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Magnesium in PDB 1o5q: Crystal Structure of Pyruvate and MG2+ Bound 2- Methylisocitrate Lyase (Prpb) From Salmonella Typhimurium

Enzymatic activity of Crystal Structure of Pyruvate and MG2+ Bound 2- Methylisocitrate Lyase (Prpb) From Salmonella Typhimurium

All present enzymatic activity of Crystal Structure of Pyruvate and MG2+ Bound 2- Methylisocitrate Lyase (Prpb) From Salmonella Typhimurium:
4.1.3.30;

Protein crystallography data

The structure of Crystal Structure of Pyruvate and MG2+ Bound 2- Methylisocitrate Lyase (Prpb) From Salmonella Typhimurium, PDB code: 1o5q was solved by D.K.Simanshu, M.R.N.Murthy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.90 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.953, 99.679, 202.396, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 25.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Pyruvate and MG2+ Bound 2- Methylisocitrate Lyase (Prpb) From Salmonella Typhimurium (pdb code 1o5q). 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 Pyruvate and MG2+ Bound 2- Methylisocitrate Lyase (Prpb) From Salmonella Typhimurium, PDB code: 1o5q:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1o5q

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Magnesium binding site 1 out of 4 in the Crystal Structure of Pyruvate and MG2+ Bound 2- Methylisocitrate Lyase (Prpb) From Salmonella Typhimurium


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 Pyruvate and MG2+ Bound 2- Methylisocitrate Lyase (Prpb) From Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1301

b:33.7
occ:0.75
 OD2 A:ASP85 2.3 41.7 1.0
O3 A:PYR1302 2.3 34.7 0.8
O2 A:PYR1302 2.4 31.7 0.8
O A:HOH1455 2.5 35.8 1.0
O A:HOH1452 2.7 53.0 1.0
C2 A:PYR1302 3.0 34.2 0.8
C1 A:PYR1302 3.0 33.5 0.8
CG A:ASP85 3.4 39.6 1.0
NH1 A:ARG158 3.7 41.6 1.0
OD1 A:ASP85 3.9 39.0 1.0
OD2 A:ASP58 4.1 36.3 1.0
N A:GLY47 4.1 29.6 1.0
O1 A:PYR1302 4.2 30.6 0.8
N A:GLY46 4.4 27.6 1.0
CA A:GLY46 4.4 27.1 1.0
O A:HOH1400 4.4 65.4 1.0
C3 A:PYR1302 4.5 29.9 0.8
CB A:ASP85 4.5 36.4 1.0
C A:GLY46 4.6 28.7 1.0
OD1 A:ASP58 4.8 34.0 1.0
CG A:ASP58 4.9 35.0 1.0
OD1 A:ASP87 4.9 58.7 1.0
CZ A:ARG158 4.9 40.8 1.0
OH A:TYR43 4.9 35.0 1.0
O A:HOH1322 4.9 77.6 1.0
CA A:GLY47 5.0 29.0 1.0

Magnesium binding site 2 out of 4 in 1o5q

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Magnesium binding site 2 out of 4 in the Crystal Structure of Pyruvate and MG2+ Bound 2- Methylisocitrate Lyase (Prpb) From Salmonella Typhimurium


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 Pyruvate and MG2+ Bound 2- Methylisocitrate Lyase (Prpb) From Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2301

b:33.0
occ:0.77
 OD2 B:ASP85 2.2 28.7 1.0
O B:HOH2454 2.2 47.2 1.0
O B:HOH2456 2.4 36.5 1.0
O3 B:PYR2302 2.4 34.3 0.8
O2 B:PYR2302 2.5 33.0 0.8
O B:HOH2400 2.5 33.3 1.0
C2 B:PYR2302 3.1 32.1 0.8
C1 B:PYR2302 3.1 31.9 0.8
CG B:ASP85 3.3 28.1 1.0
NH1 B:ARG158 3.7 40.6 1.0
N B:GLY47 3.8 22.2 1.0
OD1 B:ASP85 3.9 25.3 1.0
OD2 B:ASP58 4.0 37.3 1.0
CA B:GLY46 4.0 23.0 1.0
N B:GLY46 4.1 23.4 1.0
O B:HOH2401 4.1 56.0 1.0
C B:GLY46 4.3 22.9 1.0
O B:HOH2455 4.3 55.0 1.0
O1 B:PYR2302 4.3 27.9 0.8
C3 B:PYR2302 4.6 30.6 0.8
CB B:ASP85 4.6 23.2 1.0
OE2 B:GLU115 4.7 44.0 1.0
OD1 B:ASP58 4.7 38.5 1.0
CG B:ASP58 4.8 36.4 1.0
CA B:GLY47 4.8 21.4 1.0
CZ B:ARG158 4.8 33.4 1.0
OD1 B:ASP87 4.9 50.5 1.0
OH B:TYR43 4.9 25.3 1.0

Magnesium binding site 3 out of 4 in 1o5q

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Magnesium binding site 3 out of 4 in the Crystal Structure of Pyruvate and MG2+ Bound 2- Methylisocitrate Lyase (Prpb) From Salmonella Typhimurium


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 Pyruvate and MG2+ Bound 2- Methylisocitrate Lyase (Prpb) From Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3301

b:49.2
occ:0.83
 OD2 C:ASP85 2.1 37.0 1.0
O C:HOH3403 2.3 50.2 1.0
O3 C:PYR3302 2.3 41.4 0.9
O2 C:PYR3302 2.6 43.3 0.9
O C:HOH3379 2.8 58.4 1.0
C2 C:PYR3302 3.0 39.1 0.9
C1 C:PYR3302 3.2 40.6 0.9
CG C:ASP85 3.2 36.8 1.0
O C:HOH3401 3.6 58.4 1.0
OD1 C:ASP85 3.7 38.0 1.0
NH1 C:ARG158 4.1 46.3 1.0
N C:GLY47 4.1 38.9 1.0
O C:HOH3402 4.2 45.4 1.0
N C:GLY46 4.3 35.4 1.0
CA C:GLY46 4.3 36.0 1.0
OD2 C:ASP58 4.4 49.5 1.0
O1 C:PYR3302 4.4 36.9 0.9
CB C:ASP85 4.5 34.6 1.0
C3 C:PYR3302 4.5 37.6 0.9
C C:GLY46 4.6 37.7 1.0
OE1 C:GLU115 4.8 45.0 1.0
OH C:TYR43 4.8 32.2 1.0
OD1 C:ASP58 4.9 49.1 1.0
CE1 C:HIS113 5.0 33.0 1.0

Magnesium binding site 4 out of 4 in 1o5q

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Magnesium binding site 4 out of 4 in the Crystal Structure of Pyruvate and MG2+ Bound 2- Methylisocitrate Lyase (Prpb) From Salmonella Typhimurium


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 Pyruvate and MG2+ Bound 2- Methylisocitrate Lyase (Prpb) From Salmonella Typhimurium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg4301

b:53.3
occ:0.81
 OD2 D:ASP85 2.1 44.6 1.0
O D:HOH4377 2.2 62.9 1.0
O D:HOH4376 2.3 46.0 1.0
O3 D:PYR4302 2.4 53.3 0.9
O D:HOH4380 2.7 48.0 1.0
O2 D:PYR4302 2.7 50.9 0.9
C2 D:PYR4302 3.1 52.0 0.9
CG D:ASP85 3.2 43.5 1.0
C1 D:PYR4302 3.3 52.2 0.9
OD1 D:ASP85 3.7 44.6 1.0
NH1 D:ARG158 3.7 59.1 1.0
N D:GLY47 4.3 30.4 1.0
CA D:GLY46 4.3 29.8 1.0
N D:GLY46 4.4 31.1 1.0
O1 D:PYR4302 4.4 49.4 0.9
CB D:ASP85 4.5 42.6 1.0
OD2 D:ASP58 4.5 43.9 1.0
C3 D:PYR4302 4.6 50.3 0.9
OE1 D:GLU115 4.6 45.9 1.0
C D:GLY46 4.7 31.8 1.0
OH D:TYR43 4.8 36.2 1.0
CZ D:ARG158 4.9 57.5 1.0
CE1 D:HIS113 5.0 36.1 1.0

Reference:

D.K.Simanshu, P.S.Satheshkumar, H.S.Savithri, M.R.N.Murthy. Crystal Structure of Salmonella Typhimurium 2-Methylisocitrate Lyase (Prpb) and Its Complex with Pyruvate and Mg(2+) Biochem.Biophys.Res.Commun. V. 311 193 2003.
ISSN: ISSN 0006-291X
PubMed: 14575713
DOI: 10.1016/J.BBRC.2003.09.193
Page generated: Sun Aug 10 02:04:56 2025

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