SMTL ID : 3ovb.1

How the CCA-adding Enzyme Selects Adenine over Cytosine in Position 76 of tRNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)(Non-functional Binders)

ATP.1: 18 residues within 4Å: Chain A: G.46, S.47, R.50, E.59, D.61, T.130, H.133, K.152, Y.161, A.163, Y.173, R.224 Chain C: A.32, C.33, C.34, A.35 Ligands: MG.7, POP.13 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:S.47, A:S.47, A:S.47, A:R.50, A:R.50, A:H.133, A:Y.173, A:R.224 Water bridges: A:G.46, A:S.47, A:Y.48, A:Y.48, A:S.57, A:K.152, A:S.171, A:G.172, A:G.172 Salt bridges: A:K.152, A:K.152 ATP.8: 17 residues within 4Å: Chain B: G.46, S.47, R.50, D.61, T.130, H.133, K.152, Y.161, A.163, Y.173, R.224 Chain D: A.32, C.33, C.34, A.35 Ligands: POP.9, MG.12 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.47, B:S.47, B:R.50, B:R.50, B:H.133, B:R.224 Water bridges: B:G.172 Salt bridges: B:K.152, B:K.152 ATP.14: 4 residues within 4Å: Chain C: U.14, A.16, A.17, U.19 No protein-ligand interaction detected (PLIP)

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: R.299, R.302, K.303 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.299, A:R.302, A:K.303 SO4.10: 3 residues within 4Å: Chain B: R.299, R.302, K.303 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.299, B:R.302, B:K.303

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: W.397, E.406, R.409, E.410 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.406, A:R.409 EDO.4: 5 residues within 4Å: Chain A: V.40, E.41, L.64, L.65, F.66 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.41, A:L.65 Water bridges: A:G.39, A:E.41, A:L.65 EDO.5: 4 residues within 4Å: Chain A: K.436, D.437 Chain B: R.366 Ligands: EDO.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.437 EDO.6: 3 residues within 4Å: Chain A: H.398 Chain C: U.23, U.24 No protein-ligand interaction detected (PLIP) EDO.11: 7 residues within 4Å: Chain A: K.257, V.435, D.437, C.438, C.439 Chain B: R.366 Ligands: EDO.5 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:V.435, A:D.437, A:C.438, A:C.439, B:R.366, B:R.366

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 6 residues within 4Å: Chain A: S.47, E.59, D.61 Chain C: A.35 Ligands: ATP.1, POP.13 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.59 MG.12: 6 residues within 4Å: Chain B: S.47, E.59, D.61 Chain D: A.35 Ligands: ATP.8, POP.9 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.61

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

POP.9: 11 residues within 4Å: Chain B: G.46, S.47, R.50, K.152, Y.161, G.172, Y.173, E.176 Chain D: A.35 Ligands: ATP.8, MG.12 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.47, B:S.47, B:R.50, B:Y.161, B:Y.161, B:G.172, B:Y.173, B:E.176 Salt bridges: B:K.152, B:K.152 POP.13: 10 residues within 4Å: Chain A: G.46, S.47, R.50, D.61, K.152, Y.161, G.172 Chain C: A.35 Ligands: ATP.1, MG.7 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.47, A:S.47, A:R.50, A:Y.161, A:G.172 Water bridges: A:Y.48, A:K.152, A:K.152, A:Y.161, A:Y.173 Salt bridges: A:K.152, A:K.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pan, B. et al., How the CCA-Adding Enzyme Selects Adenine over Cytosine at Position 76 of tRNA. Science (2010)

Release Date

2010-12-01

Peptides

CCA-Adding Enzyme: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CCA-Adding Enzyme