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Sodium in PDB 2oo1: Crystal Structure of the Bromo Domain 2 of Human Bromodomain Containing Protein 3 (BRD3)

Protein crystallography data

The structure of Crystal Structure of the Bromo Domain 2 of Human Bromodomain Containing Protein 3 (BRD3), PDB code: 2oo1 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. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.837, 64.678, 91.827, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 21.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Bromo Domain 2 of Human Bromodomain Containing Protein 3 (BRD3) (pdb code 2oo1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Bromo Domain 2 of Human Bromodomain Containing Protein 3 (BRD3), PDB code: 2oo1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2oo1

Go back to Sodium Binding Sites List in 2oo1
Sodium binding site 1 out of 2 in the Crystal Structure of the Bromo Domain 2 of Human Bromodomain Containing Protein 3 (BRD3)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Bromo Domain 2 of Human Bromodomain Containing Protein 3 (BRD3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:50.0
occ:1.00
O A:LYS414 3.5 26.0 1.0
O16 C:7PE5096 3.5 48.1 1.0
O A:MET415 3.7 25.1 1.0
CG D:LYS389 3.8 19.1 1.0
C A:LYS414 3.9 24.1 1.0
C11 C:7PE5096 3.9 46.4 1.0
CA A:LYS414 4.0 21.5 1.0
C12 C:7PE5096 4.0 48.4 1.0
NZ D:LYS389 4.0 28.3 1.0
O A:ALA413 4.1 20.5 1.0
O D:HOH3010 4.1 41.0 1.0
C A:MET415 4.3 25.0 1.0
CD D:LYS389 4.4 19.6 1.0
CA A:PRO416 4.5 26.8 1.0
O D:LYS389 4.6 18.2 1.0
N A:PRO416 4.6 25.7 1.0
O D:HOH3085 4.6 37.0 1.0
N A:MET415 4.6 23.3 1.0
C9 C:7PE5096 4.7 39.0 1.0
O10 C:7PE5096 4.7 45.6 1.0
O13 C:7PE5096 4.8 52.5 1.0
CE D:LYS389 4.8 27.6 1.0
CD A:LYS414 4.8 18.8 1.0
C15 C:7PE5096 4.8 49.7 1.0
CB A:LYS414 4.9 21.0 1.0
C A:ALA413 5.0 20.3 1.0
N A:LYS414 5.0 19.1 1.0

Sodium binding site 2 out of 2 in 2oo1

Go back to Sodium Binding Sites List in 2oo1
Sodium binding site 2 out of 2 in the Crystal Structure of the Bromo Domain 2 of Human Bromodomain Containing Protein 3 (BRD3)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Bromo Domain 2 of Human Bromodomain Containing Protein 3 (BRD3) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na601

b:66.0
occ:1.00
NH2 D:ARG402 3.3 41.4 1.0
O B:HOH3037 3.5 50.7 1.0
NH1 A:ARG411 3.9 28.1 1.0
O A:ASP406 4.0 20.0 1.0
O D:HOH3053 4.1 50.9 1.0
OD2 B:ASP394 4.1 33.1 1.0
O A:HOH3061 4.1 40.3 1.0
CA A:VAL407 4.2 19.1 1.0
CZ D:ARG402 4.2 39.6 1.0
C A:ASP406 4.3 19.5 1.0
CB A:MET410 4.3 18.1 1.0
N A:VAL407 4.4 19.6 1.0
NH1 D:ARG402 4.5 39.6 1.0
CG A:MET410 4.5 18.8 1.0
NH2 A:ARG411 4.5 29.7 1.0
O A:HOH3041 4.6 32.4 1.0
CG2 A:VAL407 4.6 21.7 1.0
CZ A:ARG411 4.6 29.1 1.0
CB A:ASP406 4.8 20.7 1.0

Reference:

P.Filippakopoulos, S.Picaud, M.Mangos, T.Keates, J.P.Lambert, D.Barsyte-Lovejoy, I.Felletar, R.Volkmer, S.Muller, T.Pawson, A.C.Gingras, C.H.Arrowsmith, S.Knapp. Histone Recognition and Large-Scale Structural Analysis of the Human Bromodomain Family. Cell(Cambridge,Mass.) V. 149 214 2012.
ISSN: ISSN 0092-8674
PubMed: 22464331
DOI: 10.1016/J.CELL.2012.02.013
Page generated: Tue Dec 15 05:52:38 2020

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