SMTL ID : 1zrf.1

4 crystal structures of CAP-DNA with all base-pair substitutions at position 6, CAP-[6C;17G]ICAP38 DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

4 x CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE(Non-covalent)

CMP.1: 17 residues within 4Å: Chain E: I.30, V.49, L.61, S.62, I.70, G.71, E.72, L.73, R.82, S.83, A.84, V.86, Y.99, R.123, T.127 Chain F: L.124, S.128 14 PLIP interactions: 12 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:G.71, E:E.72, E:E.72, E:L.73, E:G.74, E:S.83, E:Y.99, E:R.123, E:T.127, F:S.128, F:S.128 Water bridges: E:S.62, E:S.83 Salt bridges: E:R.82 CMP.2: 12 residues within 4Å: Chain B: A.5, T.6 Chain E: K.57, E.58, Q.170, G.173, Q.174, G.177, C.178, S.179, R.180 Chain F: A.135 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:A.135, E:E.58, E:Q.170, E:R.180 CMP.6: 17 residues within 4Å: Chain E: L.124, S.128 Chain F: V.49, L.61, S.62, I.70, G.71, E.72, L.73, G.74, R.82, S.83, A.84, V.86, Y.99, R.123, T.127 13 PLIP interactions: 11 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:G.71, F:E.72, F:E.72, F:L.73, F:G.74, F:S.83, F:Y.99, F:R.123, E:S.128, E:S.128 Water bridges: F:S.62, F:T.127 Salt bridges: F:R.82 CMP.7: 11 residues within 4Å: Chain D: A.5 Chain E: A.135 Chain F: K.57, E.58, Q.170, G.173, Q.174, G.177, C.178, S.179, R.180 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:E.58, F:Q.170, F:R.180, F:R.180, E:A.135 pi-Cation interactions: F:K.57

5 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.3: 6 residues within 4Å: Chain E: A.144, L.148, L.190, L.195, I.196, V.205 No protein-ligand interaction detected (PLIP) DIO.4: 7 residues within 4Å: Chain E: T.10, L.11, F.14, Y.41, F.69, I.112, R.115 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.115 DIO.5: 7 residues within 4Å: Chain E: K.130, N.133, L.134, R.142, T.146, I.175, V.176 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.130 Water bridges: E:Q.145 DIO.8: 5 residues within 4Å: Chain F: A.144, L.147, L.148, I.196, V.205 No protein-ligand interaction detected (PLIP) DIO.9: 5 residues within 4Å: Chain F: K.130, R.142, T.146, I.175, V.176 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:K.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Napoli, A.A. et al., Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps. J.Mol.Biol. (2006)

Release Date

2006-03-21

Peptides

Catabolite gene activator: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

E
A

F
B

Catabolite gene activator

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