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Magnesium in PDB 1f8m: Crystal Structure of 3-Bromopyruvate Modified Isocitrate Lyase (Icl) From Mycobacterium Tuberculosis

Enzymatic activity of Crystal Structure of 3-Bromopyruvate Modified Isocitrate Lyase (Icl) From Mycobacterium Tuberculosis

All present enzymatic activity of Crystal Structure of 3-Bromopyruvate Modified Isocitrate Lyase (Icl) From Mycobacterium Tuberculosis:
4.1.3.1;

Protein crystallography data

The structure of Crystal Structure of 3-Bromopyruvate Modified Isocitrate Lyase (Icl) From Mycobacterium Tuberculosis, PDB code: 1f8m was solved by V.Sharma, S.Sharma, K.Hoener Zu Bentrup, J.D.Mckinney, D.G.Russell, W.R.Jacobs Jr., J.C.Sacchettini, Tb Structuralgenomics Consortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.86 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.310, 129.037, 166.165, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 24.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of 3-Bromopyruvate Modified Isocitrate Lyase (Icl) From Mycobacterium Tuberculosis (pdb code 1f8m). 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 3-Bromopyruvate Modified Isocitrate Lyase (Icl) From Mycobacterium Tuberculosis, PDB code: 1f8m:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1f8m

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Magnesium binding site 1 out of 4 in the Crystal Structure of 3-Bromopyruvate Modified Isocitrate Lyase (Icl) From Mycobacterium Tuberculosis


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 3-Bromopyruvate Modified Isocitrate Lyase (Icl) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg451

b:21.1
occ:1.00
 OD2 A:ASP153 2.1 17.3 1.0
O A:HOH1188 2.1 24.4 1.0
O A:HOH1148 2.4 20.8 1.0
O A:HOH2011 2.4 26.2 1.0
CG A:ASP153 3.1 15.8 1.0
O A:HOH1409 3.1 27.6 1.0
OD1 A:ASP153 3.5 16.9 1.0
NH1 A:ARG228 4.0 20.1 1.0
NZ A:LYS189 4.0 21.2 1.0
OD2 A:ASP108 4.1 20.6 1.0
N A:GLY92 4.2 14.2 1.0
CE1 A:HIS180 4.3 18.0 1.0
N A:TRP93 4.3 12.3 1.0
CB A:ASP153 4.4 17.5 1.0
O2 A:PYR500 4.5 34.2 1.0
OH A:TYR89 4.5 21.9 1.0
O A:HOH1757 4.5 29.5 1.0
CA A:GLY92 4.5 13.5 1.0
OD1 A:ASP108 4.6 18.7 1.0
CG A:GLU155 4.7 20.6 1.0
CE A:LYS189 4.7 21.5 1.0
OE2 A:GLU155 4.7 23.6 1.0
C A:GLY92 4.8 15.2 1.0
CG A:ASP108 4.8 18.9 1.0
OE1 A:GLU182 4.8 23.6 1.0
NE2 A:HIS180 4.9 20.7 1.0
CB A:TRP93 5.0 13.2 1.0

Magnesium binding site 2 out of 4 in 1f8m

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Magnesium binding site 2 out of 4 in the Crystal Structure of 3-Bromopyruvate Modified Isocitrate Lyase (Icl) From Mycobacterium Tuberculosis


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 3-Bromopyruvate Modified Isocitrate Lyase (Icl) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg452

b:28.0
occ:1.00
 O B:HOH2001 2.1 30.6 1.0
OD2 B:ASP153 2.1 15.0 1.0
O B:HOH1046 2.2 16.0 1.0
O B:HOH2015 2.3 42.2 1.0
O B:HOH1499 2.4 19.9 1.0
O B:HOH1465 3.2 24.1 1.0
CG B:ASP153 3.2 13.6 1.0
OD1 B:ASP153 3.6 14.8 1.0
NH1 B:ARG228 4.0 20.4 1.0
NZ B:LYS189 4.0 21.7 1.0
OD2 B:ASP108 4.1 19.1 1.0
N B:GLY92 4.2 16.2 1.0
N B:TRP93 4.2 14.6 1.0
NE2 B:HIS180 4.2 21.9 1.0
O B:HOH1352 4.3 26.9 1.0
OH B:TYR89 4.3 17.4 1.0
O2 B:PYR500 4.4 31.0 1.0
CB B:ASP153 4.4 14.7 1.0
OD1 B:ASP108 4.5 19.9 1.0
CA B:GLY92 4.6 16.8 1.0
CG B:GLU155 4.6 21.1 1.0
CE B:LYS189 4.7 21.1 1.0
CG B:ASP108 4.7 19.2 1.0
OE2 B:GLU155 4.8 23.7 1.0
C B:GLY92 4.8 16.3 1.0
OE1 B:GLU182 4.8 23.0 1.0
CB B:TRP93 4.8 15.8 1.0
CE1 B:HIS180 5.0 17.7 1.0

Magnesium binding site 3 out of 4 in 1f8m

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Magnesium binding site 3 out of 4 in the Crystal Structure of 3-Bromopyruvate Modified Isocitrate Lyase (Icl) From Mycobacterium Tuberculosis


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 3-Bromopyruvate Modified Isocitrate Lyase (Icl) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg453

b:32.4
occ:1.00
 O C:HOH1138 2.0 20.4 1.0
OD2 C:ASP153 2.1 16.0 1.0
O C:HOH2016 2.3 30.3 1.0
O C:HOH1454 2.5 25.0 1.0
O C:HOH1473 2.5 35.1 1.0
CG C:ASP153 3.1 15.3 1.0
OD1 C:ASP153 3.5 18.8 1.0
N C:GLY92 4.0 16.0 1.0
N C:TRP93 4.1 16.1 1.0
OD2 C:ASP108 4.1 19.5 1.0
NH1 C:ARG228 4.1 20.5 1.0
CA C:GLY92 4.3 15.8 1.0
NE2 C:HIS180 4.3 18.1 1.0
CB C:ASP153 4.3 17.3 1.0
OH C:TYR89 4.3 19.0 1.0
NZ C:LYS189 4.4 24.4 1.0
O2 C:PYR500 4.5 33.0 1.0
O C:HOH1714 4.6 40.1 1.0
OD1 C:ASP108 4.6 22.7 1.0
C C:GLY92 4.6 17.2 1.0
CG C:ASP108 4.8 22.3 1.0
OE2 C:GLU155 4.8 24.2 1.0
CG C:GLU155 4.8 19.4 1.0
CB C:TRP93 4.8 18.1 1.0
CE1 C:HIS180 4.9 17.6 1.0
OG C:SER91 4.9 18.3 1.0
OE1 C:GLU182 4.9 23.7 1.0
CA C:TRP93 5.0 18.0 1.0

Magnesium binding site 4 out of 4 in 1f8m

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Magnesium binding site 4 out of 4 in the Crystal Structure of 3-Bromopyruvate Modified Isocitrate Lyase (Icl) From Mycobacterium Tuberculosis


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 3-Bromopyruvate Modified Isocitrate Lyase (Icl) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg454

b:43.7
occ:1.00
 OD2 D:ASP153 2.2 21.0 1.0
O D:HOH1336 2.3 26.4 1.0
O D:HOH1199 2.3 19.4 1.0
O D:HOH1999 2.9 40.9 1.0
O D:HOH1299 3.1 26.7 1.0
CG D:ASP153 3.2 19.9 1.0
OD1 D:ASP153 3.5 20.9 1.0
OD2 D:ASP108 3.9 25.8 1.0
N D:TRP93 4.0 17.4 1.0
N D:GLY92 4.1 18.6 1.0
NH1 D:ARG228 4.1 24.8 1.0
NZ D:LYS189 4.2 26.5 1.0
O D:HOH1290 4.3 39.0 1.0
OD1 D:ASP108 4.4 27.8 1.0
CA D:GLY92 4.4 19.1 1.0
NE2 D:HIS180 4.5 19.8 1.0
CB D:ASP153 4.5 18.4 1.0
OH D:TYR89 4.6 26.4 1.0
CG D:ASP108 4.6 24.5 1.0
C D:GLY92 4.6 19.6 1.0
OE2 D:GLU155 4.6 27.9 1.0
O2 D:PYR500 4.6 35.2 1.0
CB D:TRP93 4.7 19.2 1.0
CE D:LYS189 4.7 25.6 1.0
CA D:TRP93 4.8 18.7 1.0
CG D:GLU155 4.8 22.1 1.0
OE1 D:GLU182 4.9 26.9 1.0

Reference:

V.Sharma, S.Sharma, K.Hoener Zu Bentrup, J.D.Mckinney, D.G.Russell, W.R.Jacobs Jr., J.C.Sacchettini. Structure of Isocitrate Lyase, A Persistence Factor of Mycobacterium Tuberculosis. Nat.Struct.Biol. V. 7 663 2000.
ISSN: ISSN 1072-8368
PubMed: 10932251
DOI: 10.1038/77964
Page generated: Sat Aug 9 20:55:10 2025

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