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Cobalt in PDB 1xcs: Structure of Oligonucleotide/Drug Complex

Protein crystallography data

The structure of Structure of Oligonucleotide/Drug Complex, PDB code: 1xcs was solved by N.Valls, R.A.Steiner, G.Wright, G.N.Murshudov, J.A.Subirana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.82 / 1.40
Space group C 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 28.659, 53.473, 40.691, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 25.1

Other elements in 1xcs:

The structure of Structure of Oligonucleotide/Drug Complex also contains other interesting chemical elements:

Barium (Ba) 1 atom
Chlorine (Cl) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Structure of Oligonucleotide/Drug Complex (pdb code 1xcs). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Structure of Oligonucleotide/Drug Complex, PDB code: 1xcs:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 1xcs

Go back to Cobalt Binding Sites List in 1xcs
Cobalt binding site 1 out of 2 in the Structure of Oligonucleotide/Drug Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of Oligonucleotide/Drug Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co64

b:34.8
occ:1.00
O A:HOH89 1.9 31.1 1.0
O A:HOH90 2.0 39.5 1.0
O A:HOH79 2.1 32.7 1.0
N7 A:DG2 2.2 23.3 1.0
O A:HOH78 2.2 34.0 1.0
O A:HOH72 2.2 33.7 1.0
C8 A:DG2 3.0 24.6 1.0
C5 A:DG2 3.3 21.7 1.0
O6 A:DG2 3.7 20.9 1.0
C6 A:DG2 3.8 20.4 1.0
O A:HOH86 4.2 47.5 1.0
N9 A:DG2 4.3 24.5 1.0
O4 A:DT3 4.4 23.2 1.0
C4 A:DG2 4.4 22.4 1.0
O3' A:DC1 4.5 38.4 1.0
OP1 A:DG2 4.5 38.1 1.0
C7 A:DT3 4.6 25.1 1.0
C4 A:DT3 5.0 23.5 1.0

Cobalt binding site 2 out of 2 in 1xcs

Go back to Cobalt Binding Sites List in 1xcs
Cobalt binding site 2 out of 2 in the Structure of Oligonucleotide/Drug Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of Oligonucleotide/Drug Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co63

b:21.6
occ:0.50
O B:HOH67 2.0 22.6 1.0
N7 B:DG12 2.1 20.0 1.0
O B:HOH66 2.1 22.6 1.0
C8 B:DG12 3.0 20.8 1.0
C5 B:DG12 3.3 20.7 1.0
O6 B:DG12 3.7 23.3 1.0
C6 B:DG12 3.9 21.7 1.0
OP2 B:DG12 4.1 21.1 1.0
O B:HOH71 4.2 28.0 1.0
N9 B:DG12 4.3 20.4 1.0
C4 B:DG12 4.4 20.0 1.0
O B:HOH86 4.6 21.8 0.5
O5' B:DG12 4.9 20.1 1.0
P B:DG12 4.9 20.8 1.0

Reference:

N.Valls, R.A.Steiner, G.Wright, G.N.Murshudov, J.A.Subirana. Variable Role of Ions in Two Drug Intercalation Complexes of Dna J.Biol.Inorg.Chem. V. 10 476 2005.
ISSN: ISSN 0949-8257
PubMed: 15926069
DOI: 10.1007/S00775-005-0655-3
Page generated: Sun Dec 13 10:36:38 2020

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