SMTL ID : 2a8q.1

2.6 Angstrom Crystal Structure of the Complex Between the Nuclear SnoRNA Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-methyl-GDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: G.72, E.93 Ligands: MN.2, POP.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:G.72, A:E.93 MN.2: 7 residues within 4Å: Chain A: G.72, E.89, E.93, D.146 Ligands: MN.1, MN.3, POP.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.89, A:E.93 MN.3: 3 residues within 4Å: Chain A: E.89 Ligands: MN.2, POP.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.89, A:E.89 MN.5: 3 residues within 4Å: Chain B: G.72, E.93 Ligands: MN.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:G.72, B:E.93 MN.6: 4 residues within 4Å: Chain B: G.72, E.89, E.93 Ligands: MN.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.89, B:E.93

1 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.4: 10 residues within 4Å: Chain A: H.37, R.63, G.72, G.73, F.74, E.89, E.93 Ligands: MN.1, MN.2, MN.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.72, A:F.74 Salt bridges: A:H.37, A:R.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scarsdale, J.N. et al., Crystal structures of U8 snoRNA decapping nudix hydrolase, X29, and its metal and cap complexes. Structure (2006)

Release Date

2006-03-28

Peptides

U8 snoRNA-binding protein X29: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

U8 snoRNA-binding protein X29

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