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Zinc in PDB 3aal: Crystal Structure of Endonuclease IV From Geobacillus Kaustophilus

Enzymatic activity of Crystal Structure of Endonuclease IV From Geobacillus Kaustophilus

All present enzymatic activity of Crystal Structure of Endonuclease IV From Geobacillus Kaustophilus:
3.1.21.2;

Protein crystallography data

The structure of Crystal Structure of Endonuclease IV From Geobacillus Kaustophilus, PDB code: 3aal was solved by R.Asano, H.Ishikawa, S.Nakane, N.Nakagawa, S.Kuramitsu, R.Masui, Rikenstructural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.42 / 1.60
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 85.170, 85.170, 140.220, 90.00, 90.00, 120.00
R / Rfree (%) 19.7 / 22.2

Other elements in 3aal:

The structure of Crystal Structure of Endonuclease IV From Geobacillus Kaustophilus also contains other interesting chemical elements:

Arsenic (As) 1 atom
Iron (Fe) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Endonuclease IV From Geobacillus Kaustophilus (pdb code 3aal). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Endonuclease IV From Geobacillus Kaustophilus, PDB code: 3aal:

Zinc binding site 1 out of 1 in 3aal

Go back to Zinc Binding Sites List in 3aal
Zinc binding site 1 out of 1 in the Crystal Structure of Endonuclease IV From Geobacillus Kaustophilus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Endonuclease IV From Geobacillus Kaustophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:10.9
occ:0.67
 O1 A:CAC300 1.9 19.5 1.0
NE2 A:HIS182 2.0 11.9 1.0
OD2 A:ASP227 2.0 16.6 1.0
NE2 A:HIS229 2.1 14.7 1.0
O2 A:CAC300 2.7 19.7 1.0
AS A:CAC300 2.8 30.4 1.0
CG A:ASP227 2.8 16.2 1.0
OD1 A:ASP227 2.9 17.5 1.0
CD2 A:HIS182 2.9 12.8 1.0
CE1 A:HIS229 3.0 14.2 1.0
CE1 A:HIS182 3.1 12.4 1.0
CD2 A:HIS229 3.1 15.6 1.0
C1 A:CAC300 3.9 20.0 1.0
CG A:HIS182 4.1 9.8 1.0
ND1 A:HIS229 4.2 14.9 1.0
ND1 A:HIS182 4.2 10.8 1.0
C2 A:CAC300 4.2 23.2 1.0
CG A:HIS229 4.2 12.7 1.0
CB A:ASP227 4.3 14.3 1.0
OD1 A:ASP179 4.3 11.7 1.0
FE A:FE302 4.5 7.5 0.7
O A:HOH306 4.6 12.9 1.0
O A:ASP227 4.7 13.6 1.0
CA A:ASP227 4.8 13.3 1.0
CG A:ASP179 4.9 10.4 1.0
C A:ASP227 4.9 12.7 1.0
OD2 A:ASP179 5.0 10.9 1.0

Reference:

R.Asano, H.Ishikawa, S.Nakane, N.Nakagawa, S.Kuramitsu, R.Masui. An Additional C-Terminal Loop in Endonuclease IV, An Apurinic/Apyrimidinic Endonuclease, Controls Binding Affinity to Dna Acta Crystallogr.,Sect.D V. 67 149 2011.
ISSN: ISSN 0907-4449
PubMed: 21358045
DOI: 10.1107/S0907444910052479
Page generated: Thu Oct 24 11:08:37 2024

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