SMTL ID : 2a8t.1

2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 snoRNA Decapping Nudix Hydrolase X29, Manganese and m7G-PPP-A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: G.72, G.73, E.93, E.150 Ligands: MN.2, MGT.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.72, A:E.93, H2O.1 MN.2: 8 residues within 4Å: Chain A: G.72, E.89, E.93, E.150 Ligands: MN.1, MN.3, MN.4, MGT.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.89, A:E.93, A:E.150, H2O.1 MN.3: 5 residues within 4Å: Chain A: R.88, E.89 Ligands: MN.2, MN.4, MGT.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.89 MN.4: 4 residues within 4Å: Chain A: E.150 Ligands: MN.2, MN.3, MGT.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.150 MN.7: 6 residues within 4Å: Chain B: G.72, G.73, E.93, E.150 Ligands: MN.8, MGT.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.72, B:E.93, H2O.4 MN.8: 7 residues within 4Å: Chain B: G.72, E.89, E.93, E.150 Ligands: MN.7, MN.9, MGT.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.89, B:E.93, B:E.150 MN.9: 3 residues within 4Å: Chain B: E.150 Ligands: MN.8, MGT.10 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.150, H2O.4

2 x MGT: 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

MGT.5: 15 residues within 4Å: Chain A: H.37, R.63, F.64, G.72, G.73, F.74, E.89, E.93, E.150 Chain B: F.49 Ligands: MN.1, MN.2, MN.3, MN.4, ADN.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.74 Water bridges: A:G.72 Salt bridges: A:H.37, A:R.63 MGT.10: 15 residues within 4Å: Chain A: F.49, R.51 Chain B: H.37, R.63, F.64, G.72, G.73, F.74, E.89, E.93, E.150 Ligands: MN.7, MN.8, MN.9, ADN.11 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:F.74, A:R.51 Water bridges: B:G.72 Salt bridges: B:H.37, B:R.63

2 x ADN: ADENOSINE(Non-covalent)

ADN.6: 11 residues within 4Å: Chain A: H.37, R.63, F.70, G.73, F.74, T.122, I.178, N.180, S.181, Q.184 Ligands: MGT.5 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.63, A:F.70, A:N.180, A:N.180, A:Q.184, A:Q.184 Water bridges: A:R.63 pi-Stacking: A:H.37 ADN.11: 10 residues within 4Å: Chain B: H.37, G.69, F.70, F.74, T.122, I.178, N.180, S.181, Q.184 Ligands: MGT.10 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:F.70, B:N.180, B:N.180, B:Q.184, B:Q.184 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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