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Zinc in PDB 3c5k: Crystal Structure of Human HDAC6 Zinc Finger Domain

Protein crystallography data

The structure of Crystal Structure of Human HDAC6 Zinc Finger Domain, PDB code: 3c5k was solved by A.Dong, M.Ravichandran, A.Schuetz, 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) 35.07 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.500, 45.109, 55.759, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 22.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human HDAC6 Zinc Finger Domain (pdb code 3c5k). 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, PDB code: 3c5k:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3c5k

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Zinc binding site 1 out of 3 in the Crystal Structure of Human HDAC6 Zinc Finger Domain


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:7.7
occ:1.00
ND1 A:HIS62 2.0 3.5 1.0
NE2 A:HIS56 2.1 5.3 1.0
SG A:CYS37 2.3 5.3 1.0
SG A:CYS40 2.4 7.5 1.0
CE1 A:HIS62 3.0 5.5 1.0
CE1 A:HIS56 3.1 5.1 1.0
CG A:HIS62 3.1 4.5 1.0
CD2 A:HIS56 3.1 4.2 1.0
CB A:CYS37 3.1 4.4 1.0
CB A:HIS62 3.5 4.0 1.0
CB A:CYS40 3.5 6.8 1.0
N A:CYS40 3.8 6.4 1.0
NE2 A:HIS62 4.1 6.4 1.0
CA A:CYS40 4.2 6.3 1.0
CD2 A:HIS62 4.2 4.5 1.0
ND1 A:HIS56 4.2 5.4 1.0
CG A:HIS56 4.2 4.3 1.0
OG A:SER60 4.2 4.8 1.0
CB A:SER39 4.5 6.1 1.0
O A:HOH312 4.6 21.3 1.0
CA A:CYS37 4.6 4.8 1.0
CB A:SER60 4.8 6.4 1.0
C A:SER39 4.8 6.4 1.0
C A:CYS40 4.8 6.5 1.0
N A:TYR41 4.9 6.0 1.0
N A:SER39 4.9 6.0 1.0
CA A:SER39 4.9 6.1 1.0
CA A:HIS62 5.0 4.0 1.0
C A:CYS37 5.0 5.1 1.0

Zinc binding site 2 out of 3 in 3c5k

Go back to Zinc Binding Sites List in 3c5k
Zinc binding site 2 out of 3 in the Crystal Structure of Human HDAC6 Zinc Finger Domain


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:7.6
occ:1.00
ND1 A:HIS52 2.1 5.5 1.0
SG A:CYS45 2.2 3.2 1.0
SG A:CYS28 2.3 6.3 1.0
SG A:CYS25 2.4 5.1 1.0
CE1 A:HIS52 3.0 5.4 1.0
CG A:HIS52 3.2 5.2 1.0
CB A:CYS25 3.3 5.7 1.0
CB A:CYS45 3.4 4.7 1.0
CB A:CYS28 3.4 8.8 1.0
CB A:HIS52 3.5 5.5 1.0
N A:CYS28 3.7 9.6 1.0
N A:CYS45 4.0 4.6 1.0
CA A:CYS28 4.1 8.6 1.0
CB A:ASN50 4.1 7.0 1.0
CG2 A:THR30 4.1 7.6 1.0
NE2 A:HIS52 4.2 7.2 1.0
CD2 A:HIS52 4.3 6.9 1.0
CA A:CYS45 4.3 4.5 1.0
ND2 A:ASN50 4.3 8.9 1.0
CB A:ASP27 4.6 10.1 1.0
N A:HIS52 4.6 5.1 1.0
CA A:HIS52 4.7 5.2 1.0
CA A:CYS25 4.7 5.9 1.0
C A:ASP27 4.8 9.9 1.0
CG A:ASN50 4.8 8.1 1.0
C A:CYS28 4.8 8.6 1.0
N A:GLY29 4.8 7.9 1.0
CA A:ASN50 5.0 6.9 1.0

Zinc binding site 3 out of 3 in 3c5k

Go back to Zinc Binding Sites List in 3c5k
Zinc binding site 3 out of 3 in the Crystal Structure of Human HDAC6 Zinc Finger Domain


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:6.4
occ:1.00
ND1 A:HIS7 2.1 3.8 1.0
SG A:CYS78 2.3 5.6 1.0
SG A:CYS5 2.4 4.3 1.0
SG A:CYS75 2.4 2.6 1.0
CE1 A:HIS7 3.0 4.2 1.0
CG A:HIS7 3.2 3.6 1.0
CB A:CYS5 3.2 4.2 1.0
CB A:CYS75 3.3 2.3 1.0
CB A:CYS78 3.4 5.2 1.0
CB A:HIS7 3.5 3.5 1.0
N A:CYS78 3.9 4.4 1.0
N A:HIS7 4.0 4.5 1.0
CD A:PRO6 4.1 4.9 1.0
NE2 A:HIS7 4.2 4.8 1.0
CD2 A:HIS7 4.2 5.0 1.0
CA A:CYS78 4.2 5.3 1.0
N A:PRO6 4.3 4.7 1.0
CA A:HIS7 4.4 4.2 1.0
CA A:CYS5 4.4 4.2 1.0
CB A:TYR77 4.5 4.5 1.0
C A:CYS5 4.5 4.7 1.0
CG A:PRO6 4.6 4.9 1.0
CA A:CYS75 4.8 2.3 1.0
O A:HOH290 4.9 8.6 1.0
C A:TYR77 4.9 4.6 1.0
C A:PRO6 4.9 4.9 1.0

Reference:

A.Dong, M.Ravichandran, A.Schuetz, 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. To Be Published.
Page generated: Wed Dec 16 04:10:10 2020

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