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Magnesium in PDB 5dql: Crystal Structure of 2-Vinyl Glyoxylate Modified Isocitrate Lyase From Mycobacterium Tuberculosis

Enzymatic activity of Crystal Structure of 2-Vinyl Glyoxylate Modified Isocitrate Lyase From Mycobacterium Tuberculosis

All present enzymatic activity of Crystal Structure of 2-Vinyl Glyoxylate Modified Isocitrate Lyase From Mycobacterium Tuberculosis:
4.1.3.1; 4.1.3.30;

Protein crystallography data

The structure of Crystal Structure of 2-Vinyl Glyoxylate Modified Isocitrate Lyase From Mycobacterium Tuberculosis, PDB code: 5dql was solved by H.-L.Huang, T.D.Meek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.27 / 1.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.086, 129.236, 167.952, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 24.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of 2-Vinyl Glyoxylate Modified Isocitrate Lyase From Mycobacterium Tuberculosis (pdb code 5dql). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of 2-Vinyl Glyoxylate Modified Isocitrate Lyase From Mycobacterium Tuberculosis, PDB code: 5dql:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5dql

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Magnesium binding site 1 out of 5 in the Crystal Structure of 2-Vinyl Glyoxylate Modified Isocitrate Lyase 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 2-Vinyl Glyoxylate Modified Isocitrate Lyase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:40.3
occ:1.00
 OD2 A:ASP153 2.1 25.0 1.0
O A:HOH647 2.3 25.6 1.0
O A:HOH787 2.5 36.0 1.0
O A:HOH604 2.5 29.9 1.0
O A:HOH879 2.6 36.5 1.0
CG A:ASP153 3.1 22.2 1.0
O A:HOH685 3.2 30.6 1.0
OD1 A:ASP153 3.5 20.2 1.0
OD2 A:ASP108 3.7 25.8 1.0
NH1 A:ARG228 4.0 34.9 1.0
N A:TRP93 4.1 20.2 1.0
NZ A:LYS189 4.1 30.9 1.0
N A:GLY92 4.2 21.0 1.0
OD1 A:ASP108 4.3 23.2 1.0
CA A:GLY92 4.4 22.4 1.0
CB A:ASP153 4.4 20.3 1.0
CG A:ASP108 4.5 24.8 1.0
C02 A:VGX503 4.5 27.6 0.7
OE2 A:GLU155 4.5 35.2 1.0
CE1 A:HIS180 4.5 25.1 1.0
CE A:LYS189 4.6 28.6 1.0
C A:GLY92 4.6 21.6 1.0
O A:HOH603 4.6 42.2 1.0
OE1 A:GLU182 4.7 29.8 1.0
OH A:TYR89 4.7 26.9 1.0
C01 A:VGX503 4.8 26.5 1.0
CB A:TRP93 4.9 19.6 1.0

Magnesium binding site 2 out of 5 in 5dql

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Magnesium binding site 2 out of 5 in the Crystal Structure of 2-Vinyl Glyoxylate Modified Isocitrate Lyase 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 2-Vinyl Glyoxylate Modified Isocitrate Lyase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:37.5
occ:1.00
 NE2 A:GLN308 2.0 33.3 1.0
O A:ALA276 2.2 39.5 1.0
O A:HOH669 2.4 38.8 1.0
O A:HOH869 2.4 41.0 1.0
O A:ALA279 2.4 37.7 1.0
O A:HOH666 2.5 44.3 1.0
CD A:GLN308 3.1 37.3 1.0
C A:ALA276 3.2 36.2 1.0
OE1 A:GLN308 3.6 34.5 1.0
C A:ALA279 3.6 35.1 1.0
CA A:ALA276 4.0 35.5 1.0
O A:ASP25 4.1 43.9 1.0
O A:HOH777 4.1 33.0 1.0
N A:ALA279 4.2 36.7 1.0
O A:HOH633 4.2 40.9 1.0
N A:PRO277 4.3 35.0 1.0
CG A:GLN308 4.4 36.6 1.0
CA A:ALA279 4.4 33.2 1.0
CA A:PRO277 4.4 40.0 1.0
CB A:ALA276 4.4 37.4 1.0
C A:PRO277 4.6 35.4 1.0
N A:ASP280 4.6 34.9 1.0
CA A:ASP280 4.8 33.0 1.0
CB A:GLN308 4.8 39.6 1.0
N A:PHE278 4.8 36.8 1.0
CB A:ASP25 4.8 47.6 1.0
CB A:ALA279 4.9 32.9 1.0
O A:HOH665 4.9 37.1 1.0
O A:HOH614 4.9 42.6 1.0
O A:PRO277 5.0 40.5 1.0

Magnesium binding site 3 out of 5 in 5dql

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Magnesium binding site 3 out of 5 in the Crystal Structure of 2-Vinyl Glyoxylate Modified Isocitrate Lyase 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 2-Vinyl Glyoxylate Modified Isocitrate Lyase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:35.9
occ:1.00
 OD2 B:ASP153 2.1 24.3 1.0
O B:HOH855 2.3 32.7 1.0
O B:HOH637 2.4 30.3 1.0
O B:HOH694 2.4 31.2 1.0
O B:HOH674 2.6 27.3 1.0
O B:HOH699 2.7 31.4 1.0
CG B:ASP153 3.3 19.4 1.0
OD2 B:ASP108 3.6 24.6 1.0
N B:TRP93 3.7 16.9 1.0
OD1 B:ASP153 3.9 22.9 1.0
N B:GLY92 3.9 19.5 1.0
C02 B:VGX502 4.0 25.5 0.4
CA B:GLY92 4.1 20.1 1.0
OD1 B:ASP108 4.3 23.1 1.0
C B:GLY92 4.3 19.7 1.0
CG B:ASP108 4.4 23.2 1.0
NH1 B:ARG228 4.4 31.1 1.0
OH B:TYR89 4.4 27.0 1.0
CB B:TRP93 4.5 17.3 1.0
CB B:ASP153 4.5 21.3 1.0
C01 B:VGX502 4.5 24.7 1.0
NZ B:LYS189 4.6 31.0 1.0
CA B:TRP93 4.6 19.5 1.0
CE1 B:HIS180 4.7 22.2 1.0
O B:HOH641 4.7 36.8 1.0
OG B:SER91 4.8 21.2 1.0
OE2 B:GLU155 4.8 29.6 1.0
CE B:LYS189 4.9 28.9 1.0

Magnesium binding site 4 out of 5 in 5dql

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Magnesium binding site 4 out of 5 in the Crystal Structure of 2-Vinyl Glyoxylate Modified Isocitrate Lyase 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 2-Vinyl Glyoxylate Modified Isocitrate Lyase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:43.1
occ:1.00
 OD2 C:ASP153 2.1 26.3 1.0
O C:HOH616 2.1 29.2 1.0
O C:HOH766 2.2 36.6 1.0
O C:HOH821 2.4 34.0 1.0
O C:HOH698 2.4 28.2 1.0
O C:HOH696 3.0 33.0 1.0
CG C:ASP153 3.2 22.9 1.0
OD2 C:ASP108 3.5 31.1 1.0
OD1 C:ASP153 3.6 23.3 1.0
N C:TRP93 3.8 20.4 1.0
N C:GLY92 4.0 19.1 1.0
OD1 C:ASP108 4.0 31.4 1.0
NZ C:LYS189 4.1 35.4 1.0
CG C:ASP108 4.2 31.4 1.0
CA C:GLY92 4.2 22.5 1.0
NH1 C:ARG228 4.3 32.6 1.0
C C:GLY92 4.4 22.6 1.0
C02 C:VGX502 4.4 31.5 1.0
CB C:ASP153 4.4 23.7 1.0
CE C:LYS189 4.5 33.6 1.0
O C:HOH605 4.5 38.6 1.0
CB C:TRP93 4.6 24.5 1.0
OE2 C:GLU155 4.6 31.6 1.0
CA C:TRP93 4.7 22.4 1.0
CE1 C:HIS180 4.7 21.5 1.0
OH C:TYR89 4.8 27.1 1.0
OE1 C:GLU182 4.9 27.1 1.0

Magnesium binding site 5 out of 5 in 5dql

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Magnesium binding site 5 out of 5 in the Crystal Structure of 2-Vinyl Glyoxylate Modified Isocitrate Lyase 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 Crystal Structure of 2-Vinyl Glyoxylate Modified Isocitrate Lyase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:45.6
occ:1.00
 OD2 D:ASP153 2.3 27.7 1.0
O D:HOH724 2.3 41.2 1.0
O D:HOH818 2.3 41.4 1.0
O D:HOH602 2.5 32.8 1.0
O D:HOH666 2.8 37.0 1.0
O D:HOH659 2.8 37.2 1.0
OD2 D:ASP108 3.3 33.6 1.0
CG D:ASP153 3.5 28.5 1.0
N D:TRP93 3.5 23.1 1.0
N D:GLY92 3.9 23.1 1.0
OD1 D:ASP153 4.0 26.7 1.0
CA D:GLY92 4.1 26.9 1.0
CG D:ASP108 4.1 35.4 1.0
C D:GLY92 4.2 26.9 1.0
OD1 D:ASP108 4.2 27.6 1.0
CB D:TRP93 4.2 29.0 1.0
CA D:TRP93 4.3 24.2 1.0
OE2 D:GLU155 4.5 32.1 1.0
NZ D:LYS189 4.5 34.6 1.0
NH1 D:ARG228 4.6 39.9 1.0
CB D:ASP153 4.6 24.4 1.0
OG D:SER91 4.7 23.5 1.0
C02 D:VGX502 4.7 35.1 1.0
OH D:TYR89 4.7 25.6 1.0
O D:HOH665 4.7 47.1 1.0
CE D:LYS189 4.9 33.1 1.0
C D:SER91 5.0 26.1 1.0

Reference:

T.V.Pham, A.S.Murkin, M.M.Moynihan, L.Harris, P.C.Tyler, N.Shetty, J.C.Sacchettini, H.L.Huang, T.D.Meek. Mechanism-Based Inactivator of Isocitrate Lyases 1 and 2 From Mycobacterium Tuberculosis. Proc. Natl. Acad. Sci. V. 114 7617 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28679637
DOI: 10.1073/PNAS.1706134114
Page generated: Sun Sep 29 02:57:26 2024

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