SMTL ID : 2gja.1

Structure of the MnmE G-domain in complex with GDP*AlF4-, Mg2+ and NH4+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.1: 14 residues within 4Å: Chain A: P.13, N.14, K.17, S.18, I.35, A.36, G.37, T.38, T.39, A.60, G.61 Ligands: MG.2, NH4.3, GDP.4 No protein-ligand interaction detected (PLIP) ALF.5: 14 residues within 4Å: Chain B: P.13, N.14, K.17, S.18, I.35, A.36, G.37, T.38, T.39, A.60, G.61 Ligands: MG.6, NH4.7, GDP.8 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.18, T.39 Ligands: ALF.1, GDP.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.18, A:T.39, H2O.3, H2O.3 MG.6: 5 residues within 4Å: Chain B: S.18, T.39, D.58 Ligands: ALF.5, GDP.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.18, B:T.39, H2O.6, H2O.6

2 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.3: 6 residues within 4Å: Chain A: N.14, T.33, I.35, T.38 Ligands: ALF.1, GDP.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.33 Water bridges: A:T.39 NH4.7: 6 residues within 4Å: Chain B: N.14, T.33, I.35, T.38 Ligands: ALF.5, GDP.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.14 Water bridges: B:T.39

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.4: 19 residues within 4Å: Chain A: N.14, A.15, G.16, K.17, S.18, S.19, V.32, T.33, D.34, N.123, K.124, D.126, I.127, S.146, A.147, R.148 Ligands: ALF.1, MG.2, NH4.3 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:N.14, A:A.15, A:G.16, A:K.17, A:S.18, A:S.19, A:S.19, A:T.33, A:T.33, A:N.123, A:K.124, A:K.124, A:S.146, A:A.147, A:R.148, A:R.148, A:R.148 Water bridges: A:S.18, A:T.39, A:G.61 Salt bridges: A:K.17, A:D.126 GDP.8: 19 residues within 4Å: Chain B: N.14, A.15, G.16, K.17, S.18, S.19, V.32, T.33, D.34, N.123, K.124, D.126, I.127, S.146, A.147, R.148 Ligands: ALF.5, MG.6, NH4.7 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:N.14, B:A.15, B:G.16, B:K.17, B:S.18, B:S.19, B:S.19, B:T.33, B:T.33, B:N.123, B:K.124, B:K.124, B:S.146, B:A.147, B:R.148, B:R.148, B:R.148 Water bridges: B:S.18, B:T.39, B:T.39, B:G.61 Salt bridges: B:K.17, B:D.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scrima, A. et al., Dimerisation-dependent GTPase reaction of MnmE: how potassium acts as GTPase-activating element. Embo J. (2006)

Release Date

2006-07-04

Peptides

tRNA modification GTPase trmE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

tRNA modification GTPase trmE

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