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Zinc in PDB 2d3k: Structural Study on Project Id PH1539 From Pyrococcus Horikoshii OT3

Enzymatic activity of Structural Study on Project Id PH1539 From Pyrococcus Horikoshii OT3

All present enzymatic activity of Structural Study on Project Id PH1539 From Pyrococcus Horikoshii OT3:
3.1.1.29;

Protein crystallography data

The structure of Structural Study on Project Id PH1539 From Pyrococcus Horikoshii OT3, PDB code: 2d3k was solved by K.Shimizu, N.Kunishima, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.06 / 1.90
Space group P 43 2 2
Cell size a, b, c (Å), α, β, γ (°) 59.855, 59.855, 128.237, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Study on Project Id PH1539 From Pyrococcus Horikoshii OT3 (pdb code 2d3k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structural Study on Project Id PH1539 From Pyrococcus Horikoshii OT3, PDB code: 2d3k:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2d3k

Go back to Zinc Binding Sites List in 2d3k
Zinc binding site 1 out of 2 in the Structural Study on Project Id PH1539 From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Study on Project Id PH1539 From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:19.9
occ:1.00
OE1 B:GLU108 2.0 20.8 1.0
OD2 B:ASP112 2.0 19.1 1.0
CD B:GLU108 2.9 20.8 1.0
OE2 B:GLU108 3.1 21.8 1.0
CG B:ASP112 3.1 19.5 1.0
CB B:ASP112 3.7 18.6 1.0
O B:GLU108 3.9 18.0 1.0
O B:HOH1009 3.9 21.3 1.0
CA B:GLU109 4.0 19.1 1.0
C B:GLU108 4.2 19.0 1.0
OD1 B:ASP112 4.2 19.9 1.0
N B:GLU109 4.2 18.4 1.0
CG B:GLU108 4.3 18.5 1.0
CG B:GLU109 4.5 21.7 0.5
NZ B:LYS8 4.6 17.3 1.0
CB B:GLU108 4.6 17.9 1.0
CB B:GLU109 4.7 20.7 1.0

Zinc binding site 2 out of 2 in 2d3k

Go back to Zinc Binding Sites List in 2d3k
Zinc binding site 2 out of 2 in the Structural Study on Project Id PH1539 From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Study on Project Id PH1539 From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:41.0
occ:1.00
OE1 B:GLU76 2.2 23.8 1.0
OE2 B:GLU76 2.6 23.6 1.0
CD B:GLU76 2.7 23.1 1.0
O B:HOH1074 4.2 43.9 1.0
CG B:GLU76 4.2 21.2 1.0
CE B:LYS72 4.3 26.4 1.0
NZ B:LYS72 4.7 26.2 1.0
CG B:LYS72 4.8 19.7 1.0
CB B:GLU76 4.8 20.0 1.0

Reference:

K.Shimizu, C.Kuroishi, M.Sugahara, N.Kunishima. Structure of Peptidyl-Trna Hydrolase 2 From Pyrococcus Horikoshii OT3: Insight Into the Functional Role of Its Dimeric State. Acta Crystallogr.,Sect.D V. 64 444 2008.
ISSN: ISSN 0907-4449
PubMed: 18391411
DOI: 10.1107/S0907444908002850
Page generated: Wed Dec 16 03:20:33 2020

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