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Cadmium 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:

Zinc (Zn) 2 atoms
Chlorine (Cl) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium 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 Cadmium atom.
In total 4 binding sites of Cadmium 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 Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 6fv4

Go back to Cadmium Binding Sites List in 6fv4
Cadmium binding site 1 out of 4 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 Cadmium with other atoms in the Cd 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:Cd403

b:35.5
occ:1.00
 NE2 A:HIS188 2.4 27.9 1.0
OE2 A:GLU122 2.5 38.2 1.0
NE2 A:HIS209 2.5 33.2 1.0
O7 A:16G402 2.7 53.1 0.8
CL A:CL405 2.7 44.7 1.0
C7 A:16G402 2.8 48.8 0.8
OE1 A:GLU122 2.9 39.0 1.0
CD A:GLU122 2.9 38.4 1.0
N2 A:16G402 3.1 48.5 0.8
CE1 A:HIS188 3.2 34.6 1.0
C2 A:16G402 3.4 43.3 0.8
ZN A:ZN401 3.4 42.4 1.0
CE1 A:HIS209 3.4 32.3 1.0
CD2 A:HIS209 3.5 30.7 1.0
CD2 A:HIS188 3.5 26.8 1.0
C8 A:16G402 3.6 46.3 0.8
NE2 A:HIS134 4.1 47.0 1.0
CG A:GLU122 4.2 30.6 1.0
C1 A:16G402 4.2 43.2 0.8
ND1 A:HIS188 4.4 33.0 1.0
CE1 A:HIS56 4.5 32.4 1.0
CG A:HIS188 4.5 29.6 1.0
O3 A:16G402 4.6 49.7 0.8
ND1 A:HIS209 4.6 31.1 1.0
CG A:HIS209 4.6 27.1 1.0
NE2 A:HIS56 4.6 33.4 1.0
C3 A:16G402 4.6 47.8 0.8
CD2 A:HIS134 4.8 48.0 1.0

Cadmium binding site 2 out of 4 in 6fv4

Go back to Cadmium Binding Sites List in 6fv4
Cadmium binding site 2 out of 4 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 Cadmium with other atoms in the Cd 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
A:Cd404

b:68.2
occ:1.00
 OE2 A:GLU260 2.7 59.5 1.0
OE1 A:GLU260 2.9 60.2 1.0
CD A:GLU260 3.1 49.3 1.0
CG A:GLU260 4.6 42.3 1.0
O A:HOH559 4.9 47.2 1.0

Cadmium binding site 3 out of 4 in 6fv4

Go back to Cadmium Binding Sites List in 6fv4
Cadmium binding site 3 out of 4 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 Cadmium with other atoms in the Cd binding site number 3 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:Cd402

b:74.9
occ:1.00
 OE2 B:GLU21 2.5 51.5 1.0
O B:HOH584 2.6 53.8 1.0
OE1 B:GLU21 2.8 41.9 1.0
CD B:GLU21 2.8 45.2 1.0
ND1 B:HIS0 3.2 51.5 1.0
CE1 B:HIS0 4.0 48.9 1.0
CG B:GLU21 4.1 44.5 1.0
CG B:HIS0 4.2 49.5 1.0
CB B:HIS0 4.4 51.7 1.0

Cadmium binding site 4 out of 4 in 6fv4

Go back to Cadmium Binding Sites List in 6fv4
Cadmium binding site 4 out of 4 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 Cadmium with other atoms in the Cd binding site number 4 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:Cd403

b:27.8
occ:1.00
 NE2 B:HIS188 2.3 22.8 1.0
OE2 B:GLU122 2.4 33.1 1.0
NE2 B:HIS209 2.5 26.4 1.0
NE2 B:HIS134 2.5 29.8 1.0
O B:HOH579 2.6 31.3 1.0
CL B:CL404 2.6 30.5 1.0
CE1 B:HIS134 3.1 36.6 1.0
CD B:GLU122 3.1 30.7 1.0
CE1 B:HIS188 3.1 27.9 1.0
OE1 B:GLU122 3.3 32.7 1.0
CD2 B:HIS209 3.3 29.1 1.0
CE1 B:HIS209 3.5 27.9 1.0
CD2 B:HIS188 3.5 21.8 1.0
ZN B:ZN401 3.6 27.0 1.0
CD2 B:HIS134 3.7 41.6 1.0
O B:GLY132 4.1 44.0 1.0
ND1 B:HIS134 4.2 41.4 1.0
CG B:GLU122 4.3 27.1 1.0
ND1 B:HIS188 4.3 23.6 1.0
CG B:HIS188 4.5 23.0 1.0
CG B:HIS209 4.5 25.4 1.0
CG B:HIS134 4.6 42.7 1.0
ND1 B:HIS209 4.6 25.6 1.0
CE1 B:HIS56 4.7 24.4 1.0
NE2 B:HIS56 4.7 24.1 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: Fri Jul 19 19:17:24 2024

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