Iron in PDB 8pkb: Staphylococcus Aureus Endonuclease IV with Bound Phosphate

All present enzymatic activity of Staphylococcus Aureus Endonuclease IV with Bound Phosphate:
3.1.21.2;

The structure of Staphylococcus Aureus Endonuclease IV with Bound Phosphate, PDB code: 8pkb was solved by M.Saper, S.Kirillov, A.Rouvinski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.548, 84.04, 103.344, 90, 90, 90
R / Rfree (%)	18.8 / 21.1

The structure of Staphylococcus Aureus Endonuclease IV with Bound Phosphate also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Iron atom in the Staphylococcus Aureus Endonuclease IV with Bound Phosphate (pdb code 8pkb). 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 with Bound Phosphate, PDB code: 8pkb:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Staphylococcus Aureus Endonuclease IV with Bound Phosphate


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 with Bound Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:24.8 occ:1.00 O A:HOH415 1.8 26.9 1.0 NE2 A:HIS109 2.1 27.6 1.0 OE1 A:GLU144 2.2 22.7 1.0 O3 A:PO4304 2.3 30.8 1.0 NE2 A:HIS68 2.3 25.9 1.0 O A:HOH425 2.3 28.2 1.0 CD A:GLU144 3.0 24.6 1.0 CD2 A:HIS109 3.1 26.7 1.0 CE1 A:HIS109 3.1 28.6 1.0 CE1 A:HIS68 3.1 26.5 1.0 HD2 A:HIS109 3.2 32.2 1.0 OE2 A:GLU144 3.2 25.1 1.0 HE1 A:HIS68 3.2 31.9 1.0 HE1 A:HIS109 3.3 34.5 1.0 CD2 A:HIS68 3.3 25.7 1.0 P A:PO4304 3.4 30.7 1.0 HE1 A:HIS213 3.4 32.7 1.0 HD2 A:HIS68 3.6 31.0 1.0 FE A:FE302 3.6 25.2 1.0 O4 A:PO4304 3.7 28.6 1.0 O2 A:PO4304 3.7 34.2 1.0 HG12 A:VAL107 3.9 29.8 1.0 HE1 A:HIS181 3.9 31.8 1.0 HH A:TYR33 4.1 34.0 1.0 CE1 A:HIS213 4.2 27.2 1.0 ND1 A:HIS109 4.2 28.4 1.0 CG A:HIS109 4.2 28.2 1.0 OE2 A:GLU258 4.2 27.6 1.0 HG11 A:VAL107 4.3 29.8 1.0 ND1 A:HIS68 4.3 25.9 1.0 CG A:HIS68 4.4 25.6 1.0 CG A:GLU144 4.4 24.6 1.0 ND1 A:HIS213 4.5 26.7 1.0 CG1 A:VAL107 4.5 24.7 1.0 HB2 A:GLU144 4.5 28.3 1.0 OH A:TYR33 4.6 28.2 1.0 O1 A:PO4304 4.6 29.6 1.0 O A:HOH473 4.6 37.4 1.0 HB3 A:GLU144 4.7 28.3 1.0 CE1 A:HIS181 4.8 26.4 1.0 CB A:GLU144 4.8 23.5 1.0 HG2 A:GLU144 4.9 29.6 1.0 OE1 A:GLU258 4.9 26.2 1.0 HG3 A:GLU144 5.0 29.6 1.0 HD1 A:HIS109 5.0 34.2 1.0

Iron binding site 2 out of 2 in the Staphylococcus Aureus Endonuclease IV with Bound Phosphate


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 with Bound Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:25.2 occ:1.00 OE2 A:GLU144 2.1 25.1 1.0 OD2 A:ASP178 2.1 23.5 1.0 OE1 A:GLU258 2.1 26.2 1.0 ND1 A:HIS213 2.2 26.7 1.0 O A:HOH415 2.2 26.9 1.0 O4 A:PO4304 2.3 28.6 1.0 CD A:GLU258 3.0 26.8 1.0 CE1 A:HIS213 3.1 27.2 1.0 CD A:GLU144 3.1 24.6 1.0 CG A:HIS213 3.2 26.1 1.0 OE2 A:GLU258 3.3 27.6 1.0 HE1 A:HIS213 3.3 32.7 1.0 CG A:ASP178 3.3 24.1 1.0 HB3 A:HIS213 3.3 29.7 1.0 HB2 A:ASP178 3.4 27.7 1.0 HB2 A:HIS213 3.5 29.7 1.0 HE1 A:HIS181 3.5 31.8 1.0 P A:PO4304 3.5 30.7 1.0 CB A:HIS213 3.6 24.6 1.0 OE1 A:GLU144 3.6 22.7 1.0 HD21 A:ASN215 3.6 28.6 1.0 FE A:FE301 3.6 24.8 1.0 O3 A:PO4304 3.7 30.8 1.0 CE1 A:HIS181 3.8 26.4 1.0 CB A:ASP178 3.9 23.0 1.0 HE1 A:HIS228 4.0 30.9 1.0 HD22 A:ASN215 4.0 28.6 1.0 ND2 A:ASN215 4.1 23.8 1.0 O2 A:PO4304 4.2 34.2 1.0 NE2 A:HIS181 4.2 24.9 1.0 NE2 A:HIS213 4.2 27.3 1.0 OD1 A:ASP178 4.3 22.7 1.0 CD2 A:HIS213 4.3 27.5 1.0 CG A:GLU144 4.4 24.6 1.0 HB3 A:ASP178 4.4 27.7 1.0 HG3 A:GLU144 4.4 29.6 1.0 CG A:GLU258 4.4 26.1 1.0 ND1 A:HIS181 4.5 24.9 1.0 HG3 A:GLU258 4.6 31.5 1.0 HG2 A:GLU144 4.6 29.6 1.0 CE1 A:HIS228 4.7 25.6 1.0 HD1 A:HIS181 4.7 29.9 1.0 HB2 A:GLU258 4.7 31.1 1.0 O1 A:PO4304 4.7 29.6 1.0 ZN A:ZN303 4.7 30.2 1.0 O A:HOH425 5.0 28.2 1.0 HA A:ASP178 5.0 27.9 1.0 HE2 A:HIS213 5.0 32.9 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.