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Calcium 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:

Zinc (Zn) 2 atoms
Sodium (Na) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Human HDAC8 Complexed with Trichostatin A, PDB code: 1t64:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1t64

Go back to Calcium Binding Sites List in 1t64
Calcium 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 Calcium with other atoms in the Ca 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:Ca389

b:25.5
occ:1.00
O A:HOH1040 2.4 38.3 1.0
O A:HOH737 2.4 38.2 1.0
O A:HOH739 2.4 32.3 1.0
O A:HOH735 2.4 29.2 1.0
O A:HOH738 2.4 37.6 1.0
O A:HOH734 2.5 30.9 1.0
O A:HOH736 2.5 22.9 1.0
O A:HOH741 2.6 36.9 1.0
OE1 A:GLU170 4.3 15.2 1.0
OE2 A:GLU170 4.5 14.1 1.0
NH2 A:ARG166 4.6 15.1 1.0
O A:HOH747 4.7 29.0 1.0
O A:HOH740 4.8 42.3 1.0
CD A:GLU170 4.9 14.9 1.0

Calcium binding site 2 out of 4 in 1t64

Go back to Calcium Binding Sites List in 1t64
Calcium 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 Calcium with other atoms in the Ca 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:Ca390

b:60.0
occ:1.00
O A:HOH842 2.2 45.8 1.0
O A:HOH844 2.4 49.7 1.0
O A:HOH843 2.4 47.6 1.0
O A:ALA68 2.5 16.9 1.0
C A:ALA68 3.7 16.8 1.0
O A:HIS71 4.0 14.0 1.0
O A:HOH818 4.2 46.7 1.0
CB A:ALA68 4.2 15.6 1.0
CA A:ALA68 4.3 16.3 1.0
N A:THR69 4.7 17.4 1.0
OD1 A:ASP73 4.9 16.2 1.0
C A:THR69 4.9 17.6 1.0
C A:HIS71 4.9 13.8 1.0
O A:THR69 4.9 17.8 1.0
O A:HOH889 5.0 51.4 1.0

Calcium binding site 3 out of 4 in 1t64

Go back to Calcium Binding Sites List in 1t64
Calcium 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 Calcium with other atoms in the Ca 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:Ca1389

b:28.4
occ:1.00
OE1 B:GLU170 4.3 21.9 1.0
OE2 B:GLU170 4.5 23.8 1.0
NH1 B:ARG166 4.5 20.4 1.0
O B:HOH578 4.5 47.4 1.0
CD B:GLU170 4.8 22.4 1.0

Calcium binding site 4 out of 4 in 1t64

Go back to Calcium Binding Sites List in 1t64
Calcium 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 Calcium with other atoms in the Ca 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:Ca1390

b:48.7
occ:1.00
O B:HOH676 2.3 47.9 1.0
O B:HOH783 2.4 38.8 1.0
O B:HOH771 2.4 38.6 1.0
O B:ALA68 2.5 15.9 1.0
C B:ALA68 3.6 15.8 1.0
O B:HIS71 4.1 11.8 1.0
CB B:ALA68 4.3 14.8 1.0
CA B:ALA68 4.3 15.1 1.0
O B:HOH925 4.4 50.1 1.0
O B:HOH622 4.6 39.1 1.0
N B:THR69 4.6 16.1 1.0
OD1 B:ASP73 4.7 15.5 1.0
C B:THR69 4.7 16.3 1.0
CA B:THR69 4.8 16.5 1.0
O B:THR69 4.9 16.5 1.0
O B:HOH498 4.9 36.6 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: Sat Dec 12 03:20:42 2020

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