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Vanadium in PDB 3mgv: Cre Recombinase-Dna Transition State

Protein crystallography data

The structure of Cre Recombinase-Dna Transition State, PDB code: 3mgv was solved by B.P.Gibb, K.Gupta, K.Ghosh, R.Sharp, J.Chen, G.D.Van Duyne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.57 / 2.29
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 136.046, 136.046, 218.431, 90.00, 90.00, 120.00
R / Rfree (%) 19.3 / 22.2

Vanadium Binding Sites:

The binding sites of Vanadium atom in the Cre Recombinase-Dna Transition State (pdb code 3mgv). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 2 binding sites of Vanadium where determined in the Cre Recombinase-Dna Transition State, PDB code: 3mgv:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in 3mgv

Go back to Vanadium Binding Sites List in 3mgv
Vanadium binding site 1 out of 2 in the Cre Recombinase-Dna Transition State


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Cre Recombinase-Dna Transition State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V690

b:18.5
occ:1.00
V B:VO4690 0.0 18.5 1.0
O3' E:DG15 1.8 15.8 1.0
O1 B:VO4690 1.9 17.2 1.0
O2 B:VO4690 1.9 15.1 1.0
OH B:TYR324 2.1 21.9 1.0
O5' F:DC1 2.1 20.9 1.0
C5' F:DC1 2.9 16.4 1.0
C3' E:DG15 3.0 18.8 1.0
CZ B:TYR324 3.0 22.1 1.0
CE1 B:TYR324 3.3 21.7 1.0
C4' E:DG15 3.4 17.7 1.0
NH2 B:ARG173 3.7 14.9 1.0
NZ B:LYS201 3.9 19.6 1.0
NE B:ARG292 3.9 14.4 1.0
NE2 B:HIS289 3.9 22.9 1.0
NE B:ARG173 4.0 16.2 1.0
O B:HOH347 4.0 11.3 1.0
C2' E:DG15 4.2 16.9 1.0
CE2 B:TYR324 4.3 21.2 1.0
NH2 B:ARG292 4.3 13.2 1.0
C4' F:DC1 4.3 18.8 1.0
CZ B:ARG173 4.3 17.1 1.0
NE1 B:TRP315 4.3 25.1 1.0
O4' E:DG15 4.3 17.1 1.0
C1' E:DG15 4.3 19.0 1.0
C5' E:DG15 4.5 18.2 1.0
CZ B:ARG292 4.6 13.0 1.0
CD1 B:TYR324 4.7 19.6 1.0
CE1 B:HIS289 4.7 20.1 1.0
O4' F:DC1 4.8 18.8 1.0
CD1 B:ILE320 4.8 19.0 1.0
CD B:ARG292 4.8 15.7 1.0
CD B:LYS201 4.9 20.0 1.0
CD2 B:HIS289 4.9 21.7 1.0
CG1 B:ILE320 5.0 22.2 1.0

Vanadium binding site 2 out of 2 in 3mgv

Go back to Vanadium Binding Sites List in 3mgv
Vanadium binding site 2 out of 2 in the Cre Recombinase-Dna Transition State


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of Cre Recombinase-Dna Transition State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:V690

b:15.2
occ:1.00
V D:VO4690 0.0 15.2 1.0
O3' I:DG15 1.8 16.2 1.0
O2 D:VO4690 1.9 15.5 1.0
O1 D:VO4690 1.9 16.7 1.0
O5' K:DC1 1.9 21.6 1.0
OH D:TYR324 2.0 14.0 1.0
C5' K:DC1 2.7 19.9 1.0
C3' I:DG15 3.0 13.8 1.0
CZ D:TYR324 3.0 14.5 1.0
CE1 D:TYR324 3.3 15.0 1.0
C4' I:DG15 3.4 13.3 1.0
NH2 D:ARG173 3.7 12.6 1.0
NE2 D:HIS289 3.9 15.2 1.0
NZ D:LYS201 3.9 19.2 1.0
NE D:ARG292 4.0 13.3 1.0
NE D:ARG173 4.0 12.7 1.0
O D:HOH351 4.0 18.0 1.0
C4' K:DC1 4.1 19.5 1.0
C2' I:DG15 4.2 13.8 1.0
CE2 D:TYR324 4.2 14.8 1.0
O4' I:DG15 4.3 17.2 1.0
CZ D:ARG173 4.3 15.1 1.0
NH2 D:ARG292 4.3 12.2 1.0
C1' I:DG15 4.3 16.1 1.0
NE1 D:TRP315 4.4 19.0 1.0
CE1 D:HIS289 4.6 14.4 1.0
C5' I:DG15 4.6 11.8 1.0
O4' K:DC1 4.6 20.4 1.0
CZ D:ARG292 4.6 15.7 1.0
CD1 D:TYR324 4.6 14.9 1.0
CD1 D:ILE320 4.8 15.9 1.0
CD D:ARG292 4.9 12.6 1.0
CD D:LYS201 4.9 18.5 1.0
CD2 D:HIS289 5.0 16.0 1.0

Reference:

B.Gibb, K.Gupta, K.Ghosh, R.Sharp, J.Chen, G.D.Van Duyne. Requirements For Catalysis in the Cre Recombinase Active Site. Nucleic Acids Res. V. 38 5817 2010.
ISSN: ISSN 0305-1048
PubMed: 20462863
DOI: 10.1093/NAR/GKQ384
Page generated: Wed Dec 16 02:30:54 2020

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