SMTL ID : 2a8r.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: G.72, E.93, E.150 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, E.150 Ligands: MN.1, MN.3, POP.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.89, A:E.93, A:E.150 MN.3: 4 residues within 4Å: Chain A: F.74, 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: 5 residues within 4Å: Chain B: G.72, E.93, E.150 Ligands: MN.6, POP.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:G.72, B:E.93 MN.6: 6 residues within 4Å: Chain B: G.72, E.89, E.93, E.150 Ligands: MN.5, POP.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.89, B:E.93, B:E.150

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

POP.4: 11 residues within 4Å: Chain A: H.37, R.63, G.72, G.73, F.74, E.89, E.93, E.150 Ligands: MN.1, MN.2, MN.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.72, A:F.74, A:E.150 Salt bridges: A:H.37, A:R.63 POP.7: 10 residues within 4Å: Chain B: H.37, R.63, G.72, G.73, F.74, E.89, E.93, E.150 Ligands: MN.5, MN.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.72, B:F.74, B:E.150 Salt bridges: B:H.37, B: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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