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Cadmium in PDB 5y4a: Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis.

Enzymatic activity of Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis.

All present enzymatic activity of Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis.:
2.4.2.7;

Protein crystallography data

The structure of Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis., PDB code: 5y4a was solved by G.C.Pavithra, U.A.Ramagopal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.34
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.216, 77.547, 90.388, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 25.5

Other elements in 5y4a:

The structure of Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis. also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis. (pdb code 5y4a). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis., PDB code: 5y4a:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 5y4a

Go back to Cadmium Binding Sites List in 5y4a
Cadmium binding site 1 out of 5 in the Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd404

b:31.2
occ:1.00
 O A:HOH520 2.3 26.1 1.0
O A:HOH518 2.4 10.7 1.0
OD1 A:ASP130 2.5 14.2 1.0
OD1 A:ASP131 2.5 15.2 1.0
OD2 A:ASP130 2.6 14.9 1.0
O A:HOH508 2.6 6.9 1.0
O A:HOH509 2.7 18.6 1.0
CG A:ASP130 2.9 14.2 1.0
CG A:ASP131 3.5 14.5 1.0
OG1 A:THR67 3.5 11.9 0.5
OD2 A:ASP131 3.7 13.6 1.0
N A:ASP131 4.2 14.1 1.0
O4 A:SO4402 4.3 20.2 1.0
CB A:ASP130 4.3 14.3 1.0
O A:HOH519 4.3 28.7 1.0
O A:LEU132 4.4 16.2 1.0
N A:GLY71 4.5 13.3 1.0
N A:LEU132 4.5 15.5 1.0
CB A:ASP131 4.8 14.6 1.0
CA A:GLY71 4.9 12.9 1.0
O A:HOH506 4.9 12.6 1.0
CB A:THR67 4.9 12.1 0.5
CB A:ARG70 4.9 16.9 1.0
O A:THR67 4.9 11.9 0.5
CB A:LEU132 4.9 16.3 1.0
CA A:ASP130 4.9 14.0 1.0

Cadmium binding site 2 out of 5 in 5y4a

Go back to Cadmium Binding Sites List in 5y4a
Cadmium binding site 2 out of 5 in the Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd405

b:24.0
occ:1.00
 OE2 A:GLU102 2.5 19.1 1.0
OE1 A:GLU102 2.6 18.2 1.0
CD A:GLU102 2.9 19.0 1.0
CG A:GLU102 4.4 19.2 1.0
NH1 A:ARG148 4.5 23.7 1.0
CD A:LYS144 4.6 21.4 1.0
CD A:ARG148 4.7 23.6 1.0

Cadmium binding site 3 out of 5 in 5y4a

Go back to Cadmium Binding Sites List in 5y4a
Cadmium binding site 3 out of 5 in the Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd201

b:58.5
occ:0.50
 OE1 B:GLU54 3.3 60.7 1.0
OE2 B:GLU58 3.9 57.1 1.0
CD B:GLU54 4.4 60.9 1.0
OG B:SER57 4.6 41.8 1.0
OE1 B:GLU58 4.7 55.7 1.0
CD B:GLU58 4.7 54.2 1.0
OE2 B:GLU54 4.8 64.1 1.0

Cadmium binding site 4 out of 5 in 5y4a

Go back to Cadmium Binding Sites List in 5y4a
Cadmium binding site 4 out of 5 in the Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd204

b:48.9
occ:1.00
 O B:HOH307 2.3 36.7 1.0
OD1 B:ASP130 2.4 24.4 1.0
OD1 B:ASP131 2.5 23.7 1.0
O B:HOH304 2.6 17.4 1.0
O B:HOH303 2.6 15.5 1.0
OD2 B:ASP130 2.8 23.7 1.0
CG B:ASP130 2.9 23.2 1.0
O B:HOH312 3.1 29.1 1.0
CG B:ASP131 3.6 22.7 1.0
OG1 B:THR67 3.9 23.9 1.0
O3 B:SO4203 4.0 27.1 1.0
OD2 B:ASP131 4.1 23.4 1.0
N B:GLY71 4.3 17.8 1.0
N B:ASP131 4.3 20.6 1.0
CB B:ASP130 4.4 22.4 1.0
N B:LEU132 4.5 24.9 1.0
O B:LEU132 4.6 28.6 1.0
CB B:ASP131 4.8 21.8 1.0
CA B:GLY71 4.8 17.5 1.0
CB B:ARG70 5.0 20.8 1.0
CA B:ASP131 5.0 21.5 1.0
OG1 B:THR138 5.0 29.5 1.0

Cadmium binding site 5 out of 5 in 5y4a

Go back to Cadmium Binding Sites List in 5y4a
Cadmium binding site 5 out of 5 in the Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd205

b:83.7
occ:1.00
 NE2 B:HIS155 2.3 62.0 1.0
O B:HOH318 2.6 49.2 1.0
ND1 B:HIS177 2.9 73.2 1.0
CE1 B:HIS155 2.9 62.9 1.0
CE1 B:HIS177 3.1 76.2 1.0
CD2 B:HIS155 3.4 61.6 1.0
CG2 B:VAL154 4.0 56.3 1.0
ND1 B:HIS155 4.1 63.0 1.0
CG B:HIS177 4.2 70.4 1.0
NE2 B:HIS177 4.3 77.2 1.0
CG B:HIS155 4.4 60.0 1.0
CD2 B:HIS177 4.9 75.2 1.0
CB B:HIS177 4.9 60.4 1.0

Reference:

G.C.Pavithra, U.A.Ramagopal. Cadmium Directed Assembly of Adenine Phosphoribosyltransferase From Yersinia Pseudotuberculosis. To Be Published.
Page generated: Thu Jul 10 14:45:08 2025

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