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Zinc in PDB 2b4y: Crystal Structure of Human Sirtuin Homolog 5

Protein crystallography data

The structure of Crystal Structure of Human Sirtuin Homolog 5, PDB code: 2b4y was solved by J.R.Min, T.Antoshenko, A.Dong, A.Schuetz, P.Loppnau, J.Weigelt, M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, A.N.Plotnikov, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.30 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.574, 58.756, 104.965, 93.50, 92.75, 94.98
R / Rfree (%) 18.3 / 23.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Sirtuin Homolog 5 (pdb code 2b4y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human Sirtuin Homolog 5, PDB code: 2b4y:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2b4y

Go back to Zinc Binding Sites List in 2b4y
Zinc binding site 1 out of 4 in the Crystal Structure of Human Sirtuin Homolog 5


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 Sirtuin Homolog 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:23.9
occ:1.00
SG A:CYS207 2.1 20.8 1.0
SG A:CYS169 2.3 25.5 1.0
SG A:CYS166 2.4 22.7 1.0
SG A:CYS212 2.4 26.3 1.0
CB A:CYS166 3.1 21.1 1.0
CB A:CYS207 3.1 20.8 1.0
CB A:CYS169 3.2 26.3 1.0
CB A:CYS212 3.3 27.8 1.0
N A:CYS169 3.7 26.7 1.0
CA A:CYS169 4.1 26.0 1.0
CG A:GLU209 4.3 33.8 1.0
CB A:GLU209 4.4 30.9 1.0
CB A:SER168 4.6 26.4 1.0
CA A:CYS166 4.6 21.1 1.0
CA A:CYS207 4.6 20.3 1.0
N A:GLY214 4.7 24.1 1.0
O A:HOH1040 4.7 22.0 1.0
CA A:CYS212 4.7 28.4 1.0
C A:CYS169 4.8 25.9 1.0
C A:SER168 4.8 27.1 1.0
O A:HOH1132 4.9 43.2 1.0
CA A:GLY214 4.9 22.4 1.0
N A:GLY170 4.9 24.9 1.0

Zinc binding site 2 out of 4 in 2b4y

Go back to Zinc Binding Sites List in 2b4y
Zinc binding site 2 out of 4 in the Crystal Structure of Human Sirtuin Homolog 5


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 Sirtuin Homolog 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2001

b:22.9
occ:1.00
SG B:CYS207 2.3 19.0 1.0
SG B:CYS169 2.3 24.8 1.0
SG B:CYS212 2.3 26.4 1.0
SG B:CYS166 2.4 21.4 1.0
CB B:CYS166 3.1 18.1 1.0
CB B:CYS207 3.1 21.2 1.0
CB B:CYS212 3.2 26.4 1.0
CB B:CYS169 3.4 25.8 1.0
N B:CYS169 3.8 25.2 1.0
CA B:CYS169 4.2 24.5 1.0
CB B:GLU209 4.4 26.1 1.0
CG B:GLU209 4.5 27.1 1.0
N B:GLY214 4.5 21.7 1.0
CA B:CYS207 4.6 20.7 1.0
CA B:CYS166 4.6 19.5 1.0
CA B:CYS212 4.7 26.6 1.0
CB B:SER168 4.7 25.6 1.0
O B:HOH2048 4.8 33.4 1.0
CA B:GLY214 4.8 20.9 1.0
C B:CYS169 4.9 24.2 1.0
O B:HOH2092 4.9 38.2 1.0
O B:HOH2027 5.0 17.3 1.0
C B:SER168 5.0 25.7 1.0
N B:GLY213 5.0 24.2 1.0

Zinc binding site 3 out of 4 in 2b4y

Go back to Zinc Binding Sites List in 2b4y
Zinc binding site 3 out of 4 in the Crystal Structure of Human Sirtuin Homolog 5


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 Sirtuin Homolog 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn3001

b:19.3
occ:1.00
SG C:CYS169 2.3 16.7 1.0
SG C:CYS166 2.4 19.0 1.0
SG C:CYS207 2.4 20.1 1.0
SG C:CYS212 2.4 20.2 1.0
CB C:CYS207 3.0 20.1 1.0
CB C:CYS166 3.2 15.7 1.0
CB C:CYS212 3.3 21.7 1.0
CB C:CYS169 3.5 18.1 1.0
N C:CYS169 3.8 16.9 1.0
CA C:CYS169 4.2 17.2 1.0
CA C:CYS207 4.5 20.9 1.0
N C:GLY214 4.5 18.8 1.0
CA C:CYS166 4.6 15.3 1.0
CA C:CYS212 4.7 22.1 1.0
CB C:GLU209 4.7 26.8 1.0
CA C:GLY214 4.8 18.4 1.0
CB C:SER168 4.8 16.8 1.0
O C:HOH3027 4.9 20.5 1.0
C C:SER168 4.9 16.9 1.0
CG C:GLU209 4.9 29.2 1.0
C C:CYS169 4.9 17.8 1.0
N C:GLY170 5.0 16.7 1.0
N C:GLY213 5.0 20.9 1.0

Zinc binding site 4 out of 4 in 2b4y

Go back to Zinc Binding Sites List in 2b4y
Zinc binding site 4 out of 4 in the Crystal Structure of Human Sirtuin Homolog 5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human Sirtuin Homolog 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn4001

b:20.4
occ:1.00
SG D:CYS169 2.3 20.4 1.0
SG D:CYS207 2.3 21.7 1.0
SG D:CYS212 2.4 20.0 1.0
SG D:CYS166 2.4 18.7 1.0
CB D:CYS207 3.1 21.4 1.0
CB D:CYS166 3.1 17.1 1.0
CB D:CYS169 3.3 21.6 1.0
CB D:CYS212 3.3 22.3 1.0
N D:CYS169 3.7 20.8 1.0
CA D:CYS169 4.0 21.2 1.0
CA D:CYS207 4.5 21.7 1.0
CA D:CYS166 4.6 17.0 1.0
N D:GLY214 4.6 19.2 1.0
CB D:GLU209 4.6 29.3 1.0
CA D:CYS212 4.7 22.7 1.0
CG D:GLU209 4.8 31.9 1.0
CB D:SER168 4.8 16.5 1.0
CA D:GLY214 4.8 18.3 1.0
C D:CYS169 4.8 21.9 1.0
C D:SER168 4.8 19.6 1.0
O D:HOH4109 4.9 21.5 1.0
N D:GLY170 4.9 20.5 1.0

Reference:

T.Antoshenko, J.R.Min, A.Schuetz, P.Loppnau, A.M.Edwards, C.H.Arrowsmith, A.Bochkarev, A.N.Plotnikov. Crystal Structure of Human Sirtuin Homolog 5 in Complex with Nad To Be Published.
Page generated: Wed Dec 16 03:18:05 2020

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