Atomistry » Magnesium » PDB 1xfy-1xon » 1xg3
Atomistry »
  Magnesium »
    PDB 1xfy-1xon »
      1xg3 »

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

Go back to Magnesium Binding Sites List in 1xg3
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

Go back to Magnesium Binding Sites List in 1xg3
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: Tue Aug 13 17:39:49 2024

Last articles

Cl in 3LK9
Cl in 3LLC
Cl in 3LL1
Cl in 3LKW
Cl in 3LK0
Cl in 3LK7
Cl in 3LJX
Cl in 3LJY
Cl in 3LJ7
Cl in 3LJ6
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy