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Zinc in PDB 6ajd: Crystal Structure of A Monometallic Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 Reveals No Lysine Carbamylation Within the Active Site

Enzymatic activity of Crystal Structure of A Monometallic Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 Reveals No Lysine Carbamylation Within the Active Site

All present enzymatic activity of Crystal Structure of A Monometallic Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 Reveals No Lysine Carbamylation Within the Active Site:
3.5.2.2;

Protein crystallography data

The structure of Crystal Structure of A Monometallic Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 Reveals No Lysine Carbamylation Within the Active Site, PDB code: 6ajd was solved by Y.H.Huang, C.Y.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.28 / 2.22
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 88.375, 110.169, 112.660, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 23.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Monometallic Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 Reveals No Lysine Carbamylation Within the Active Site (pdb code 6ajd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of A Monometallic Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 Reveals No Lysine Carbamylation Within the Active Site, PDB code: 6ajd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6ajd

Go back to Zinc Binding Sites List in 6ajd
Zinc binding site 1 out of 2 in the Crystal Structure of A Monometallic Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 Reveals No Lysine Carbamylation Within the Active Site


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 A Monometallic Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 Reveals No Lysine Carbamylation Within the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:45.5
occ:1.00
 OD1 A:ASP316 2.3 27.2 1.0
NE2 A:HIS59 2.7 21.2 1.0
O A:HOH619 2.7 23.6 1.0
NE2 A:HIS61 2.7 21.1 1.0
O A:HOH718 2.8 27.9 1.0
O A:HOH757 2.9 35.0 1.0
CG A:ASP316 3.3 28.6 1.0
NE2 A:HIS239 3.4 25.2 1.0
CE1 A:HIS59 3.4 21.7 1.0
CD2 A:HIS61 3.5 22.4 1.0
CD2 A:HIS59 3.7 20.4 1.0
CE1 A:HIS61 3.8 19.1 1.0
OD2 A:ASP316 3.9 27.3 1.0
CD2 A:HIS239 3.9 23.5 1.0
O A:HOH755 4.1 29.9 1.0
NZ A:LYS150 4.4 18.5 1.0
CB A:ASP316 4.4 22.5 1.0
O A:HOH663 4.5 28.3 1.0
CE1 A:HIS239 4.5 25.8 1.0
ND1 A:HIS59 4.6 19.5 1.0
ND1 A:HIS183 4.6 25.1 1.0
CG A:HIS59 4.7 24.7 1.0
CG A:HIS61 4.7 23.3 1.0
ND1 A:HIS61 4.8 20.7 1.0
CA A:ASP316 4.9 21.9 1.0

Zinc binding site 2 out of 2 in 6ajd

Go back to Zinc Binding Sites List in 6ajd
Zinc binding site 2 out of 2 in the Crystal Structure of A Monometallic Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 Reveals No Lysine Carbamylation Within the Active Site


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 A Monometallic Dihydropyrimidinase From Pseudomonas Aeruginosa PAO1 Reveals No Lysine Carbamylation Within the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:49.3
occ:1.00
 OD1 B:ASP316 2.3 27.9 1.0
O B:HOH611 2.6 23.8 1.0
NE2 B:HIS59 2.6 23.8 1.0
NE2 B:HIS61 2.7 25.6 1.0
O B:HOH714 2.7 29.1 1.0
O B:HOH670 2.8 24.8 1.0
NE2 B:HIS239 3.2 27.3 1.0
CG B:ASP316 3.3 29.6 1.0
CE1 B:HIS59 3.4 25.6 1.0
CD2 B:HIS61 3.6 23.3 1.0
CD2 B:HIS59 3.6 20.3 1.0
CE1 B:HIS61 3.7 21.2 1.0
CD2 B:HIS239 3.8 28.0 1.0
OD2 B:ASP316 3.8 29.4 1.0
O B:HOH709 4.2 29.9 1.0
NZ B:LYS150 4.3 24.2 1.0
CE1 B:HIS239 4.3 22.1 1.0
O B:HOH696 4.3 29.7 1.0
CB B:ASP316 4.4 25.0 1.0
ND1 B:HIS59 4.5 23.1 1.0
ND1 B:HIS183 4.6 28.0 1.0
CG B:HIS59 4.7 23.2 1.0
CG B:HIS61 4.8 26.2 1.0
ND1 B:HIS61 4.8 23.3 1.0
CA B:ASP316 5.0 26.6 1.0
O B:SER289 5.0 23.4 1.0

Reference:

J.H.Cheng, Y.H.Huang, J.J.Lin, C.Y.Huang. Crystal Structures of Monometallic Dihydropyrimidinase and the Human Dihydroorotase Domain K1556A Mutant Reveal No Lysine Carbamylation Within the Active Site Biochem. Biophys. Res. V. 505 439 2018COMMUN..
ISSN: ESSN 1090-2104
PubMed: 30268498
DOI: 10.1016/J.BBRC.2018.09.153
Page generated: Thu Aug 21 12:25:21 2025

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