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Cadmium in PDB 7dit: Structure of PFGRX1 in the Intermediate State with Cadmium and Cesium

Enzymatic activity of Structure of PFGRX1 in the Intermediate State with Cadmium and Cesium

All present enzymatic activity of Structure of PFGRX1 in the Intermediate State with Cadmium and Cesium:
1.8.4.2;

Protein crystallography data

The structure of Structure of PFGRX1 in the Intermediate State with Cadmium and Cesium, PDB code: 7dit was solved by Y.Manickam, A.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.22 / 1.80
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 48.435, 48.435, 82.737, 90, 90, 120
R / Rfree (%) 16.7 / 20

Other elements in 7dit:

The structure of Structure of PFGRX1 in the Intermediate State with Cadmium and Cesium also contains other interesting chemical elements:

Caesium (Cs) 2 atoms
Chlorine (Cl) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of PFGRX1 in the Intermediate State with Cadmium and Cesium (pdb code 7dit). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the Structure of PFGRX1 in the Intermediate State with Cadmium and Cesium, PDB code: 7dit:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in 7dit

Go back to Cadmium Binding Sites List in 7dit
Cadmium binding site 1 out of 7 in the Structure of PFGRX1 in the Intermediate State with Cadmium and Cesium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of PFGRX1 in the Intermediate State with Cadmium and Cesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:20.7
occ:0.56
 OD2 A:ASP90 2.5 20.5 1.0
O A:HOH310 2.5 33.9 1.0
O A:HOH393 2.6 34.0 1.0
O A:HOH425 2.7 42.4 1.0
CL A:CL213 2.7 36.7 0.8
CL A:CL212 2.8 31.0 0.8
OD1 A:ASP90 3.1 18.6 1.0
CG A:ASP90 3.2 22.4 1.0
O A:HOH384 3.9 31.2 1.0
O A:HOH325 4.0 20.4 1.0
O A:HOH352 4.5 37.6 1.0
CB A:ASP90 4.6 15.0 1.0
N A:GLY87 4.6 16.8 1.0
NH2 A:ARG77 4.7 14.6 0.5
O A:HOH390 4.7 37.3 1.0
CA A:GLY86 4.8 16.8 1.0
O A:HOH324 5.0 25.9 1.0

Cadmium binding site 2 out of 7 in 7dit

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Cadmium binding site 2 out of 7 in the Structure of PFGRX1 in the Intermediate State with Cadmium and Cesium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of PFGRX1 in the Intermediate State with Cadmium and Cesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:32.6
occ:0.43
 OE1 A:GLU51 2.4 24.9 1.0
O A:HOH423 2.7 51.0 1.0
O A:HOH317 2.7 44.0 1.0
CE1 A:HIS49 2.7 30.1 1.0
O A:HOH392 2.8 35.6 1.0
NE2 A:HIS49 2.8 25.9 1.0
O A:HOH356 2.8 50.0 1.0
CD A:GLU51 3.3 26.4 1.0
OE2 A:GLU51 3.5 23.6 1.0
ND1 A:HIS49 4.0 29.2 1.0
O A:HOH369 4.1 40.6 1.0
O A:HOH407 4.1 51.7 1.0
CD2 A:HIS49 4.2 26.6 1.0
O A:VAL50 4.6 17.7 1.0
CG A:GLU51 4.6 19.7 1.0
CG A:HIS49 4.8 26.4 1.0
CB A:GLU51 4.8 15.4 1.0
CA A:GLU51 4.9 17.6 1.0

Cadmium binding site 3 out of 7 in 7dit

Go back to Cadmium Binding Sites List in 7dit
Cadmium binding site 3 out of 7 in the Structure of PFGRX1 in the Intermediate State with Cadmium and Cesium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of PFGRX1 in the Intermediate State with Cadmium and Cesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:39.7
occ:0.41
 OD2 A:ASP83 2.6 29.6 0.5
OD1 A:ASP83 2.7 26.1 0.5
O A:HOH318 2.8 46.6 1.0
CG A:ASP83 3.0 24.8 0.5
NH2 A:ARG103 4.2 25.6 1.0
O A:HOH328 4.3 25.3 1.0
CB A:ASP83 4.4 17.5 0.5
CB A:ASP83 4.5 17.5 0.5
O A:VAL84 4.5 19.6 1.0
NH1 A:ARG103 4.5 30.8 1.0
OD1 A:ASP83 4.6 30.3 0.5
CG A:ASP83 4.7 24.4 0.5
CZ A:ARG103 4.9 27.8 1.0
NZ A:LYS99 4.9 52.8 1.0

Cadmium binding site 4 out of 7 in 7dit

Go back to Cadmium Binding Sites List in 7dit
Cadmium binding site 4 out of 7 in the Structure of PFGRX1 in the Intermediate State with Cadmium and Cesium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of PFGRX1 in the Intermediate State with Cadmium and Cesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:41.9
occ:0.47
 ND1 A:HIS49 2.5 29.2 1.0
O A:HOH418 2.7 50.3 1.0
O A:HOH311 2.8 27.1 0.5
O A:HOH386 2.9 26.4 1.0
O A:HOH407 2.9 51.7 1.0
CE1 A:HIS49 3.4 30.1 1.0
CG A:HIS49 3.5 26.4 1.0
CB A:HIS49 3.8 26.6 1.0
O A:HOH421 3.8 34.7 1.0
CA A:HIS49 3.8 19.4 1.0
O A:MET48 3.9 22.9 1.0
CS A:CS210 4.0 29.6 0.6
O A:HOH311 4.2 29.2 0.5
NE2 A:HIS49 4.5 25.9 1.0
CD2 A:HIS49 4.6 26.6 1.0
N A:VAL50 4.6 18.7 1.0
O A:HOH395 4.7 53.6 1.0
C A:HIS49 4.8 21.7 1.0
O A:HOH341 4.8 44.5 1.0
C A:MET48 4.8 20.5 1.0
N A:HIS49 4.8 15.7 1.0
O A:HOH354 4.8 29.3 1.0

Cadmium binding site 5 out of 7 in 7dit

Go back to Cadmium Binding Sites List in 7dit
Cadmium binding site 5 out of 7 in the Structure of PFGRX1 in the Intermediate State with Cadmium and Cesium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of PFGRX1 in the Intermediate State with Cadmium and Cesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:56.9
occ:0.33
 OD2 A:ASP58 2.7 28.9 1.0
OD1 A:ASP58 2.8 23.9 1.0
O A:HOH416 2.9 49.3 1.0
CG A:ASP58 3.1 23.9 1.0
O A:HOH389 3.6 59.2 1.0
CB A:ASP58 4.6 21.4 1.0
CG A:PRO57 4.6 27.9 1.0
O A:HOH337 4.9 29.1 1.0
CB A:PRO57 5.0 27.1 1.0

Cadmium binding site 6 out of 7 in 7dit

Go back to Cadmium Binding Sites List in 7dit
Cadmium binding site 6 out of 7 in the Structure of PFGRX1 in the Intermediate State with Cadmium and Cesium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of PFGRX1 in the Intermediate State with Cadmium and Cesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:44.8
occ:0.20
 OE1 A:GLU18 2.7 36.9 1.0
O A:HOH413 2.8 40.1 1.0
OE1 A:GLU18 2.9 36.4 0.0
O A:HOH308 3.0 25.8 0.7
CD A:GLU18 3.6 38.2 0.0
OE2 A:GLU18 3.6 39.5 0.0
CD A:GLU18 3.8 40.1 1.0
OE2 A:GLU18 4.2 39.6 1.0
O A:HOH349 4.4 42.0 1.0
O A:HOH360 4.5 30.3 1.0
CB A:LYS14 4.7 26.5 1.0
CG A:GLU18 4.9 36.4 0.0

Cadmium binding site 7 out of 7 in 7dit

Go back to Cadmium Binding Sites List in 7dit
Cadmium binding site 7 out of 7 in the Structure of PFGRX1 in the Intermediate State with Cadmium and Cesium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structure of PFGRX1 in the Intermediate State with Cadmium and Cesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd209

b:77.8
occ:0.53
 OE2 A:GLU28 2.5 58.1 1.0
OE1 A:GLU28 2.8 42.6 1.0
O A:HOH370 3.0 39.4 1.0
CD A:GLU28 3.0 46.9 1.0
CG A:GLU28 4.5 40.4 1.0

Reference:

Y.Manickam, A.Sharma. Interaction of Metals with PFGRX1 To Be Published.
Page generated: Thu Nov 25 08:15:44 2021

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