Cobalt in PDB 3gx4: Crystal Structure Analysis of S. Pombe Atl in Complex with Dna

The structure of Crystal Structure Analysis of S. Pombe Atl in Complex with Dna, PDB code: 3gx4 was solved by J.L.Tubbs, A.S.Arvai, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.04 / 2.70
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	59.728, 59.728, 238.028, 90.00, 90.00, 120.00
R / Rfree (%)	22.7 / 29.6

The binding sites of Cobalt atom in the Crystal Structure Analysis of S. Pombe Atl in Complex with Dna (pdb code 3gx4). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure Analysis of S. Pombe Atl in Complex with Dna, PDB code: 3gx4:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure Analysis of S. Pombe Atl in Complex with Dna


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure Analysis of S. Pombe Atl in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ Y:Co302 b:0.4 occ:1.00 CO Y:NCO302 0.0 0.4 1.0 N3 Y:NCO302 2.0 0.2 1.0 N2 Y:NCO302 2.0 0.0 1.0 N1 Y:NCO302 2.0 0.4 1.0 N5 Y:NCO302 2.0 0.1 1.0 N6 Y:NCO302 2.0 0.1 1.0 N4 Y:NCO302 2.0 0.7 1.0 C2' Y:DG206 3.9 26.9 1.0 O5' Y:6OG207 4.0 21.2 1.0 C1' Y:DG206 4.0 32.1 1.0 C3' Y:6OG207 4.1 19.1 1.0 O5' Y:DC208 4.1 25.0 1.0 NE X:ARG39 4.1 21.9 1.0 N3 Y:DG206 4.2 33.5 1.0 NH1 X:ARG39 4.2 24.5 1.0 CB X:ARG39 4.4 17.2 1.0 N9 Y:DG206 4.4 31.9 1.0 OP2 Y:DC208 4.4 22.2 1.0 C5' Y:DC208 4.5 26.0 1.0 C4 Y:DG206 4.5 31.6 1.0 C6 Y:DC208 4.5 26.6 1.0 CG X:ARG39 4.5 18.0 1.0 O3' Y:DG206 4.6 35.1 1.0 O4' Y:DC208 4.6 25.1 1.0 P Y:DC208 4.6 26.1 1.0 CA X:ARG39 4.6 21.1 1.0 O X:ARG39 4.6 23.6 1.0 C5' Y:6OG207 4.7 28.1 1.0 CZ X:ARG39 4.7 26.0 1.0 C2' Y:6OG207 4.7 25.4 1.0 C5 Y:DC208 4.8 22.1 1.0 P Y:6OG207 4.8 32.3 1.0 OE1 X:GLN43 4.8 61.9 1.0 C3' Y:DG206 4.8 35.7 1.0 C4' Y:6OG207 4.9 24.5 1.0 O3' Y:6OG207 4.9 23.3 1.0 C2 Y:DG206 5.0 34.2 1.0 CD X:ARG39 5.0 19.8 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure Analysis of S. Pombe Atl in Complex with Dna


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure Analysis of S. Pombe Atl in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ Z:Co303 b:0.9 occ:1.00 CO Z:NCO303 0.0 0.9 1.0 N5 Z:NCO303 2.0 0.9 1.0 N4 Z:NCO303 2.1 0.2 1.0 N2 Z:NCO303 2.1 0.3 1.0 N3 Z:NCO303 2.1 1.0 1.0 N1 Z:NCO303 2.1 0.9 1.0 N6 Z:NCO303 2.1 0.7 1.0 O6 Z:DG226 3.3 40.9 1.0 O6 Y:DG201 3.9 26.9 1.0 C6 Z:DG226 4.4 39.4 1.0 N7 Z:DG225 4.4 35.0 1.0 N7 Z:DG226 4.5 38.3 1.0 N4 Y:DC202 4.6 36.8 1.0 O6 Z:DG225 4.7 32.1 1.0 C5 Z:DG226 4.9 39.9 1.0 C5 Z:DG225 5.0 34.5 1.0

J.L.Tubbs, V.Latypov, S.Kanugula, A.Butt, M.Melikishvili, R.Kraehenbuehl, O.Fleck, A.Marriott, A.J.Watson, B.Verbeek, G.Mcgown, M.Thorncroft, M.F.Santibanez-Koref, C.Millington, A.S.Arvai, M.D.Kroeger, L.A.Peterson, D.M.Williams, M.G.Fried, G.P.Margison, A.E.Pegg, J.A.Tainer. Flipping of Alkylated Dna Damage Bridges Base and Nucleotide Excision Repair. Nature V. 459 808 2009.
ISSN: ISSN 0028-0836
PubMed: 19516334
DOI: 10.1038/NATURE08076