Cobalt in PDB 4r4a: Racemic Crystal Structure of A Cobalt-Bound B-Dna Duplex

The structure of Racemic Crystal Structure of A Cobalt-Bound B-Dna Duplex, PDB code: 4r4a was solved by P.K.Mandal, G.W.Collie, B.Kauffmann, I.Huc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.33 / 1.49
Space group	P -1
Cell size a, b, c (Å), α, β, γ (°)	26.286, 32.352, 33.500, 62.25, 73.14, 68.56
R / Rfree (%)	20.9 / 23.3

The binding sites of Cobalt atom in the Racemic Crystal Structure of A Cobalt-Bound B-Dna Duplex (pdb code 4r4a). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 5 binding sites of Cobalt where determined in the Racemic Crystal Structure of A Cobalt-Bound B-Dna Duplex, PDB code: 4r4a:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5;

Cobalt binding site 1 out of 5 in the Racemic Crystal Structure of A Cobalt-Bound B-Dna Duplex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Racemic Crystal Structure of A Cobalt-Bound B-Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:8.5 occ:1.00 O A:HOH202 2.0 12.0 1.0 O A:HOH201 2.1 11.0 1.0 O B:HOH212 2.1 10.4 1.0 O A:HOH208 2.1 10.7 1.0 O A:HOH204 2.1 9.4 1.0 N7 A:DG3 2.2 8.2 1.0 C8 A:DG3 3.0 8.7 1.0 C5 A:DG3 3.3 6.7 1.0 O6 A:DG3 3.7 7.0 1.0 C6 A:DG3 3.9 6.7 1.0 O A:HOH229 3.9 14.2 0.7 O A:HOH215 4.0 14.8 1.0 OP2 A:DG3 4.2 14.0 1.0 O A:HOH231 4.2 20.4 0.9 N9 A:DG3 4.3 7.9 1.0 O B:HOH233 4.3 17.9 0.8 O B:HOH225 4.3 17.4 0.8 O6 A:DG4 4.3 7.1 1.0 C4 A:DG3 4.4 7.4 1.0 C6 A:DC2 4.9 8.7 1.0 C5 A:DC2 5.0 7.9 1.0

Cobalt binding site 2 out of 5 in the Racemic Crystal Structure of A Cobalt-Bound B-Dna Duplex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Racemic Crystal Structure of A Cobalt-Bound B-Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:9.2 occ:1.00 O A:HOH203 2.0 10.8 1.0 O A:HOH207 2.1 13.1 1.0 O A:HOH212 2.1 11.2 1.0 N7 A:DG9 2.2 6.9 1.0 O6 A:DG10 2.2 7.6 1.0 C8 A:DG9 3.0 7.9 1.0 C6 A:DG10 3.1 7.7 1.0 C5 A:DG9 3.2 6.6 1.0 N7 A:DG10 3.7 9.8 1.0 C5 A:DG10 3.7 7.9 1.0 O6 A:DG9 3.7 7.7 1.0 C6 A:DG9 3.8 6.6 1.0 C2' A:DC8 4.0 17.3 1.0 N4 B:DC1 4.0 7.3 0.6 N4 B:DC1 4.1 8.0 0.4 N9 A:DG9 4.2 7.8 1.0 N1 A:DG10 4.3 6.5 1.0 OP2 A:DG9 4.3 15.8 1.0 C4 A:DG9 4.3 6.8 1.0 C8 A:DG10 4.9 9.6 1.0 C3' A:DC8 4.9 15.9 1.0 C4 A:DG10 5.0 8.2 1.0

Cobalt binding site 3 out of 5 in the Racemic Crystal Structure of A Cobalt-Bound B-Dna Duplex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Racemic Crystal Structure of A Cobalt-Bound B-Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co103 b:8.4 occ:0.53 O A:HOH216 1.9 17.2 1.0 O A:HOH248 2.0 22.8 1.0 O B:HOH220 2.0 20.9 1.0 O B:HOH207 2.0 19.2 1.0 O B:HOH230 2.1 24.7 1.0 O A:HOH220 2.3 18.2 1.0 O B:HOH239 3.9 18.3 0.7 O A:HOH250 4.2 36.4 1.0 O4' B:DC7 4.3 10.5 1.0 N3 A:DA6 4.4 8.4 1.0 O4' A:DC7 4.6 11.6 1.0 C4' A:DC7 4.7 11.9 1.0 O B:HOH226 4.7 12.7 1.0 N3 B:DA6 4.7 8.2 1.0 C5' A:DC7 4.9 11.6 1.0 C2 A:DA6 4.9 8.1 1.0 C1' B:DC7 5.0 9.2 1.0

Cobalt binding site 4 out of 5 in the Racemic Crystal Structure of A Cobalt-Bound B-Dna Duplex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Racemic Crystal Structure of A Cobalt-Bound B-Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Co102 b:7.9 occ:1.00 O B:HOH202 2.1 9.4 1.0 O B:HOH211 2.1 9.4 1.0 O B:HOH209 2.1 9.6 1.0 O B:HOH213 2.1 8.3 1.0 O B:HOH210 2.1 10.8 1.0 N7 B:DG9 2.2 6.1 1.0 C8 B:DG9 3.0 6.7 1.0 C5 B:DG9 3.3 6.1 1.0 O6 B:DG9 3.8 6.9 1.0 C6 B:DG9 3.9 6.5 1.0 OP2 B:DG9 3.9 9.5 1.0 O B:HOH208 4.1 14.6 0.9 O B:HOH214 4.2 11.6 0.9 O B:HOH206 4.2 12.3 0.9 N9 B:DG9 4.3 6.4 1.0 O6 B:DG10 4.3 6.7 1.0 O A:HOH235 4.4 22.5 0.9 C4 B:DG9 4.4 5.7 1.0 O A:HOH218 4.4 15.6 1.0 C6 B:DC8 4.9 7.1 1.0 N4 A:DC1 5.0 7.4 0.6

Cobalt binding site 5 out of 5 in the Racemic Crystal Structure of A Cobalt-Bound B-Dna Duplex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Racemic Crystal Structure of A Cobalt-Bound B-Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Co103 b:11.5 occ:1.00 O B:HOH203 2.0 14.4 1.0 O B:HOH215 2.1 16.2 1.0 O B:HOH218 2.1 15.4 1.0 N7 B:DG3 2.2 8.9 1.0 C8 B:DG3 3.0 10.6 1.0 C5 B:DG3 3.3 8.8 1.0 O6 B:DG3 3.7 10.2 1.0 C6 B:DG3 3.9 8.4 1.0 O B:HOH222 4.0 17.0 1.0 N9 B:DG3 4.3 10.3 1.0 OP2 B:DG3 4.3 15.1 1.0 O B:HOH251 4.4 26.9 0.9 O6 B:DG4 4.4 10.1 1.0 O A:HOH224 4.4 18.6 0.9 C4 B:DG3 4.4 8.9 1.0 C2' B:DC2 4.9 14.0 1.0

P.K.Mandal, G.W.Collie, B.Kauffmann, I.Huc. Racemic Dna Crystallography. Angew.Chem.Int.Ed.Engl. 2014.
ISSN: ESSN 1521-3773
PubMed: 25358289
DOI: 10.1002/ANIE.201409014