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Cadmium in PDB 1jdy: Rabbit Muscle Phosphoglucomutase

Enzymatic activity of Rabbit Muscle Phosphoglucomutase

All present enzymatic activity of Rabbit Muscle Phosphoglucomutase:
5.4.2.2;

Protein crystallography data

The structure of Rabbit Muscle Phosphoglucomutase, PDB code: 1jdy was solved by W.J.Ray Junior, S.Baranidharan, Y.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.70
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 174.420, 174.420, 101.120, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 24.4

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Rabbit Muscle Phosphoglucomutase (pdb code 1jdy). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Rabbit Muscle Phosphoglucomutase, PDB code: 1jdy:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 1jdy

Go back to Cadmium Binding Sites List in 1jdy
Cadmium binding site 1 out of 2 in the Rabbit Muscle Phosphoglucomutase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Rabbit Muscle Phosphoglucomutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd562

b:2.0
occ:1.00
O2P A:SEP116 2.0 46.7 1.0
OD1 A:ASP287 2.2 26.3 1.0
OD2 A:ASP289 2.2 43.2 1.0
OD1 A:ASP291 2.2 35.0 1.0
CG A:ASP289 3.0 38.0 1.0
OD1 A:ASP289 3.1 42.8 1.0
CG A:ASP287 3.2 26.3 1.0
P A:SEP116 3.4 44.5 1.0
CG A:ASP291 3.4 27.6 1.0
OD2 A:ASP287 3.6 29.4 1.0
OG A:SEP116 3.8 40.8 1.0
CB A:SEP116 3.9 30.5 1.0
O1P A:SEP116 4.0 39.7 1.0
OD2 A:ASP291 4.2 28.6 1.0
CB A:ASP291 4.2 23.3 1.0
CG A:ARG292 4.3 20.6 1.0
CA A:SEP116 4.4 24.2 1.0
N A:ASP291 4.4 23.8 1.0
O3P A:SEP116 4.4 41.8 1.0
NE A:ARG292 4.4 22.6 1.0
CB A:ASP289 4.4 30.3 1.0
CB A:ASP287 4.5 22.3 1.0
O A:HOH579 4.5 47.7 1.0
N A:ARG292 4.7 18.9 1.0
CA A:ASP291 4.7 21.2 1.0
CB A:ARG292 4.7 20.8 1.0
O A:HOH699 4.7 22.4 1.0
N A:ASP289 4.8 21.5 1.0
NZ A:LYS388 4.8 39.2 1.0
C A:ASP291 4.8 19.5 1.0
CD A:ARG292 4.9 24.4 1.0
N A:HIS117 4.9 28.1 1.0
C A:SEP116 5.0 26.1 1.0
CA A:ASP289 5.0 24.6 1.0

Cadmium binding site 2 out of 2 in 1jdy

Go back to Cadmium Binding Sites List in 1jdy
Cadmium binding site 2 out of 2 in the Rabbit Muscle Phosphoglucomutase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Rabbit Muscle Phosphoglucomutase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd562

b:2.0
occ:1.00
O2P B:SEP116 2.0 49.8 1.0
OD2 B:ASP291 2.1 19.7 1.0
OD2 B:ASP289 2.2 43.9 1.0
OD2 B:ASP287 2.2 24.3 1.0
OD1 B:ASP289 2.9 39.7 1.0
CG B:ASP289 2.9 35.1 1.0
CG B:ASP291 3.2 21.3 1.0
CG B:ASP287 3.2 23.4 1.0
P B:SEP116 3.5 47.7 1.0
CB B:SEP116 3.6 29.0 1.0
OD1 B:ASP291 3.6 23.4 1.0
OD1 B:ASP287 3.7 25.8 1.0
OG B:SEP116 4.0 42.1 1.0
O3P B:SEP116 4.1 46.1 1.0
CA B:SEP116 4.2 22.0 1.0
NE B:ARG292 4.2 23.3 1.0
CB B:ASP289 4.3 27.7 1.0
CG B:ARG292 4.4 13.6 1.0
CB B:ASP291 4.4 15.2 1.0
O1P B:SEP116 4.4 47.4 1.0
N B:ASP291 4.4 16.4 1.0
CB B:ASP287 4.4 19.0 1.0
N B:ASP289 4.7 19.6 1.0
C B:SEP116 4.7 19.8 1.0
O B:HOH569 4.7 11.2 1.0
N B:ARG292 4.7 13.4 1.0
N B:HIS117 4.8 23.6 1.0
CD B:ARG292 4.8 17.1 1.0
CA B:ASP291 4.8 13.8 1.0
CB B:ARG292 4.9 14.5 1.0
CA B:ASP289 4.9 24.8 1.0
C B:ASP291 4.9 13.4 1.0
NH2 B:ARG292 5.0 24.3 1.0
CZ B:ARG292 5.0 25.3 1.0

Reference:

S.Baranidharan, Y.Liu, W.J.Ray Junior. To Be Published.
Page generated: Wed Oct 28 09:53:39 2020
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