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Magnesium in PDB 1xg4: Crystal Structure of the C123S 2-Methylisocitrate Lyase Mutant From Escherichia Coli in Complex with the Inhibitor Isocitrate

Enzymatic activity of Crystal Structure of the C123S 2-Methylisocitrate Lyase Mutant From Escherichia Coli in Complex with the Inhibitor Isocitrate

All present enzymatic activity of Crystal Structure of the C123S 2-Methylisocitrate Lyase Mutant From Escherichia Coli in Complex with the Inhibitor Isocitrate:
4.1.3.30;

Protein crystallography data

The structure of Crystal Structure of the C123S 2-Methylisocitrate Lyase Mutant From Escherichia Coli in Complex with the Inhibitor Isocitrate, PDB code: 1xg4 was solved by S.Liu, Z.Lu, Y.Han, E.Melamud, D.Dunaway-Mariano, O.Herzberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.29 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 159.061, 84.561, 99.756, 90.00, 108.15, 90.00
R / Rfree (%) 18.1 / 20.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the C123S 2-Methylisocitrate Lyase Mutant From Escherichia Coli in Complex with the Inhibitor Isocitrate (pdb code 1xg4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the C123S 2-Methylisocitrate Lyase Mutant From Escherichia Coli in Complex with the Inhibitor Isocitrate, PDB code: 1xg4:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 1xg4

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Magnesium binding site 1 out of 3 in the Crystal Structure of the C123S 2-Methylisocitrate Lyase Mutant From Escherichia Coli in Complex with the Inhibitor 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 the C123S 2-Methylisocitrate Lyase Mutant From Escherichia Coli in Complex with the Inhibitor Isocitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1101

b:26.1
occ:1.00
O A:HOH1360 2.1 21.0 1.0
OD2 A:ASP85 2.2 18.4 1.0
O A:HOH1361 2.4 23.4 1.0
O2 A:ICT1105 2.4 24.0 1.0
O A:HOH1362 2.4 23.9 1.0
O7 A:ICT1105 2.6 29.0 1.0
C1 A:ICT1105 3.3 27.6 1.0
CG A:ASP85 3.3 16.8 1.0
C2 A:ICT1105 3.4 26.9 1.0
OD1 A:ASP85 3.7 18.0 1.0
NZ A:LYS121 3.8 27.6 1.0
N A:GLY47 3.9 15.4 1.0
OD2 A:ASP58 3.9 20.2 1.0
OD1 A:ASP87 4.0 30.5 1.0
NH1 A:ARG158 4.1 21.5 1.0
C3 A:ICT1105 4.1 25.7 1.0
O6 A:ICT1105 4.1 23.5 1.0
N A:GLY46 4.1 12.8 1.0
CA A:GLY46 4.2 14.9 1.0
OD1 A:ASP58 4.3 20.5 1.0
C A:GLY46 4.4 15.3 1.0
O1 A:ICT1105 4.4 29.2 1.0
CG A:ASP58 4.5 20.7 1.0
CB A:ASP85 4.5 16.8 1.0
C6 A:ICT1105 4.6 25.0 1.0
CA A:GLY47 4.7 15.1 1.0
CE A:LYS121 4.8 26.9 1.0
OH A:TYR43 4.9 16.7 1.0
OE1 A:GLU115 4.9 25.2 1.0

Magnesium binding site 2 out of 3 in 1xg4

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Magnesium binding site 2 out of 3 in the Crystal Structure of the C123S 2-Methylisocitrate Lyase Mutant From Escherichia Coli in Complex with the Inhibitor 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 the C123S 2-Methylisocitrate Lyase Mutant From Escherichia Coli in Complex with the Inhibitor Isocitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1201

b:28.6
occ:1.00
OD2 B:ASP85 2.0 21.9 1.0
O B:HOH1467 2.3 24.2 1.0
O B:HOH1465 2.3 22.7 1.0
O2 B:ICT1205 2.4 27.4 1.0
O B:HOH1466 2.5 29.2 1.0
O7 B:ICT1205 2.7 29.6 1.0
CG B:ASP85 3.1 19.6 1.0
C1 B:ICT1205 3.2 28.4 1.0
C2 B:ICT1205 3.4 26.6 1.0
OD1 B:ASP85 3.7 20.6 1.0
N B:GLY47 3.9 15.6 1.0
NZ B:LYS121 4.0 29.1 1.0
OD2 B:ASP58 4.0 19.4 1.0
N B:GLY46 4.0 14.8 1.0
CA B:GLY46 4.0 16.1 1.0
OD1 B:ASP87 4.0 27.9 1.0
C3 B:ICT1205 4.1 26.4 1.0
NH1 B:ARG158 4.2 20.3 1.0
O6 B:ICT1205 4.3 24.1 1.0
O1 B:ICT1205 4.3 30.5 1.0
C B:GLY46 4.3 16.0 1.0
CB B:ASP85 4.3 18.7 1.0
OD1 B:ASP58 4.5 20.6 1.0
C6 B:ICT1205 4.6 24.6 1.0
CG B:ASP58 4.6 20.9 1.0
OH B:TYR43 4.7 17.9 1.0
CA B:GLY47 4.8 15.5 1.0
OE1 B:GLU115 4.9 24.6 1.0
CE1 B:HIS113 4.9 18.2 1.0
CE B:LYS121 5.0 27.7 1.0

Magnesium binding site 3 out of 3 in 1xg4

Go back to Magnesium Binding Sites List in 1xg4
Magnesium binding site 3 out of 3 in the Crystal Structure of the C123S 2-Methylisocitrate Lyase Mutant From Escherichia Coli in Complex with the Inhibitor Isocitrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the C123S 2-Methylisocitrate Lyase Mutant From Escherichia Coli in Complex with the Inhibitor Isocitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1401

b:25.2
occ:1.00
OD2 D:ASP85 2.1 22.4 1.0
O D:HOH1633 2.3 20.5 1.0
O D:HOH1635 2.3 21.7 1.0
O D:HOH1634 2.4 21.6 1.0
O2 D:ICT1405 2.4 27.7 1.0
O7 D:ICT1405 2.6 28.8 1.0
CG D:ASP85 3.2 20.1 1.0
C1 D:ICT1405 3.2 27.6 1.0
C2 D:ICT1405 3.4 26.1 1.0
OD1 D:ASP85 3.6 18.8 1.0
NZ D:LYS121 3.9 24.4 1.0
OD2 D:ASP58 3.9 21.7 1.0
N D:GLY47 3.9 14.1 1.0
OD2 D:ASP87 3.9 30.4 1.0
NH1 D:ARG158 4.1 24.6 1.0
C3 D:ICT1405 4.1 25.1 1.0
N D:GLY46 4.1 14.6 1.0
CA D:GLY46 4.1 14.2 1.0
O6 D:ICT1405 4.2 23.1 1.0
O1 D:ICT1405 4.3 28.3 1.0
C D:GLY46 4.4 13.9 1.0
CB D:ASP85 4.4 17.8 1.0
OD1 D:ASP58 4.5 20.0 1.0
C6 D:ICT1405 4.6 24.7 1.0
CG D:ASP58 4.6 22.0 1.0
CA D:GLY47 4.8 15.1 1.0
OH D:TYR43 4.8 19.0 1.0
CE D:LYS121 4.8 23.1 1.0
OE1 D:GLU115 4.9 25.8 1.0
CE1 D:HIS113 5.0 17.7 1.0

Reference:

S.Liu, Z.Lu, Y.Han, E.Melamud, D.Dunaway-Mariano, O.Herzberg. Crystal Structures of 2-Methylisocitrate Lyase in Complex with Product and with Isocitrate Inhibitor Provide Insight Into Lyase Substrate Specificity, Catalysis and Evolution Biochemistry V. 44 2949 2005.
ISSN: ISSN 0006-2960
PubMed: 15723538
DOI: 10.1021/BI0479712
Page generated: Sun Aug 10 07:04:57 2025

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