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Cobalt in PDB 4mnb: Crystal Structure of A Complex Between the Marine Anticancer Drug Variolin B and Dna

Protein crystallography data

The structure of Crystal Structure of A Complex Between the Marine Anticancer Drug Variolin B and Dna, PDB code: 4mnb was solved by A.Canals, R.Arribas-Bosacoma, M.Alvarez, F.Albericio, J.Aymami, M.Coll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.79 / 1.40
Space group C 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 28.700, 53.400, 40.800, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.3

Other elements in 4mnb:

The structure of Crystal Structure of A Complex Between the Marine Anticancer Drug Variolin B and Dna also contains other interesting chemical elements:

Sodium (Na) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of A Complex Between the Marine Anticancer Drug Variolin B and Dna (pdb code 4mnb). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Crystal Structure of A Complex Between the Marine Anticancer Drug Variolin B and Dna, PDB code: 4mnb:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 4mnb

Go back to Cobalt Binding Sites List in 4mnb
Cobalt binding site 1 out of 4 in the Crystal Structure of A Complex Between the Marine Anticancer Drug Variolin B and Dna


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of A Complex Between the Marine Anticancer Drug Variolin B and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co103

b:21.7
occ:1.00
CO A:NCO103 0.0 21.7 1.0
N5 A:NCO103 2.0 24.1 1.0
N3 A:NCO103 2.0 21.8 1.0
N1 A:NCO103 2.0 20.8 1.0
N6 A:NCO103 2.1 43.9 1.0
N7 A:DG2 2.2 13.9 1.0
N4 A:NCO103 2.2 36.2 1.0
C8 A:DG2 3.0 13.9 1.0
C5 A:DG2 3.3 11.8 1.0
O6 A:DG2 3.6 12.0 1.0
C6 A:DG2 3.8 11.0 1.0
O A:HOH205 4.0 20.6 1.0
N9 A:DG2 4.3 14.8 1.0
O4 A:DT3 4.4 15.1 1.0
C4 A:DG2 4.4 12.1 1.0
O A:HOH203 4.5 39.7 1.0
OP2 A:DG2 4.5 38.3 1.0
C7 A:DT3 4.5 15.3 1.0
OP1 A:DG2 4.7 30.2 1.0
C4 A:DT3 4.9 15.7 1.0

Cobalt binding site 2 out of 4 in 4mnb

Go back to Cobalt Binding Sites List in 4mnb
Cobalt binding site 2 out of 4 in the Crystal Structure of A Complex Between the Marine Anticancer Drug Variolin B and Dna


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of A Complex Between the Marine Anticancer Drug Variolin B and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co104

b:51.8
occ:0.25
OP1 A:DG6 3.7 37.0 1.0
O3' A:DC5 4.7 25.1 1.0
P A:DG6 4.9 28.6 1.0

Cobalt binding site 3 out of 4 in 4mnb

Go back to Cobalt Binding Sites List in 4mnb
Cobalt binding site 3 out of 4 in the Crystal Structure of A Complex Between the Marine Anticancer Drug Variolin B and Dna


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of A Complex Between the Marine Anticancer Drug Variolin B and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co101

b:13.5
occ:0.50
CO B:NCO101 0.0 13.5 0.5
N4 B:NCO101 2.0 16.5 0.5
N6 B:NCO101 2.0 8.0 0.5
N1 B:NCO101 2.1 11.4 0.5
N5 B:NCO101 2.1 16.6 0.5
N7 B:DG12 2.2 13.3 1.0
C8 B:DG12 3.1 13.3 1.0
C5 B:DG12 3.4 13.4 1.0
O6 B:DG12 3.8 16.9 1.0
C6 B:DG12 3.9 14.8 1.0
OP2 B:DG12 4.2 13.5 1.0
O B:HOH202 4.3 25.6 1.0
N9 B:DG12 4.3 12.4 1.0
C4 B:DG12 4.5 11.8 1.0
O B:HOH209 4.8 31.6 0.5
O5' B:DG12 5.0 11.6 1.0
P B:DG12 5.0 12.8 1.0

Cobalt binding site 4 out of 4 in 4mnb

Go back to Cobalt Binding Sites List in 4mnb
Cobalt binding site 4 out of 4 in the Crystal Structure of A Complex Between the Marine Anticancer Drug Variolin B and Dna


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of A Complex Between the Marine Anticancer Drug Variolin B and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co102

b:39.9
occ:1.00
CO B:NCO102 0.0 39.9 1.0
N2 B:NCO102 2.0 29.8 1.0
N1 B:NCO102 2.0 38.5 1.0
N7 B:DG8 2.3 20.5 1.0
C8 B:DG8 3.3 20.2 1.0
C5 B:DG8 3.4 15.4 1.0
O6 B:DG8 3.6 16.0 1.0
O1 A:VAR101 3.9 33.1 0.5
C6 B:DG8 3.9 14.6 1.0
O B:HOH210 3.9 32.2 1.0
N6 A:VAR102 4.0 31.2 0.5
N7 A:VAR102 4.5 31.1 0.5
N9 B:DG8 4.5 17.5 1.0
C12 A:VAR102 4.5 28.4 0.5
C4 B:DG8 4.6 15.4 1.0
OP1 B:DG8 4.7 36.1 1.0
N6 A:VAR101 4.8 19.3 0.5
C1 A:VAR101 4.9 26.1 0.5

Reference:

A.Canals, R.Arribas-Bosacoma, M.Alvarez, F.Albericio, J.Aymami, M.Coll. Crystal Structure of A Complex Between the Marine Anticancer Drug Variolin B and Dna To Be Published.
Page generated: Sun Dec 13 10:45:14 2020

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