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Sodium in PDB 5amf: Crystal Structure of the Bromodomain of Human Surface Epitope Engineered BRD1A in Complex with 3D Consortium Fragment Ethyl 4,5,6,7-Tetrahydro-1H-Indazole-5- Carboxylate (Sgc - Diamond I04-1 Fragment Screening)

Protein crystallography data

The structure of Crystal Structure of the Bromodomain of Human Surface Epitope Engineered BRD1A in Complex with 3D Consortium Fragment Ethyl 4,5,6,7-Tetrahydro-1H-Indazole-5- Carboxylate (Sgc - Diamond I04-1 Fragment Screening), PDB code: 5amf was solved by N.M.Pearce, M.Fairhead, C.Strain-Damerell, R.Talon, N.Wright, J.T.Ng, A.Bradley, O.Cox, D.Bowkett, P.Collins, J.Brandao-Neto, A.Douangamath, T.Krojer, N.Burgess-Brown, P.Brennan, C.H.Arrowsmith, E.Edwards, C.Bountra, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.275 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.550, 56.330, 101.690, 90.00, 90.00, 90.00
R / Rfree (%) 17.55 / 21.26

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Bromodomain of Human Surface Epitope Engineered BRD1A in Complex with 3D Consortium Fragment Ethyl 4,5,6,7-Tetrahydro-1H-Indazole-5- Carboxylate (Sgc - Diamond I04-1 Fragment Screening) (pdb code 5amf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the Bromodomain of Human Surface Epitope Engineered BRD1A in Complex with 3D Consortium Fragment Ethyl 4,5,6,7-Tetrahydro-1H-Indazole-5- Carboxylate (Sgc - Diamond I04-1 Fragment Screening), PDB code: 5amf:

Sodium binding site 1 out of 1 in 5amf

Go back to Sodium Binding Sites List in 5amf
Sodium binding site 1 out of 1 in the Crystal Structure of the Bromodomain of Human Surface Epitope Engineered BRD1A in Complex with 3D Consortium Fragment Ethyl 4,5,6,7-Tetrahydro-1H-Indazole-5- Carboxylate (Sgc - Diamond I04-1 Fragment Screening)


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 Bromodomain of Human Surface Epitope Engineered BRD1A in Complex with 3D Consortium Fragment Ethyl 4,5,6,7-Tetrahydro-1H-Indazole-5- Carboxylate (Sgc - Diamond I04-1 Fragment Screening) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1145

b:22.6
occ:1.00
O B:MET107 2.3 17.7 1.0
O B:ASN110 2.3 20.5 1.0
O A:LYS108 2.4 21.1 1.0
O A:HOH2089 2.4 22.4 1.0
O A:HOH2090 2.4 18.6 1.0
C A:LYS108 3.4 18.0 1.0
C B:ASN110 3.5 26.1 1.0
C B:MET107 3.5 20.5 1.0
CE2 B:TYR117 3.6 17.4 1.0
CD2 B:TYR117 3.7 16.4 1.0
CA A:LYS108 3.9 17.4 0.4
CA A:LYS108 4.0 17.3 0.6
O B:LYS108 4.0 19.1 1.0
CA B:ALA111 4.0 20.5 1.0
O A:HOH2097 4.1 25.7 1.0
O A:MET107 4.1 20.5 1.0
O A:ASN110 4.2 21.2 1.0
N B:ALA111 4.2 21.6 1.0
C B:ALA111 4.2 18.6 1.0
N B:ARG112 4.2 21.0 1.0
C B:LYS108 4.3 17.7 1.0
CA B:LYS108 4.3 18.7 0.4
CA B:LYS108 4.4 18.7 0.6
N B:LYS108 4.4 18.4 1.0
CA B:MET107 4.5 20.6 1.0
N B:ASN110 4.5 21.4 1.0
CA B:ASN110 4.6 23.7 1.0
N A:TYR109 4.6 18.1 1.0
C A:ASN110 4.6 24.2 1.0
C A:TYR109 4.7 20.5 1.0
O A:TYR109 4.8 21.8 1.0
CZ B:TYR117 4.8 19.7 1.0
O B:ALA111 4.9 20.9 1.0
C A:MET107 4.9 19.8 1.0
CB A:LYS108 4.9 17.9 0.4
N A:ASN110 4.9 16.5 1.0
N A:LYS108 4.9 16.8 1.0
CA A:TYR109 5.0 17.5 1.0

Reference:

N.M.Pearce, M.Fairhead, C.Strain-Damerell, R.Talon, N.Wright, J.T.Ng, A.Bradley, O.Cox, D.Bowkett, P.Collins, J.Brandao-Neto, A.Douangamath, T.Krojer, N.Burgess-Brown, P.Brennan, C.H.Arrowsmith, E.Edwards, C.Bountra, F.Von Delft. Crystal Structure of the Bromodomain of Human Surface Epitope Engineered BRD1A in Complex with 3D Consortium Fragment Ethyl 4,5,6,7-Tetrahydro-1H- Indazole-5-Carboxylate To Be Published.
Page generated: Tue Dec 15 10:23:27 2020

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