Atomistry » Sodium » PDB 1t4b-1u8r » 1t64
Atomistry »
  Sodium »
    PDB 1t4b-1u8r »
      1t64 »

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: Tue Dec 15 05:36:18 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy