Cobalt in PDB 2f7n: Structure of D. Radiodurans Dps-1

The structure of Structure of D. Radiodurans Dps-1, PDB code: 2f7n was solved by Y.H.Lee, S.G.Kim, G.Bhattacharyya, A.Grove, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.00
Space group	P 2 3
Cell size a, b, c (Å), α, β, γ (°)	90.130, 90.130, 90.130, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 22

The binding sites of Cobalt atom in the Structure of D. Radiodurans Dps-1 (pdb code 2f7n). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Structure of D. Radiodurans Dps-1, PDB code: 2f7n:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Structure of D. Radiodurans Dps-1


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of D. Radiodurans Dps-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co208 b:23.0 occ:0.33 OD1 A:ASP93 2.2 21.3 1.0 O A:HOH286 2.4 72.2 0.3 OD2 A:ASP93 2.6 19.1 1.0 CG A:ASP93 2.7 19.4 1.0 CB A:ASP93 4.2 18.8 1.0 O A:HOH318 4.2 23.9 1.0 N A:ASP93 4.8 17.2 1.0 CA A:ASP93 4.8 18.4 1.0 CD2 A:PHE90 5.0 22.3 1.0

Cobalt binding site 2 out of 4 in the Structure of D. Radiodurans Dps-1


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of D. Radiodurans Dps-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co209 b:22.2 occ:1.00 OE2 A:GLU114 2.3 18.3 1.0 OD2 A:ASP110 2.3 15.6 1.0 OD1 A:ASP110 2.5 18.6 1.0 CG A:ASP110 2.7 18.1 1.0 CD A:GLU114 2.9 17.6 1.0 OE1 A:GLU114 3.2 16.2 1.0 O A:HOH257 3.8 24.0 1.0 CG A:GLU114 4.1 18.1 1.0 CB A:ASP110 4.2 17.5 1.0 O A:HOH259 4.8 23.8 1.0

Cobalt binding site 3 out of 4 in the Structure of D. Radiodurans Dps-1


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of D. Radiodurans Dps-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co210 b:29.4 occ:1.00 OD1 A:ASP36 1.9 22.9 1.0 NE2 A:HIS50 2.1 25.0 1.0 NE2 A:HIS39 2.1 28.4 1.0 OE2 A:GLU55 2.2 26.0 1.0 CG A:ASP36 2.7 24.7 1.0 OE1 A:GLU55 2.8 25.9 1.0 CD A:GLU55 2.9 24.0 1.0 OD2 A:ASP36 2.9 22.2 1.0 CE1 A:HIS50 3.0 22.6 1.0 CD2 A:HIS39 3.0 28.2 1.0 CE1 A:HIS39 3.1 28.0 1.0 CD2 A:HIS50 3.1 22.3 1.0 NE2 A:GLN59 3.8 34.1 1.0 ND1 A:HIS50 4.2 21.8 1.0 ND1 A:HIS39 4.2 26.9 1.0 CG A:HIS39 4.2 28.0 1.0 CB A:ASP36 4.2 25.1 1.0 CG A:HIS50 4.2 23.1 1.0 CD2 A:PHE58 4.3 22.9 1.0 CB A:ALA38 4.3 23.6 1.0 CG A:GLU55 4.3 22.7 1.0 CE2 A:PHE58 4.5 24.4 1.0

Cobalt binding site 4 out of 4 in the Structure of D. Radiodurans Dps-1


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of D. Radiodurans Dps-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co211 b:38.3 occ:0.33 OD1 A:ASP181 2.5 29.5 1.0 O A:HOH328 2.6 38.7 1.0 OD2 A:ASP181 3.1 29.1 1.0 CG A:ASP181 3.1 26.8 1.0 CB A:ASP181 4.6 24.1 1.0 O A:ASP181 4.8 19.9 1.0

S.G.Kim, G.Bhattacharyya, A.Grove, Y.H.Lee. Crystal Structure of Dps-1, A Functionally Distinct Dps Protein From Deinococcus Radiodurans. J.Mol.Biol. V. 361 105 2006.
ISSN: ISSN 0022-2836
PubMed: 16828801
DOI: 10.1016/J.JMB.2006.06.010