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Magnesium in PDB 5h3f: Crystal Structure of Mouse Isocitrate Dehydrogenases 2 Complexed with Isocitrate

Enzymatic activity of Crystal Structure of Mouse Isocitrate Dehydrogenases 2 Complexed with Isocitrate

All present enzymatic activity of Crystal Structure of Mouse Isocitrate Dehydrogenases 2 Complexed with Isocitrate:
1.1.1.42;

Protein crystallography data

The structure of Crystal Structure of Mouse Isocitrate Dehydrogenases 2 Complexed with Isocitrate, PDB code: 5h3f was solved by Y.Xu, L.Liu, T.Miyakawa, A.Nakamura, M.Tanokura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.89 / 3.29
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 135.853, 135.853, 220.162, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 22.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mouse Isocitrate Dehydrogenases 2 Complexed with Isocitrate (pdb code 5h3f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Mouse Isocitrate Dehydrogenases 2 Complexed with Isocitrate, PDB code: 5h3f:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5h3f

Go back to Magnesium Binding Sites List in 5h3f
Magnesium binding site 1 out of 2 in the Crystal Structure of Mouse Isocitrate Dehydrogenases 2 Complexed with Isocitrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Mouse Isocitrate Dehydrogenases 2 Complexed with Isocitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:93.2
occ:1.00
O2 A:ICT501 2.3 0.0 1.0
OD1 A:ASP314 2.4 0.9 1.0
OD2 B:ASP291 2.6 1.0 1.0
O7 A:ICT501 2.8 0.6 1.0
OD1 A:ASP318 3.2 1.0 1.0
C1 A:ICT501 3.3 0.4 1.0
CG B:ASP291 3.5 0.2 1.0
CG A:ASP314 3.5 0.4 1.0
O A:ASP314 3.5 0.2 1.0
C2 A:ICT501 3.6 0.6 1.0
CB B:ASP291 3.7 0.9 1.0
CG A:ASP318 3.8 0.3 1.0
OD2 A:ASP318 3.8 0.7 1.0
NH1 A:ARG149 4.0 0.7 1.0
OD2 A:ASP314 4.1 0.5 1.0
C A:ASP314 4.3 0.2 1.0
O1 A:ICT501 4.4 0.1 1.0
CA A:ASP314 4.5 0.1 1.0
CB A:ASP314 4.6 0.4 1.0
O6 A:ICT501 4.7 0.5 1.0
OD1 B:ASP291 4.7 0.8 1.0
OG A:SER317 4.8 0.8 1.0
NZ B:LYS251 4.9 0.9 1.0
C3 A:ICT501 4.9 0.2 1.0

Magnesium binding site 2 out of 2 in 5h3f

Go back to Magnesium Binding Sites List in 5h3f
Magnesium binding site 2 out of 2 in the Crystal Structure of Mouse Isocitrate Dehydrogenases 2 Complexed with Isocitrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Mouse Isocitrate Dehydrogenases 2 Complexed with Isocitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:97.3
occ:1.00
OD2 A:ASP291 2.6 0.5 1.0
O7 B:ICT501 2.6 0.1 1.0
O1 B:ICT501 2.6 0.2 1.0
OD1 B:ASP314 2.7 0.0 1.0
OD2 B:ASP318 3.0 0.8 1.0
OD1 B:ASP318 3.4 0.7 1.0
C1 B:ICT501 3.5 0.8 1.0
C2 B:ICT501 3.5 0.8 1.0
CG B:ASP318 3.5 0.6 1.0
CG A:ASP291 3.6 0.2 1.0
CG B:ASP314 3.9 0.8 1.0
O B:ASP314 4.0 0.6 1.0
CB A:ASP291 4.0 0.2 1.0
NH1 B:ARG149 4.1 0.8 1.0
OD2 B:ASP314 4.6 0.3 1.0
O2 B:ICT501 4.7 0.8 1.0
OD1 A:ASP291 4.7 0.2 1.0
O5 B:ICT501 4.7 0.5 1.0
C B:ASP314 4.8 0.5 1.0
NH2 B:ARG149 4.8 0.6 1.0
CZ B:ARG149 4.9 0.4 1.0
C3 B:ICT501 4.9 0.2 1.0
CA B:ASP314 4.9 0.8 1.0
CB B:ASP318 5.0 0.6 1.0

Reference:

Y.Xu, L.Liu, A.Nakamura, S.Someya, T.Miyakawa, M.Tanokura. Studies on the Regulatory Mechanism of Isocitrate Dehydrogenase 2 Using Acetylation Mimics Sci Rep V. 7 9785 2017.
ISSN: ESSN 2045-2322
PubMed: 28852116
DOI: 10.1038/S41598-017-10337-7
Page generated: Sun Sep 29 15:40:54 2024

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