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Zinc in PDB 3pkj: Human SIRT6 Crystal Structure in Complex with 2'-N-Acetyl Adp Ribose

Protein crystallography data

The structure of Human SIRT6 Crystal Structure in Complex with 2'-N-Acetyl Adp Ribose, PDB code: 3pkj was solved by P.W.Pan, A.Dong, W.Qiu, P.Loppnau, J.Wang, M.Ravichandran, J.R.Walker, C.Bountra, J.Weigelt, C.H.Arrowsmith, J.Min, A.M.Edwards, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.50 / 2.12
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.042, 135.780, 89.105, 90.00, 120.02, 90.00
R / Rfree (%) 23.4 / 26.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Human SIRT6 Crystal Structure in Complex with 2'-N-Acetyl Adp Ribose (pdb code 3pkj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Human SIRT6 Crystal Structure in Complex with 2'-N-Acetyl Adp Ribose, PDB code: 3pkj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3pkj

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Zinc binding site 1 out of 6 in the Human SIRT6 Crystal Structure in Complex with 2'-N-Acetyl Adp Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human SIRT6 Crystal Structure in Complex with 2'-N-Acetyl Adp Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn354

b:47.0
occ:1.00
SG A:CYS142 2.2 46.8 1.0
SG A:CYS164 2.3 53.1 1.0
SG A:CYS175 2.4 58.2 1.0
SG A:CYS139 2.6 38.2 1.0
CB A:CYS164 3.0 49.2 1.0
CB A:CYS175 3.2 54.3 1.0
CB A:CYS139 3.4 34.5 1.0
CB A:CYS142 3.5 42.8 1.0
N A:CYS142 3.9 42.3 1.0
CA A:CYS142 4.3 42.2 1.0
CA A:CYS164 4.5 48.7 1.0
N A:GLY177 4.5 49.8 1.0
CA A:CYS175 4.6 54.1 1.0
CA A:GLY177 4.7 48.9 1.0
OG1 A:THR144 4.7 53.6 1.0
CA A:CYS139 4.9 34.2 1.0
CB A:THR144 4.9 51.9 1.0
CB A:LYS141 4.9 43.5 1.0
C A:CYS175 5.0 56.5 1.0
C A:CYS142 5.0 44.9 1.0
N A:ARG176 5.0 52.3 1.0

Zinc binding site 2 out of 6 in 3pkj

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Zinc binding site 2 out of 6 in the Human SIRT6 Crystal Structure in Complex with 2'-N-Acetyl Adp Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human SIRT6 Crystal Structure in Complex with 2'-N-Acetyl Adp Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn354

b:59.1
occ:1.00
SG B:CYS142 2.2 44.0 1.0
SG B:CYS139 2.2 44.1 1.0
SG B:CYS175 2.3 58.5 1.0
SG B:CYS164 2.7 58.3 1.0
CB B:CYS139 3.2 39.8 1.0
CB B:CYS164 3.2 54.4 1.0
CB B:CYS142 3.3 40.0 1.0
CB B:CYS175 3.4 54.5 1.0
N B:CYS142 3.5 39.7 1.0
CA B:CYS142 3.9 39.4 1.0
CG2 B:VAL166 4.2 63.5 1.0
N B:GLY177 4.4 44.6 1.0
CB B:LYS141 4.5 41.9 1.0
CA B:GLY177 4.5 43.4 1.0
C B:LYS141 4.6 43.1 1.0
CA B:CYS139 4.6 38.8 1.0
C B:CYS142 4.7 42.1 1.0
CA B:CYS164 4.7 54.2 1.0
CA B:CYS175 4.8 54.2 1.0
N B:LYS143 4.9 37.9 1.0
CA B:LYS141 4.9 39.2 1.0
OG1 B:THR144 4.9 45.5 1.0
N B:LYS141 4.9 39.3 1.0

Zinc binding site 3 out of 6 in 3pkj

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Zinc binding site 3 out of 6 in the Human SIRT6 Crystal Structure in Complex with 2'-N-Acetyl Adp Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human SIRT6 Crystal Structure in Complex with 2'-N-Acetyl Adp Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn354

b:49.6
occ:1.00
SG C:CYS142 2.2 48.1 1.0
SG C:CYS139 2.3 45.1 1.0
SG C:CYS175 2.5 54.1 1.0
SG C:CYS164 2.5 45.8 1.0
CB C:CYS164 3.1 42.2 1.0
CB C:CYS139 3.2 41.2 1.0
CB C:CYS175 3.4 50.4 1.0
CB C:CYS142 3.4 44.1 1.0
N C:CYS142 3.7 43.9 1.0
CA C:CYS142 4.1 43.5 1.0
N C:GLY177 4.4 48.8 1.0
CA C:CYS164 4.6 42.5 1.0
CA C:GLY177 4.6 47.7 1.0
CA C:CYS139 4.6 41.0 1.0
CB C:LYS141 4.7 47.1 1.0
CA C:CYS175 4.8 50.2 1.0
C C:CYS142 4.8 45.9 1.0
OG1 C:THR144 4.8 45.0 1.0
C C:LYS141 4.8 48.2 1.0
CB C:THR144 4.9 44.5 1.0
N C:LYS143 5.0 42.1 1.0

Zinc binding site 4 out of 6 in 3pkj

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Zinc binding site 4 out of 6 in the Human SIRT6 Crystal Structure in Complex with 2'-N-Acetyl Adp Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human SIRT6 Crystal Structure in Complex with 2'-N-Acetyl Adp Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn354

b:46.5
occ:1.00
SG D:CYS164 2.3 53.7 1.0
SG D:CYS142 2.4 34.2 1.0
SG D:CYS139 2.5 43.4 1.0
CB D:CYS164 2.8 49.8 1.0
O D:ARG176 2.9 55.8 1.0
CB D:CYS139 3.3 39.3 1.0
CB D:CYS142 3.6 31.2 1.0
N D:ARG176 3.8 52.1 1.0
N D:CYS142 3.8 33.4 1.0
C D:ARG176 3.8 56.2 1.0
CG1 D:VAL166 4.2 59.4 1.0
CA D:CYS142 4.2 31.9 1.0
CA D:CYS164 4.3 49.4 1.0
CA D:ARG176 4.4 52.1 1.0
CA D:CYS139 4.7 38.7 1.0
CB D:LYS141 4.8 40.8 1.0
N D:GLY177 4.8 52.5 1.0
C D:LYS141 4.8 38.9 1.0
C D:CYS142 4.9 36.9 1.0
N D:LYS143 5.0 34.4 1.0

Zinc binding site 5 out of 6 in 3pkj

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Zinc binding site 5 out of 6 in the Human SIRT6 Crystal Structure in Complex with 2'-N-Acetyl Adp Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human SIRT6 Crystal Structure in Complex with 2'-N-Acetyl Adp Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn354

b:57.1
occ:1.00
SG E:CYS175 2.3 56.7 1.0
SG E:CYS142 2.3 49.6 1.0
SG E:CYS164 2.4 51.7 1.0
SG E:CYS139 2.4 48.0 1.0
CB E:CYS164 2.9 48.1 1.0
CB E:CYS175 3.2 52.7 1.0
CB E:CYS139 3.4 43.9 1.0
CB E:CYS142 3.5 45.7 1.0
N E:CYS142 3.9 45.7 1.0
CG2 E:VAL166 4.0 58.7 1.0
CA E:CYS142 4.3 45.2 1.0
N E:GLY177 4.3 48.6 1.0
CA E:CYS164 4.4 48.1 1.0
CA E:GLY177 4.5 47.6 1.0
CA E:CYS175 4.5 52.2 1.0
CB E:LYS141 4.8 48.3 1.0
C E:CYS175 4.8 55.6 1.0
CA E:CYS139 4.8 43.4 1.0
N E:ARG176 4.9 51.3 1.0
OG1 E:THR144 5.0 45.3 1.0
C E:LYS141 5.0 49.5 1.0

Zinc binding site 6 out of 6 in 3pkj

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Zinc binding site 6 out of 6 in the Human SIRT6 Crystal Structure in Complex with 2'-N-Acetyl Adp Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human SIRT6 Crystal Structure in Complex with 2'-N-Acetyl Adp Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn354

b:40.2
occ:1.00
SG F:CYS142 2.2 41.7 1.0
SG F:CYS164 2.2 52.8 1.0
SG F:CYS175 2.5 54.2 1.0
SG F:CYS139 2.6 40.3 1.0
CB F:CYS164 2.9 49.1 1.0
CB F:CYS175 3.2 50.5 1.0
CB F:CYS139 3.4 35.9 1.0
CB F:CYS142 3.5 37.9 1.0
N F:CYS142 4.0 38.1 1.0
CA F:CYS142 4.3 37.8 1.0
CA F:CYS164 4.4 48.9 1.0
N F:GLY177 4.5 48.6 1.0
CA F:CYS175 4.6 50.4 1.0
CA F:GLY177 4.7 48.2 1.0
OG1 F:THR144 4.8 45.5 1.0
CB F:THR144 4.9 45.9 1.0
CA F:CYS139 4.9 35.2 1.0
C F:CYS142 5.0 42.1 1.0
C F:CYS175 5.0 53.4 1.0
N F:ARG176 5.0 49.6 1.0

Reference:

P.W.Pan, J.L.Feldman, M.K.Devries, A.Dong, A.M.Edwards, J.M.Denu. Structure and Biochemical Functions of SIRT6. J.Biol.Chem. V. 286 14575 2011.
ISSN: ISSN 0021-9258
PubMed: 21362626
DOI: 10.1074/JBC.M111.218990
Page generated: Wed Dec 16 04:43:15 2020

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