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Zinc in PDB 3gv4: Crystal Structure of Human HDAC6 Zinc Finger Domain and Ubiquitin C- Terminal Peptide Rlrgg

Enzymatic activity of Crystal Structure of Human HDAC6 Zinc Finger Domain and Ubiquitin C- Terminal Peptide Rlrgg

All present enzymatic activity of Crystal Structure of Human HDAC6 Zinc Finger Domain and Ubiquitin C- Terminal Peptide Rlrgg:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Human HDAC6 Zinc Finger Domain and Ubiquitin C- Terminal Peptide Rlrgg, PDB code: 3gv4 was solved by A.Dong, M.Ravichandran, P.Loppnau, Y.Li, F.Mackenzie, I.Kozieradzki, A.M.Edwards, C.H.Arrowsmith, J.Weigelt, C.Bountra, A.Bochkarev, S.Dhe-Paganon, J.Min, H.Ouyang, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.45 / 1.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 31.657, 36.093, 88.998, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 23

Other elements in 3gv4:

The structure of Crystal Structure of Human HDAC6 Zinc Finger Domain and Ubiquitin C- Terminal Peptide Rlrgg also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human HDAC6 Zinc Finger Domain and Ubiquitin C- Terminal Peptide Rlrgg (pdb code 3gv4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Human HDAC6 Zinc Finger Domain and Ubiquitin C- Terminal Peptide Rlrgg, PDB code: 3gv4:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3gv4

Go back to Zinc Binding Sites List in 3gv4
Zinc binding site 1 out of 3 in the Crystal Structure of Human HDAC6 Zinc Finger Domain and Ubiquitin C- Terminal Peptide Rlrgg


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human HDAC6 Zinc Finger Domain and Ubiquitin C- Terminal Peptide Rlrgg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:18.3
occ:1.00
 NE2 A:HIS56 2.0 17.3 1.0
ND1 A:HIS62 2.1 17.0 1.0
SG A:CYS40 2.3 17.2 1.0
SG A:CYS37 2.3 15.3 1.0
CE1 A:HIS56 2.9 18.4 1.0
CE1 A:HIS62 3.0 19.5 1.0
CD2 A:HIS56 3.1 17.2 1.0
CG A:HIS62 3.2 16.0 1.0
CB A:CYS37 3.2 15.6 1.0
CB A:CYS40 3.4 16.0 1.0
CB A:HIS62 3.5 15.2 1.0
N A:CYS40 3.7 15.9 1.0
CA A:CYS40 4.1 16.2 1.0
ND1 A:HIS56 4.1 19.0 1.0
NE2 A:HIS62 4.2 19.3 1.0
CG A:HIS56 4.2 17.4 1.0
OG A:SER60 4.2 17.3 1.0
CD2 A:HIS62 4.3 18.7 1.0
O A:HOH244 4.3 47.1 1.0
CB A:SER39 4.4 16.1 1.0
CA A:CYS37 4.6 15.1 1.0
C A:SER39 4.7 16.2 1.0
CB A:SER60 4.7 17.8 1.0
C A:CYS40 4.8 16.1 1.0
N A:TYR41 4.9 15.8 1.0
CA A:SER39 4.9 16.1 1.0
N A:SER39 4.9 15.3 1.0

Zinc binding site 2 out of 3 in 3gv4

Go back to Zinc Binding Sites List in 3gv4
Zinc binding site 2 out of 3 in the Crystal Structure of Human HDAC6 Zinc Finger Domain and Ubiquitin C- Terminal Peptide Rlrgg


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human HDAC6 Zinc Finger Domain and Ubiquitin C- Terminal Peptide Rlrgg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:19.3
occ:1.00
 ND1 A:HIS52 2.0 19.0 1.0
SG A:CYS28 2.3 19.2 1.0
SG A:CYS25 2.4 16.3 1.0
SG A:CYS45 2.4 17.5 1.0
CE1 A:HIS52 3.0 20.2 1.0
CG A:HIS52 3.1 18.1 1.0
CB A:CYS25 3.3 17.1 1.0
CB A:CYS45 3.3 15.6 1.0
CB A:CYS28 3.4 19.8 1.0
CB A:HIS52 3.4 16.0 1.0
N A:CYS28 3.7 20.1 1.0
CB A:ASN50 4.0 18.7 1.0
N A:CYS45 4.0 15.4 1.0
NE2 A:HIS52 4.1 20.4 1.0
CA A:CYS28 4.1 20.1 1.0
CD2 A:HIS52 4.2 19.4 1.0
OG1 A:THR30 4.2 21.0 1.0
CA A:CYS45 4.3 15.8 1.0
ND2 A:ASN50 4.4 23.0 1.0
N A:HIS52 4.5 15.9 1.0
CA A:HIS52 4.6 16.1 1.0
CB A:ASP27 4.6 19.5 1.0
CA A:CYS25 4.7 17.4 1.0
C A:ASP27 4.7 20.1 1.0
CG A:ASN50 4.7 20.4 1.0
CA A:ASN50 4.8 17.8 1.0
C A:CYS28 4.9 20.2 1.0
N A:ASP27 4.9 19.2 1.0
CA A:ASP27 5.0 19.8 1.0
N A:GLY29 5.0 19.7 1.0
C A:ASN50 5.0 17.3 1.0

Zinc binding site 3 out of 3 in 3gv4

Go back to Zinc Binding Sites List in 3gv4
Zinc binding site 3 out of 3 in the Crystal Structure of Human HDAC6 Zinc Finger Domain and Ubiquitin C- Terminal Peptide Rlrgg


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human HDAC6 Zinc Finger Domain and Ubiquitin C- Terminal Peptide Rlrgg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:16.9
occ:1.00
 ND1 A:HIS7 2.1 15.3 1.0
SG A:CYS78 2.3 16.8 1.0
SG A:CYS5 2.3 15.8 1.0
SG A:CYS75 2.3 15.3 1.0
CG A:HIS7 3.1 15.4 1.0
CE1 A:HIS7 3.1 16.6 1.0
CB A:CYS5 3.2 16.0 1.0
CB A:CYS75 3.3 14.2 1.0
CB A:CYS78 3.3 15.6 1.0
CB A:HIS7 3.4 15.2 1.0
N A:CYS78 3.9 15.6 1.0
N A:HIS7 4.0 15.1 1.0
CA A:CYS78 4.2 16.0 1.0
CD A:PRO6 4.2 15.7 1.0
NE2 A:HIS7 4.2 15.1 1.0
CD2 A:HIS7 4.2 13.0 1.0
CA A:HIS7 4.3 15.3 1.0
N A:PRO6 4.5 15.8 1.0
CA A:CYS5 4.5 15.7 1.0
C A:CYS5 4.6 16.0 1.0
CG A:PRO6 4.6 16.3 1.0
CA A:CYS75 4.7 14.3 1.0
CB A:TYR77 4.8 14.9 1.0
C A:TYR77 4.9 14.8 1.0
C A:PRO6 5.0 15.6 1.0

Reference:

A.Dong, M.Ravichandran, P.Loppnau, Y.Li, F.Mackenzie, I.Kozieradzki, A.M.Edwards, C.H.Arrowsmith, J.Weigelt, C.Bountra, A.Bochkarev, S.Dhe-Paganon, J.Min, H.Ouyang. Crystal Structure of Human HDAC6 Zinc Finger Domain and Ubiquitin C-Terminal Peptide Rlrgg To Be Published.
Page generated: Thu Oct 24 14:01:50 2024

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