Iron in PDB 8axy: Staphylococcus Aureus Endonuclease IV Orthorhombic Crystal Form

All present enzymatic activity of Staphylococcus Aureus Endonuclease IV Orthorhombic Crystal Form:
3.1.21.2;

The structure of Staphylococcus Aureus Endonuclease IV Orthorhombic Crystal Form, PDB code: 8axy was solved by A.Rouvinski, S.Kirillov, M.A.Saper, R.Wiener, M.N.Isupov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.55 / 1.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.857, 82.581, 105.091, 90, 90, 90
R / Rfree (%)	13.6 / 15.8

The structure of Staphylococcus Aureus Endonuclease IV Orthorhombic Crystal Form also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Iron atom in the Staphylococcus Aureus Endonuclease IV Orthorhombic Crystal Form (pdb code 8axy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Staphylococcus Aureus Endonuclease IV Orthorhombic Crystal Form, PDB code: 8axy:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Staphylococcus Aureus Endonuclease IV Orthorhombic Crystal Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Staphylococcus Aureus Endonuclease IV Orthorhombic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:9.3 occ:1.00 O A:HOH435 1.9 11.4 1.0 OE1 A:GLU144 2.1 9.8 1.0 O3 A:SO4304 2.1 12.4 1.0 NE2 A:HIS109 2.1 9.4 1.0 O A:HOH486 2.2 12.2 1.0 NE2 A:HIS68 2.2 8.9 1.0 CD A:GLU144 3.1 8.8 1.0 CE1 A:HIS68 3.1 8.5 1.0 CD2 A:HIS109 3.1 9.0 1.0 CE1 A:HIS109 3.1 10.8 1.0 S A:SO4304 3.2 13.5 1.0 HE1 A:HIS68 3.2 8.6 1.0 CD2 A:HIS68 3.2 8.7 1.0 HD2 A:HIS109 3.3 9.2 1.0 HE1 A:HIS109 3.3 10.4 1.0 OE2 A:GLU144 3.4 9.9 1.0 HD2 A:HIS68 3.4 8.7 1.0 O2 A:SO4304 3.5 16.3 1.0 FE A:FE302 3.5 9.2 1.0 HE1 A:HIS213 3.6 9.0 1.0 O1 A:SO4304 3.6 12.1 1.0 HE1 A:HIS181 3.8 10.4 1.0 HG11 A:VAL107 4.0 9.0 1.0 ND1 A:HIS68 4.2 9.4 1.0 OE2 A:GLU258 4.2 10.2 1.0 HG12 A:VAL107 4.2 9.2 1.0 ND1 A:HIS109 4.3 10.8 1.0 CG A:HIS109 4.3 9.7 1.0 CE1 A:HIS213 4.3 9.1 1.0 CG A:HIS68 4.3 8.3 1.0 CG A:GLU144 4.4 8.6 1.0 O4 A:SO4304 4.5 13.5 1.0 ND1 A:HIS213 4.5 8.5 1.0 OH A:TYR33 4.5 11.6 1.0 CG1 A:VAL107 4.6 9.1 1.0 HB2 A:GLU144 4.6 8.6 1.0 O A:HOH660 4.7 22.1 1.0 CE1 A:HIS181 4.7 10.5 1.0 HH A:TYR33 4.7 11.5 0.0 HD2 A:TYR71 4.7 20.8 0.5 HB3 A:GLU144 4.8 8.7 1.0 OE1 A:GLU258 4.8 8.9 1.0 HE1 A:MET146 4.9 11.6 1.0 CB A:GLU144 4.9 8.7 1.0 HG2 A:GLU144 5.0 8.7 1.0 CD A:GLU258 5.0 9.1 1.0 HG3 A:GLU144 5.0 8.6 1.0 HD1 A:HIS68 5.0 9.4 0.0

Iron binding site 2 out of 2 in the Staphylococcus Aureus Endonuclease IV Orthorhombic Crystal Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Staphylococcus Aureus Endonuclease IV Orthorhombic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:9.2 occ:1.00 O A:HOH435 2.0 11.4 1.0 OE2 A:GLU144 2.1 9.9 1.0 OD2 A:ASP178 2.1 9.4 1.0 O1 A:SO4304 2.1 12.1 1.0 OE1 A:GLU258 2.1 8.9 1.0 ND1 A:HIS213 2.2 8.5 1.0 CD A:GLU258 3.1 9.1 1.0 CD A:GLU144 3.1 8.8 1.0 CE1 A:HIS213 3.1 9.1 1.0 HE1 A:HIS213 3.2 9.0 1.0 CG A:ASP178 3.2 8.7 1.0 S A:SO4304 3.3 13.5 1.0 CG A:HIS213 3.3 8.5 1.0 OE2 A:GLU258 3.3 10.2 1.0 HB2 A:ASP178 3.4 8.0 1.0 HB3 A:HIS213 3.4 7.9 1.0 O3 A:SO4304 3.5 12.4 1.0 FE A:FE301 3.5 9.3 1.0 OE1 A:GLU144 3.5 9.8 1.0 HB2 A:HIS213 3.5 7.8 1.0 CB A:HIS213 3.6 7.8 1.0 HD21 A:ASN215 3.7 8.9 1.0 HE1 A:HIS181 3.7 10.4 1.0 HE1 A:HIS228 3.8 11.8 1.0 CB A:ASP178 3.8 8.0 1.0 O2 A:SO4304 3.9 16.3 1.0 CE1 A:HIS181 3.9 10.5 1.0 HD22 A:ASN215 4.0 9.1 1.0 ND2 A:ASN215 4.2 9.1 1.0 NE2 A:HIS213 4.3 9.5 1.0 OD1 A:ASP178 4.3 9.5 1.0 HB3 A:ASP178 4.3 8.1 1.0 CG A:GLU144 4.4 8.6 1.0 CD2 A:HIS213 4.4 8.9 1.0 HG3 A:GLU144 4.4 8.6 1.0 NE2 A:HIS181 4.4 11.2 1.0 CG A:GLU258 4.4 9.2 1.0 O4 A:SO4304 4.4 13.5 1.0 ND1 A:HIS181 4.5 9.3 1.0 CE1 A:HIS228 4.5 12.1 1.0 HB2 A:GLU258 4.6 9.0 1.0 HG2 A:GLU144 4.6 8.7 1.0 HG3 A:GLU258 4.6 9.2 1.0 HD1 A:HIS181 4.6 9.3 0.0 HG A:CYS176 4.8 10.0 0.0 O A:HOH486 4.8 12.2 1.0 ZN A:ZN303 4.8 16.9 1.0 HD2 A:HIS68 4.8 8.7 1.0 NE2 A:HIS228 4.9 13.0 1.0 HA A:ASP178 5.0 8.1 1.0 NE2 A:HIS68 5.0 8.9 1.0

S.Kirillov, M.N.Isupov, N.Paterson, R.Wiener, S.Abeldenov, M.A.Saper, A.Rouvinski. Octahedrally Coordinated Iron in the Catalytic Site of Endonuclease IV From Staphylococcus Aureus To Be Published.