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Sodium in PDB 1vkg: Crystal Structure of Human HDAC8 Complexed with Cra-19156

Protein crystallography data

The structure of Crystal Structure of Human HDAC8 Complexed with Cra-19156, PDB code: 1vkg was solved by J.R.Somoza, R.J.Skene, B.A.Katz, C.Mol, J.D.Ho, A.J.Jennings, C.Luong, A.Arvai, J.J.Buggy, E.Chi, J.Tang, B.-C.Sang, E.Verner, R.Wynands, E.M.Leahy, D.R.Dougan, G.Snell, M.Navre, M.W.Knuth, R.V.Swanson, D.E.Mcree, L.W.Tari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.630, 92.710, 98.760, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 30.4

Other elements in 1vkg:

The structure of Crystal Structure of Human HDAC8 Complexed with Cra-19156 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human HDAC8 Complexed with Cra-19156 (pdb code 1vkg). 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 Human HDAC8 Complexed with Cra-19156, PDB code: 1vkg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1vkg

Go back to Sodium Binding Sites List in 1vkg
Sodium binding site 1 out of 2 in the Crystal Structure of Human HDAC8 Complexed with Cra-19156


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 Human HDAC8 Complexed with Cra-19156 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:39.6
occ:1.00
OH A:TYR240 2.5 40.5 1.0
O A:LEU177 2.5 28.2 1.0
HG23 A:THR268 2.8 25.6 1.0
O A:ASP178 2.9 46.2 1.0
HA A:LEU177 2.9 28.7 1.0
O A:LEU200 3.0 29.9 1.0
HE1 A:PHE277 3.0 32.1 1.0
C A:LEU177 3.0 32.0 1.0
HB2 A:LEU200 3.0 39.7 1.0
HH A:TYR240 3.2 35.8 1.0
HE1 A:TYR240 3.2 32.4 1.0
CZ A:TYR240 3.4 29.7 1.0
HA A:LEU179 3.4 24.4 1.0
CA A:LEU177 3.5 30.9 1.0
C A:ASP178 3.5 33.5 1.0
HA A:HIS201 3.6 27.1 1.0
C A:LEU200 3.7 25.4 1.0
CG2 A:THR268 3.7 28.4 1.0
CE1 A:TYR240 3.7 33.3 1.0
HG22 A:THR268 3.7 25.6 1.0
N A:ASP178 3.8 28.7 1.0
HB3 A:LEU200 3.9 40.6 1.0
CB A:LEU200 3.9 41.2 1.0
CE1 A:PHE277 3.9 32.3 1.0
HB3 A:LEU177 3.9 31.5 1.0
H2 A:HOH465 3.9 42.0 1.0
N A:LEU179 4.0 28.8 1.0
HG21 A:THR268 4.1 26.4 1.0
CA A:LEU179 4.2 20.0 1.0
CA A:ASP178 4.3 32.9 1.0
CB A:LEU177 4.3 29.8 1.0
O A:ASP176 4.3 40.4 1.0
HD1 A:PHE277 4.4 39.0 1.0
N A:HIS201 4.4 27.6 1.0
CA A:LEU200 4.4 37.2 1.0
H A:LEU200 4.4 38.1 1.0
H A:ASP178 4.4 32.8 1.0
CA A:HIS201 4.5 22.8 1.0
HA A:ASP178 4.5 32.5 1.0
HD22 A:LEU177 4.6 39.1 1.0
CD1 A:PHE277 4.6 40.9 1.0
HD12 A:ILE231 4.6 31.4 1.0
CE2 A:TYR240 4.6 23.3 1.0
HD21 A:LEU177 4.7 39.0 1.0
O A:HOH465 4.7 42.6 1.0
N A:LEU177 4.7 27.1 1.0
HZ A:PHE277 4.7 31.9 1.0
CZ A:PHE277 4.8 28.0 1.0
H A:LEU179 4.8 26.0 1.0
N A:LEU200 4.8 38.8 1.0
CB A:THR268 4.9 26.1 1.0
HE2 A:TYR240 4.9 27.4 1.0
C A:LEU179 4.9 28.8 1.0
C A:ASP176 4.9 39.0 1.0
HB A:THR268 5.0 23.9 1.0
HB2 A:LEU177 5.0 31.0 1.0
CD1 A:TYR240 5.0 35.0 1.0

Sodium binding site 2 out of 2 in 1vkg

Go back to Sodium Binding Sites List in 1vkg
Sodium binding site 2 out of 2 in the Crystal Structure of Human HDAC8 Complexed with Cra-19156


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 Human HDAC8 Complexed with Cra-19156 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:30.1
occ:1.00
O B:LEU200 2.3 15.5 1.0
HB3 B:HIS201 2.4 15.1 1.0
O B:ASP178 2.4 51.9 1.0
O B:HIS180 2.6 28.6 1.0
OD1 B:ASP176 2.6 30.9 1.0
O B:ASP176 2.7 38.5 1.0
H B:ASP178 2.8 32.9 1.0
OG B:SER199 3.0 30.7 1.0
H B:LEU200 3.1 31.9 1.0
C B:LEU200 3.4 24.2 1.0
H1 B:HOH492 3.4 52.4 1.0
N B:ASP178 3.4 31.9 1.0
CB B:HIS201 3.4 19.4 1.0
CG B:ASP176 3.5 33.3 1.0
HG B:SER199 3.5 29.3 1.0
C B:ASP176 3.5 38.5 1.0
C B:ASP178 3.5 39.0 1.0
C B:HIS180 3.6 24.9 1.0
HB3 B:ASP176 3.6 32.0 1.0
N B:LEU200 3.7 37.4 1.0
HA B:HIS201 3.7 13.1 1.0
HA B:HIS181 3.7 27.3 1.0
O B:HOH492 3.8 51.5 1.0
HA B:LEU177 3.8 40.0 1.0
CA B:HIS201 3.9 11.4 1.0
HD2 B:HIS201 4.0 21.8 1.0
HA B:SER199 4.0 29.2 1.0
HB3 B:ASP178 4.0 25.6 1.0
CB B:ASP176 4.0 27.3 1.0
HB2 B:HIS201 4.1 18.1 1.0
CA B:ASP178 4.1 36.5 1.0
N B:HIS201 4.1 12.7 1.0
CB B:SER199 4.2 29.0 1.0
H B:GLY182 4.2 29.9 1.0
C B:LEU177 4.2 37.1 1.0
N B:LEU177 4.2 39.8 1.0
CA B:LEU177 4.3 39.3 1.0
C B:SER199 4.3 30.1 1.0
CA B:SER199 4.3 29.6 1.0
CA B:LEU200 4.3 28.2 1.0
CG B:HIS201 4.3 25.1 1.0
N B:HIS180 4.4 28.9 1.0
CA B:ASP176 4.4 28.0 1.0
N B:HIS181 4.4 29.2 1.0
CA B:HIS181 4.5 28.4 1.0
OD2 B:ASP176 4.5 38.6 1.0
H B:HIS180 4.5 29.2 1.0
CD2 B:HIS201 4.5 21.4 1.0
HB2 B:LEU200 4.5 33.1 1.0
CA B:HIS180 4.5 22.5 1.0
H2 B:HOH492 4.5 52.1 1.0
C B:LEU179 4.6 24.8 1.0
CB B:ASP178 4.6 27.8 1.0
N B:LEU179 4.6 28.6 1.0
HE1 B:HIS142 4.7 21.8 1.0
HE21 B:GLN263 4.7 30.1 1.0
HB2 B:SER199 4.7 29.9 1.0
N B:GLY182 4.8 29.0 1.0
HD1 B:HIS142 4.8 16.7 1.0
O B:LEU179 4.9 24.4 1.0
HB3 B:SER199 4.9 30.6 1.0
HD21 B:LEU177 5.0 31.7 1.0

Reference:

J.R.Somoza, R.J.Skene, B.A.Katz, C.Mol, J.D.Ho, A.J.Jennings, C.Luong, A.Arvai, J.J.Buggy, E.Chi, J.Tang, B.-C.Sang, E.Verner, R.Wynands, E.M.Leahy, D.R.Dougan, G.Snell, M.Navre, M.W.Knuth, R.V.Swanson, D.E.Mcree, L.W.Tari. Structural Snapshots of Human HDAC8 Provide Insights Into the Class I Histone Deacetylases Structure V. 12 1325 2004.
ISSN: ISSN 0969-2126
PubMed: 15242608
DOI: 10.1016/J.STR.2004.04.012
Page generated: Tue Dec 15 05:37:40 2020

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