Chlorine in PDB 8edd: Staphylococcus Aureus Endonuclease IV Y33F Mutant

All present enzymatic activity of Staphylococcus Aureus Endonuclease IV Y33F Mutant:
3.1.21.2;

The structure of Staphylococcus Aureus Endonuclease IV Y33F Mutant, PDB code: 8edd was solved by M.A.Saper, S.Kirillov, M.N.Isupov, R.Wiener, A.Rouvinski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.49 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.477, 41.987, 152.773, 90, 90, 90
R / Rfree (%)	17 / 20.4

The structure of Staphylococcus Aureus Endonuclease IV Y33F Mutant also contains other interesting chemical elements:

Iron	(Fe)	2 atoms
Zinc	(Zn)	1 atom

The binding sites of Chlorine atom in the Staphylococcus Aureus Endonuclease IV Y33F Mutant (pdb code 8edd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Staphylococcus Aureus Endonuclease IV Y33F Mutant, PDB code: 8edd:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Staphylococcus Aureus Endonuclease IV Y33F Mutant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Staphylococcus Aureus Endonuclease IV Y33F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl306 b:27.2 occ:1.00 HZ1 A:LYS255 2.4 24.5 1.0 H A:LEU2 2.4 27.9 1.0 H A:ASP252 2.5 34.7 1.0 HA A:MET1 3.0 36.4 1.0 NZ A:LYS255 3.2 20.4 1.0 HA A:LYS251 3.2 36.6 1.0 N A:LEU2 3.3 23.2 1.0 N A:ASP252 3.3 28.9 1.0 HB2 A:LEU2 3.4 28.1 1.0 HZ2 A:LYS255 3.4 24.5 1.0 O A:HOH589 3.6 38.4 1.0 HA A:ASP252 3.7 36.9 1.0 HG A:LEU2 3.7 29.9 1.0 HE3 A:LYS255 3.7 24.8 1.0 HZ3 A:LYS255 3.7 24.5 1.0 CA A:MET1 3.8 30.3 1.0 HD2 A:LYS251 3.8 59.9 1.0 HD12 A:LEU2 3.9 30.8 1.0 H2 A:MET1 3.9 38.6 1.0 HD3 A:LYS251 3.9 59.9 1.0 H A:ILE253 3.9 28.3 1.0 CE A:LYS255 4.0 20.7 1.0 C A:MET1 4.0 27.3 1.0 CA A:ASP252 4.0 30.7 1.0 CB A:LEU2 4.0 23.4 1.0 O A:PHE250 4.1 23.5 1.0 CA A:LYS251 4.1 30.5 1.0 HE2 A:LYS255 4.1 24.8 1.0 C A:LYS251 4.2 28.8 1.0 CA A:LEU2 4.2 22.4 1.0 CG A:LEU2 4.2 24.9 1.0 N A:MET1 4.3 32.2 1.0 CD A:LYS251 4.3 49.9 1.0 O A:ILE253 4.4 19.4 1.0 N A:ILE253 4.5 23.6 1.0 H1 A:MET1 4.5 38.6 1.0 SD A:MET1 4.5 36.3 1.0 CD1 A:LEU2 4.5 25.7 1.0 O A:HOH423 4.6 21.1 1.0 C A:ASP252 4.7 26.2 1.0 HE2 A:MET1 4.7 41.5 1.0 OD2 A:ASP252 4.9 50.4 1.0 O A:LEU2 4.9 20.9 1.0 HB3 A:LEU2 4.9 28.1 1.0 C A:PHE250 4.9 24.3 1.0 HE1 A:MET1 5.0 41.5 1.0 HA A:LEU2 5.0 26.8 1.0 N A:LYS251 5.0 27.0 1.0 CB A:MET1 5.0 33.3 1.0 C A:LEU2 5.0 20.8 1.0 HG3 A:LYS251 5.0 52.7 1.0 CB A:LYS251 5.0 37.3 1.0

Chlorine binding site 2 out of 3 in the Staphylococcus Aureus Endonuclease IV Y33F Mutant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Staphylococcus Aureus Endonuclease IV Y33F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl307 b:24.7 occ:1.00 H A:ARG221 2.4 22.8 1.0 HE1 A:HIS183 2.9 20.2 1.0 O A:HOH444 3.0 35.5 1.0 HA A:ASP220 3.1 21.4 1.0 HB2 A:ASP220 3.2 23.6 1.0 N A:ARG221 3.2 19.0 1.0 HB3 A:TYR235 3.3 23.6 1.0 HB2 A:ARG221 3.5 25.6 1.0 HD2 A:TYR235 3.5 25.6 1.0 HB3 A:ARG221 3.6 25.6 1.0 CA A:ASP220 3.7 17.8 1.0 CB A:ASP220 3.7 19.7 1.0 CE1 A:HIS183 3.7 16.8 1.0 HB3 A:ASP220 3.8 23.6 1.0 CB A:ARG221 3.9 21.3 1.0 C A:ASP220 4.0 17.9 1.0 CA A:ARG221 4.2 19.4 1.0 CD2 A:TYR235 4.2 21.3 1.0 CB A:TYR235 4.2 19.7 1.0 HE2 A:HIS183 4.2 19.1 1.0 HD2 A:LYS190 4.3 41.4 1.0 O A:TYR235 4.3 19.6 1.0 NE2 A:HIS183 4.4 16.0 1.0 HD3 A:LYS190 4.5 41.4 1.0 HB2 A:TYR235 4.6 23.6 1.0 O A:HOH560 4.6 35.4 1.0 HA A:ARG221 4.6 23.3 1.0 CG A:TYR235 4.6 18.7 1.0 ND1 A:HIS183 4.8 15.6 1.0 CD A:LYS190 4.9 34.5 1.0

Chlorine binding site 3 out of 3 in the Staphylococcus Aureus Endonuclease IV Y33F Mutant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Staphylococcus Aureus Endonuclease IV Y33F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl308 b:27.1 occ:1.00 HH22 A:ARG172 2.4 22.0 1.0 HH12 A:ARG172 2.5 22.7 1.0 H A:ASP136 2.7 65.6 1.0 H A:ASN135 2.7 74.0 1.0 HD22 A:ASN137 2.8 37.1 1.0 NH2 A:ARG172 3.2 18.4 1.0 HB2 A:ASN137 3.2 32.9 1.0 H A:THR134 3.2 53.8 1.0 H A:ASN137 3.2 44.8 1.0 N A:ASP136 3.2 54.6 1.0 N A:ASN135 3.2 61.6 1.0 HG21 A:ILE95 3.3 22.1 1.0 NH1 A:ARG172 3.3 18.9 1.0 HB2 A:ASP136 3.5 72.2 1.0 ND2 A:ASN137 3.6 30.9 1.0 N A:ASN137 3.6 37.4 1.0 HA A:LEU133 3.6 36.5 1.0 N A:THR134 3.6 44.8 1.0 CZ A:ARG172 3.7 18.7 1.0 OG1 A:THR134 3.7 61.0 1.0 HD13 A:ILE95 3.8 23.6 1.0 HA A:ASN135 3.8 75.2 1.0 HH21 A:ARG172 3.9 22.0 1.0 C A:ASN135 3.9 57.7 1.0 CA A:ASN135 3.9 62.7 1.0 CB A:ASN137 4.0 27.4 1.0 C A:THR134 4.0 57.7 1.0 CA A:ASP136 4.0 55.0 1.0 HG22 A:ILE95 4.0 22.1 1.0 HH11 A:ARG172 4.0 22.7 1.0 CG2 A:ILE95 4.1 18.4 1.0 HD21 A:ASN137 4.1 37.1 1.0 O A:HOH454 4.1 25.6 1.0 C A:ASP136 4.2 49.6 1.0 CB A:ASP136 4.2 60.2 1.0 CA A:THR134 4.2 53.3 1.0 CG A:ASN137 4.3 29.0 1.0 HG1 A:THR134 4.3 73.2 1.0 CA A:ASN137 4.3 28.5 1.0 C A:LEU133 4.3 38.4 1.0 O A:VAL132 4.3 24.6 1.0 O A:ASN137 4.3 22.9 1.0 HD12 A:ILE95 4.4 23.6 1.0 CA A:LEU133 4.4 30.4 1.0 HG23 A:THR134 4.5 71.0 1.0 CB A:THR134 4.5 58.1 1.0 CD1 A:ILE95 4.6 19.7 1.0 C A:ASN137 4.7 23.8 1.0 HG23 A:ILE95 4.7 22.1 1.0 HD23 A:LEU133 4.7 31.9 1.0 HB3 A:ASN137 4.8 32.9 1.0 HB3 A:ASP136 4.9 72.2 1.0 O A:ASN135 4.9 56.9 1.0 HD22 A:LEU133 4.9 31.9 1.0 HB A:ILE95 4.9 21.5 1.0 O A:THR134 4.9 57.7 1.0 HA A:ASP136 4.9 66.0 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.