Sodium in the structure of Crystal Structure Of the Bromo Domain 2 of Human Bromodomain Containing Protein 3 (BRD3) (pdb 2oo1)

The binding sites of Sodium atom in the structure of Crystal Structure Of the Bromo Domain 2 of Human Bromodomain Containing Protein 3 (BRD3) (pdb code 2oo1). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2oo1 structure was solved by P.FILIPPAKOPOULOS, A.BULLOCK, E.PAPAGRIGORIOU, T.KEATES, C.COOPER, C.SMEE, E.UGOCHUKWU, J.DEBRECZENI, F.VON DELFT, C.ARROWSMITH, A.EDWARDS, J.WEIGELT, M.SUNDSTROM, S.KNAPP, STRUCTURAL GENOMICS CONSORTIUM (SGC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-1.7 Space group P21212 a (A) 103.837 b (A) 64.678 c (A) 91.827 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 18.6 Rfree (%) 21.3 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2oo1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2oo1. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Ala413, A: Lys414, A: Met415, A: Pro416, D: Lys389, C: 7pe5096, D: Hoh3010, D: Hoh3085, conact list: Atom Atom Distance (A) Na O A:Ala413 4.12 Na C A:Ala413 4.98 Na O A:Lys414 3.52 Na N A:Lys414 4.99 Na CB A:Lys414 4.90 Na CD A:Lys414 4.83 Na C A:Lys414 3.86 Na CA A:Lys414 4.00 Na O A:Met415 3.72 Na N A:Met415 4.64 Na C A:Met415 4.27 Na N A:Pro416 4.60 Na CA A:Pro416 4.46 Na O D:Lys389 4.59 Na CE D:Lys389 4.82 Na CD D:Lys389 4.43 Na CG D:Lys389 3.79 Na NZ D:Lys389 4.02 Na C9 C:7pe5096 4.69 Na O10 C:7pe5096 4.73 Na C12 C:7pe5096 4.00 Na O13 C:7pe5096 4.77 Na C11 C:7pe5096 3.88 Na O16 C:7pe5096 3.55 Na C15 C:7pe5096 4.84 Na O D:Hoh3010 4.12 Na O D:Hoh3085 4.64 interactive model: Sodium binding site 2 out of 2 in 2oo1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2oo1. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asp406, A: Val407, A: Met410, A: Arg411, B: Asp394, D: Arg402, A: Hoh3041, A: Hoh3061, B: Hoh3037, D: Hoh3053, conact list: Atom Atom Distance (A) Na O A:Asp406 4.04 Na CB A:Asp406 4.80 Na C A:Asp406 4.32 Na N A:Val407 4.36 Na CG2 A:Val407 4.63 Na CA A:Val407 4.24 Na CB A:Met410 4.35 Na CG A:Met410 4.53 Na CZ A:Arg411 4.64 Na NH2 A:Arg411 4.55 Na NH1 A:Arg411 3.92 Na OD2 B:Asp394 4.14 Na CZ D:Arg402 4.25 Na NH2 D:Arg402 3.34 Na NH1 D:Arg402 4.49 Na O A:Hoh3041 4.58 Na O A:Hoh3061 4.15 Na O B:Hoh3037 3.52 Na O D:Hoh3053 4.10 interactive model: