Atomistry » Magnesium » PDB 1f7d-1fnt » 1f8i
Atomistry »
  Magnesium »
    PDB 1f7d-1fnt »
      1f8i »

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

Go back to Magnesium Binding Sites List in 1f8i
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

Go back to Magnesium Binding Sites List in 1f8i
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

Go back to Magnesium Binding Sites List in 1f8i
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

Go back to Magnesium Binding Sites List in 1f8i
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: Tue Aug 13 03:11:40 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy