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Sodium in PDB 8cza: Crystal Structure of the First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075

Protein crystallography data

The structure of Crystal Structure of the First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075, PDB code: 8cza was solved by A.Chan, E.Schonbrunn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.40 / 2.96
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 94.801, 175.737, 143.071, 90, 90, 90
R / Rfree (%) 20.4 / 26.8

Other elements in 8cza:

The structure of Crystal Structure of the First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075 also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075 (pdb code 8cza). 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 First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075, PDB code: 8cza:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 8cza

Go back to Sodium Binding Sites List in 8cza
Sodium binding site 1 out of 2 in the Crystal Structure of the First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075


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 First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na202

b:36.2
occ:0.50
O C:LEU107 2.5 58.5 1.0
O C:TYR106 2.8 50.2 1.0
HA C:LEU107 3.1 73.0 1.0
O C:ASN109 3.1 55.9 1.0
C C:LEU107 3.2 60.7 1.0
CA C:LEU107 3.6 60.9 1.0
C C:TYR106 3.8 54.5 1.0
C C:ASN109 3.9 56.0 1.0
H C:ASN109 4.1 63.7 1.0
HA C:LYS110 4.1 82.2 1.0
N C:ASN109 4.2 53.0 1.0
N C:LEU107 4.2 59.5 1.0
N C:TYR108 4.2 59.2 1.0
C C:TYR108 4.4 56.9 1.0
N C:LYS110 4.6 61.1 1.0
CA C:ASN109 4.7 55.2 1.0
CA C:TYR108 4.8 57.8 1.0
HA C:TYR108 4.8 69.4 1.0
H C:TYR108 4.8 71.1 1.0
CA C:LYS110 4.9 68.5 1.0
HD23 C:LEU107 4.9 71.2 1.0
HB3 C:LEU107 4.9 74.5 1.0
CB C:LEU107 4.9 62.1 1.0
O C:TYR108 4.9 59.4 1.0

Sodium binding site 2 out of 2 in 8cza

Go back to Sodium Binding Sites List in 8cza
Sodium binding site 2 out of 2 in the Crystal Structure of the First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075


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 First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na201

b:41.4
occ:0.50
O D:ASN109 2.5 63.4 1.0
O D:LEU107 2.7 63.8 1.0
O D:TYR106 2.7 57.5 1.0
H D:ASN109 3.5 53.9 1.0
C D:LEU107 3.5 59.0 1.0
C D:ASN109 3.6 57.4 1.0
HA D:LEU107 3.6 61.5 1.0
N D:ASN109 3.8 44.9 1.0
C D:TYR106 3.8 53.5 1.0
CA D:LEU107 4.0 51.2 1.0
HD3 D:PRO111 4.1 66.5 1.0
CA D:ASN109 4.3 55.2 1.0
HA D:LYS110 4.4 69.8 1.0
N D:LEU107 4.4 45.1 1.0
C D:TYR108 4.5 48.9 1.0
N D:TYR108 4.5 56.9 1.0
HG3 D:PRO111 4.5 69.2 1.0
HD12 D:LEU107 4.6 74.0 1.0
N D:LYS110 4.6 63.3 1.0
CA D:LYS110 4.9 58.1 1.0
CD D:PRO111 4.9 55.4 1.0
HA D:ASN109 4.9 66.2 1.0
HA D:TYR106 5.0 61.7 1.0
CA D:TYR108 5.0 52.3 1.0

Reference:

X.Guan, N.Cheryala, R.M.Karim, A.Chan, N.Berndt, J.Qi, G.I.Georg, E.Schonbrunn. Bivalent Bet Bromodomain Inhibitors Confer Increased Potency and Selectivity For Brdt Via Protein Conformational Plasticity. J.Med.Chem. V. 65 10441 2022.
ISSN: ISSN 0022-2623
PubMed: 35867655
DOI: 10.1021/ACS.JMEDCHEM.2C00453
Page generated: Wed Oct 9 11:19:37 2024

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