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Cobalt in PDB 1xcu: Oligonucleotid/Drug Complex

Protein crystallography data

The structure of Oligonucleotid/Drug Complex, PDB code: 1xcu 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) 25.00 / 2.00
Space group C 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 29.056, 52.856, 40.084, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 25.2

Other elements in 1xcu:

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

Barium (Ba) 1 atom
Sodium (Na) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Oligonucleotid/Drug Complex (pdb code 1xcu). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Oligonucleotid/Drug Complex, PDB code: 1xcu:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in 1xcu

Go back to Cobalt Binding Sites List in 1xcu
Cobalt binding site 1 out of 3 in the Oligonucleotid/Drug Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Oligonucleotid/Drug Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co33

b:53.4
occ:1.00
O A:HOH43 2.2 52.0 1.0
O A:HOH49 2.2 49.7 1.0
O A:HOH52 2.2 52.4 1.0
O A:HOH48 2.2 51.9 1.0
O A:HOH51 2.2 53.6 1.0
N7 A:DG2 2.3 33.6 1.0
C8 A:DG2 3.2 36.9 1.0
C5 A:DG2 3.3 36.4 1.0
O6 A:DG2 3.6 33.8 1.0
C6 A:DG2 3.8 35.6 1.0
O A:HOH42 4.0 42.5 1.0
O3' A:DC1 4.3 60.4 1.0
N9 A:DG2 4.4 36.3 1.0
C4 A:DG2 4.5 36.5 1.0
O4 A:DT3 4.5 36.1 1.0
C7 A:DT3 4.6 44.3 1.0
OP1 A:DG2 4.7 58.3 1.0

Cobalt binding site 2 out of 3 in 1xcu

Go back to Cobalt Binding Sites List in 1xcu
Cobalt binding site 2 out of 3 in the Oligonucleotid/Drug Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Oligonucleotid/Drug Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co35

b:40.4
occ:0.25
O A:HOH53 1.9 39.1 0.2
OP1 A:DG6 2.1 50.1 1.0
P A:DG6 3.3 52.5 1.0
O3' A:DC5 3.4 46.5 1.0
O5' A:DG6 4.0 49.5 1.0
O A:HOH44 4.0 33.7 0.5
C3' A:DC5 4.4 44.9 1.0
OP2 A:DG6 4.6 50.7 1.0
C4' A:DC5 4.7 43.8 1.0
O A:HOH44 4.8 37.8 0.5

Cobalt binding site 3 out of 3 in 1xcu

Go back to Cobalt Binding Sites List in 1xcu
Cobalt binding site 3 out of 3 in the Oligonucleotid/Drug Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Oligonucleotid/Drug Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co32

b:35.9
occ:0.50
O B:HOH49 2.0 38.0 1.0
O B:HOH46 2.1 37.7 1.0
N7 B:DG12 2.2 32.9 1.0
C8 B:DG12 3.1 34.5 1.0
C5 B:DG12 3.4 37.4 1.0
O6 B:DG12 3.8 36.5 1.0
C6 B:DG12 4.0 40.1 1.0
OP2 B:DG12 4.0 35.2 1.0
BA B:BA34 4.2 37.7 0.2
O B:HOH48 4.3 47.4 1.0
N9 B:DG12 4.3 33.3 1.0
O B:HOH55 4.4 43.5 1.0
C4 B:DG12 4.5 33.9 1.0
P B:DG12 5.0 37.2 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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