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Sodium in PDB 1t64: Crystal Structure of Human HDAC8 Complexed with Trichostatin A

Protein crystallography data

The structure of Crystal Structure of Human HDAC8 Complexed with Trichostatin A, PDB code: 1t64 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) 81.65 / 1.90
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 81.014, 81.014, 114.178, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 22.1

Other elements in 1t64:

The structure of Crystal Structure of Human HDAC8 Complexed with Trichostatin A also contains other interesting chemical elements:

Calcium (Ca) 4 atoms
Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human HDAC8 Complexed with Trichostatin A (pdb code 1t64). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Human HDAC8 Complexed with Trichostatin A, PDB code: 1t64:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 1t64

Go back to Sodium Binding Sites List in 1t64
Sodium binding site 1 out of 4 in the Crystal Structure of Human HDAC8 Complexed with Trichostatin A


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 Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na391

b:28.1
occ:1.00
 O A:VAL195 2.3 12.3 1.0
O A:PHE189 2.3 13.8 1.0
O A:HOH426 2.3 25.1 1.0
O A:THR192 2.4 11.8 1.0
O A:HOH560 2.9 37.9 1.0
C A:PHE189 3.4 13.7 1.0
O A:TYR225 3.5 12.0 1.0
C A:VAL195 3.5 12.9 1.0
C A:THR192 3.6 12.5 1.0
CB A:TYR225 3.7 12.8 1.0
C A:TYR225 4.0 12.4 1.0
CB A:PHE189 4.0 13.8 1.0
N A:THR192 4.2 12.6 1.0
N A:SER190 4.2 13.5 1.0
CA A:SER190 4.3 14.2 1.0
CG2 A:THR192 4.3 11.8 1.0
OG A:SER226 4.3 15.8 1.0
CA A:PHE189 4.3 13.8 1.0
CA A:THR192 4.4 12.4 1.0
C A:SER190 4.4 13.6 1.0
CA A:MET196 4.4 12.8 1.0
N A:MET196 4.4 12.7 1.0
CA A:TYR225 4.5 12.2 1.0
CA A:VAL195 4.5 12.6 1.0
O A:SER190 4.5 13.1 1.0
O A:GLY222 4.6 13.8 1.0
N A:VAL195 4.6 12.6 1.0
N A:SER193 4.7 12.6 1.0
CA A:GLY222 4.7 13.9 1.0
N A:SER226 4.7 11.9 1.0
CB A:VAL195 4.8 13.3 1.0
CA A:SER193 4.9 13.1 1.0
N A:THR197 4.9 12.1 1.0
CG A:TYR225 4.9 12.6 1.0
N A:PHE191 4.9 13.5 1.0
CB A:THR192 5.0 12.9 1.0

Sodium binding site 2 out of 4 in 1t64

Go back to Sodium Binding Sites List in 1t64
Sodium binding site 2 out of 4 in the Crystal Structure of Human HDAC8 Complexed with Trichostatin A


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 Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na392

b:22.9
occ:1.00
 O A:ASP178 2.3 13.0 1.0
O A:LEU200 2.4 14.7 1.0
OD1 A:ASP176 2.5 14.4 1.0
O A:HIS180 2.6 12.4 1.0
O A:ASP176 2.7 14.4 1.0
OG A:SER199 3.0 14.4 1.0
C A:ASP178 3.3 13.6 1.0
N A:ASP178 3.4 14.5 1.0
C A:ASP176 3.4 14.4 1.0
C A:LEU200 3.4 13.7 1.0
CG A:ASP176 3.4 17.1 1.0
C A:HIS180 3.6 12.7 1.0
CA A:ASP178 3.8 13.4 1.0
CB A:HIS201 3.8 13.4 1.0
C A:LEU177 3.8 14.5 1.0
CB A:ASP178 3.9 13.3 1.0
CB A:ASP176 3.9 14.8 1.0
N A:LEU200 4.0 13.4 1.0
N A:LEU177 4.0 14.1 1.0
CA A:LEU177 4.1 14.2 1.0
CA A:HIS201 4.2 13.6 1.0
CB A:SER199 4.2 13.2 1.0
N A:HIS201 4.2 13.7 1.0
N A:HIS180 4.2 12.9 1.0
CA A:ASP176 4.3 14.8 1.0
O A:HOH396 4.3 21.2 1.0
CA A:LEU200 4.4 13.5 1.0
ND1 A:HIS201 4.4 13.9 1.0
OD2 A:ASP176 4.4 17.8 1.0
N A:HIS181 4.4 12.6 1.0
C A:LEU179 4.4 12.9 1.0
N A:LEU179 4.5 12.9 1.0
CA A:SER199 4.5 13.5 1.0
CA A:HIS181 4.5 13.4 1.0
N A:GLY182 4.5 14.0 1.0
C A:SER199 4.5 13.2 1.0
O A:LEU177 4.6 14.8 1.0
CA A:HIS180 4.6 12.6 1.0
CG A:HIS201 4.6 14.2 1.0
O A:LEU179 4.8 12.9 1.0
CE1 A:HIS142 4.8 17.7 1.0
C A:HIS181 4.8 13.7 1.0
CA A:LEU179 4.9 12.6 1.0

Sodium binding site 3 out of 4 in 1t64

Go back to Sodium Binding Sites List in 1t64
Sodium binding site 3 out of 4 in the Crystal Structure of Human HDAC8 Complexed with Trichostatin A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Human HDAC8 Complexed with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1391

b:26.3
occ:1.00
 O B:LEU200 2.4 11.2 1.0
O B:ASP178 2.4 13.0 1.0
OD1 B:ASP176 2.6 15.7 1.0
O B:HIS180 2.6 12.1 1.0
O B:ASP176 2.7 12.7 1.0
OG B:SER199 2.9 14.1 1.0
C B:ASP176 3.4 13.3 1.0
C B:ASP178 3.4 13.2 1.0
CG B:ASP176 3.4 16.0 1.0
C B:LEU200 3.5 11.5 1.0
N B:ASP178 3.5 13.0 1.0
C B:HIS180 3.7 12.3 1.0
CB B:HIS201 3.8 11.4 1.0
N B:LEU200 3.8 11.7 1.0
CA B:ASP178 3.8 13.0 1.0
CB B:ASP176 3.8 13.9 1.0
CB B:ASP178 3.9 13.1 1.0
C B:LEU177 3.9 12.7 1.0
N B:LEU177 4.0 12.7 1.0
CB B:SER199 4.1 12.7 1.0
CA B:LEU177 4.2 12.3 1.0
CA B:ASP176 4.2 13.6 1.0
CA B:HIS201 4.3 11.6 1.0
N B:HIS201 4.3 11.7 1.0
ND1 B:HIS201 4.3 11.4 1.0
O B:HOH420 4.3 24.6 1.0
CA B:LEU200 4.3 12.0 1.0
N B:HIS180 4.3 12.6 1.0
CA B:SER199 4.3 12.8 1.0
C B:SER199 4.4 12.7 1.0
OD2 B:ASP176 4.4 16.8 1.0
N B:HIS181 4.4 12.3 1.0
N B:GLY182 4.4 14.6 1.0
CA B:HIS181 4.5 13.0 1.0
C B:LEU179 4.5 12.9 1.0
CG B:HIS201 4.5 10.4 1.0
N B:LEU179 4.6 13.1 1.0
CA B:HIS180 4.6 12.6 1.0
O B:LEU177 4.7 13.2 1.0
C B:HIS181 4.8 13.8 1.0
O B:LEU179 4.8 12.8 1.0
CE1 B:HIS142 4.9 16.3 1.0
CA B:LEU179 5.0 12.9 1.0

Sodium binding site 4 out of 4 in 1t64

Go back to Sodium Binding Sites List in 1t64
Sodium binding site 4 out of 4 in the Crystal Structure of Human HDAC8 Complexed with Trichostatin A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Human HDAC8 Complexed with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1392

b:24.2
occ:1.00
 O B:HOH439 2.1 22.1 1.0
O B:PHE189 2.2 12.9 1.0
O B:VAL195 2.3 12.4 1.0
O B:THR192 2.4 13.4 1.0
C B:PHE189 3.3 13.6 1.0
O B:HOH548 3.5 39.7 1.0
C B:VAL195 3.6 12.6 1.0
O B:TYR225 3.6 13.4 1.0
C B:THR192 3.6 12.7 1.0
CB B:TYR225 3.6 12.3 1.0
C B:TYR225 4.0 12.7 1.0
CB B:PHE189 4.1 13.6 1.0
N B:THR192 4.1 12.3 1.0
CA B:SER190 4.2 13.9 1.0
N B:SER190 4.2 13.5 1.0
OG B:SER226 4.2 13.7 1.0
CG2 B:THR192 4.2 12.0 1.0
C B:SER190 4.3 13.5 1.0
CA B:PHE189 4.3 13.4 1.0
CA B:THR192 4.3 12.7 1.0
CA B:MET196 4.4 14.0 1.0
N B:MET196 4.4 12.9 1.0
CA B:TYR225 4.4 12.3 1.0
O B:GLY222 4.5 9.4 1.0
O B:SER190 4.5 12.5 1.0
CA B:VAL195 4.5 11.7 1.0
N B:VAL195 4.6 12.6 1.0
N B:SER193 4.6 12.6 1.0
N B:SER226 4.7 12.9 1.0
CA B:GLY222 4.7 9.8 1.0
N B:PHE191 4.8 12.8 1.0
CB B:VAL195 4.8 10.9 1.0
CA B:SER193 4.8 12.7 1.0
CG B:TYR225 4.9 11.2 1.0
CB B:THR192 4.9 12.8 1.0
N B:THR197 5.0 14.4 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: Sun Oct 6 22:37:56 2024

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