Cobalt in PDB 2b1d: 5'-D(*Gp*Cp*Ap*Gp*Ap*Cp*Gp*Tp*Cp*Tp*Gp*C)-3' Methionine Repressor Binding Site

The structure of 5'-D(*Gp*Cp*Ap*Gp*Ap*Cp*Gp*Tp*Cp*Tp*Gp*C)-3' Methionine Repressor Binding Site, PDB code: 2b1d was solved by H.M.Berman, J.W.Locasale, A.A.Napoli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.84 / 2.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	39.980, 40.346, 40.255, 82.15, 69.13, 81.44
R / Rfree (%)	23.5 / 28.4

The structure of 5'-D(*Gp*Cp*Ap*Gp*Ap*Cp*Gp*Tp*Cp*Tp*Gp*C)-3' Methionine Repressor Binding Site also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Cobalt atom in the 5'-D(*Gp*Cp*Ap*Gp*Ap*Cp*Gp*Tp*Cp*Tp*Gp*C)-3' Methionine Repressor Binding Site (pdb code 2b1d). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the 5'-D(*Gp*Cp*Ap*Gp*Ap*Cp*Gp*Tp*Cp*Tp*Gp*C)-3' Methionine Repressor Binding Site, PDB code: 2b1d:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the 5'-D(*Gp*Cp*Ap*Gp*Ap*Cp*Gp*Tp*Cp*Tp*Gp*C)-3' Methionine Repressor Binding Site


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of 5'-D(*Gp*Cp*Ap*Gp*Ap*Cp*Gp*Tp*Cp*Tp*Gp*C)-3' Methionine Repressor Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Co2505 b:63.8 occ:1.00 CO A:NCO2505 0.0 63.8 1.0 N6 A:NCO2505 1.9 55.1 1.0 N1 A:NCO2505 1.9 64.8 1.0 N5 A:NCO2505 2.0 69.8 1.0 N4 A:NCO2505 2.0 49.3 1.0 N2 A:NCO2505 2.0 71.1 1.0 N3 A:NCO2505 2.0 55.5 1.0 O A:HOH2553 4.1 71.3 1.0 O6 A:DG4 4.1 10.8 1.0 OP2 C:DG4 4.2 42.2 1.0 N7 A:DG4 4.3 11.6 1.0 O A:HOH2512 4.7 75.4 1.0 OP1 C:DG4 4.8 52.0 1.0 OP1 F:DA15 4.9 63.4 1.0 OP2 F:DA15 4.9 72.5 1.0 C6 A:DG4 4.9 8.8 1.0

Cobalt binding site 2 out of 3 in the 5'-D(*Gp*Cp*Ap*Gp*Ap*Cp*Gp*Tp*Cp*Tp*Gp*C)-3' Methionine Repressor Binding Site


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of 5'-D(*Gp*Cp*Ap*Gp*Ap*Cp*Gp*Tp*Cp*Tp*Gp*C)-3' Methionine Repressor Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Co2507 b:64.7 occ:1.00 CO C:NCO2507 0.0 64.7 1.0 N1 C:NCO2507 1.9 61.7 1.0 N6 C:NCO2507 1.9 56.5 1.0 N4 C:NCO2507 2.0 50.0 1.0 N3 C:NCO2507 2.0 53.9 1.0 N5 C:NCO2507 2.0 73.8 1.0 N2 C:NCO2507 2.0 55.8 1.0 O C:HOH2636 4.0 76.2 1.0 OP2 E:DC6 4.0 71.3 1.0 OP2 A:DG4 4.0 29.2 1.0 O6 C:DG4 4.1 13.6 1.0 N7 C:DG4 4.2 19.9 1.0 C6 C:DG4 4.9 27.0 1.0 OP1 A:DG4 4.9 49.1 1.0 C5 C:DG4 5.0 23.4 1.0 N7 C:DA3 5.0 29.2 1.0 P A:DG4 5.0 37.7 1.0

Cobalt binding site 3 out of 3 in the 5'-D(*Gp*Cp*Ap*Gp*Ap*Cp*Gp*Tp*Cp*Tp*Gp*C)-3' Methionine Repressor Binding Site


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of 5'-D(*Gp*Cp*Ap*Gp*Ap*Cp*Gp*Tp*Cp*Tp*Gp*C)-3' Methionine Repressor Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ F:Co2506 b:72.7 occ:1.00 CO F:NCO2506 0.0 72.7 1.0 N3 F:NCO2506 1.9 83.5 1.0 N1 F:NCO2506 1.9 64.7 1.0 N4 F:NCO2506 1.9 77.7 1.0 N6 F:NCO2506 2.0 76.4 1.0 N2 F:NCO2506 2.0 73.7 1.0 N5 F:NCO2506 2.0 89.0 1.0 O6 F:DG16 4.1 37.7 1.0 OP1 A:DA3 4.2 48.8 1.0 OP1 C:DA3 4.2 47.5 1.0 N7 F:DG16 4.3 30.9 1.0 OP2 C:DA3 4.6 40.8 1.0 O A:HOH2571 4.7 84.2 1.0 O4 E:DT8 4.9 51.3 1.0 C6 F:DG16 4.9 34.4 1.0 P C:DA3 4.9 37.0 1.0 C5 F:DG16 4.9 41.5 1.0

J.W.Locasale, A.A.Napoli, S.Chen, H.M.Berman, C.L.Lawson. Signatures of Protein-Dna Recognition in Free Dna Binding Sites. J.Mol.Biol. V. 386 1054 2009.
ISSN: ISSN 0022-2836
PubMed: 19244617