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Zinc in PDB 6fv3: Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase From Mycobacterium Smegmatis.

Enzymatic activity of Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase From Mycobacterium Smegmatis.

All present enzymatic activity of Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase From Mycobacterium Smegmatis.:
3.5.1.25;

Protein crystallography data

The structure of Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase From Mycobacterium Smegmatis., PDB code: 6fv3 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) 51.95 / 2.58
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 60.450, 86.390, 89.930, 88.12, 75.58, 69.79
R / Rfree (%) 24.7 / 29.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase From Mycobacterium Smegmatis. (pdb code 6fv3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase From Mycobacterium Smegmatis., PDB code: 6fv3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6fv3

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Zinc binding site 1 out of 8 in the Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase From Mycobacterium Smegmatis.


Mono view


Stereo pair view

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

b:40.3
occ:1.00
 O A:HOH539 2.0 35.4 1.0
NE2 A:HIS58 2.1 34.9 1.0
NE2 A:HIS56 2.1 37.4 1.0
OD1 A:ASP267 2.1 35.8 1.0
OE1 A:GLU122 2.1 43.4 1.0
CD A:GLU122 2.9 45.9 1.0
CE1 A:HIS56 3.0 40.5 1.0
CE1 A:HIS58 3.0 36.2 1.0
CG A:ASP267 3.0 39.1 1.0
OE2 A:GLU122 3.1 52.2 1.0
CD2 A:HIS56 3.1 36.0 1.0
CD2 A:HIS58 3.2 34.5 1.0
OD2 A:ASP267 3.3 39.5 1.0
ZN A:ZN402 3.5 38.9 1.0
O A:HOH572 3.5 45.9 1.0
ND1 A:HIS56 4.1 35.3 1.0
ND1 A:HIS58 4.1 40.5 1.0
CG A:HIS56 4.2 35.3 1.0
CG A:HIS58 4.2 37.6 1.0
CG A:GLU122 4.3 41.9 1.0
CB A:ASP267 4.4 23.0 1.0
CD2 A:HIS209 4.5 38.4 1.0
NE2 A:HIS209 4.7 43.1 1.0
CB A:GLU122 4.7 39.4 1.0
CA A:ASP267 4.9 29.2 1.0
O A:HOH575 5.0 45.6 1.0

Zinc binding site 2 out of 8 in 6fv3

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Zinc binding site 2 out of 8 in the Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase From Mycobacterium Smegmatis.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase From Mycobacterium Smegmatis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:38.9
occ:1.00
 O A:HOH539 2.1 35.4 1.0
OE2 A:GLU122 2.1 52.2 1.0
NE2 A:HIS188 2.1 42.9 1.0
NE2 A:HIS209 2.1 43.1 1.0
O A:HOH572 2.2 45.9 1.0
CD A:GLU122 2.8 45.9 1.0
CE1 A:HIS188 3.0 37.1 1.0
CD2 A:HIS209 3.0 38.4 1.0
CE1 A:HIS209 3.1 36.7 1.0
OE1 A:GLU122 3.2 43.4 1.0
CD2 A:HIS188 3.2 37.4 1.0
ZN A:ZN401 3.5 40.3 1.0
O A:HOH575 3.7 45.6 1.0
CG A:GLU122 4.0 41.9 1.0
ND1 A:HIS188 4.2 39.4 1.0
CG A:HIS209 4.2 31.3 1.0
ND1 A:HIS209 4.2 37.0 1.0
CG A:HIS188 4.3 39.2 1.0
CE1 A:HIS56 4.3 40.5 1.0
NE2 A:HIS134 4.4 54.5 1.0
NE2 A:HIS56 4.6 37.4 1.0
OD2 A:ASP267 4.6 39.5 1.0
CG2 A:THR208 4.7 36.3 1.0
OD1 A:ASP267 4.8 35.8 1.0

Zinc binding site 3 out of 8 in 6fv3

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Zinc binding site 3 out of 8 in the Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase From Mycobacterium Smegmatis.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase From Mycobacterium Smegmatis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:37.7
occ:1.00
 NE2 B:HIS58 2.1 42.9 1.0
NE2 B:HIS56 2.1 37.5 1.0
OD1 B:ASP267 2.1 47.4 1.0
OE1 B:GLU122 2.1 45.3 1.0
O B:HOH526 2.7 40.8 1.0
CD B:GLU122 2.8 41.9 1.0
OE2 B:GLU122 2.8 48.2 1.0
CE1 B:HIS56 2.9 42.7 1.0
CG B:ASP267 3.0 46.7 1.0
CE1 B:HIS58 3.1 41.3 1.0
CD2 B:HIS58 3.1 39.5 1.0
CD2 B:HIS56 3.1 37.9 1.0
OD2 B:ASP267 3.2 48.0 1.0
ZN B:ZN402 3.4 39.7 1.0
ND1 B:HIS56 4.1 46.7 1.0
ND1 B:HIS58 4.2 44.4 1.0
CG B:HIS56 4.2 34.0 1.0
CG B:GLU122 4.2 43.3 1.0
CG B:HIS58 4.2 43.0 1.0
CB B:ASP267 4.4 35.5 1.0
CD2 B:HIS209 4.5 39.9 1.0
NE2 B:HIS209 4.6 44.0 1.0
CB B:GLU122 4.7 44.5 1.0
O B:HOH563 4.8 37.0 1.0
CA B:ASP267 4.9 39.6 1.0

Zinc binding site 4 out of 8 in 6fv3

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Zinc binding site 4 out of 8 in the Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase From Mycobacterium Smegmatis.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase From Mycobacterium Smegmatis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:39.7
occ:1.00
 NE2 B:HIS188 2.1 43.0 1.0
OE2 B:GLU122 2.1 48.2 1.0
NE2 B:HIS209 2.1 44.0 1.0
O B:HOH526 2.4 40.8 1.0
O B:HOH563 2.6 37.0 1.0
CD B:GLU122 3.0 41.9 1.0
CE1 B:HIS188 3.0 39.9 1.0
CD2 B:HIS209 3.0 39.9 1.0
CE1 B:HIS209 3.1 37.1 1.0
CD2 B:HIS188 3.2 37.1 1.0
OE1 B:GLU122 3.4 45.3 1.0
ZN B:ZN401 3.4 37.7 1.0
CG B:GLU122 4.1 43.3 1.0
ND1 B:HIS188 4.1 39.2 1.0
CG B:HIS209 4.2 33.0 1.0
OD2 B:ASP267 4.2 48.0 1.0
ND1 B:HIS209 4.2 35.6 1.0
O B:HOH516 4.3 51.4 1.0
CG B:HIS188 4.3 38.2 1.0
CE1 B:HIS56 4.3 42.7 1.0
NE2 B:HIS134 4.4 48.5 1.0
NE2 B:HIS56 4.5 37.5 1.0
CG2 B:THR208 4.7 29.9 1.0
OD1 B:ASP267 4.8 47.4 1.0
CG B:ASP267 4.9 46.7 1.0
CD2 B:HIS134 4.9 54.0 1.0

Zinc binding site 5 out of 8 in 6fv3

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Zinc binding site 5 out of 8 in the Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase From Mycobacterium Smegmatis.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase From Mycobacterium Smegmatis. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:36.6
occ:1.00
 O C:HOH510 2.1 30.3 1.0
NE2 C:HIS56 2.1 38.8 1.0
NE2 C:HIS58 2.1 35.5 1.0
OD1 C:ASP267 2.1 41.3 1.0
OE1 C:GLU122 2.1 46.7 1.0
O C:HOH530 2.8 34.8 1.0
CD C:GLU122 2.9 46.7 1.0
CG C:ASP267 3.0 38.0 1.0
CE1 C:HIS56 3.0 38.5 1.0
OE2 C:GLU122 3.0 53.1 1.0
CD2 C:HIS58 3.1 37.8 1.0
CE1 C:HIS58 3.1 36.9 1.0
CD2 C:HIS56 3.1 34.5 1.0
OD2 C:ASP267 3.2 42.4 1.0
ZN C:ZN402 3.7 44.1 1.0
ND1 C:HIS56 4.1 36.3 1.0
ND1 C:HIS58 4.2 37.4 1.0
CG C:HIS56 4.2 35.3 1.0
CG C:HIS58 4.2 33.3 1.0
CG C:GLU122 4.3 40.8 1.0
CB C:ASP267 4.4 31.2 1.0
CD2 C:HIS209 4.6 34.9 1.0
O C:HOH576 4.6 39.6 1.0
NE2 C:HIS209 4.8 40.9 1.0
CB C:GLU122 4.8 43.6 1.0
CA C:ASP267 4.9 35.2 1.0

Zinc binding site 6 out of 8 in 6fv3

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Zinc binding site 6 out of 8 in the Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase From Mycobacterium Smegmatis.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase From Mycobacterium Smegmatis. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:44.1
occ:1.00
 O C:HOH510 2.1 30.3 1.0
OE2 C:GLU122 2.1 53.1 1.0
NE2 C:HIS188 2.1 38.8 1.0
NE2 C:HIS209 2.1 40.9 1.0
O C:HOH576 2.5 39.6 1.0
CE1 C:HIS188 2.9 43.3 1.0
CD2 C:HIS209 3.0 34.9 1.0
CE1 C:HIS209 3.1 28.8 1.0
CD2 C:HIS188 3.2 42.7 1.0
CD C:GLU122 3.3 46.7 1.0
O C:HOH530 3.5 34.8 1.0
ZN C:ZN401 3.7 36.6 1.0
OE1 C:GLU122 4.0 46.7 1.0
ND1 C:HIS188 4.1 46.5 1.0
OD2 C:ASP267 4.2 42.4 1.0
ND1 C:HIS209 4.2 33.0 1.0
CG C:HIS209 4.2 31.1 1.0
CG C:HIS188 4.2 45.5 1.0
CG C:GLU122 4.4 40.8 1.0
NE2 C:HIS134 4.5 45.8 1.0
CE1 C:HIS56 4.6 38.5 1.0
NE2 C:HIS56 4.8 38.8 1.0
CG2 C:THR208 4.9 33.0 1.0
CB C:ALA213 4.9 35.3 1.0

Zinc binding site 7 out of 8 in 6fv3

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Zinc binding site 7 out of 8 in the Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase From Mycobacterium Smegmatis.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase From Mycobacterium Smegmatis. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:42.0
occ:1.00
 NE2 D:HIS58 2.1 45.2 1.0
NE2 D:HIS56 2.1 36.8 1.0
OD1 D:ASP267 2.1 53.1 1.0
OE1 D:GLU122 2.1 51.1 1.0
O D:HOH524 2.3 43.3 1.0
CD D:GLU122 2.8 47.1 1.0
OE2 D:GLU122 2.9 46.6 1.0
CE1 D:HIS56 2.9 42.5 1.0
CD2 D:HIS58 3.1 42.3 1.0
CG D:ASP267 3.1 47.0 1.0
CE1 D:HIS58 3.1 42.0 1.0
CD2 D:HIS56 3.2 40.6 1.0
ZN D:ZN402 3.4 46.1 1.0
OD2 D:ASP267 3.5 38.9 1.0
ND1 D:HIS56 4.1 44.7 1.0
ND1 D:HIS58 4.2 40.8 1.0
CG D:GLU122 4.2 43.2 1.0
CG D:HIS56 4.2 40.6 1.0
CG D:HIS58 4.2 41.1 1.0
CB D:ASP267 4.3 39.5 1.0
CD2 D:HIS209 4.4 42.5 1.0
NE2 D:HIS209 4.4 44.7 1.0
CB D:GLU122 4.6 40.5 1.0
CE1 D:HIS134 4.9 56.3 1.0
CA D:ASP267 4.9 39.1 1.0

Zinc binding site 8 out of 8 in 6fv3

Go back to Zinc Binding Sites List in 6fv3
Zinc binding site 8 out of 8 in the Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase From Mycobacterium Smegmatis.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase From Mycobacterium Smegmatis. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:46.1
occ:1.00
 NE2 D:HIS188 2.1 42.1 1.0
OE2 D:GLU122 2.1 46.6 1.0
NE2 D:HIS209 2.1 44.7 1.0
O D:HOH524 2.8 43.3 1.0
O D:HOH572 2.8 37.7 1.0
CD D:GLU122 2.9 47.1 1.0
CE1 D:HIS188 3.0 38.9 1.0
CE1 D:HIS209 3.0 38.4 1.0
CD2 D:HIS209 3.1 42.5 1.0
CD2 D:HIS188 3.2 38.7 1.0
OE1 D:GLU122 3.3 51.1 1.0
ZN D:ZN401 3.4 42.0 1.0
CE1 D:HIS134 3.9 56.3 1.0
CG D:GLU122 4.1 43.2 1.0
ND1 D:HIS188 4.1 37.1 1.0
ND1 D:HIS209 4.2 39.8 1.0
CG D:HIS209 4.2 42.1 1.0
CG D:HIS188 4.3 38.4 1.0
NE2 D:HIS134 4.3 53.2 1.0
CE1 D:HIS56 4.4 42.5 1.0
NE2 D:HIS56 4.6 36.8 1.0
OD2 D:ASP267 4.6 38.9 1.0
ND1 D:HIS134 4.8 65.7 1.0
OD1 D:ASP267 4.8 53.1 1.0
CG2 D:THR208 4.8 30.4 1.0
CG D:ASP267 5.0 47.0 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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