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Zinc in PDB 6fv4: The Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase D267A Mutant From Mycobacterium Smegmatis in Complex with N-Acetyl-D- Glucosamine-6-Phosphate

Enzymatic activity of The Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase D267A Mutant From Mycobacterium Smegmatis in Complex with N-Acetyl-D- Glucosamine-6-Phosphate

All present enzymatic activity of The Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase D267A Mutant From Mycobacterium Smegmatis in Complex with N-Acetyl-D- Glucosamine-6-Phosphate:
3.5.1.25;

Protein crystallography data

The structure of The Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase D267A Mutant From Mycobacterium Smegmatis in Complex with N-Acetyl-D- Glucosamine-6-Phosphate, PDB code: 6fv4 was solved by M.S.Ahangar, C.M.Furze, C.S.Guy, C.Cooper, K.S.Maskew, B.Graham, A.D.Cameron, E.Fullam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.56 / 1.97
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 164.766, 54.437, 110.262, 90.00, 123.22, 90.00
R / Rfree (%) 18.4 / 23.5

Other elements in 6fv4:

The structure of The Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase D267A Mutant From Mycobacterium Smegmatis in Complex with N-Acetyl-D- Glucosamine-6-Phosphate also contains other interesting chemical elements:

Cadmium (Cd) 4 atoms
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the The Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase D267A Mutant From Mycobacterium Smegmatis in Complex with N-Acetyl-D- Glucosamine-6-Phosphate (pdb code 6fv4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase D267A Mutant From Mycobacterium Smegmatis in Complex with N-Acetyl-D- Glucosamine-6-Phosphate, PDB code: 6fv4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6fv4

Go back to Zinc Binding Sites List in 6fv4
Zinc binding site 1 out of 2 in the The Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase D267A Mutant From Mycobacterium Smegmatis in Complex with N-Acetyl-D- Glucosamine-6-Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase D267A Mutant From Mycobacterium Smegmatis in Complex with N-Acetyl-D- Glucosamine-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:42.4
occ:1.00
 NE2 A:HIS58 2.1 41.4 1.0
OE1 A:GLU122 2.1 39.0 1.0
NE2 A:HIS56 2.1 33.4 1.0
CL A:CL405 2.2 44.7 1.0
CE1 A:HIS58 2.8 36.5 1.0
CE1 A:HIS56 3.0 32.4 1.0
CD A:GLU122 3.0 38.4 1.0
CD2 A:HIS56 3.2 30.8 1.0
CD2 A:HIS58 3.3 34.3 1.0
OE2 A:GLU122 3.4 38.2 1.0
CD A:CD403 3.4 35.5 1.0
C8 A:16G402 3.9 46.3 0.8
ND1 A:HIS58 4.0 36.5 1.0
ND1 A:HIS56 4.2 31.0 1.0
CG A:HIS58 4.3 33.2 1.0
CG A:HIS56 4.3 30.3 1.0
CG A:GLU122 4.4 30.6 1.0
C7 A:16G402 4.4 48.8 0.8
CB A:ALA267 4.4 32.6 1.0
CB A:GLU122 4.6 32.6 1.0
CD2 A:HIS209 4.7 30.7 1.0
N2 A:16G402 4.7 48.5 0.8
NE2 A:HIS209 4.7 33.2 1.0
CB A:SER91 4.8 30.7 1.0
O7 A:16G402 4.9 53.1 0.8
CA A:ALA267 5.0 29.0 1.0

Zinc binding site 2 out of 2 in 6fv4

Go back to Zinc Binding Sites List in 6fv4
Zinc binding site 2 out of 2 in the The Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase D267A Mutant From Mycobacterium Smegmatis in Complex with N-Acetyl-D- Glucosamine-6-Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase D267A Mutant From Mycobacterium Smegmatis in Complex with N-Acetyl-D- Glucosamine-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:27.0
occ:1.00
 OE1 B:GLU122 2.1 32.7 1.0
NE2 B:HIS58 2.1 30.8 1.0
NE2 B:HIS56 2.1 24.1 1.0
CL B:CL404 2.2 30.5 1.0
CD B:GLU122 3.0 30.7 1.0
CE1 B:HIS58 3.0 28.1 1.0
CE1 B:HIS56 3.1 24.4 1.0
CD2 B:HIS58 3.1 26.7 1.0
CD2 B:HIS56 3.1 26.0 1.0
OE2 B:GLU122 3.3 33.1 1.0
CD B:CD403 3.6 27.8 1.0
NE2 B:HIS134 3.7 29.8 1.0
CE1 B:HIS134 4.0 36.6 1.0
ND1 B:HIS58 4.2 29.1 1.0
ND1 B:HIS56 4.2 25.3 1.0
CG B:HIS58 4.2 28.9 1.0
CG B:HIS56 4.3 26.5 1.0
CB B:ALA267 4.3 26.0 1.0
CG B:GLU122 4.3 27.1 1.0
CB B:GLU122 4.6 32.3 1.0
CD2 B:HIS209 4.7 29.1 1.0
CA B:ALA267 4.8 30.4 1.0
NE2 B:HIS209 4.8 26.4 1.0
CE B:MET269 4.9 29.6 0.4
CD2 B:HIS134 4.9 41.6 1.0
CB B:SER91 4.9 29.8 1.0

Reference:

M.S.Ahangar, C.M.Furze, C.S.Guy, C.Cooper, K.S.Maskew, B.Graham, A.D.Cameron, E.Fullam. Structural and Functional Determination of Homologs of Themycobacterium Tuberculosis N-Acetylglucosamine-6-Phosphate Deacetylase (Naga). J. Biol. Chem. V. 293 9770 2018.
ISSN: ESSN 1083-351X
PubMed: 29728457
DOI: 10.1074/JBC.RA118.002597
Page generated: Mon Oct 28 21:27:16 2024

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