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Zinc in PDB 5nof: Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis

Enzymatic activity of Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis

All present enzymatic activity of Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis:
2.4.2.18;

Protein crystallography data

The structure of Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis, PDB code: 5nof was solved by S.Perveen, N.Rashid, A.C.Papageorgiou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.19 / 2.42
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.605, 81.389, 179.392, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 25.5

Other elements in 5nof:

The structure of Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis (pdb code 5nof). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis, PDB code: 5nof:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5nof

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Zinc binding site 1 out of 6 in the Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:43.8
occ:1.00
 OE2 A:GLU48 2.0 42.3 1.0
O A:HOH605 2.0 30.0 1.0
OE2 A:GLU198 2.0 44.0 1.0
OD2 B:ASP296 2.1 39.0 1.0
OE1 B:GLU295 2.3 51.3 1.0
CD A:GLU198 2.9 46.0 1.0
CG B:ASP296 2.9 37.6 1.0
CD A:GLU48 3.0 47.6 1.0
ZN A:ZN504 3.1 46.0 1.0
OE1 A:GLU198 3.2 44.5 1.0
CB B:ASP296 3.2 33.0 1.0
OE1 A:GLU48 3.3 41.2 1.0
CD B:GLU295 3.4 49.6 1.0
OE2 B:GLU295 3.6 48.1 1.0
OD1 B:ASP296 4.1 59.4 1.0
O B:HOH514 4.2 40.2 1.0
CG A:GLU198 4.2 45.8 1.0
CG A:GLU48 4.3 41.7 1.0
CA B:ASP296 4.5 37.9 1.0
N B:ASP296 4.7 43.5 1.0
CG B:GLU295 4.7 47.4 1.0
O B:GLU295 5.0 34.1 1.0
C B:GLU295 5.0 34.4 1.0

Zinc binding site 2 out of 6 in 5nof

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Zinc binding site 2 out of 6 in the Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:71.7
occ:1.00
 O A:HOH619 2.0 52.0 1.0
OD1 A:ASP217 2.0 64.3 1.0
O A:HOH601 2.2 51.9 1.0
OE2 A:GLU218 2.3 68.2 1.0
OD2 A:ASP78 3.0 94.2 1.0
CG A:ASP217 3.0 47.9 1.0
CD A:GLU218 3.0 73.5 1.0
OE1 A:GLU218 3.1 79.4 1.0
OD2 A:ASP217 3.3 52.7 1.0
CG A:ASP78 3.5 0.9 1.0
OD1 A:ASP78 3.6 0.0 1.0
O A:HOH635 3.8 53.7 1.0
CB A:ASP217 4.4 45.9 1.0
CG A:GLU218 4.5 58.3 1.0
N A:ASP217 4.6 41.7 1.0
O A:ASP217 4.6 45.5 1.0
CB A:ASP78 4.7 98.6 1.0
CA A:ASP217 4.8 44.5 1.0
C A:ASP217 4.8 39.4 1.0
CA A:GLY76 4.8 54.1 1.0
OG1 A:THR82 5.0 60.4 1.0

Zinc binding site 3 out of 6 in 5nof

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Zinc binding site 3 out of 6 in the Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:53.9
occ:1.00
 OE2 A:GLU118 2.0 74.7 1.0
O A:HOH634 2.2 52.1 1.0
O A:HOH643 2.4 31.7 1.0
O A:HOH639 2.5 31.1 1.0
CD A:GLU118 2.8 69.3 1.0
OE1 A:GLU118 3.0 78.6 1.0
O A:HOH650 3.3 39.4 1.0
CG A:GLU118 4.3 65.6 1.0

Zinc binding site 4 out of 6 in 5nof

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Zinc binding site 4 out of 6 in the Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:46.0
occ:1.00
 OE2 B:GLU295 2.0 48.1 1.0
O A:HOH637 2.1 17.0 1.0
O A:HOH605 2.2 30.0 1.0
OE1 A:GLU198 2.2 44.5 1.0
CD B:GLU295 2.9 49.6 1.0
CD A:GLU198 3.1 46.0 1.0
ZN A:ZN501 3.1 43.8 1.0
OE1 B:GLU295 3.2 51.3 1.0
OE2 A:GLU198 3.5 44.0 1.0
OE1 A:GLU48 3.9 41.2 1.0
N A:GLY47 3.9 39.1 1.0
OE2 A:GLU48 4.3 42.3 1.0
CG A:GLU198 4.3 45.8 1.0
CG B:GLU295 4.3 47.4 1.0
CD A:GLU48 4.5 47.6 1.0
CB A:GLU198 4.5 42.2 1.0
CA A:GLY47 4.5 42.3 1.0
O B:GLU295 4.6 34.1 1.0
CB A:THR46 4.7 52.8 1.0
CG A:GLU194 4.8 0.6 1.0
CB B:ASP296 4.8 33.0 1.0
CA A:THR46 4.8 46.0 1.0
C A:THR46 4.8 45.5 1.0
OD2 B:ASP296 5.0 39.0 1.0

Zinc binding site 5 out of 6 in 5nof

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Zinc binding site 5 out of 6 in the Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:79.7
occ:1.00
 OE2 B:GLU218 2.0 78.9 1.0
OD1 B:ASP217 2.3 61.4 1.0
CD B:GLU218 2.9 87.3 1.0
OE1 B:GLU218 3.1 0.1 1.0
CG B:ASP217 3.2 61.7 1.0
OD2 B:ASP217 3.3 72.1 1.0
OD2 B:ASP78 3.5 85.0 1.0
O B:HOH516 3.8 47.8 1.0
CG B:GLU218 4.2 66.8 1.0
CG B:ASP78 4.4 79.2 1.0
O B:ASP217 4.5 49.0 1.0
CB B:ASP217 4.6 51.2 1.0
CB B:ASP78 4.7 94.8 1.0
C B:ASP217 4.9 42.8 1.0
N B:ASP217 5.0 42.3 1.0
CA B:GLY76 5.0 73.4 1.0

Zinc binding site 6 out of 6 in 5nof

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Zinc binding site 6 out of 6 in the Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Anthranilate Phosphoribosyltransferase From Thermococcus Kodakaraensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:78.2
occ:1.00
 O B:HOH540 2.1 57.4 1.0
O B:HOH509 2.1 65.5 1.0
O B:HOH536 2.9 52.1 1.0
OE2 B:GLU235 3.1 90.1 1.0
OE1 B:GLU235 3.7 95.9 1.0
CD B:GLU235 3.8 99.4 1.0
OH B:TYR289 4.0 69.9 1.0
OE1 B:GLU229 4.5 40.3 1.0
O A:HOH623 4.7 50.0 1.0
OE2 B:GLU229 4.8 43.9 1.0
CD B:GLU229 5.0 38.6 1.0

Reference:

S.Perveen, N.Rashid, X.F.Tang, T.Imanaka, A.C.Papageorgiou. Anthranilate Phosphoribosyltransferase From the Hyperthermophilic Archaeon Thermococcus Kodakarensis Shows Maximum Activity with Zinc and Forms A Unique Dimeric Structure. Febs Open Bio V. 7 1217 2017.
ISSN: ESSN 2211-5463
PubMed: 28781961
DOI: 10.1002/2211-5463.12264
Page generated: Wed Dec 16 06:36:29 2020

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