Cadmium in PDB 5hv4: Crystal Structure of A Prolyl 4-Hydroxylase Complexed with Alpha- Ketoglutarate From the Pathogenic Bacterium Bacillus Anthracis in C2221

The structure of Crystal Structure of A Prolyl 4-Hydroxylase Complexed with Alpha- Ketoglutarate From the Pathogenic Bacterium Bacillus Anthracis in C2221, PDB code: 5hv4 was solved by N.J.Schnicker, M.Dey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.37 / 2.35
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	42.551, 146.189, 75.075, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 24.5

The structure of Crystal Structure of A Prolyl 4-Hydroxylase Complexed with Alpha- Ketoglutarate From the Pathogenic Bacterium Bacillus Anthracis in C2221 also contains other interesting chemical elements:

Potassium

(K)

6 atoms

The binding sites of Cadmium atom in the Crystal Structure of A Prolyl 4-Hydroxylase Complexed with Alpha- Ketoglutarate From the Pathogenic Bacterium Bacillus Anthracis in C2221 (pdb code 5hv4). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Crystal Structure of A Prolyl 4-Hydroxylase Complexed with Alpha- Ketoglutarate From the Pathogenic Bacterium Bacillus Anthracis in C2221, PDB code: 5hv4:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Crystal Structure of A Prolyl 4-Hydroxylase Complexed with Alpha- Ketoglutarate From the Pathogenic Bacterium Bacillus Anthracis in C2221


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of A Prolyl 4-Hydroxylase Complexed with Alpha- Ketoglutarate From the Pathogenic Bacterium Bacillus Anthracis in C2221 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:22.0 occ:1.00 NE2 A:HIS193 2.7 15.0 1.0 OD1 A:ASP129 2.7 22.8 1.0 O5 A:AKG306 2.7 41.8 1.0 NE2 A:HIS127 2.7 22.6 1.0 O2 A:AKG306 2.7 30.3 1.0 OD2 A:ASP129 3.2 15.6 1.0 CG A:ASP129 3.2 21.6 1.0 C2 A:AKG306 3.4 41.2 1.0 C1 A:AKG306 3.4 35.4 1.0 CE1 A:HIS127 3.4 25.0 1.0 CD2 A:HIS193 3.4 15.1 1.0 O A:HOH432 3.6 25.8 1.0 CD2 A:HIS127 3.6 24.4 1.0 CE1 A:HIS193 3.7 21.4 1.0 ND1 A:HIS127 4.5 20.8 1.0 O1 A:AKG306 4.5 39.2 1.0 CE2 A:TYR124 4.6 32.6 1.0 NE1 A:TRP209 4.6 18.8 1.0 CG A:HIS193 4.6 16.8 1.0 CB A:ASP129 4.6 20.1 1.0 CG A:HIS127 4.7 16.9 1.0 ND1 A:HIS193 4.7 18.9 1.0 C3 A:AKG306 4.8 43.2 1.0 CZ A:PHE178 5.0 14.8 1.0

Cadmium binding site 2 out of 5 in the Crystal Structure of A Prolyl 4-Hydroxylase Complexed with Alpha- Ketoglutarate From the Pathogenic Bacterium Bacillus Anthracis in C2221


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of A Prolyl 4-Hydroxylase Complexed with Alpha- Ketoglutarate From the Pathogenic Bacterium Bacillus Anthracis in C2221 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:56.2 occ:1.00 OD1 A:ASN104 2.7 40.4 1.0 OD2 A:ASP17 3.2 40.2 1.0 ND2 A:ASN104 3.2 36.4 1.0 CG A:ASN104 3.3 29.2 1.0 OD1 A:ASP17 3.6 32.3 1.0 CG A:ASP17 3.8 37.3 1.0 O A:HOH490 4.5 31.2 1.0 CB A:ASN104 4.8 28.0 1.0

Cadmium binding site 3 out of 5 in the Crystal Structure of A Prolyl 4-Hydroxylase Complexed with Alpha- Ketoglutarate From the Pathogenic Bacterium Bacillus Anthracis in C2221


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of A Prolyl 4-Hydroxylase Complexed with Alpha- Ketoglutarate From the Pathogenic Bacterium Bacillus Anthracis in C2221 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd303 b:37.1 occ:1.00 ND1 A:HIS18 2.7 20.2 1.0 O A:HOH461 2.7 29.9 1.0 O A:HOH499 2.8 41.2 1.0 O A:HOH484 3.5 41.4 1.0 CG A:HIS18 3.6 28.1 1.0 CE1 A:HIS18 3.7 23.0 1.0 CB A:HIS18 3.7 22.0 1.0 CA A:HIS18 3.9 25.9 1.0 N A:LYS19 4.4 29.0 1.0 C A:HIS18 4.7 27.3 1.0 O A:LYS19 4.7 25.3 1.0 O A:VAL22 4.7 21.5 1.0 CG2 A:ILE23 4.8 19.8 1.0 CD2 A:HIS18 4.8 19.3 1.0 NE2 A:HIS18 4.8 25.4 1.0 CA A:ILE23 4.9 22.4 1.0 CG1 A:ILE23 5.0 25.8 1.0 N A:HIS18 5.0 29.2 1.0

Cadmium binding site 4 out of 5 in the Crystal Structure of A Prolyl 4-Hydroxylase Complexed with Alpha- Ketoglutarate From the Pathogenic Bacterium Bacillus Anthracis in C2221


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of A Prolyl 4-Hydroxylase Complexed with Alpha- Ketoglutarate From the Pathogenic Bacterium Bacillus Anthracis in C2221 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd304 b:29.6 occ:1.00 OD2 A:ASP121 2.7 29.1 1.0 OD1 A:ASP121 2.7 31.5 1.0 CG A:ASP121 3.0 25.2 1.0 CB A:ASP121 4.5 28.8 1.0 O A:ASP121 4.9 28.4 1.0

Cadmium binding site 5 out of 5 in the Crystal Structure of A Prolyl 4-Hydroxylase Complexed with Alpha- Ketoglutarate From the Pathogenic Bacterium Bacillus Anthracis in C2221


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of A Prolyl 4-Hydroxylase Complexed with Alpha- Ketoglutarate From the Pathogenic Bacterium Bacillus Anthracis in C2221 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd305 b:57.8 occ:1.00 OE1 A:GLU55 2.1 67.4 1.0 CD A:GLU55 2.6 50.6 1.0 OE2 A:GLU55 2.7 54.0 1.0 CG A:GLU55 3.9 40.9 1.0

N.J.Schnicker, M.Dey. Structural Analysis of Cofactor Binding For A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis. Acta Crystallogr D Struct V. 72 675 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 27139630
DOI: 10.1107/S2059798316004198