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Magnesium in PDB 1xg3: Crystal Structure of the C123S 2-Methylisocitrate Lyase Mutant From Escherichia Coli in Complex with the Reaction Product, Mg(II)-Pyruvate and Succinate

Enzymatic activity of Crystal Structure of the C123S 2-Methylisocitrate Lyase Mutant From Escherichia Coli in Complex with the Reaction Product, Mg(II)-Pyruvate and Succinate

All present enzymatic activity of Crystal Structure of the C123S 2-Methylisocitrate Lyase Mutant From Escherichia Coli in Complex with the Reaction Product, Mg(II)-Pyruvate and Succinate:
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 Reaction Product, Mg(II)-Pyruvate and Succinate, PDB code: 1xg3 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) 25.85 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 159.358, 85.993, 99.597, 90.00, 108.28, 90.00
R / Rfree (%) 16.1 / 19.5

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 Reaction Product, Mg(II)-Pyruvate and Succinate (pdb code 1xg3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the C123S 2-Methylisocitrate Lyase Mutant From Escherichia Coli in Complex with the Reaction Product, Mg(II)-Pyruvate and Succinate, PDB code: 1xg3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1xg3

Go back to Magnesium Binding Sites List in 1xg3
Magnesium binding site 1 out of 4 in the Crystal Structure of the C123S 2-Methylisocitrate Lyase Mutant From Escherichia Coli in Complex with the Reaction Product, Mg(II)-Pyruvate and Succinate


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 Reaction Product, Mg(II)-Pyruvate and Succinate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2101

b:15.6
occ:1.00
 O A:HOH2355 2.0 18.6 1.0
OD2 A:ASP85 2.0 12.2 1.0
O A:HOH2356 2.1 12.9 1.0
O A:HOH2354 2.2 14.6 1.0
O1 A:PYR2105 2.2 14.7 1.0
O3 A:PYR2105 2.3 17.5 1.0
C2 A:PYR2105 2.9 17.2 1.0
C1 A:PYR2105 3.0 16.8 1.0
CG A:ASP85 3.1 12.2 1.0
OD1 A:ASP85 3.6 12.8 1.0
OD1 A:ASP87 3.7 22.4 1.0
NZ A:LYS121 3.8 16.6 1.0
OD2 A:ASP58 3.9 17.8 1.0
N A:GLY47 3.9 13.1 1.0
NH1 A:ARG158 4.1 18.8 1.0
N A:GLY46 4.1 13.2 1.0
CA A:GLY46 4.1 12.2 1.0
O2 A:PYR2105 4.2 17.4 1.0
O4 A:SIN2106 4.2 30.6 1.0
OD1 A:ASP58 4.3 18.3 1.0
CB A:ASP85 4.4 12.3 1.0
C A:GLY46 4.4 14.2 1.0
C3 A:PYR2105 4.5 16.5 1.0
CG A:ASP58 4.5 18.8 1.0
OE1 A:GLU115 4.6 17.5 1.0
OH A:TYR43 4.6 15.8 1.0
C3 A:SIN2106 4.7 35.5 1.0
CE1 A:HIS113 4.8 15.7 1.0
C4 A:SIN2106 4.8 35.3 1.0
CE A:LYS121 4.8 16.8 1.0
CG A:ASP87 4.9 21.8 1.0
CA A:GLY47 4.9 11.7 1.0

Magnesium binding site 2 out of 4 in 1xg3

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Magnesium binding site 2 out of 4 in the Crystal Structure of the C123S 2-Methylisocitrate Lyase Mutant From Escherichia Coli in Complex with the Reaction Product, Mg(II)-Pyruvate and Succinate


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 Reaction Product, Mg(II)-Pyruvate and Succinate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2201

b:15.2
occ:1.00
 O B:HOH2483 2.0 15.1 1.0
OD2 B:ASP85 2.0 16.0 1.0
O B:HOH2481 2.1 10.8 1.0
O1 B:PYR2205 2.2 16.0 1.0
O B:HOH2482 2.2 13.3 1.0
O3 B:PYR2205 2.3 16.7 1.0
C2 B:PYR2205 3.0 16.4 1.0
C1 B:PYR2205 3.0 14.9 1.0
CG B:ASP85 3.1 13.3 1.0
OD1 B:ASP85 3.5 11.1 1.0
NZ B:LYS121 3.7 16.7 1.0
OD1 B:ASP87 3.7 17.5 1.0
N B:GLY47 3.9 10.9 1.0
OD2 B:ASP58 3.9 15.2 1.0
N B:GLY46 4.1 11.0 1.0
CA B:GLY46 4.1 12.0 1.0
NH1 B:ARG158 4.2 17.3 1.0
O4 B:SIN2206 4.2 22.2 1.0
O2 B:PYR2205 4.2 13.2 1.0
OD1 B:ASP58 4.3 15.8 1.0
C B:GLY46 4.4 10.5 1.0
CB B:ASP85 4.4 14.8 1.0
C3 B:PYR2205 4.5 16.6 1.0
CG B:ASP58 4.5 15.0 1.0
C3 B:SIN2206 4.6 27.6 1.0
OE1 B:GLU115 4.7 15.4 1.0
OH B:TYR43 4.7 16.3 1.0
CE B:LYS121 4.7 19.1 1.0
CE1 B:HIS113 4.7 12.9 1.0
CA B:GLY47 4.7 9.9 1.0
C4 B:SIN2206 4.8 27.0 1.0
CG B:ASP87 4.9 19.0 1.0

Magnesium binding site 3 out of 4 in 1xg3

Go back to Magnesium Binding Sites List in 1xg3
Magnesium binding site 3 out of 4 in the Crystal Structure of the C123S 2-Methylisocitrate Lyase Mutant From Escherichia Coli in Complex with the Reaction Product, Mg(II)-Pyruvate and Succinate


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 Reaction Product, Mg(II)-Pyruvate and Succinate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2301

b:17.8
occ:1.00
 O C:HOH2571 2.0 20.7 1.0
OD2 C:ASP85 2.1 14.8 1.0
O1 C:PYR2305 2.2 18.9 1.0
O C:HOH2570 2.3 16.6 1.0
O C:HOH2572 2.3 17.8 1.0
O3 C:PYR2305 2.4 16.6 1.0
C1 C:PYR2305 3.0 18.4 1.0
C2 C:PYR2305 3.0 18.5 1.0
CG C:ASP85 3.2 12.3 1.0
OD1 C:ASP85 3.7 14.8 1.0
O C:HOH2522 4.0 30.0 1.0
OD2 C:ASP58 4.0 21.2 1.0
N C:GLY47 4.0 12.5 1.0
CA C:GLY46 4.1 12.8 1.0
N C:GLY46 4.2 11.1 1.0
O C:HOH2521 4.2 37.6 1.0
O2 C:PYR2305 4.2 19.0 1.0
NH1 C:ARG158 4.3 34.9 1.0
C C:GLY46 4.4 13.6 1.0
CB C:ASP85 4.5 12.8 1.0
OD1 C:ASP58 4.5 17.4 1.0
C3 C:PYR2305 4.5 18.0 1.0
CG C:ASP58 4.7 18.6 1.0
CZ C:ARG158 4.7 32.1 1.0
OH C:TYR43 4.8 15.4 1.0
OE2 C:GLU115 4.8 17.5 1.0
CE1 C:HIS113 4.8 11.9 1.0
NH2 C:ARG158 4.9 35.3 1.0
CA C:GLY47 5.0 12.6 1.0

Magnesium binding site 4 out of 4 in 1xg3

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Magnesium binding site 4 out of 4 in the Crystal Structure of the C123S 2-Methylisocitrate Lyase Mutant From Escherichia Coli in Complex with the Reaction Product, Mg(II)-Pyruvate and Succinate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the C123S 2-Methylisocitrate Lyase Mutant From Escherichia Coli in Complex with the Reaction Product, Mg(II)-Pyruvate and Succinate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2401

b:14.9
occ:1.00
 OD2 D:ASP85 2.0 14.0 1.0
O D:HOH2671 2.1 7.7 1.0
O1 D:PYR2405 2.1 13.2 1.0
O3 D:PYR2405 2.1 14.4 1.0
O D:HOH2673 2.1 12.6 1.0
O D:HOH2672 2.1 14.9 1.0
C2 D:PYR2405 2.8 13.6 1.0
C1 D:PYR2405 2.9 15.0 1.0
CG D:ASP85 3.1 12.8 1.0
OD1 D:ASP85 3.5 14.5 1.0
OD2 D:ASP87 3.8 17.7 1.0
NZ D:LYS121 3.9 16.2 1.0
N D:GLY47 3.9 10.3 1.0
NH1 D:ARG158 4.0 16.6 1.0
OD2 D:ASP58 4.0 14.7 1.0
O2 D:PYR2405 4.1 12.6 1.0
N D:GLY46 4.1 10.3 1.0
CA D:GLY46 4.1 9.9 1.0
O4 D:SIN2406 4.1 18.4 1.0
C3 D:PYR2405 4.3 14.1 1.0
CB D:ASP85 4.3 13.3 1.0
OD1 D:ASP58 4.4 14.7 1.0
C D:GLY46 4.4 10.5 1.0
C3 D:SIN2406 4.5 22.3 1.0
OH D:TYR43 4.6 13.8 1.0
C4 D:SIN2406 4.6 24.2 1.0
CG D:ASP58 4.6 15.9 1.0
CE1 D:HIS113 4.6 14.4 1.0
OE1 D:GLU115 4.7 16.4 1.0
CA D:GLY47 4.9 9.8 1.0
CG D:ASP87 4.9 17.2 1.0
CE D:LYS121 5.0 16.2 1.0
CZ D:ARG158 5.0 16.4 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: Mon Dec 14 07:04:11 2020

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