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Cadmium in PDB 5yzi: Crystal Structure of Mouse Cytosolic Isocitrate Dehydrogenase Complexed with Cadmium

Enzymatic activity of Crystal Structure of Mouse Cytosolic Isocitrate Dehydrogenase Complexed with Cadmium

All present enzymatic activity of Crystal Structure of Mouse Cytosolic Isocitrate Dehydrogenase Complexed with Cadmium:
1.1.1.42;

Protein crystallography data

The structure of Crystal Structure of Mouse Cytosolic Isocitrate Dehydrogenase Complexed with Cadmium, PDB code: 5yzi was solved by H.J.Cho, B.S.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.87 / 2.52
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 98.246, 91.428, 109.724, 90.00, 113.65, 90.00
R / Rfree (%) 18.8 / 23.1

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Mouse Cytosolic Isocitrate Dehydrogenase Complexed with Cadmium (pdb code 5yzi). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Crystal Structure of Mouse Cytosolic Isocitrate Dehydrogenase Complexed with Cadmium, PDB code: 5yzi:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 5yzi

Go back to Cadmium Binding Sites List in 5yzi
Cadmium binding site 1 out of 3 in the Crystal Structure of Mouse Cytosolic Isocitrate Dehydrogenase Complexed with Cadmium


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 Mouse Cytosolic Isocitrate Dehydrogenase Complexed with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd501

b:74.4
occ:1.00
OD1 A:ASP275 2.7 55.9 1.0
OD2 B:ASP252 2.8 49.3 1.0
OD1 A:ASP279 3.1 50.6 1.0
CG A:ASP275 3.4 52.0 1.0
CG B:ASP252 3.6 46.4 1.0
CB B:ASP252 3.7 40.0 1.0
OD2 A:ASP275 3.7 54.9 1.0
CG A:ASP279 3.7 47.8 1.0
OD2 A:ASP279 3.8 50.4 1.0
O A:ASP275 3.9 34.1 1.0
O A:ALA308 4.0 41.3 1.0
O A:HOH643 4.2 44.5 1.0
NH1 A:ARG109 4.3 41.5 1.0
C A:ASP275 4.4 35.5 1.0
CA A:ASP275 4.5 39.7 1.0
CB A:ASP275 4.6 45.8 1.0
C5N A:NAP502 4.6 31.3 1.0
NZ B:LYS212 4.7 44.1 1.0
C4N A:NAP502 4.8 31.6 1.0
OD1 B:ASP252 4.8 49.2 1.0
OG A:SER278 4.9 38.3 1.0

Cadmium binding site 2 out of 3 in 5yzi

Go back to Cadmium Binding Sites List in 5yzi
Cadmium binding site 2 out of 3 in the Crystal Structure of Mouse Cytosolic Isocitrate Dehydrogenase Complexed with Cadmium


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 Mouse Cytosolic Isocitrate Dehydrogenase Complexed with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd501

b:1.0
occ:1.00
OD1 B:ASP275 2.8 63.2 1.0
OD2 B:ASP279 3.1 57.9 1.0
OD2 A:ASP252 3.4 54.9 1.0
O B:ALA308 3.6 62.6 1.0
NH1 B:ARG109 3.7 38.4 1.0
CG B:ASP275 3.7 59.3 1.0
CG B:ASP279 4.0 56.6 1.0
OD1 B:ASP279 4.2 60.7 1.0
OD2 B:ASP275 4.2 60.6 1.0
C4N B:NAP503 4.2 83.5 0.8
C5N B:NAP503 4.3 83.6 0.8
CG A:ASP252 4.4 52.1 1.0
O B:ASP275 4.4 48.6 1.0
CB A:ASP252 4.5 49.1 1.0
CZ B:ARG109 4.7 41.5 1.0
CA B:ASP275 4.7 47.0 1.0
C B:ALA308 4.8 60.3 1.0
NH2 B:ARG109 4.8 44.7 1.0
CB B:ASP275 4.8 52.9 1.0
C B:ASP275 4.8 45.9 1.0
NH1 B:ARG132 4.8 39.3 1.0

Cadmium binding site 3 out of 3 in 5yzi

Go back to Cadmium Binding Sites List in 5yzi
Cadmium binding site 3 out of 3 in the Crystal Structure of Mouse Cytosolic Isocitrate Dehydrogenase Complexed with Cadmium


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 Mouse Cytosolic Isocitrate Dehydrogenase Complexed with Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd502

b:0.3
occ:1.00
SG B:CYS245 3.0 54.4 1.0
O B:HOH642 3.3 46.3 1.0
CB B:GLU247 3.5 44.0 1.0
OE1 B:GLU247 3.6 55.3 1.0
CB B:CYS245 3.7 53.4 1.0
CD B:GLU247 4.1 54.5 1.0
CE1 B:TYR208 4.1 33.1 1.0
O B:TYR246 4.2 36.5 1.0
C B:TYR246 4.2 36.3 1.0
OH B:TYR208 4.3 33.6 1.0
CG B:GLU247 4.3 50.2 1.0
N B:GLU247 4.4 36.6 1.0
C B:CYS245 4.5 44.2 1.0
CZ B:TYR208 4.5 32.3 1.0
CA B:GLU247 4.5 39.4 1.0
N B:TYR246 4.5 40.1 1.0
CA B:CYS245 4.7 49.0 1.0
O B:CYS245 4.8 44.0 1.0
OE2 B:GLU247 4.8 57.1 1.0
CA B:TYR246 4.8 35.9 1.0
CD1 B:TYR208 5.0 32.3 1.0

Reference:

H.J.Cho, H.Y.Cho, J.W.Park, O.S.Kwon, H.S.Lee, T.L.Huh, B.S.Kang. Nadp+-Dependent Cytosolic Isocitrate Dehydrogenase Provides Nadph in the Presence of Cadmium Due to the Moderate Chelating Effect of Glutathione. J. Biol. Inorg. Chem. V. 23 849 2018.
ISSN: ESSN 1432-1327
PubMed: 29923039
DOI: 10.1007/S00775-018-1581-5
Page generated: Sat Dec 12 08:28:03 2020

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