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Zinc in PDB 5tpr: Desmethyl-4-Deoxygadusol Synthase From Anabaena Variabilis (AVA_3858) with Nad+ and ZN2+ Bound

Enzymatic activity of Desmethyl-4-Deoxygadusol Synthase From Anabaena Variabilis (AVA_3858) with Nad+ and ZN2+ Bound

All present enzymatic activity of Desmethyl-4-Deoxygadusol Synthase From Anabaena Variabilis (AVA_3858) with Nad+ and ZN2+ Bound:
4.2.3.4;

Protein crystallography data

The structure of Desmethyl-4-Deoxygadusol Synthase From Anabaena Variabilis (AVA_3858) with Nad+ and ZN2+ Bound, PDB code: 5tpr was solved by K.M.Kean, P.A.Karplus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.63 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.500, 120.261, 133.260, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 18.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Desmethyl-4-Deoxygadusol Synthase From Anabaena Variabilis (AVA_3858) with Nad+ and ZN2+ Bound (pdb code 5tpr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Desmethyl-4-Deoxygadusol Synthase From Anabaena Variabilis (AVA_3858) with Nad+ and ZN2+ Bound, PDB code: 5tpr:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5tpr

Go back to Zinc Binding Sites List in 5tpr
Zinc binding site 1 out of 2 in the Desmethyl-4-Deoxygadusol Synthase From Anabaena Variabilis (AVA_3858) with Nad+ and ZN2+ Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Desmethyl-4-Deoxygadusol Synthase From Anabaena Variabilis (AVA_3858) with Nad+ and ZN2+ Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:20.0
occ:0.50
OE2 A:GLU198 2.0 20.0 1.0
NE2 A:HIS271 2.1 16.3 1.0
O A:HOH852 2.1 19.8 0.5
NE2 A:HIS287 2.1 16.2 1.0
O A:HOH608 2.3 22.8 0.5
CE1 A:HIS271 2.9 16.9 1.0
H5N A:NAD503 3.0 32.3 1.0
CD A:GLU198 3.0 20.2 1.0
HE1 A:HIS271 3.0 20.3 1.0
CE1 A:HIS287 3.0 16.8 1.0
HE1 A:HIS287 3.2 20.1 1.0
CD2 A:HIS271 3.2 16.1 1.0
HG21 A:VAL291 3.2 14.8 1.0
CD2 A:HIS287 3.2 16.7 1.0
HD2 A:HIS287 3.4 20.0 1.0
HD2 A:HIS271 3.4 19.4 1.0
OE1 A:GLU198 3.5 20.8 1.0
C5N A:NAD503 3.5 26.9 1.0
OD2 A:ASP150 3.6 35.4 1.0
HZ3 A:LYS201 4.0 24.4 1.0
O A:HOH983 4.0 25.4 0.5
CG2 A:VAL291 4.1 12.4 1.0
C6N A:NAD503 4.1 26.2 1.0
ND1 A:HIS271 4.1 16.1 1.0
H6N A:NAD503 4.1 31.5 1.0
O A:HOH830 4.1 36.8 1.0
HG22 A:VAL291 4.2 14.8 1.0
C4N A:NAD503 4.2 28.3 1.0
ND1 A:HIS287 4.2 16.3 1.0
H4N A:NAD503 4.2 34.0 1.0
CG A:HIS271 4.2 14.5 1.0
CG A:GLU198 4.3 16.9 1.0
HG3 A:GLU198 4.3 20.3 1.0
CG A:HIS287 4.3 15.5 1.0
HG23 A:VAL291 4.4 14.8 1.0
HG2 A:GLU198 4.5 20.3 1.0
HG11 A:VAL291 4.6 14.2 1.0
HZ2 A:LYS201 4.7 24.4 1.0
NZ A:LYS201 4.8 20.4 1.0
CG A:ASP150 4.9 31.3 1.0
HD1 A:HIS271 4.9 19.4 1.0
H2D A:NAD503 4.9 31.3 1.0
HD12 A:ILE146 4.9 19.9 1.0
HD1 A:HIS287 5.0 19.6 1.0
O A:HOH910 5.0 34.2 1.0

Zinc binding site 2 out of 2 in 5tpr

Go back to Zinc Binding Sites List in 5tpr
Zinc binding site 2 out of 2 in the Desmethyl-4-Deoxygadusol Synthase From Anabaena Variabilis (AVA_3858) with Nad+ and ZN2+ Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Desmethyl-4-Deoxygadusol Synthase From Anabaena Variabilis (AVA_3858) with Nad+ and ZN2+ Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:18.5
occ:0.50
OE2 B:GLU198 2.0 21.0 1.0
NE2 B:HIS287 2.1 15.2 1.0
NE2 B:HIS271 2.1 17.6 1.0
O B:HOH625 2.6 18.6 0.5
H5N B:NAD502 2.9 32.4 0.8
CD B:GLU198 3.0 20.1 1.0
CE1 B:HIS271 3.0 17.2 1.0
CE1 B:HIS287 3.0 15.3 1.0
O B:HOH1001 3.1 34.9 0.5
CD2 B:HIS287 3.1 15.0 1.0
CD2 B:HIS271 3.1 16.8 1.0
HE1 B:HIS271 3.2 20.7 1.0
HE1 B:HIS287 3.2 18.4 1.0
HG21 B:VAL291 3.2 15.6 1.0
HD2 B:HIS287 3.3 18.1 1.0
HD2 B:HIS271 3.3 20.2 1.0
C5N B:NAD502 3.4 27.0 0.8
OE1 B:GLU198 3.5 21.4 1.0
OD2 B:ASP150 3.6 38.6 1.0
HZ3 B:LYS201 4.0 29.5 1.0
C6N B:NAD502 4.1 26.5 0.8
C4N B:NAD502 4.1 26.9 0.8
CG2 B:VAL291 4.1 13.0 1.0
H4N B:NAD502 4.1 32.3 0.8
H6N B:NAD502 4.1 31.9 0.8
ND1 B:HIS287 4.2 15.3 1.0
ND1 B:HIS271 4.2 16.4 1.0
HG22 B:VAL291 4.2 15.6 1.0
HG3 B:GLU198 4.2 20.1 1.0
CG B:HIS287 4.2 14.5 1.0
CG B:HIS271 4.3 16.5 1.0
CG B:GLU198 4.3 16.8 1.0
HG23 B:VAL291 4.4 15.6 1.0
HG2 B:GLU198 4.6 20.1 1.0
HG11 B:VAL291 4.7 14.1 1.0
NZ B:LYS201 4.8 24.6 1.0
CG B:ASP150 4.8 34.1 1.0
HZ2 B:LYS201 4.8 29.5 1.0
O B:HOH927 4.9 33.1 1.0
O B:HOH1000 4.9 48.2 1.0
H2D B:NAD502 4.9 27.2 0.8
HD12 B:ILE146 4.9 23.5 1.0
HD1 B:HIS287 5.0 18.4 1.0
HD1 B:HIS271 5.0 19.7 1.0
HD3 B:LYS201 5.0 27.4 1.0

Reference:

A.R.Osborn, K.M.Kean, K.M.Alseud, K.H.Almabruk, S.Asamizu, J.A.Lee, P.A.Karplus, T.Mahmud. Evolution and Distribution of C7-Cyclitol Synthases in Prokaryotes and Eukaryotes. Acs Chem. Biol. V. 12 979 2017.
ISSN: ESSN 1554-8937
PubMed: 28182402
DOI: 10.1021/ACSCHEMBIO.7B00066
Page generated: Wed Dec 16 10:56:35 2020

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