Iron in PDB 3aal: 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;

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

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

Arsenic	(As)	1 atom
Zinc	(Zn)	1 atom

The binding sites of Iron 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 Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Endonuclease IV From Geobacillus Kaustophilus, PDB code: 3aal:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Endonuclease IV From Geobacillus Kaustophilus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe301 b:18.2 occ:1.00 NE2 A:HIS110 2.0 15.7 1.0 C1 A:CAC300 2.1 20.0 1.0 OE2 A:GLU145 2.2 17.1 1.0 NE2 A:HIS69 2.2 14.4 1.0 CD2 A:HIS110 3.0 13.4 1.0 CE1 A:HIS69 3.0 12.2 1.0 CE1 A:HIS110 3.0 16.5 1.0 CD A:GLU145 3.1 14.3 1.0 CD2 A:HIS69 3.3 12.8 1.0 AS A:CAC300 3.3 30.4 1.0 OE1 A:GLU145 3.4 12.0 1.0 FE A:FE302 3.5 7.5 0.7 C2 A:CAC300 3.8 23.2 1.0 O2 A:CAC300 3.8 19.7 1.0 ND1 A:HIS110 4.1 16.1 1.0 CG A:HIS110 4.2 12.3 1.0 OE2 A:GLU259 4.2 14.0 1.0 ND1 A:HIS69 4.2 10.8 1.0 CE1 A:HIS214 4.3 11.9 1.0 CG A:HIS69 4.4 11.2 1.0 ND1 A:HIS214 4.5 11.3 1.0 CG A:GLU145 4.5 11.3 1.0 OH A:TYR34 4.5 13.2 1.0 CE1 A:HIS182 4.7 12.4 1.0 CG1 A:VAL108 4.7 10.6 1.0 O1 A:CAC300 4.8 19.5 1.0 CB A:GLU145 4.9 9.7 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Endonuclease IV From Geobacillus Kaustophilus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Endonuclease IV From Geobacillus Kaustophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:7.5 occ:0.67 O2 A:CAC300 2.0 19.7 1.0 OD1 A:ASP179 2.1 11.7 1.0 OE1 A:GLU145 2.2 12.0 1.0 OE1 A:GLU259 2.2 10.6 1.0 ND1 A:HIS214 2.4 11.3 1.0 CD A:GLU259 3.0 12.2 1.0 OE2 A:GLU259 3.1 14.0 1.0 CD A:GLU145 3.2 14.3 1.0 AS A:CAC300 3.2 30.4 1.0 CE1 A:HIS214 3.2 11.9 1.0 CG A:ASP179 3.3 10.4 1.0 CG A:HIS214 3.4 10.2 1.0 FE A:FE301 3.5 18.2 1.0 OE2 A:GLU145 3.5 17.1 1.0 C1 A:CAC300 3.6 20.0 1.0 CB A:HIS214 3.7 9.7 1.0 CE1 A:HIS182 3.8 12.4 1.0 CB A:ASP179 3.9 10.1 1.0 C2 A:CAC300 4.0 23.2 1.0 NE2 A:HIS182 4.1 11.9 1.0 ND2 A:ASN216 4.2 10.8 1.0 OD2 A:ASP179 4.4 10.9 1.0 NE2 A:HIS214 4.4 10.8 1.0 ND1 A:HIS182 4.4 10.8 1.0 CD2 A:HIS214 4.4 11.6 1.0 CG A:GLU259 4.5 12.9 1.0 CG A:GLU145 4.5 11.3 1.0 CE1 A:HIS229 4.5 14.2 1.0 ZN A:ZN303 4.5 10.9 0.7 O1 A:CAC300 4.6 19.5 1.0 NE2 A:HIS229 4.9 14.7 1.0 CD2 A:HIS182 5.0 12.8 1.0

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