Atomistry » Magnesium » PDB 6uy0-6vck » 6vb9
Atomistry »
  Magnesium »
    PDB 6uy0-6vck »
      6vb9 »

Magnesium in PDB 6vb9: Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis

Enzymatic activity of Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis

All present enzymatic activity of Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis:
4.1.3.1;

Protein crystallography data

The structure of Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis, PDB code: 6vb9 was solved by I.V.Krieger, T.V.Pham, T.D.Meek, J.C.Sacchettini, Tb Structural Genomicsconsortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.94 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.065, 129.065, 167.825, 90, 90, 90
R / Rfree (%) 17.9 / 22.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis (pdb code 6vb9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis, PDB code: 6vb9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 6vb9

Go back to Magnesium Binding Sites List in 6vb9
Magnesium binding site 1 out of 7 in the Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 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 Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:18.4
occ:1.00
 OD2 A:ASP153 2.0 16.6 1.0
O5 A:OXD503 2.0 17.9 0.5
O5 A:OXD503 2.0 17.9 0.5
O A:HOH643 2.0 19.3 1.0
O6 A:OXD503 2.1 20.4 0.5
O6 A:OXD503 2.1 20.4 0.5
O A:HOH606 2.2 18.1 1.0
O A:HOH622 2.2 14.6 1.0
C2 A:OXD503 2.9 18.9 0.5
C2 A:OXD503 2.9 18.9 0.5
C1 A:OXD503 3.0 20.3 0.5
C1 A:OXD503 3.0 20.3 0.5
CG A:ASP153 3.0 16.1 1.0
OD1 A:ASP153 3.4 18.4 1.0
OD2 A:ASP108 3.9 15.3 1.0
NZ A:LYS189 4.0 15.7 1.0
O3 A:OXD503 4.0 21.0 0.7
N A:TRP93 4.1 13.9 1.0
O4 A:OXD503 4.1 19.0 0.5
O4 A:OXD503 4.1 19.0 0.5
NH1 A:ARG228 4.1 21.4 1.0
O01 A:QVA191 4.2 19.3 1.0
OD1 A:ASP108 4.3 18.3 1.0
N A:GLY92 4.3 17.8 1.0
CB A:ASP153 4.3 18.0 1.0
CA A:GLY92 4.3 18.9 1.0
CE A:LYS189 4.4 19.8 1.0
CE1 A:HIS180 4.4 19.0 1.0
CG A:GLU155 4.4 22.8 1.0
OE1 A:GLU155 4.4 19.5 1.0
OE1 A:GLU182 4.5 18.2 1.0
CG A:ASP108 4.5 17.6 1.0
C A:GLY92 4.5 17.3 1.0
C02 A:QVA191 4.8 24.0 1.0
CD A:GLU155 4.8 16.4 1.0
OH A:TYR89 4.8 24.3 1.0

Magnesium binding site 2 out of 7 in 6vb9

Go back to Magnesium Binding Sites List in 6vb9
Magnesium binding site 2 out of 7 in the Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 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 Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:28.1
occ:1.00
 O A:ALA276 2.2 29.6 1.0
O A:HOH765 2.2 30.8 1.0
OE1 A:GLN308 2.3 27.8 1.0
O A:HOH818 2.5 34.8 1.0
O A:ALA279 2.5 25.9 1.0
O A:HOH827 2.7 25.5 1.0
CD A:GLN308 3.3 27.2 1.0
C A:ALA276 3.3 28.0 1.0
NE2 A:GLN308 3.7 26.7 1.0
C A:ALA279 3.7 28.4 1.0
CA A:ALA276 4.0 30.1 1.0
O A:HOH702 4.1 28.6 1.0
O A:ASP25 4.2 35.4 1.0
N A:ALA279 4.3 22.7 1.0
N A:PRO277 4.3 29.7 1.0
CB A:ALA276 4.4 28.3 1.0
CA A:PRO277 4.5 30.0 1.0
O A:HOH679 4.5 29.7 1.0
CA A:ALA279 4.6 26.9 1.0
CG A:GLN308 4.6 28.7 1.0
N A:ASP280 4.7 24.9 1.0
C A:PRO277 4.7 31.8 1.0
O A:HOH767 4.7 31.6 1.0
CA A:ASP280 4.7 21.7 1.0
N A:PHE278 4.9 30.7 1.0

Magnesium binding site 3 out of 7 in 6vb9

Go back to Magnesium Binding Sites List in 6vb9
Magnesium binding site 3 out of 7 in the Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 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 Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:19.5
occ:1.00
 O6 B:OXD503 2.0 22.4 1.0
OD2 B:ASP153 2.1 19.0 1.0
O B:HOH645 2.1 17.3 1.0
O B:HOH619 2.2 15.8 1.0
O5 B:OXD503 2.2 23.6 1.0
O B:HOH602 2.2 16.5 1.0
C1 B:OXD503 2.9 26.2 1.0
C2 B:OXD503 3.0 22.0 1.0
CG B:ASP153 3.1 17.3 1.0
OD1 B:ASP153 3.5 18.0 1.0
OD2 B:ASP108 3.9 18.4 1.0
O4 B:OXD503 4.0 24.9 0.6
NZ B:LYS189 4.0 18.5 1.0
N B:TRP93 4.0 16.6 1.0
O01 B:QVA191 4.1 22.8 1.0
O3 B:OXD503 4.2 23.1 1.0
N B:GLY92 4.2 17.4 1.0
NH1 B:ARG228 4.2 25.4 1.0
CA B:GLY92 4.2 20.8 1.0
OD1 B:ASP108 4.2 16.1 1.0
CG B:GLU155 4.3 21.6 1.0
CE B:LYS189 4.3 17.0 1.0
OE2 B:GLU155 4.3 20.4 1.0
CB B:ASP153 4.4 16.4 1.0
CG B:ASP108 4.5 17.1 1.0
C B:GLY92 4.5 18.5 1.0
CE1 B:HIS180 4.6 21.0 1.0
OE1 B:GLU182 4.6 24.4 1.0
CD B:GLU155 4.7 20.0 1.0
C02 B:QVA191 4.7 24.5 1.0
OH B:TYR89 4.9 23.5 1.0
CB B:TRP93 4.9 19.2 1.0
CA B:TRP93 5.0 18.6 1.0

Magnesium binding site 4 out of 7 in 6vb9

Go back to Magnesium Binding Sites List in 6vb9
Magnesium binding site 4 out of 7 in the Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 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 Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:21.5
occ:1.00
 OD2 C:ASP153 2.0 21.2 1.0
O C:HOH628 2.0 17.4 1.0
O5 C:OXD504 2.1 23.2 0.5
O5 C:OXD504 2.1 23.2 0.5
O C:HOH640 2.1 18.0 1.0
O C:HOH614 2.2 16.9 1.0
O4 C:OXD504 2.2 21.4 0.5
O4 C:OXD504 2.2 21.4 0.5
C1 C:OXD504 2.8 22.6 0.5
C1 C:OXD504 2.8 22.6 0.5
C2 C:OXD504 2.8 24.1 0.5
C2 C:OXD504 2.8 24.2 0.5
CG C:ASP153 3.1 20.8 1.0
OD1 C:ASP153 3.4 18.5 1.0
NZ C:LYS189 3.9 18.2 1.0
OD2 C:ASP108 3.9 21.1 1.0
N C:TRP93 4.0 18.0 1.0
O6 C:OXD504 4.0 23.7 0.5
O6 C:OXD504 4.0 23.8 0.5
O3 C:OXD504 4.1 23.4 0.5
N C:GLY92 4.1 18.1 1.0
OD1 C:ASP108 4.2 18.2 1.0
CE C:LYS189 4.2 17.6 1.0
CA C:GLY92 4.2 15.7 1.0
CG C:GLU155 4.2 19.9 1.0
O03 C:QVA191 4.3 22.1 1.0
OE2 C:GLU155 4.3 20.2 1.0
CB C:ASP153 4.3 19.5 1.0
NH1 C:ARG228 4.4 24.0 1.0
C C:GLY92 4.5 20.8 1.0
CG C:ASP108 4.5 20.5 1.0
CE1 C:HIS180 4.5 18.0 1.0
OE1 C:GLU182 4.6 16.1 1.0
CD C:GLU155 4.6 19.8 1.0
OH C:TYR89 4.9 23.9 1.0
C02 C:QVA191 4.9 26.2 1.0
CA C:TRP93 4.9 19.1 1.0
CB C:TRP93 5.0 22.8 1.0

Magnesium binding site 5 out of 7 in 6vb9

Go back to Magnesium Binding Sites List in 6vb9
Magnesium binding site 5 out of 7 in the Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:29.3
occ:1.00
 O C:ALA276 2.3 26.6 1.0
O C:ALA279 2.4 22.9 1.0
O C:HOH636 2.4 27.6 1.0
OE1 C:GLN308 2.4 25.0 1.0
O C:HOH814 2.6 26.9 1.0
O C:HOH800 2.6 26.1 1.0
CD C:GLN308 3.4 27.6 1.0
C C:ALA276 3.4 21.5 1.0
C C:ALA279 3.5 26.5 1.0
NE2 C:GLN308 3.7 26.4 1.0
O C:HOH778 3.9 26.9 1.0
CA C:ALA276 4.1 23.0 1.0
N C:ALA279 4.2 26.1 1.0
O C:ASP25 4.2 28.5 1.0
CA C:ALA279 4.4 24.2 1.0
N C:PRO277 4.4 20.7 1.0
N C:ASP280 4.5 18.8 1.0
O C:HOH716 4.5 34.4 1.0
O C:HOH764 4.5 37.8 1.0
CB C:ALA276 4.5 26.2 1.0
CA C:PRO277 4.5 24.9 1.0
O C:HOH766 4.6 27.3 1.0
CA C:ASP280 4.6 25.3 1.0
C C:PRO277 4.6 26.4 1.0
CG C:GLN308 4.8 30.0 1.0
C C:ASP280 4.9 28.2 1.0
O C:ASP280 4.9 26.7 1.0
N C:PHE278 4.9 21.2 1.0
CB C:ALA279 4.9 26.3 1.0
O C:PRO277 4.9 24.6 1.0

Magnesium binding site 6 out of 7 in 6vb9

Go back to Magnesium Binding Sites List in 6vb9
Magnesium binding site 6 out of 7 in the Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:30.8
occ:1.00
 O D:HOH730 2.3 24.7 1.0
O D:ALA276 2.4 24.2 1.0
OE1 D:GLN308 2.4 26.2 1.0
O D:HOH738 2.4 26.7 1.0
O D:ALA279 2.5 25.0 1.0
O D:HOH796 2.5 28.1 1.0
CD D:GLN308 3.3 28.9 1.0
C D:ALA276 3.5 22.0 1.0
NE2 D:GLN308 3.6 24.7 1.0
C D:ALA279 3.6 29.4 1.0
O D:HOH696 4.1 26.9 1.0
O D:ASP25 4.1 33.1 1.0
CA D:ALA276 4.2 26.4 1.0
N D:ALA279 4.2 26.0 1.0
O D:HOH646 4.3 33.5 1.0
N D:PRO277 4.4 25.2 1.0
CA D:ALA279 4.5 27.8 1.0
CA D:PRO277 4.5 24.7 1.0
CB D:ALA276 4.6 28.7 1.0
O D:HOH720 4.6 27.1 1.0
N D:ASP280 4.6 25.2 1.0
C D:PRO277 4.7 26.4 1.0
CA D:ASP280 4.7 24.4 1.0
CG D:GLN308 4.7 27.2 1.0
CB D:ALA279 4.9 29.4 1.0
N D:PHE278 4.9 23.0 1.0
C D:ASP280 5.0 23.8 1.0

Magnesium binding site 7 out of 7 in 6vb9

Go back to Magnesium Binding Sites List in 6vb9
Magnesium binding site 7 out of 7 in the Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:24.7
occ:1.00
 OD2 D:ASP153 2.0 24.5 1.0
O4 D:OXD503 2.0 23.5 0.5
O4 D:OXD503 2.0 23.5 0.5
O D:HOH605 2.1 18.2 1.0
O D:HOH620 2.1 20.9 1.0
O5 D:OXD503 2.1 23.8 0.5
O5 D:OXD503 2.1 23.8 0.5
O D:HOH633 2.3 27.2 1.0
C2 D:OXD503 2.8 23.1 0.5
C2 D:OXD503 2.8 23.1 0.5
C1 D:OXD503 3.0 23.5 0.5
C1 D:OXD503 3.0 23.5 0.5
CG D:ASP153 3.1 21.6 1.0
OD1 D:ASP153 3.6 19.5 1.0
O3 D:OXD503 3.8 25.0 0.5
N D:TRP93 3.8 19.9 1.0
OD2 D:ASP108 3.9 21.9 1.0
N D:GLY92 4.0 19.3 1.0
O6 D:OXD503 4.0 23.2 0.5
O6 D:OXD503 4.0 23.2 0.5
NZ D:LYS189 4.1 20.2 1.0
CA D:GLY92 4.1 18.9 1.0
OD1 D:ASP108 4.1 22.5 1.0
CG D:GLU155 4.2 23.0 1.0
CB D:ASP153 4.3 17.1 1.0
C D:GLY92 4.3 22.8 1.0
NH1 D:ARG228 4.3 25.4 1.0
O01 D:QVA191 4.3 26.0 1.0
OE2 D:GLU155 4.3 23.4 1.0
CE D:LYS189 4.4 22.7 1.0
CG D:ASP108 4.5 25.8 1.0
CE1 D:HIS180 4.6 19.9 1.0
CD D:GLU155 4.6 19.2 1.0
CA D:TRP93 4.8 18.9 1.0
CB D:TRP93 4.8 21.3 1.0
OE1 D:GLU182 4.8 23.9 1.0
OH D:TYR89 4.9 23.9 1.0

Reference:

T.V.Pham, K.Chen, I.K.Krieger, J.C.Sacchettini, T.Emde, T.D.Meek. Covalent Inactivation of Mycobacterium Tuberculosis Isocitrate Lyase By Cis-2,3-Epoxy-Succinate To Be Published.
Page generated: Tue Oct 1 21:27:08 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