Magnesium in PDB 8zxg: Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI

The structure of Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI, PDB code: 8zxg was solved by A.A.Azman, N.D.Muhd Noor, A.T.C.Leow, S.A.Mohd Noor, M.S.Mohamad Ali, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.01 / 1.49
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	77.823, 77.823, 135.266, 90, 90, 90
R / Rfree (%)	19.3 / n/a

The structure of Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 58;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI (pdb code 8zxg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 58 binding sites of Magnesium where determined in the Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI, PDB code: 8zxg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 58 in the Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg408 b:43.4 occ:1.00 O A:HOH545 2.9 24.4 1.0 O A:ALA183 3.0 31.2 1.0 CG2 A:THR214 3.2 27.2 1.0 CE1 A:TYR211 3.2 32.3 1.0 CD1 A:TYR211 3.3 33.9 1.0 CD2 A:LEU215 3.5 35.2 1.0 CB A:ALA183 3.7 26.0 1.0 O A:TYR211 3.7 27.5 1.0 C A:ALA183 3.7 25.8 1.0 CB A:THR214 3.7 24.5 1.0 CA A:ALA183 3.7 24.4 1.0 CZ A:TYR211 3.9 33.1 1.0 CG A:LEU215 3.9 32.0 1.0 CG A:TYR211 4.0 28.8 1.0 N A:LEU215 4.2 27.6 1.0 CA A:TYR211 4.5 26.4 1.0 C A:TYR211 4.5 27.6 1.0 C A:THR214 4.5 27.7 1.0 O A:PRO161 4.5 24.8 1.0 CE2 A:TYR211 4.5 36.2 1.0 OH A:TYR211 4.5 40.9 1.0 CD2 A:TYR211 4.6 35.2 1.0 CA A:THR214 4.7 27.6 1.0 CA A:LEU215 4.7 28.9 1.0 OG1 A:THR214 4.8 26.4 1.0 CB A:TYR211 4.8 27.4 1.0 O A:THR160 4.9 22.6 1.0 CB A:LEU215 4.9 31.1 1.0 N A:LEU184 4.9 26.1 1.0 CD1 A:LEU218 5.0 37.0 1.0

Magnesium binding site 2 out of 58 in the Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg409 b:44.4 occ:1.00 N A:GLU173 3.0 30.7 1.0 O A:GLU154 3.0 31.1 1.0 O A:TYR171 3.0 26.5 1.0 OG1 A:THR156 3.3 30.3 0.5 CB A:GLU173 3.5 38.8 1.0 O A:HOH543 3.7 35.0 1.0 N A:THR156 3.7 25.4 1.0 CA A:ARG172 3.7 27.9 1.0 CG2 A:THR156 3.8 32.4 0.5 CA A:GLU173 3.8 33.2 1.0 C A:ARG172 3.8 30.5 1.0 CB A:THR156 3.9 28.5 0.5 C A:TYR171 3.9 24.7 1.0 C A:GLU154 3.9 28.4 1.0 C A:PHE155 3.9 25.5 1.0 CB A:THR156 4.0 32.4 0.5 CA A:PHE155 4.0 25.2 1.0 N A:ARG172 4.2 26.0 1.0 N A:PHE155 4.4 27.1 1.0 CA A:THR156 4.4 26.6 0.5 CA A:THR156 4.5 27.4 0.5 CD2 A:TYR171 4.5 32.7 1.0 O A:PHE155 4.7 29.4 1.0

Magnesium binding site 3 out of 58 in the Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg410 b:42.9 occ:1.00 O A:HIS230 2.6 28.3 1.0 O A:GLU232 2.7 30.1 1.0 N A:GLY186 2.7 34.8 1.0 CB A:SER228 3.5 30.4 1.0 N A:GLU232 3.5 30.0 1.0 CA A:GLY186 3.6 34.6 1.0 OG A:SER228 3.6 37.0 1.0 C A:GLY231 3.6 29.5 1.0 CG2 A:ILE185 3.7 34.9 1.0 C A:ILE185 3.7 33.7 1.0 CA A:ILE185 3.7 31.9 1.0 C A:HIS230 3.8 25.5 1.0 C A:GLU232 3.8 27.3 1.0 CA A:GLY231 3.9 29.9 1.0 MG A:MG411 3.9 48.5 1.0 ND1 A:HIS187 4.1 46.3 1.0 O A:GLY231 4.2 29.4 1.0 CB A:ILE185 4.2 33.5 1.0 CA A:GLU232 4.3 29.5 1.0 N A:GLY231 4.3 29.6 1.0 CG2 A:VAL234 4.4 32.2 1.0 N A:HIS187 4.4 39.7 1.0 C A:GLY186 4.6 41.2 1.0 CE1 A:HIS187 4.6 48.2 1.0 O A:HOH550 4.6 51.2 1.0 O A:LEU184 4.8 37.0 1.0 O A:ILE185 4.8 36.6 1.0 O A:HOH519 4.9 33.4 1.0 N A:ASP233 4.9 30.4 1.0 CG1 A:ILE185 4.9 33.9 1.0 N A:ILE185 5.0 31.9 1.0 CA A:SER228 5.0 24.9 1.0

Magnesium binding site 4 out of 58 in the Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg411 b:48.5 occ:1.00 ND1 A:HIS187 2.8 46.3 1.0 N A:GLU232 2.9 30.0 1.0 CG A:HIS187 3.4 47.1 1.0 CB A:HIS187 3.5 43.9 1.0 CA A:GLY231 3.5 29.9 1.0 C A:GLY231 3.7 29.5 1.0 CE1 A:HIS187 3.7 48.2 1.0 CB A:GLU232 3.9 35.6 1.0 CA A:GLU232 3.9 29.5 1.0 MG A:MG410 3.9 42.9 1.0 N A:HIS187 4.0 39.7 1.0 CG A:GLU232 4.1 41.0 1.0 CA A:HIS187 4.4 44.4 1.0 O A:GLU232 4.4 30.1 1.0 CD2 A:HIS187 4.4 54.0 1.0 NE2 A:HIS187 4.6 54.4 1.0 C A:GLY186 4.6 41.2 1.0 C A:GLU232 4.6 27.3 1.0 O A:HOH550 4.6 51.2 1.0 CA A:GLY186 4.7 34.6 1.0 N A:GLY231 4.8 29.6 1.0 O A:HIS230 4.8 28.3 1.0 O A:GLY231 4.9 29.4 1.0 N A:GLY186 5.0 34.8 1.0

Magnesium binding site 5 out of 58 in the Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg412 b:36.2 occ:1.00 MG A:MG413 2.7 41.5 1.0 O A:GLU45 2.8 25.5 1.0 O A:TYR53 2.9 26.4 1.0 N A:ALA49 3.5 24.3 1.0 CB A:ALA49 3.6 28.9 1.0 CA A:LYS54 3.6 26.2 1.0 C A:GLU45 3.6 22.2 1.0 CA A:ALA49 3.8 26.4 1.0 CA A:GLU45 3.8 22.4 1.0 CB A:LEU48 3.9 23.8 1.0 C A:TYR53 3.9 24.8 1.0 CB A:GLU45 4.1 22.6 1.0 C A:LEU48 4.2 24.3 1.0 N A:LYS54 4.2 25.1 1.0 N A:VAL55 4.4 25.8 1.0 CB A:LYS54 4.4 28.8 1.0 C A:LYS54 4.4 25.0 1.0 CG A:LYS54 4.5 34.2 1.0 CA A:LEU48 4.6 23.6 1.0 CG A:GLU45 4.7 26.0 1.0 N A:LYS46 4.9 23.7 1.0 O A:LEU48 4.9 26.6 1.0 CD1 A:LEU48 4.9 23.6 1.0

Magnesium binding site 6 out of 58 in the Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg413 b:41.5 occ:1.00 MG A:MG412 2.7 36.2 1.0 N A:VAL55 2.9 25.8 1.0 CA A:LYS54 3.4 26.2 1.0 CG2 A:VAL55 3.5 28.6 1.0 C A:LYS54 3.6 25.0 1.0 CG A:GLU45 3.7 26.0 1.0 CB A:VAL55 3.8 27.1 1.0 CB A:LYS54 3.8 28.8 1.0 CA A:VAL55 3.9 25.0 1.0 CB A:GLU45 4.0 22.6 1.0 MG A:MG440 4.1 44.9 1.0 CD A:GLU45 4.2 29.5 1.0 CA A:GLU45 4.3 22.4 1.0 CG A:LYS54 4.3 34.2 1.0 OE1 A:GLU45 4.4 34.2 1.0 O A:TYR53 4.7 26.4 1.0 N A:LYS54 4.7 25.1 1.0 O A:GLU45 4.7 25.5 1.0 O A:LYS54 4.8 24.6 1.0

Magnesium binding site 7 out of 58 in the Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg414 b:48.8 occ:1.00 O A:HOH560 2.6 37.6 1.0 O A:HOH511 2.8 25.6 1.0 OD1 A:ASN36 3.0 25.6 1.0 CG2 A:ILE76 3.6 25.7 1.0 CG A:ASN36 3.7 24.1 1.0 ND2 A:ASN36 3.9 30.1 1.0 CB A:ASP75 4.1 25.2 1.0 OD2 A:ASP75 4.1 39.3 1.0 CD2 A:LEU73 4.3 22.7 1.0 O A:GLY72 4.5 22.4 1.0 CG A:ASP75 4.6 33.2 1.0 CA A:LEU73 4.7 20.8 1.0 N A:ILE76 4.7 22.4 1.0 CB A:ASN36 4.8 21.1 1.0 CA A:ASP75 4.9 23.6 1.0 O A:HOH564 4.9 41.8 1.0 N A:ASP75 4.9 22.0 1.0 O A:LEU73 5.0 22.3 1.0

Magnesium binding site 8 out of 58 in the Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg415 b:29.1 occ:1.00 O A:LEU63 2.8 21.2 1.0 O A:THR166 2.8 22.4 1.0 ND2 A:ASN89 2.9 21.7 1.0 N A:HIS86 3.0 20.2 1.0 O A:THR64 3.2 20.6 1.0 CB A:HIS86 3.4 20.5 1.0 C A:THR64 3.4 19.2 1.0 CG1 A:ILE168 3.6 21.9 1.0 CD1 A:ILE168 3.7 24.8 1.0 C A:LEU63 3.7 20.8 1.0 N A:HIS65 3.8 19.1 1.0 CA A:HIS86 3.8 19.9 1.0 CA A:GLY85 3.8 21.8 1.0 C A:GLY85 3.9 20.7 1.0 CA A:HIS65 3.9 19.7 1.0 CG A:ASN89 4.0 22.6 1.0 C A:THR166 4.1 21.3 1.0 CG2 A:ILE168 4.1 22.7 1.0 CA A:THR64 4.1 20.3 1.0 OD1 A:ASN89 4.2 22.3 1.0 CB A:ILE168 4.4 21.3 1.0 N A:THR64 4.4 21.4 1.0 CB A:LEU63 4.4 24.4 1.0 N A:ILE168 4.4 20.9 1.0 CB A:THR166 4.7 19.9 1.0 CG A:HIS86 4.7 22.1 1.0 CA A:LEU63 4.7 20.1 1.0 O A:HIS86 4.7 21.5 1.0 C A:HIS86 4.8 20.3 1.0 C A:HIS65 4.8 18.9 1.0 CA A:THR166 4.9 20.9 1.0 C A:HIS167 4.9 21.3 1.0 CA A:HIS167 4.9 20.5 1.0 CB A:HIS65 5.0 19.8 1.0 N A:HIS167 5.0 21.0 1.0

Magnesium binding site 9 out of 58 in the Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg416 b:40.9 occ:1.00 N A:ILE149 2.8 27.9 1.0 O A:PHE155 2.8 29.4 1.0 O A:LEU152 2.8 27.4 1.0 C A:PHE155 3.4 25.5 1.0 CB A:ILE149 3.5 25.7 1.0 O A:ILE149 3.5 27.9 1.0 CB A:PHE155 3.6 25.9 1.0 CA A:ILE149 3.6 27.5 1.0 C A:ARG148 3.7 28.0 1.0 CA A:ARG148 3.7 29.9 1.0 CB A:LEU152 3.7 25.5 1.0 C A:LEU152 3.8 26.3 1.0 CG1 A:ILE149 3.9 28.3 1.0 CA A:PHE155 3.9 25.2 1.0 C A:ILE149 4.0 26.5 1.0 N A:PHE155 4.2 27.1 1.0 CD1 A:ILE149 4.3 28.6 1.0 CB A:ARG148 4.3 36.1 1.0 N A:THR156 4.3 25.4 1.0 CA A:LEU152 4.3 26.9 1.0 CA A:THR156 4.6 27.4 0.5 O A:ASP147 4.6 27.6 1.0 CA A:THR156 4.7 26.6 0.5 CG2 A:ILE149 4.8 26.9 1.0 CD1 A:LEU152 4.8 26.5 1.0 O A:ARG148 4.8 35.7 1.0 N A:LEU152 4.8 25.6 1.0 N A:PRO153 4.9 28.5 1.0 CG A:PHE155 4.9 26.1 1.0 CG A:LEU152 4.9 26.4 1.0 N A:ARG148 4.9 28.7 1.0

Magnesium binding site 10 out of 58 in the Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg417 b:42.1 occ:1.00 O A:HOH549 2.7 30.7 1.0 OE1 A:GLU59 2.7 44.2 1.0 CD A:GLU59 3.6 41.8 1.0 ND2 A:ASN82 3.6 32.4 1.0 OE2 A:GLU59 3.7 44.0 1.0 CB A:ALA150 3.7 34.3 1.0 OG1 A:THR60 3.9 26.2 1.0 N A:SER151 4.0 26.5 1.0 CB A:SER151 4.0 27.5 1.0 MG A:MG452 4.3 49.9 1.0 CA A:SER151 4.3 26.8 1.0 C A:ALA150 4.4 29.2 1.0 CA A:ALA150 4.6 33.4 1.0 CG A:ASN82 4.7 27.9 1.0 OG1 A:THR27 4.8 30.8 1.0 OG A:SER151 4.8 26.3 1.0 CG A:GLU59 5.0 36.9 1.0

A.A.Azman, N.D.Muhd Noor, A.T.C.Leow, S.A.Mohd Noor, M.S.Mohamad Ali. Crystal Structure of Paraoxonase From Bacillus Sp. Strain S3WAHI To Be Published.