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Zinc in PDB 4r8m: Human SIRT2 Crystal Structure in Complex with Bhjh-TM1

Protein crystallography data

The structure of Human SIRT2 Crystal Structure in Complex with Bhjh-TM1, PDB code: 4r8m was solved by Y.B.Teng, Q.Hao, H.N.Lin, H.Jing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.11 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 36.936, 116.799, 70.905, 90.00, 91.77, 90.00
R / Rfree (%) 22.1 / 27.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Human SIRT2 Crystal Structure in Complex with Bhjh-TM1 (pdb code 4r8m). 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 SIRT2 Crystal Structure in Complex with Bhjh-TM1, PDB code: 4r8m:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4r8m

Go back to Zinc Binding Sites List in 4r8m
Zinc binding site 1 out of 2 in the Human SIRT2 Crystal Structure in Complex with Bhjh-TM1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human SIRT2 Crystal Structure in Complex with Bhjh-TM1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:47.2
occ:1.00
SG A:CYS221 2.2 43.5 1.0
SG A:CYS200 2.3 62.3 1.0
SG A:CYS195 2.4 50.9 1.0
SG A:CYS224 2.5 47.8 1.0
CB A:CYS221 3.0 43.9 1.0
CB A:CYS200 3.2 60.8 1.0
CB A:CYS195 3.2 45.4 1.0
CB A:CYS224 3.5 47.0 1.0
N A:CYS224 3.9 49.5 1.0
CA A:CYS224 4.2 46.5 1.0
OG A:SER197 4.4 49.3 1.0
CB A:HIS202 4.4 58.9 1.0
CA A:CYS221 4.5 45.8 1.0
CB A:ASP223 4.6 56.7 1.0
CA A:CYS200 4.6 61.8 1.0
CA A:CYS195 4.6 44.8 1.0
N A:HIS202 4.7 54.6 1.0
CB A:SER226 4.7 40.8 1.0
C A:CYS224 4.8 43.0 1.0
C A:CYS200 4.9 60.9 1.0
N A:ARG201 4.9 59.8 1.0
C A:ASP223 4.9 52.8 1.0
N A:GLN225 4.9 45.2 1.0
N A:SER226 5.0 40.5 1.0

Zinc binding site 2 out of 2 in 4r8m

Go back to Zinc Binding Sites List in 4r8m
Zinc binding site 2 out of 2 in the Human SIRT2 Crystal Structure in Complex with Bhjh-TM1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human SIRT2 Crystal Structure in Complex with Bhjh-TM1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:38.8
occ:1.00
SG B:CYS200 2.3 41.3 1.0
SG B:CYS195 2.3 44.4 1.0
SG B:CYS221 2.3 35.0 1.0
SG B:CYS224 2.4 38.3 1.0
CB B:CYS200 3.0 42.2 1.0
CB B:CYS195 3.1 37.5 1.0
CB B:CYS221 3.2 37.1 1.0
CB B:CYS224 3.3 38.9 1.0
N B:CYS224 3.8 40.2 1.0
CA B:CYS224 4.1 38.9 1.0
CB B:HIS202 4.3 39.2 1.0
CA B:CYS200 4.4 43.7 1.0
N B:HIS202 4.5 37.7 1.0
CA B:CYS195 4.6 34.3 1.0
N B:ARG201 4.6 38.5 1.0
CB B:SER197 4.6 47.9 1.0
C B:CYS224 4.7 36.6 1.0
CA B:CYS221 4.7 38.0 1.0
CB B:ASP223 4.7 47.9 1.0
C B:CYS200 4.8 42.3 1.0
OG B:SER226 4.8 37.9 1.0
CB B:SER226 4.8 36.4 1.0
N B:GLN225 4.9 38.0 1.0
C B:ASP223 4.9 44.3 1.0
N B:SER226 5.0 36.2 1.0

Reference:

Y.B.Teng, H.Jing, P.Aramsangtienchai, B.He, S.Khan, J.Hu, H.Lin, Q.Hao. Efficient Demyristoylase Activity of SIRT2 Revealed By Kinetic and Structural Studies Sci Rep V. 5 8529 2015.
ISSN: ESSN 2045-2322
PubMed: 25704306
DOI: 10.1038/SREP08529
Page generated: Wed Dec 16 05:45:27 2020

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