245 Hydrogen bonds: A:Q.244, A:Q.244

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.99, E.102, D.107, F.109, N.110, E.112 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.99, A:D.107, A:F.109, A:E.112, H2O.4, H2O.4 CA.3: 4 residues within 4Å: Chain A: D.201, T.203, T.205, T.207 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.201, A:D.201, A:T.203, A:T.205, H2O.7

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: N.7, E.39 Ligands: PO4.5 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.39, H2O.1, H2O.2, H2O.2, H2O.8

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 7 residues within 4Å: Chain A: N.7, E.39, H.134, D.168, N.170, H.252 Ligands: MG.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.7, A:D.168, A:N.170 Water bridges: A:Y.175 Salt bridges: A:H.134, A:H.252

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.6: 6 residues within 4Å: Chain A: W.187, T.188, S.189, P.190, F.192, W.194 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.189, A:F.192 Water bridges: A:W.194

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.7: 2 residues within 4Å: Chain A: C.104, N.106 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parsiegla, G. et al., The Structure of Human DNase I Bound to Magnesium and Phosphate Ions Points to a Catalytic Mechanism Common to Members of the DNase I-Like Superfamily. Biochemistry (2012)

Release Date

2013-01-09

Peptides

DEOXYRIBONUCLEASE-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DEOXYRIBONUCLEASE-1