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Cadmium in PDB 7dim: Structure of PFGRX1 with Cadmium

Enzymatic activity of Structure of PFGRX1 with Cadmium

All present enzymatic activity of Structure of PFGRX1 with Cadmium:
1.8.4.2;

Protein crystallography data

The structure of Structure of PFGRX1 with Cadmium, PDB code: 7dim 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) 24.18 / 1.68
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 48.35, 48.35, 83.002, 90, 90, 120
R / Rfree (%) 15.7 / 19.1

Other elements in 7dim:

The structure of Structure of PFGRX1 with Cadmium also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Cadmium atom in the Structure of PFGRX1 with Cadmium (pdb code 7dim). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 13 binding sites of Cadmium where determined in the Structure of PFGRX1 with Cadmium, PDB code: 7dim:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 13 in 7dim

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Cadmium binding site 1 out of 13 in the Structure of PFGRX1 with Cadmium


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 with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:17.6
occ:0.74
 OD2 A:ASP90 2.4 17.7 1.0
O A:HOH322 2.5 22.9 1.0
O A:HOH401 2.5 25.4 1.0
O A:HOH399 2.6 25.7 1.0
CL A:CL217 2.6 22.8 0.9
CL A:CL216 2.7 23.9 0.9
CG A:ASP90 3.2 17.6 1.0
OD1 A:ASP90 3.2 17.9 1.0
O A:HOH374 4.0 29.7 1.0
O A:HOH442 4.1 40.6 1.0
O A:HOH339 4.1 16.7 1.0
O A:HOH380 4.4 28.2 1.0
CE A:LYS72 4.6 29.5 0.6
N A:GLY87 4.6 13.8 1.0
CB A:ASP90 4.6 12.7 1.0
CE A:LYS72 4.6 29.4 0.4
CA A:GLY86 4.7 13.6 1.0
NZ A:LYS72 4.7 30.9 0.4
NH2 A:ARG77 4.8 14.4 1.0
O A:HOH366 4.9 32.6 1.0
CG A:LYS72 5.0 24.8 0.4

Cadmium binding site 2 out of 13 in 7dim

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Cadmium binding site 2 out of 13 in the Structure of PFGRX1 with Cadmium


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 with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:22.6
occ:0.53
 OE1 A:GLU51 2.3 21.7 1.0
NE2 A:HIS49 2.5 27.3 1.0
O A:HOH309 2.6 34.2 1.0
O A:HOH408 2.7 31.4 1.0
O A:HOH429 2.7 44.1 1.0
O A:HOH341 2.8 36.0 1.0
CE1 A:HIS49 2.8 28.5 1.0
CD A:GLU51 3.2 21.4 1.0
OE2 A:GLU51 3.5 20.9 1.0
CD2 A:HIS49 3.9 27.9 1.0
ND1 A:HIS49 4.1 26.4 1.0
O A:HOH358 4.5 26.6 1.0
O A:HOH393 4.5 43.6 1.0
CG A:GLU51 4.5 17.5 1.0
O A:VAL50 4.6 16.4 1.0
CG A:HIS49 4.7 24.1 1.0
CB A:GLU51 4.7 14.2 1.0
CA A:GLU51 4.9 13.3 1.0

Cadmium binding site 3 out of 13 in 7dim

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Cadmium binding site 3 out of 13 in the Structure of PFGRX1 with Cadmium


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 with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:27.9
occ:0.41
 OD2 A:ASP83 2.6 23.5 0.6
OD1 A:ASP83 2.6 27.4 0.6
O A:HOH303 2.7 48.9 1.0
O A:HOH369 2.7 40.8 1.0
O A:HOH404 2.7 54.7 1.0
CG A:ASP83 2.9 22.3 0.6
NH2 A:ARG103 4.1 25.5 1.0
CB A:ASP83 4.4 16.0 0.4
O A:HOH325 4.4 23.9 1.0
CB A:ASP83 4.4 15.9 0.6
NH1 A:ARG103 4.5 24.6 1.0
O A:VAL84 4.5 16.5 1.0
CG A:ASP83 4.6 21.5 0.4
CZ A:ARG103 4.8 22.5 1.0
OD1 A:ASP83 4.8 28.0 0.4

Cadmium binding site 4 out of 13 in 7dim

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Cadmium binding site 4 out of 13 in the Structure of PFGRX1 with Cadmium


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 with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:41.7
occ:0.31
 CD A:CD214 1.5 59.7 0.3
O A:HOH314 2.1 46.3 0.5
O A:HOH314 2.3 45.7 0.5
O A:HOH367 2.3 37.6 0.7
ND1 A:HIS49 2.6 26.4 1.0
O A:HOH424 2.7 38.2 0.7
CE1 A:HIS49 3.3 28.5 1.0
CG A:HIS49 3.3 24.1 1.0
OD1 A:ASN19 3.7 19.5 1.0
CB A:HIS49 3.7 21.4 1.0
O A:HOH430 3.9 23.4 0.4
NE2 A:HIS49 4.2 27.3 1.0
CD2 A:HIS49 4.2 27.9 1.0
O A:HOH383 4.4 36.3 1.0
CA A:HIS49 4.4 16.5 1.0
CG A:ASN19 4.4 22.6 1.0
O A:HOH375 4.5 22.5 1.0
ND2 A:ASN19 4.5 18.9 1.0
O A:MET48 4.6 17.4 1.0

Cadmium binding site 5 out of 13 in 7dim

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Cadmium binding site 5 out of 13 in the Structure of PFGRX1 with Cadmium


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 with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:54.5
occ:0.45
 OD2 A:ASP58 2.6 26.0 1.0
OD1 A:ASP58 2.8 22.7 1.0
O A:HOH328 2.8 42.0 0.7
CG A:ASP58 3.0 22.7 1.0
O A:HOH433 3.4 37.0 1.0
CB A:ASP58 4.5 17.3 1.0
CG A:PRO57 4.8 25.0 1.0
O A:HOH323 4.8 28.0 1.0

Cadmium binding site 6 out of 13 in 7dim

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Cadmium binding site 6 out of 13 in the Structure of PFGRX1 with Cadmium


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 with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:52.1
occ:0.43
 O A:HOH407 2.3 30.3 1.0
OD1 A:ASN43 2.5 26.3 0.5
O A:HOH444 2.5 43.9 0.8
O A:HOH411 2.8 42.9 1.0
O A:HOH400 2.9 45.0 0.8
CG A:ASN43 3.5 29.4 0.5
ND2 A:ASN43 3.9 32.8 0.5
CD A:CD212 3.9 74.4 0.3
O A:HOH418 4.3 46.8 0.8
O A:LYS40 4.4 21.6 1.0
O A:GLY41 4.6 22.5 1.0
O A:HOH440 4.7 40.2 1.0
CB A:ASN43 4.9 23.8 0.5
CB A:ASN43 4.9 23.9 0.5
CA A:GLY41 4.9 18.2 1.0
OD1 A:ASN43 4.9 33.0 0.5
C A:GLY41 4.9 20.9 1.0

Cadmium binding site 7 out of 13 in 7dim

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Cadmium binding site 7 out of 13 in the Structure of PFGRX1 with Cadmium


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 with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd209

b:30.5
occ:0.23
 O A:HOH413 2.7 34.7 1.0
OE1 A:GLU18 2.7 31.9 1.0
OE2 A:GLU18 2.7 27.1 1.0
O A:HOH414 2.7 36.6 1.0
O A:HOH403 2.8 44.0 1.0
O A:HOH438 2.8 42.3 1.0
CD A:GLU18 3.0 36.3 1.0
O A:HOH383 4.0 36.3 1.0
CG A:GLU18 4.5 27.4 1.0
O A:HOH362 4.7 31.2 1.0
CB A:LYS14 4.7 21.6 1.0
O A:HOH304 4.8 27.7 1.0
O A:HOH424 5.0 38.2 0.7
O A:HOH427 5.0 50.0 1.0

Cadmium binding site 8 out of 13 in 7dim

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Cadmium binding site 8 out of 13 in the Structure of PFGRX1 with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structure of PFGRX1 with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd210

b:41.0
occ:0.32
 O A:HOH422 2.7 39.6 1.0
O A:HOH315 2.7 27.8 1.0
O A:HOH409 2.7 25.4 1.0
N A:GLU6 3.0 41.1 1.0
N A:ALA7 4.1 31.2 1.0
N A:VAL8 4.2 21.8 1.0
CA A:GLU6 4.3 33.4 1.0
CG2 A:VAL8 4.4 28.6 1.0
CB A:VAL8 4.4 22.5 1.0
C A:GLU6 4.5 33.2 1.0
O A:HOH433 4.5 37.0 1.0
CA A:VAL8 5.0 20.1 1.0

Cadmium binding site 9 out of 13 in 7dim

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Cadmium binding site 9 out of 13 in the Structure of PFGRX1 with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Structure of PFGRX1 with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd211

b:87.4
occ:0.59
 OE2 A:GLU28 2.7 32.8 0.5
O A:HOH349 3.2 52.9 1.0
OE1 A:GLU28 3.5 33.6 0.5
CD A:GLU28 3.7 35.5 0.5
CD A:CD215 3.7 72.1 0.5
OE1 A:GLU28 4.1 34.0 0.5
CD A:GLU28 4.7 34.0 0.5
CG A:GLU28 4.9 30.6 0.5

Cadmium binding site 10 out of 13 in 7dim

Go back to Cadmium Binding Sites List in 7dim
Cadmium binding site 10 out of 13 in the Structure of PFGRX1 with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Structure of PFGRX1 with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd212

b:74.4
occ:0.31
 O A:HOH407 2.2 30.3 1.0
O A:HOH370 2.3 34.8 1.0
O A:HOH440 2.3 40.2 1.0
O A:GLY41 2.5 22.5 1.0
O A:HOH412 3.5 38.0 1.0
C A:GLY41 3.6 20.9 1.0
CD A:CD208 3.9 52.1 0.4
O A:HOH411 4.1 42.9 1.0
ND2 A:ASN43 4.3 32.8 0.5
O A:HOH405 4.3 33.2 0.9
CA A:GLY41 4.3 18.2 1.0
OD1 A:ASN43 4.6 26.3 0.5
N A:TYR42 4.7 18.1 1.0
CG A:ASN43 4.7 29.4 0.5
CA A:TYR42 4.8 23.8 1.0
O A:HOH444 5.0 43.9 0.8

Reference:

Y.Manickam, A.Sharma. Interaction of Metals with PFGRX1 To Be Published.
Page generated: Thu Jul 10 15:23:43 2025

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