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

Protein crystallography data

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

Other elements in 5hv4:

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

Cadmium Binding Sites:

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 5hv4

Go back to Cadmium Binding Sites List in 5hv4
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 5hv4

Go back to Cadmium Binding Sites List in 5hv4
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 5hv4

Go back to Cadmium Binding Sites List in 5hv4
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 5hv4

Go back to Cadmium Binding Sites List in 5hv4
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 5hv4

Go back to Cadmium Binding Sites List in 5hv4
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

Reference:

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
Page generated: Sat Dec 12 08:26:49 2020

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