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Zinc in PDB 4g1c: Human SIRT5 Bound to Succ-IDH2 and Carba-Nad

Protein crystallography data

The structure of Human SIRT5 Bound to Succ-IDH2 and Carba-Nad, PDB code: 4g1c was solved by H.Dai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.40 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.239, 84.425, 95.740, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 24.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Human SIRT5 Bound to Succ-IDH2 and Carba-Nad (pdb code 4g1c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human SIRT5 Bound to Succ-IDH2 and Carba-Nad, PDB code: 4g1c:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4g1c

Go back to Zinc Binding Sites List in 4g1c
Zinc binding site 1 out of 2 in the Human SIRT5 Bound to Succ-IDH2 and Carba-Nad


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human SIRT5 Bound to Succ-IDH2 and Carba-Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:41.4
occ:1.00
SG A:CYS169 2.1 37.8 1.0
SG A:CYS212 2.4 44.9 1.0
SG A:CYS207 2.4 47.9 1.0
SG A:CYS166 2.4 36.1 1.0
CB A:CYS166 3.1 36.2 1.0
CB A:CYS207 3.1 32.5 1.0
CB A:CYS212 3.2 47.3 1.0
CB A:CYS169 3.3 39.3 1.0
N A:CYS169 3.8 40.3 1.0
CA A:CYS169 4.1 33.8 1.0
CB A:GLU209 4.4 68.6 1.0
N A:GLY214 4.5 47.3 1.0
CA A:CYS166 4.6 33.5 1.0
CA A:CYS207 4.6 38.9 1.0
O A:HOH613 4.6 39.8 1.0
CA A:CYS212 4.6 50.8 1.0
CB A:SER168 4.8 41.5 1.0
CA A:GLY214 4.8 41.3 1.0
C A:CYS169 4.8 37.5 1.0
C A:SER168 4.9 39.8 1.0
N A:GLY213 4.9 44.4 1.0
N A:GLY170 5.0 36.5 1.0

Zinc binding site 2 out of 2 in 4g1c

Go back to Zinc Binding Sites List in 4g1c
Zinc binding site 2 out of 2 in the Human SIRT5 Bound to Succ-IDH2 and Carba-Nad


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human SIRT5 Bound to Succ-IDH2 and Carba-Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:44.3
occ:1.00
SG B:CYS169 2.1 47.3 1.0
SG B:CYS207 2.3 45.2 1.0
SG B:CYS212 2.3 52.1 1.0
SG B:CYS166 2.4 43.4 1.0
CB B:CYS207 2.9 45.0 1.0
CB B:CYS212 3.1 42.0 1.0
CB B:CYS166 3.1 35.6 1.0
CB B:CYS169 3.3 55.1 1.0
N B:CYS169 3.7 43.9 1.0
CA B:CYS169 4.1 44.2 1.0
CA B:CYS207 4.4 47.1 1.0
CA B:CYS212 4.6 46.6 1.0
CA B:CYS166 4.6 34.6 1.0
CB B:SER168 4.7 50.6 1.0
N B:GLY214 4.7 46.2 1.0
C B:CYS169 4.8 46.3 1.0
C B:SER168 4.8 49.9 1.0
N B:GLY170 4.9 44.7 1.0
O B:GLU209 4.9 51.8 1.0
CA B:GLY214 4.9 44.8 1.0
C B:CYS212 5.0 46.4 1.0

Reference:

B.G.Szczepankiewicz, H.Dai, K.J.Koppetsch, D.Qian, F.Jiang, C.Mao, R.B.Perni. Synthesis of Carba-Nad and the Structures of Its Ternary Complexes with SIRT3 and SIRT5. J.Org.Chem. V. 77 7319 2012.
ISSN: ISSN 0022-3263
PubMed: 22849721
DOI: 10.1021/JO301067E
Page generated: Wed Dec 16 05:18:49 2020

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