Calcium in PDB 5d9i: SV40 Large T Antigen Origin Binding Domain Bound to Artificial Dna Fork

The structure of SV40 Large T Antigen Origin Binding Domain Bound to Artificial Dna Fork, PDB code: 5d9i was solved by G.Meinke, A.Bohm, P.A.Bullock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	94.192, 63.393, 64.891, 90.00, 92.42, 90.00
R / Rfree (%)	18 / 22.3

The binding sites of Calcium atom in the SV40 Large T Antigen Origin Binding Domain Bound to Artificial Dna Fork (pdb code 5d9i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the SV40 Large T Antigen Origin Binding Domain Bound to Artificial Dna Fork, PDB code: 5d9i:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the SV40 Large T Antigen Origin Binding Domain Bound to Artificial Dna Fork


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of SV40 Large T Antigen Origin Binding Domain Bound to Artificial Dna Fork within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:45.7 occ:0.50 O B:HOH433 2.2 34.1 1.0 O B:ALA212 2.6 29.0 1.0 OH B:CME216 2.7 48.8 1.0 O B:CME216 2.8 31.1 1.0 CZ B:CME216 3.4 47.3 1.0 N B:CME216 3.4 31.1 1.0 CB B:CME216 3.5 36.5 1.0 CE B:LYS167 3.6 30.5 1.0 C B:ALA212 3.6 26.2 1.0 O B:GLN213 3.6 26.4 1.0 C B:CME216 3.7 30.7 1.0 NZ B:LYS167 3.7 27.4 1.0 CD1 B:LEU221 3.8 21.4 1.0 CA B:CME216 3.8 32.7 1.0 CA B:GLN213 3.8 24.7 1.0 C B:GLN213 3.9 26.6 1.0 N B:GLN213 4.2 25.6 1.0 N B:LEU215 4.5 26.7 1.0 O B:HOH447 4.5 39.0 1.0 C B:LEU215 4.5 28.4 1.0 CB B:LEU215 4.6 26.7 1.0 SG B:CME216 4.8 44.2 1.0 CE B:CME216 4.8 44.5 1.0 CA B:LEU215 4.8 28.1 1.0 CA B:ALA212 4.8 25.8 1.0 N B:LYS214 4.9 26.9 1.0 CB B:LEU221 5.0 21.6 1.0 N B:THR217 5.0 30.7 1.0 CD B:LYS167 5.0 28.0 1.0 CG B:LEU221 5.0 21.6 1.0

Calcium binding site 2 out of 2 in the SV40 Large T Antigen Origin Binding Domain Bound to Artificial Dna Fork


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of SV40 Large T Antigen Origin Binding Domain Bound to Artificial Dna Fork within 5.0Å range: probe atom residue distance (Å) B Occ Y:Ca101 b:26.7 occ:1.00 OP2 Y:DG22 2.4 38.9 1.0 O Y:HOH201 2.4 25.8 1.0 P Y:DG22 3.6 38.5 1.0 OP1 Y:DG22 4.1 38.2 1.0 N1 X:DG1 4.2 42.0 1.0 O Y:HOH202 4.3 36.3 1.0 O A:HOH450 4.3 27.8 1.0 O5' Y:DG22 4.3 38.9 1.0 C8 Y:DG22 4.5 40.7 1.0 OXT Y:ACT102 4.5 29.3 1.0 N2 X:DG1 4.7 40.6 1.0 O6 X:DG1 4.8 44.1 1.0 O3' Y:DG21 4.8 38.5 1.0 C6 X:DG1 4.9 43.1 1.0 C2 X:DG1 4.9 41.2 1.0

G.Meinke, P.J.Phelan, A.Fradet-Turcotte, A.Bohm, J.Archambault, P.A.Bullock. Structure-Based Analysis of the Interaction Between the Simian Virus 40 T-Antigen Origin Binding Domain and Single-Stranded Dna. J. Virol. V. 85 818 2011.
ISSN: ESSN 1098-5514
PubMed: 20980496
DOI: 10.1128/JVI.01738-10