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Magnesium in PDB 1f8i: Crystal Structure of Isocitrate Lyase:Nitropropionate:Glyoxylate Complex From Mycobacterium Tuberculosis

Enzymatic activity of Crystal Structure of Isocitrate Lyase:Nitropropionate:Glyoxylate Complex From Mycobacterium Tuberculosis

All present enzymatic activity of Crystal Structure of Isocitrate Lyase:Nitropropionate:Glyoxylate Complex From Mycobacterium Tuberculosis:
4.1.3.1;

Protein crystallography data

The structure of Crystal Structure of Isocitrate Lyase:Nitropropionate:Glyoxylate Complex From Mycobacterium Tuberculosis, PDB code: 1f8i 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) 35.02 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.291, 129.018, 166.962, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 21

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Isocitrate Lyase:Nitropropionate:Glyoxylate Complex From Mycobacterium Tuberculosis (pdb code 1f8i). 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 Isocitrate Lyase:Nitropropionate:Glyoxylate Complex From Mycobacterium Tuberculosis, PDB code: 1f8i:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1f8i

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Magnesium binding site 1 out of 4 in the Crystal Structure of Isocitrate Lyase:Nitropropionate:Glyoxylate Complex 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 Isocitrate Lyase:Nitropropionate:Glyoxylate Complex From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg451

b:24.8
occ:1.00
 OD2 A:ASP153 2.0 16.1 1.0
O2 A:GLV461 2.0 38.1 1.0
O A:HOH1001 2.1 16.6 1.0
O A:HOH1002 2.2 22.7 1.0
O A:HOH1003 2.2 18.5 1.0
O1 A:GLV461 2.2 39.1 1.0
C2 A:GLV461 2.8 36.2 1.0
C1 A:GLV461 2.8 36.3 1.0
CG A:ASP153 3.1 16.3 1.0
OD1 A:ASP153 3.5 13.6 1.0
OD2 A:ASP108 3.8 24.0 1.0
O3 A:GLV461 4.0 32.6 1.0
O2 A:SIN471 4.1 38.9 1.0
N A:TRP93 4.2 16.5 1.0
N A:GLY92 4.2 15.6 1.0
NZ A:LYS189 4.2 24.0 1.0
NH1 A:ARG228 4.2 19.2 1.0
OD1 A:ASP108 4.3 22.6 1.0
CB A:ASP153 4.4 15.2 1.0
CA A:GLY92 4.4 15.6 1.0
NE2 A:HIS180 4.4 18.6 1.0
C1 A:SIN471 4.4 38.1 1.0
CG A:ASP108 4.5 22.9 1.0
C2 A:SIN471 4.6 37.1 1.0
C A:GLY92 4.6 16.4 1.0
OE1 A:GLU182 4.6 18.4 1.0
OH A:TYR89 4.7 19.3 1.0
OE2 A:GLU155 4.7 22.3 1.0
CE A:LYS189 4.7 24.4 1.0
CG A:GLU155 4.8 18.7 1.0
CB A:TRP93 4.9 15.8 1.0
CA A:TRP93 5.0 14.7 1.0

Magnesium binding site 2 out of 4 in 1f8i

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Magnesium binding site 2 out of 4 in the Crystal Structure of Isocitrate Lyase:Nitropropionate:Glyoxylate Complex 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 Isocitrate Lyase:Nitropropionate:Glyoxylate Complex From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg452

b:25.1
occ:1.00
 O B:HOH1005 2.0 31.4 1.0
O2 B:GLV462 2.0 33.1 1.0
O B:HOH1006 2.1 19.6 1.0
OD2 B:ASP153 2.2 19.1 1.0
O B:HOH1004 2.2 15.0 1.0
O1 B:GLV462 2.4 37.2 1.0
C2 B:GLV462 2.8 34.7 1.0
C1 B:GLV462 3.0 35.4 1.0
CG B:ASP153 3.3 16.3 1.0
OD2 B:ASP108 3.6 22.4 1.0
OD1 B:ASP153 3.7 15.8 1.0
O2 B:SIN472 3.8 42.1 1.0
OD1 B:ASP108 3.9 22.9 1.0
N B:TRP93 3.9 17.5 1.0
O3 B:GLV462 4.0 29.2 1.0
NZ B:LYS189 4.0 22.1 1.0
N B:GLY92 4.1 15.9 1.0
CG B:ASP108 4.2 21.6 1.0
CA B:GLY92 4.2 17.2 1.0
NH1 B:ARG228 4.2 22.1 1.0
CG B:GLU155 4.3 25.7 1.0
C B:GLY92 4.4 17.9 1.0
CE B:LYS189 4.5 26.5 1.0
C1 B:SIN472 4.5 40.4 1.0
CB B:ASP153 4.5 14.6 1.0
C2 B:SIN472 4.7 40.5 1.0
OE1 B:GLU182 4.7 20.4 1.0
NE2 B:HIS180 4.7 16.9 1.0
CB B:TRP93 4.8 18.3 1.0
CA B:TRP93 4.8 17.5 1.0
OE2 B:GLU155 4.8 26.1 1.0
CD B:GLU155 4.8 26.5 1.0
OH B:TYR89 4.9 17.2 1.0

Magnesium binding site 3 out of 4 in 1f8i

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Magnesium binding site 3 out of 4 in the Crystal Structure of Isocitrate Lyase:Nitropropionate:Glyoxylate Complex 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 Isocitrate Lyase:Nitropropionate:Glyoxylate Complex From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg453

b:24.3
occ:1.00
 O C:HOH1007 2.1 16.6 1.0
O C:HOH1009 2.1 22.9 1.0
OD2 C:ASP153 2.1 15.9 1.0
O C:HOH1008 2.2 22.5 1.0
O1 C:GLV463 2.2 39.0 1.0
O2 C:GLV463 2.3 37.9 1.0
C1 C:GLV463 2.9 37.1 1.0
C2 C:GLV463 3.0 37.4 1.0
CG C:ASP153 3.1 15.8 1.0
OD1 C:ASP153 3.4 16.0 1.0
OD2 C:ASP108 3.9 24.1 1.0
O2 C:SIN473 4.0 40.6 1.0
NZ C:LYS189 4.1 27.0 1.0
NH1 C:ARG228 4.1 22.4 1.0
O3 C:GLV463 4.2 34.9 1.0
N C:GLY92 4.3 19.2 1.0
N C:TRP93 4.3 19.9 1.0
NE2 C:HIS180 4.3 18.6 1.0
OD1 C:ASP108 4.4 23.3 1.0
C1 C:SIN473 4.4 39.6 1.0
CB C:ASP153 4.4 15.7 1.0
CA C:GLY92 4.5 19.1 1.0
OE1 C:GLU182 4.5 23.2 1.0
CG C:ASP108 4.5 22.0 1.0
CG C:GLU155 4.6 22.6 1.0
CE C:LYS189 4.7 27.6 1.0
OH C:TYR89 4.7 20.4 1.0
C C:GLY92 4.8 20.2 1.0
C2 C:SIN473 4.8 39.3 1.0
OE2 C:GLU155 4.8 25.2 1.0
O1 C:SIN473 5.0 42.5 1.0
CZ C:ARG228 5.0 22.8 1.0

Magnesium binding site 4 out of 4 in 1f8i

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Magnesium binding site 4 out of 4 in the Crystal Structure of Isocitrate Lyase:Nitropropionate:Glyoxylate Complex 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 Isocitrate Lyase:Nitropropionate:Glyoxylate Complex From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg454

b:25.6
occ:1.00
 OD2 D:ASP153 2.0 18.1 1.0
O D:HOH1012 2.0 18.0 1.0
O D:HOH1010 2.0 21.6 1.0
O D:HOH1011 2.1 26.5 1.0
O1 D:GLV464 2.1 41.0 1.0
O2 D:GLV464 2.2 39.0 1.0
C1 D:GLV464 2.8 39.0 1.0
C2 D:GLV464 2.8 38.4 1.0
CG D:ASP153 3.1 18.8 1.0
OD1 D:ASP153 3.5 20.1 1.0
OD2 D:ASP108 3.8 24.2 1.0
O2 D:SIN474 4.1 43.2 1.0
O3 D:GLV464 4.1 35.5 1.0
NZ D:LYS189 4.1 27.3 1.0
N D:GLY92 4.2 20.6 1.0
N D:TRP93 4.2 20.3 1.0
NH1 D:ARG228 4.2 26.6 1.0
OD1 D:ASP108 4.3 27.2 1.0
CG D:GLU155 4.3 26.6 1.0
CB D:ASP153 4.3 18.9 1.0
CA D:GLY92 4.4 20.2 1.0
CG D:ASP108 4.5 25.6 1.0
OE1 D:GLU182 4.5 21.8 1.0
NE2 D:HIS180 4.5 15.4 1.0
CE D:LYS189 4.6 28.7 1.0
OE2 D:GLU155 4.6 28.4 1.0
C1 D:SIN474 4.6 42.9 1.0
C D:GLY92 4.6 21.9 1.0
C2 D:SIN474 4.7 41.1 1.0
CD D:GLU155 4.8 28.1 1.0
OH D:TYR89 4.9 23.1 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 20:55:03 2025

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