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Zinc in PDB 4f56: The Bicyclic Intermediate Structure Provides Insights Into the Desuccinylation Mechanism of SIRT5

Protein crystallography data

The structure of The Bicyclic Intermediate Structure Provides Insights Into the Desuccinylation Mechanism of SIRT5, PDB code: 4f56 was solved by Y.Zhou, Q.Hao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.403, 66.755, 156.861, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 23.3

Zinc Binding Sites:

The binding sites of Zinc atom in the The Bicyclic Intermediate Structure Provides Insights Into the Desuccinylation Mechanism of SIRT5 (pdb code 4f56). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The Bicyclic Intermediate Structure Provides Insights Into the Desuccinylation Mechanism of SIRT5, PDB code: 4f56:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4f56

Go back to Zinc Binding Sites List in 4f56
Zinc binding site 1 out of 2 in the The Bicyclic Intermediate Structure Provides Insights Into the Desuccinylation Mechanism of SIRT5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Bicyclic Intermediate Structure Provides Insights Into the Desuccinylation Mechanism of SIRT5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:35.4
occ:1.00
SG A:CYS166 2.3 27.8 1.0
SG A:CYS169 2.3 38.6 1.0
SG A:CYS207 2.4 32.1 1.0
SG A:CYS212 2.4 39.8 1.0
CB A:CYS166 3.0 27.1 1.0
CB A:CYS207 3.1 30.0 1.0
CB A:CYS212 3.2 39.8 1.0
CB A:CYS169 3.2 34.3 1.0
N A:CYS169 3.7 35.0 1.0
CA A:CYS169 4.0 35.0 1.0
CG1 A:VAL171 4.1 33.8 1.0
CA A:CYS166 4.5 24.6 1.0
CA A:CYS207 4.6 28.4 1.0
N A:GLY214 4.6 29.6 1.0
CA A:CYS212 4.6 42.4 1.0
C A:CYS169 4.7 34.9 1.0
CB A:SER168 4.8 35.4 1.0
CA A:GLY214 4.8 28.9 1.0
C A:SER168 4.8 34.8 1.0
N A:GLY170 4.8 32.6 1.0
CB A:GLU209 4.9 39.0 1.0

Zinc binding site 2 out of 2 in 4f56

Go back to Zinc Binding Sites List in 4f56
Zinc binding site 2 out of 2 in the The Bicyclic Intermediate Structure Provides Insights Into the Desuccinylation Mechanism of SIRT5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Bicyclic Intermediate Structure Provides Insights Into the Desuccinylation Mechanism of SIRT5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:33.0
occ:1.00
SG B:CYS169 2.3 35.0 1.0
SG B:CYS207 2.3 30.4 1.0
SG B:CYS166 2.3 28.1 1.0
SG B:CYS212 2.4 35.1 1.0
CB B:CYS207 2.9 30.3 1.0
CB B:CYS166 3.1 23.8 1.0
CB B:CYS212 3.2 37.2 1.0
CB B:CYS169 3.3 36.5 1.0
N B:CYS169 3.8 35.4 1.0
CA B:CYS169 4.1 36.3 1.0
CA B:CYS207 4.4 31.4 1.0
N B:GLY214 4.5 30.1 1.0
CB B:GLU209 4.5 42.3 1.0
CG B:GLU209 4.6 39.8 1.0
CA B:CYS166 4.6 21.4 1.0
CA B:CYS212 4.7 38.5 1.0
CB B:SER168 4.7 34.4 1.0
N B:GLY213 4.8 35.3 1.0
C B:CYS169 4.8 34.7 1.0
CA B:GLY214 4.9 29.7 1.0
O B:HOH662 4.9 33.6 1.0
N B:GLY170 5.0 34.0 1.0
C B:SER168 5.0 36.3 1.0

Reference:

Y.Zhou, H.Zhang, B.He, J.Du, H.Lin, R.A.Cerione, Q.Hao. The Bicyclic Intermediate Structure Provides Insights Into the Desuccinylation Mechanism of Human Sirtuin 5 (SIRT5) J.Biol.Chem. V. 287 28307 2012.
ISSN: ISSN 0021-9258
PubMed: 22767592
DOI: 10.1074/JBC.M112.384511
Page generated: Wed Dec 16 05:16:54 2020

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