Magnesium in PDB 9b86: Fetb Apo From Porphyromonas Gingivalis Without Heme Group

The structure of Fetb Apo From Porphyromonas Gingivalis Without Heme Group, PDB code: 9b86 was solved by S.F.Ataide, A.Kwan, Y.Phonok, J.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.80 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.631, 49.817, 98.912, 90, 90, 90
R / Rfree (%)	20.2 / 22.5

The binding sites of Magnesium atom in the Fetb Apo From Porphyromonas Gingivalis Without Heme Group (pdb code 9b86). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Fetb Apo From Porphyromonas Gingivalis Without Heme Group, PDB code: 9b86:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Fetb Apo From Porphyromonas Gingivalis Without Heme Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Fetb Apo From Porphyromonas Gingivalis Without Heme Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:25.7 occ:1.00 O A:HOH495 3.0 25.3 1.0 NH1 A:ARG137 3.1 24.4 1.0 CB A:ARG137 3.6 16.5 1.0 CG A:ARG137 3.6 19.7 1.0 CD A:ARG137 3.6 19.0 1.0 CG2 A:ILE255 4.0 17.7 1.0 CA A:ARG137 4.0 17.2 1.0 CZ A:ARG137 4.1 23.7 1.0 CG1 A:ILE255 4.2 18.9 1.0 NE A:ARG137 4.3 19.5 1.0 O A:HOH431 4.5 34.3 1.0 CD1 A:ILE255 4.5 20.0 1.0 CB A:ILE255 4.7 18.1 1.0 O A:HOH524 4.8 29.8 1.0 N A:ARG137 4.8 17.2 1.0

Magnesium binding site 2 out of 5 in the Fetb Apo From Porphyromonas Gingivalis Without Heme Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Fetb Apo From Porphyromonas Gingivalis Without Heme Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:33.1 occ:1.00 O A:ASP254 2.8 19.9 1.0 NZ A:LYS30 3.0 24.5 1.0 O A:HOH510 3.1 30.8 1.0 O3 A:GOL306 3.6 35.0 1.0 C A:ASP254 3.7 17.2 1.0 CB A:ASP254 3.8 18.2 1.0 CE A:LYS30 3.8 20.9 1.0 CD A:LYS30 3.8 21.9 1.0 CA A:ASP254 3.9 16.3 1.0 CD2 A:LEU244 4.3 20.9 1.0 CD1 A:LEU244 4.4 21.7 1.0 OD1 A:ASP254 4.5 22.0 1.0 CG A:ASP254 4.5 22.4 1.0 NH1 A:ARG259 4.6 20.6 1.0 O A:HOH533 4.7 29.3 1.0 C3 A:GOL306 4.9 28.5 1.0 N A:ILE255 4.9 18.7 1.0 CG A:LEU244 5.0 22.3 1.0

Magnesium binding site 3 out of 5 in the Fetb Apo From Porphyromonas Gingivalis Without Heme Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Fetb Apo From Porphyromonas Gingivalis Without Heme Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:28.6 occ:1.00 OD2 A:ASP254 2.6 19.2 1.0 O A:PHE249 2.7 21.3 1.0 O A:HOH480 2.7 24.9 1.0 O A:HOH455 2.8 22.4 1.0 CG A:ASP254 3.4 22.4 1.0 OG1 A:THR27 3.6 20.2 1.0 OD1 A:ASP254 3.6 22.0 1.0 C A:PHE249 3.8 18.2 1.0 CD1 A:LEU244 3.9 21.7 1.0 CA A:SER250 4.0 15.3 1.0 N A:ALA251 4.1 17.3 1.0 C A:SER250 4.2 17.3 1.0 CB A:ASN248 4.3 21.3 1.0 N A:SER250 4.4 16.1 1.0 CB A:ALA212 4.4 20.9 1.0 CG A:LEU244 4.4 22.3 1.0 O A:ALA23 4.5 23.3 1.0 CB A:ALA251 4.7 19.7 1.0 CB A:ALA23 4.8 30.5 1.0 CB A:ASP254 4.8 18.2 1.0 O A:HOH488 4.8 25.5 1.0 N A:ALA212 4.9 18.3 1.0 O A:SER250 4.9 16.9 1.0 C A:ALA23 4.9 25.7 1.0 ND2 A:ASN248 5.0 28.4 1.0 CB A:THR27 5.0 21.1 1.0

Magnesium binding site 4 out of 5 in the Fetb Apo From Porphyromonas Gingivalis Without Heme Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Fetb Apo From Porphyromonas Gingivalis Without Heme Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:30.0 occ:1.00 OH A:TYR163 2.7 27.4 1.0 O A:LEU208 2.8 20.4 1.0 O A:HOH578 2.9 31.4 1.0 N A:HIS153 3.0 24.7 1.0 CA A:GLY152 3.5 20.2 1.0 CZ A:TYR163 3.5 24.2 1.0 CE1 A:TYR163 3.6 22.0 1.0 C A:GLY152 3.7 24.6 1.0 C A:LEU208 3.9 20.6 1.0 CB A:HIS153 4.0 28.7 1.0 CG A:MET209 4.0 25.7 1.0 CA A:HIS153 4.0 25.3 1.0 O A:HOH475 4.2 25.0 1.0 CE A:MET209 4.3 24.9 1.0 CA A:MET209 4.4 18.6 1.0 CB A:MET209 4.6 19.7 1.0 N A:MET209 4.6 19.0 1.0 CG1 A:VAL89 4.6 26.8 1.0 CB A:VAL89 4.6 24.0 1.0 CE2 A:TYR163 4.7 27.7 1.0 CG2 A:VAL89 4.7 26.0 1.0 N A:GLY152 4.8 19.5 1.0 SD A:MET209 4.8 26.3 1.0 N A:GLY154 4.9 27.6 1.0 O A:HOH534 4.9 27.6 1.0 CD1 A:TYR163 4.9 21.1 1.0 O A:GLY152 4.9 24.7 1.0 O A:MET151 4.9 19.5 1.0 CB A:LEU208 5.0 18.6 1.0 CA A:LEU208 5.0 18.8 1.0

Magnesium binding site 5 out of 5 in the Fetb Apo From Porphyromonas Gingivalis Without Heme Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Fetb Apo From Porphyromonas Gingivalis Without Heme Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg305 b:37.5 occ:1.00 N A:VAL89 3.2 22.6 1.0 N A:ILE90 3.4 24.8 1.0 CB A:HIS88 3.7 24.7 1.0 CG1 A:ILE90 3.7 28.5 1.0 O A:HOH541 3.8 32.2 1.0 CB A:VAL89 3.9 24.0 1.0 CA A:VAL89 3.9 21.1 1.0 O A:ILE90 4.0 25.7 1.0 CA A:HIS88 4.1 24.3 1.0 C A:HIS88 4.1 26.0 1.0 C A:VAL89 4.1 23.6 1.0 CA A:ILE90 4.4 27.5 1.0 O A:HOH578 4.4 31.4 1.0 CG2 A:VAL89 4.5 26.0 1.0 CB A:ILE90 4.6 24.6 1.0 O A:HOH534 4.6 27.6 1.0 CG A:HIS88 4.6 28.7 1.0 O A:HOH548 4.6 39.5 1.0 C A:ILE90 4.6 23.5 1.0 CD1 A:ILE90 4.8 29.6 1.0 CD2 A:HIS88 4.8 28.6 1.0 OH A:TYR163 4.9 27.4 1.0

S.F.Ataide, A.Kwan, Y.Phonok, J.Gao. Fetb Apo From Porphyromonas Gingivalis Without Heme Group To Be Published.