Cadmium in PDB 5hv0: Structural Analysis of Cofactor Binding of A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis

The structure of Structural Analysis of Cofactor Binding of A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis, PDB code: 5hv0 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)	39.12 / 1.63
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	90.336, 90.336, 51.423, 90.00, 90.00, 120.00
R / Rfree (%)	17.4 / 21.5

The structure of Structural Analysis of Cofactor Binding of A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis also contains other interesting chemical elements:

Potassium

(K)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Cadmium atom in the Structural Analysis of Cofactor Binding of A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis (pdb code 5hv0). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 16 binding sites of Cadmium where determined in the Structural Analysis of Cofactor Binding of A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis, PDB code: 5hv0:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 16 in the Structural Analysis of Cofactor Binding of A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structural Analysis of Cofactor Binding of A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:12.6 occ:1.00 O2 A:AKG310 2.3 15.6 1.0 OD1 A:ASP129 2.3 12.7 1.0 O5 A:AKG310 2.4 16.9 1.0 NE2 A:HIS193 2.4 12.2 1.0 NE2 A:HIS127 2.5 15.7 1.0 OD2 A:ASP129 2.8 11.0 1.0 C1 A:AKG310 2.8 29.4 1.0 CG A:ASP129 2.8 11.3 1.0 C2 A:AKG310 2.9 18.9 1.0 CE1 A:HIS193 3.3 10.9 1.0 CD2 A:HIS193 3.3 9.8 1.0 CD2 A:HIS127 3.3 17.0 1.0 CE1 A:HIS127 3.4 17.2 1.0 O1 A:AKG310 4.1 16.5 1.0 O A:HOH522 4.1 22.4 1.0 CB A:ASP129 4.3 13.5 1.0 C3 A:AKG310 4.4 18.9 1.0 ND1 A:HIS193 4.4 11.6 1.0 CG A:HIS193 4.4 10.4 1.0 CG A:HIS127 4.5 15.9 1.0 NE1 A:TRP209 4.5 9.2 1.0 ND1 A:HIS127 4.5 18.9 1.0 CE2 A:TYR124 4.7 29.6 1.0 CZ A:PHE178 4.8 12.8 1.0 CA A:ASP129 4.9 9.9 1.0

Cadmium binding site 2 out of 16 in the Structural Analysis of Cofactor Binding of A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structural Analysis of Cofactor Binding of A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:49.5 occ:0.33 OE1 A:GLU90 2.7 43.1 1.0 OE2 A:GLU90 2.7 51.4 1.0 O A:HOH532 2.8 53.6 1.0 CD A:GLU90 3.0 33.0 1.0 O A:HOH491 4.5 49.8 1.0 CG A:GLU90 4.5 20.4 1.0 O A:HOH595 4.9 34.5 1.0

Cadmium binding site 3 out of 16 in the Structural Analysis of Cofactor Binding of A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structural Analysis of Cofactor Binding of A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd303 b:55.9 occ:0.33 OE2 A:GLU51 2.7 68.1 1.0 OE1 A:GLU51 2.8 50.4 1.0 CD A:GLU51 2.9 74.7 1.0 O A:HOH403 3.0 29.4 1.0 O A:HOH538 4.0 48.2 0.3 CG A:GLU51 4.1 31.2 1.0 O A:HOH407 4.2 35.4 1.0 OE2 A:GLU55 4.4 27.4 1.0 O A:HOH408 4.5 16.3 1.0

Cadmium binding site 4 out of 16 in the Structural Analysis of Cofactor Binding of A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structural Analysis of Cofactor Binding of A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd304 b:30.3 occ:0.49 O A:HOH432 2.7 37.7 1.0 O A:HOH615 3.4 40.0 1.0 O A:HOH606 3.6 43.7 1.0 O A:ASN104 3.9 12.2 1.0 ND2 A:ASN104 4.6 21.8 1.0 CG2 A:ILE15 4.7 15.5 1.0

Cadmium binding site 5 out of 16 in the Structural Analysis of Cofactor Binding of A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structural Analysis of Cofactor Binding of A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd305 b:23.3 occ:0.74 ND1 A:HIS18 2.7 17.0 1.0 O A:HOH414 2.7 23.1 1.0 O A:HOH550 2.7 22.7 1.0 O A:HOH586 2.7 40.4 1.0 O A:HOH565 2.8 22.5 1.0 CG A:HIS18 3.5 10.0 1.0 CE1 A:HIS18 3.6 19.5 1.0 CB A:HIS18 3.7 12.8 1.0 CA A:HIS18 3.9 15.5 1.0 O A:HOH493 4.2 37.6 1.0 N A:LYS19 4.4 20.5 1.0 O A:VAL22 4.6 15.0 1.0 O A:LYS19 4.6 26.4 1.0 C A:HIS18 4.7 24.2 1.0 CD2 A:HIS18 4.7 12.3 1.0 NE2 A:HIS18 4.7 20.4 1.0 CG1 A:ILE23 4.8 12.8 1.0 CA A:ILE23 4.8 12.2 1.0 O A:HOH503 4.9 22.6 1.0 CG2 A:ILE23 4.9 16.2 1.0

Cadmium binding site 6 out of 16 in the Structural Analysis of Cofactor Binding of A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structural Analysis of Cofactor Binding of A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd306 b:20.3 occ:0.69 OE2 A:GLU119 2.7 28.3 1.0 OE1 A:GLU119 2.7 25.8 1.0 CD A:GLU119 3.0 70.7 1.0 O A:GLY201 3.3 29.0 1.0 C A:GLY201 3.7 21.4 1.0 CB A:GLU202 4.1 19.8 0.6 CB A:GLU202 4.2 4.5 0.4 CA A:GLY201 4.2 17.3 1.0 CG2 A:VAL120 4.3 26.6 1.0 N A:GLU202 4.3 11.3 1.0 CG A:GLU119 4.5 32.5 1.0 CG A:GLU202 4.6 8.4 0.6 OE1 A:GLU202 4.6 47.5 0.6 CA A:GLU202 4.6 12.8 0.4 CA A:GLU202 4.6 14.7 0.6 CD A:GLU202 4.7 51.1 0.6 N A:VAL120 4.7 17.4 1.0 N A:GLY201 4.7 19.9 1.0 CG A:GLU202 4.9 29.2 0.4 CB A:VAL120 5.0 20.6 1.0

Cadmium binding site 7 out of 16 in the Structural Analysis of Cofactor Binding of A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structural Analysis of Cofactor Binding of A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd307 b:49.5 occ:0.54 OD2 A:ASP121 2.7 63.5 1.0 OD1 A:ASP121 2.7 37.8 1.0 CG A:ASP121 2.9 63.6 1.0 CB A:ASP121 4.3 27.7 1.0 O A:HOH525 4.6 33.2 1.0 CG1 A:VAL120 5.0 39.0 1.0

Cadmium binding site 8 out of 16 in the Structural Analysis of Cofactor Binding of A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structural Analysis of Cofactor Binding of A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd308 b:37.2 occ:0.83 OE1 A:GLU154 2.6 45.4 1.0 OE2 A:GLU154 2.6 50.8 1.0 CD A:GLU154 2.9 34.2 1.0 CG A:GLU154 4.3 78.7 1.0 CD A:LYS200 4.4 26.9 1.0 NZ A:LYS200 4.8 35.1 1.0 CE A:LYS200 4.9 46.2 1.0

Cadmium binding site 9 out of 16 in the Structural Analysis of Cofactor Binding of A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Structural Analysis of Cofactor Binding of A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd309 b:31.0 occ:0.50 CD A:CD309 0.0 31.0 0.5 CD A:CD309 2.0 36.5 0.5 NE2 A:HIS134 2.6 22.7 1.0 O A:HOH574 2.7 41.6 1.0 CE1 A:HIS134 3.3 34.4 1.0 CD2 A:HIS134 3.7 25.0 1.0 ND1 A:HIS134 4.5 24.3 1.0 CG A:HIS134 4.8 22.0 1.0

Cadmium binding site 10 out of 16 in the Structural Analysis of Cofactor Binding of A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Structural Analysis of Cofactor Binding of A Prolyl 4-Hydroxylase From the Pathogenic Bacterium Bacillus Anthracis within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd309 b:36.5 occ:0.50 CD A:CD309 0.0 36.5 0.5 CD A:CD309 2.0 31.0 0.5 CE1 A:HIS134 2.6 34.4 1.0 NE2 A:HIS134 2.6 22.7 1.0 O A:HOH574 2.8 41.6 1.0 ND1 A:HIS134 3.9 24.3 1.0 CD2 A:HIS134 4.0 25.0 1.0 CG A:HIS134 4.6 22.0 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