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Magnesium in PDB 3lcb: The Crystal Structure of Isocitrate Dehydrogenase Kinase/Phosphatase in Complex with Its Substrate, Isocitrate Dehydrogenase, From Escherichia Coli.

Enzymatic activity of The Crystal Structure of Isocitrate Dehydrogenase Kinase/Phosphatase in Complex with Its Substrate, Isocitrate Dehydrogenase, From Escherichia Coli.

All present enzymatic activity of The Crystal Structure of Isocitrate Dehydrogenase Kinase/Phosphatase in Complex with Its Substrate, Isocitrate Dehydrogenase, From Escherichia Coli.:
1.1.1.42; 2.7.11.5;

Protein crystallography data

The structure of The Crystal Structure of Isocitrate Dehydrogenase Kinase/Phosphatase in Complex with Its Substrate, Isocitrate Dehydrogenase, From Escherichia Coli., PDB code: 3lcb was solved by J.Zheng, Z.Jia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.90
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 196.801, 196.801, 156.458, 90.00, 90.00, 120.00
R / Rfree (%) 19 / 22.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Crystal Structure of Isocitrate Dehydrogenase Kinase/Phosphatase in Complex with Its Substrate, Isocitrate Dehydrogenase, From Escherichia Coli. (pdb code 3lcb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Crystal Structure of Isocitrate Dehydrogenase Kinase/Phosphatase in Complex with Its Substrate, Isocitrate Dehydrogenase, From Escherichia Coli., PDB code: 3lcb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3lcb

Go back to Magnesium Binding Sites List in 3lcb
Magnesium binding site 1 out of 2 in the The Crystal Structure of Isocitrate Dehydrogenase Kinase/Phosphatase in Complex with Its Substrate, Isocitrate Dehydrogenase, From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of Isocitrate Dehydrogenase Kinase/Phosphatase in Complex with Its Substrate, Isocitrate Dehydrogenase, From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg579

b:79.3
occ:1.00
O1A A:ATP1760 1.9 64.0 1.0
O1G A:ATP1760 2.3 69.4 1.0
OD1 A:ASN462 2.3 62.3 1.0
O1B A:ATP1760 2.4 67.4 1.0
OD2 A:ASP475 2.7 70.5 1.0
O3B A:ATP1760 2.8 69.4 1.0
OD1 A:ASP475 2.8 71.0 1.0
PB A:ATP1760 3.0 67.4 1.0
PG A:ATP1760 3.0 70.4 1.0
CG A:ASP475 3.1 69.5 1.0
PA A:ATP1760 3.1 64.5 1.0
O3A A:ATP1760 3.3 65.3 1.0
CG A:ASN462 3.4 62.0 1.0
O3' A:ATP1760 3.6 65.3 1.0
O3G A:ATP1760 3.6 70.2 1.0
C5' A:ATP1760 3.9 64.4 1.0
O5' A:ATP1760 4.0 64.4 1.0
ND2 A:ASN462 4.1 61.7 1.0
C3' A:ATP1760 4.1 64.8 1.0
CD A:LYS461 4.2 61.4 1.0
O A:LYS461 4.2 62.0 1.0
CE A:LYS461 4.3 61.1 1.0
O2A A:ATP1760 4.4 64.3 1.0
O2G A:ATP1760 4.4 70.4 1.0
CG A:LYS461 4.4 61.6 1.0
O2B A:ATP1760 4.5 67.3 1.0
CB A:ASP475 4.5 68.1 1.0
C4' A:ATP1760 4.6 64.6 1.0
CB A:ASN462 4.6 62.0 1.0
C A:LYS461 4.8 62.0 1.0
CA A:ASN462 4.8 62.2 1.0
OD2 A:ASP477 4.8 68.8 1.0
NZ A:LYS461 4.9 60.2 1.0

Magnesium binding site 2 out of 2 in 3lcb

Go back to Magnesium Binding Sites List in 3lcb
Magnesium binding site 2 out of 2 in the The Crystal Structure of Isocitrate Dehydrogenase Kinase/Phosphatase in Complex with Its Substrate, Isocitrate Dehydrogenase, From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of Isocitrate Dehydrogenase Kinase/Phosphatase in Complex with Its Substrate, Isocitrate Dehydrogenase, From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg579

b:72.3
occ:1.00
O1B B:ATP1761 1.9 68.2 1.0
OD1 B:ASN462 2.2 54.6 1.0
PB B:ATP1761 2.3 67.5 1.0
O3A B:ATP1761 2.4 64.8 1.0
C5' B:ATP1761 2.8 58.0 1.0
O2B B:ATP1761 2.9 68.0 1.0
PA B:ATP1761 2.9 62.3 1.0
O5' B:ATP1761 2.9 60.1 1.0
O2A B:ATP1761 2.9 62.8 1.0
CG B:ASN462 3.3 54.1 1.0
C4' B:ATP1761 3.3 57.7 1.0
C3' B:ATP1761 3.4 57.8 1.0
OD2 B:ASP475 3.4 59.1 1.0
CG B:ASP475 3.4 59.0 1.0
CB B:ASP475 3.5 59.2 1.0
O3' B:ATP1761 3.5 57.6 1.0
O3B B:ATP1761 3.8 67.2 1.0
OD1 B:ASP475 4.0 59.0 1.0
ND2 B:ASN462 4.0 53.5 1.0
O1G B:ATP1761 4.2 67.1 1.0
CE2 B:TYR474 4.3 57.1 1.0
O1A B:ATP1761 4.3 61.9 1.0
CB B:ASN462 4.4 54.4 1.0
CA B:ASN462 4.4 54.4 1.0
O B:LYS461 4.4 55.6 1.0
PG B:ATP1761 4.7 67.0 1.0
O4' B:ATP1761 4.7 57.4 1.0
CA B:ASP475 4.7 59.2 1.0
CD2 B:TYR474 4.8 57.5 1.0
C2' B:ATP1761 4.8 57.5 1.0
C B:LYS461 4.9 55.2 1.0

Reference:

J.Zheng, Z.Jia. Structure of the Bifunctional Isocitrate Dehydrogenase Kinase/Phosphatase. Nature V. 465 961 2010.
ISSN: ISSN 0028-0836
PubMed: 20505668
DOI: 10.1038/NATURE09088
Page generated: Mon Dec 14 08:24:06 2020

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