SMTL ID : 2a8s.1

2.45 Angstrom Crystal Structure of the Complex Between the Nuclear SnoRNA Decapping Nudix Hydrolase X29, Manganese and GTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: G.72, G.73, E.93 Ligands: MN.2, GTP.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:G.72, A:E.93, A:E.93 MN.2: 7 residues within 4Å: Chain A: E.89, E.92, E.93, E.150 Ligands: MN.1, MN.3, GTP.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.89, A:E.93, A:E.150 MN.3: 5 residues within 4Å: Chain A: R.88, E.89, E.92 Ligands: MN.2, GTP.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.89 MN.4: 2 residues within 4Å: Chain A: E.150 Ligands: GTP.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.150 MN.6: 5 residues within 4Å: Chain B: G.72, G.73, E.93 Ligands: MN.7, GTP.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:G.72, B:E.93 MN.7: 5 residues within 4Å: Chain B: G.72, E.89, E.93 Ligands: MN.6, GTP.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.89, B:E.93 MN.8: 5 residues within 4Å: Chain B: E.92, K.145, D.146, E.150 Ligands: GTP.10 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.92 MN.9: 2 residues within 4Å: Chain B: E.89 Ligands: GTP.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.89, B:E.89

2 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.5: 20 residues within 4Å: Chain A: H.37, R.63, F.70, G.72, G.73, F.74, E.89, E.92, E.93, T.122, E.150, I.178, G.179, N.180, S.181, Q.184 Ligands: MN.1, MN.2, MN.3, MN.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:F.70, A:F.74, A:T.122, A:G.179, A:N.180, A:N.180, A:Q.184, A:Q.184 Salt bridges: A:H.37, A:R.63 pi-Stacking: A:H.37, A:H.37 GTP.10: 20 residues within 4Å: Chain B: H.37, R.63, G.69, F.70, G.72, G.73, F.74, E.89, E.93, C.120, T.122, E.150, I.178, N.180, S.181, Q.184 Ligands: MN.6, MN.7, MN.8, MN.9 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:F.70, B:F.74, B:Q.184, B:Q.184, B:Q.184 Water bridges: B:R.63 Salt bridges: B:H.37, B:R.63 pi-Stacking: B:H.37, B:H.37

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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