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Magnesium in PDB 3st8: Crystal Structure of Glmu From Mycobacterium Tuberculosis in Complex with Coenzyme A, Glucosamine 1-Phosphate and Uridine-Diphosphate-N- Acetylglucosamine

Enzymatic activity of Crystal Structure of Glmu From Mycobacterium Tuberculosis in Complex with Coenzyme A, Glucosamine 1-Phosphate and Uridine-Diphosphate-N- Acetylglucosamine

All present enzymatic activity of Crystal Structure of Glmu From Mycobacterium Tuberculosis in Complex with Coenzyme A, Glucosamine 1-Phosphate and Uridine-Diphosphate-N- Acetylglucosamine:
2.3.1.157; 2.7.7.23;

Protein crystallography data

The structure of Crystal Structure of Glmu From Mycobacterium Tuberculosis in Complex with Coenzyme A, Glucosamine 1-Phosphate and Uridine-Diphosphate-N- Acetylglucosamine, PDB code: 3st8 was solved by P.A.Jagtap, B.Prakash, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.71 / 1.98
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 110.312, 110.312, 360.537, 90.00, 90.00, 120.00
R / Rfree (%) 16.7 / 20.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Glmu From Mycobacterium Tuberculosis in Complex with Coenzyme A, Glucosamine 1-Phosphate and Uridine-Diphosphate-N- Acetylglucosamine (pdb code 3st8). 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 Glmu From Mycobacterium Tuberculosis in Complex with Coenzyme A, Glucosamine 1-Phosphate and Uridine-Diphosphate-N- Acetylglucosamine, PDB code: 3st8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3st8

Go back to Magnesium Binding Sites List in 3st8
Magnesium binding site 1 out of 4 in the Crystal Structure of Glmu From Mycobacterium Tuberculosis in Complex with Coenzyme A, Glucosamine 1-Phosphate and Uridine-Diphosphate-N- Acetylglucosamine


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 Glmu From Mycobacterium Tuberculosis in Complex with Coenzyme A, Glucosamine 1-Phosphate and Uridine-Diphosphate-N- Acetylglucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg496

b:25.9
occ:1.00
 O2A A:UD1502 2.0 19.3 1.0
O A:HOH946 2.1 25.4 1.0
OD2 A:ASP114 2.1 24.9 1.0
O1B A:UD1502 2.2 23.2 1.0
O A:HOH945 2.2 24.2 1.0
OD1 A:ASN239 2.3 24.1 1.0
CG A:ASP114 3.1 28.2 1.0
CG A:ASN239 3.2 24.7 1.0
PA A:UD1502 3.4 22.6 1.0
OD1 A:ASP114 3.4 29.4 1.0
PB A:UD1502 3.5 26.5 1.0
ND2 A:ASN239 3.6 25.8 1.0
O3A A:UD1502 3.7 23.5 1.0
NZ A:LYS26 3.7 28.0 1.0
O6' A:UD1502 4.0 28.0 1.0
O5B A:UD1502 4.3 19.5 1.0
C5B A:UD1502 4.3 17.0 1.0
CB A:ASP114 4.4 23.3 1.0
O5' A:UD1502 4.4 25.8 1.0
O2B A:UD1502 4.5 26.3 1.0
O A:VAL238 4.5 24.2 1.0
O1A A:UD1502 4.5 21.2 1.0
O1' A:UD1502 4.5 24.6 1.0
CB A:ASN239 4.6 21.7 1.0
O3B A:UD1502 4.6 21.2 1.0
C3B A:UD1502 4.7 22.3 1.0
C A:VAL238 4.8 25.7 1.0
C1' A:UD1502 4.8 20.7 1.0
CE A:LYS26 4.8 30.8 1.0
C4B A:UD1502 4.9 23.0 1.0
N A:ASN239 4.9 24.5 1.0
CA A:ASN239 4.9 20.3 1.0

Magnesium binding site 2 out of 4 in 3st8

Go back to Magnesium Binding Sites List in 3st8
Magnesium binding site 2 out of 4 in the Crystal Structure of Glmu From Mycobacterium Tuberculosis in Complex with Coenzyme A, Glucosamine 1-Phosphate and Uridine-Diphosphate-N- Acetylglucosamine


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 Glmu From Mycobacterium Tuberculosis in Complex with Coenzyme A, Glucosamine 1-Phosphate and Uridine-Diphosphate-N- Acetylglucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg497

b:16.9
occ:0.33
 OD2 A:ASP417 2.1 17.1 1.0
O A:HOH1031 2.7 23.0 0.3
CG A:ASP417 3.0 17.0 1.0
OD1 A:ASP417 3.1 16.0 1.0
O A:HOH537 3.3 24.0 1.0
MG A:MG501 3.8 19.9 0.3
CB A:ASP417 4.4 15.8 1.0
O A:ASP417 4.7 16.0 1.0
CA A:GLY435 4.8 16.4 1.0

Magnesium binding site 3 out of 4 in 3st8

Go back to Magnesium Binding Sites List in 3st8
Magnesium binding site 3 out of 4 in the Crystal Structure of Glmu From Mycobacterium Tuberculosis in Complex with Coenzyme A, Glucosamine 1-Phosphate and Uridine-Diphosphate-N- Acetylglucosamine


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 Glmu From Mycobacterium Tuberculosis in Complex with Coenzyme A, Glucosamine 1-Phosphate and Uridine-Diphosphate-N- Acetylglucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg500

b:21.4
occ:0.33
 O A:HOH597 3.3 20.3 1.0
CA A:ALA451 3.7 19.4 1.0
N A:GLY452 4.2 21.6 1.0
CB A:ALA451 4.2 19.9 1.0
O A:HOH1031 4.3 23.0 0.3
C A:ALA451 4.5 22.6 1.0
O A:SER450 4.6 20.9 1.0
N A:ALA451 4.7 19.5 1.0
C A:SER450 5.0 19.8 1.0

Magnesium binding site 4 out of 4 in 3st8

Go back to Magnesium Binding Sites List in 3st8
Magnesium binding site 4 out of 4 in the Crystal Structure of Glmu From Mycobacterium Tuberculosis in Complex with Coenzyme A, Glucosamine 1-Phosphate and Uridine-Diphosphate-N- Acetylglucosamine


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 Glmu From Mycobacterium Tuberculosis in Complex with Coenzyme A, Glucosamine 1-Phosphate and Uridine-Diphosphate-N- Acetylglucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:19.9
occ:0.33
 O A:HOH507 2.1 14.8 1.0
OD1 A:ASP417 2.2 16.0 1.0
CG A:ASP417 3.1 17.0 1.0
OD2 A:ASP417 3.7 17.1 1.0
MG A:MG497 3.8 16.9 0.3
OG A:SER392 4.1 17.4 1.0
CB A:ASP417 4.2 15.8 1.0
O A:SER392 4.3 14.1 1.0
CE A:MET419 4.6 14.2 1.0
CA A:ASP417 4.7 15.2 1.0
CB A:SER392 4.9 15.0 1.0

Reference:

P.A.Jagtap, B.Prakash. Structure of Mycobacterium Tuberculosis Glmu in Complex with Acetyl Coa To Be Published.
Page generated: Mon Dec 14 08:51:57 2020

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