Atomistry » Cadmium » PDB 6fv4-6ozy » 6fv4
Atomistry »
  Cadmium »
    PDB 6fv4-6ozy »
      6fv4 »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy