Zinc in PDB 1guq: Structure of Nucleotidyltransferase Complexed with Udp-Glucose

All present enzymatic activity of Structure of Nucleotidyltransferase Complexed with Udp-Glucose:
2.7.7.10;

The structure of Structure of Nucleotidyltransferase Complexed with Udp-Glucose, PDB code: 1guq was solved by J.B.Thoden, I.Rayment, H.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.400, 57.500, 188.900, 90.00, 100.13, 90.00
R / Rfree (%)	n/a / n/a

The structure of Structure of Nucleotidyltransferase Complexed with Udp-Glucose also contains other interesting chemical elements:

Potassium	(K)	4 atoms
Iron	(Fe)	4 atoms

The binding sites of Zinc atom in the Structure of Nucleotidyltransferase Complexed with Udp-Glucose (pdb code 1guq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Nucleotidyltransferase Complexed with Udp-Glucose, PDB code: 1guq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Nucleotidyltransferase Complexed with Udp-Glucose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Nucleotidyltransferase Complexed with Udp-Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn350 b:18.7 occ:1.00 ND1 A:HIS164 1.9 13.4 1.0 ND1 A:HIS115 2.1 15.0 1.0 SG A:CYS52 2.3 15.4 1.0 SG A:CYS55 2.4 16.6 1.0 CE1 A:HIS164 2.9 16.0 1.0 CE1 A:HIS115 3.0 34.0 1.0 CB A:CYS52 3.0 10.7 1.0 CG A:HIS164 3.1 10.3 1.0 CG A:HIS115 3.1 18.7 1.0 CB A:CYS55 3.5 10.7 1.0 CB A:HIS115 3.5 21.4 1.0 N A:CYS55 3.5 12.8 1.0 CB A:HIS164 3.5 20.6 1.0 CA A:CYS55 3.7 18.4 1.0 NE2 A:HIS164 4.0 13.2 1.0 NE2 A:HIS115 4.1 25.1 1.0 C A:LEU54 4.1 13.3 1.0 CD2 A:HIS115 4.2 19.8 1.0 CD2 A:HIS164 4.2 10.5 1.0 CA A:HIS164 4.2 21.5 1.0 CA A:HIS115 4.3 18.0 1.0 CA A:CYS52 4.4 12.9 1.0 CB A:LEU54 4.5 19.5 1.0 CB A:ASP49 4.6 28.2 1.0 CA A:LEU54 4.6 26.7 1.0 N A:LEU54 4.7 25.0 1.0 O A:LEU54 4.7 11.1 1.0 C A:CYS52 4.8 15.6 1.0 N A:HIS164 4.8 18.1 1.0 O A:CYS52 4.8 25.3 1.0 N A:ASP49 4.9 14.6 1.0 O A:ASP49 5.0 16.9 1.0

Zinc binding site 2 out of 4 in the Structure of Nucleotidyltransferase Complexed with Udp-Glucose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Nucleotidyltransferase Complexed with Udp-Glucose within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn350 b:22.0 occ:1.00 ND1 B:HIS164 2.0 14.2 1.0 ND1 B:HIS115 2.1 19.1 1.0 SG B:CYS52 2.3 18.8 1.0 SG B:CYS55 2.4 22.4 1.0 CE1 B:HIS115 2.9 19.6 1.0 CB B:CYS52 2.9 14.8 1.0 CE1 B:HIS164 3.0 16.0 1.0 CG B:HIS164 3.1 19.2 1.0 CG B:HIS115 3.1 18.0 1.0 CB B:CYS55 3.4 18.0 1.0 CB B:HIS164 3.5 20.6 1.0 N B:CYS55 3.5 12.9 1.0 CB B:HIS115 3.6 22.0 1.0 CA B:CYS55 3.7 16.5 1.0 NE2 B:HIS115 4.0 24.9 1.0 NE2 B:HIS164 4.1 17.3 1.0 C B:LEU54 4.1 15.6 1.0 CD2 B:HIS115 4.2 20.8 1.0 CD2 B:HIS164 4.2 25.1 1.0 CA B:HIS115 4.3 26.5 1.0 CA B:HIS164 4.3 27.0 1.0 CA B:CYS52 4.3 17.5 1.0 CB B:LEU54 4.5 25.5 1.0 CB B:ASP49 4.5 21.1 1.0 N B:LEU54 4.6 22.7 1.0 CA B:LEU54 4.6 25.4 1.0 O B:LEU54 4.7 20.1 1.0 C B:CYS52 4.7 28.3 1.0 N B:ASP49 4.8 33.1 1.0 N B:HIS164 4.8 24.4 1.0 O B:CYS52 4.9 27.0 1.0 O B:ASP49 4.9 28.2 1.0 O B:HOH385 4.9 24.5 1.0

Zinc binding site 3 out of 4 in the Structure of Nucleotidyltransferase Complexed with Udp-Glucose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Nucleotidyltransferase Complexed with Udp-Glucose within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn350 b:21.0 occ:1.00 ND1 C:HIS115 2.0 24.4 1.0 ND1 C:HIS164 2.0 31.2 1.0 SG C:CYS52 2.1 19.2 1.0 SG C:CYS55 2.4 19.1 1.0 CE1 C:HIS115 2.7 15.8 1.0 CB C:CYS52 2.8 16.6 1.0 CG C:HIS164 3.0 22.4 1.0 CE1 C:HIS164 3.0 17.2 1.0 CG C:HIS115 3.2 25.3 1.0 CB C:HIS164 3.3 22.3 1.0 CB C:CYS55 3.4 12.0 1.0 N C:CYS55 3.5 20.5 1.0 CA C:CYS55 3.7 16.0 1.0 CB C:HIS115 3.8 21.6 1.0 NE2 C:HIS115 4.0 16.7 1.0 C C:LEU54 4.1 22.9 1.0 NE2 C:HIS164 4.1 23.1 1.0 CD2 C:HIS164 4.2 22.8 1.0 CA C:HIS115 4.2 39.8 1.0 CD2 C:HIS115 4.2 31.8 1.0 CA C:HIS164 4.3 22.9 1.0 CA C:CYS52 4.3 16.5 1.0 CB C:ASP49 4.4 0.0 1.0 O C:LEU54 4.6 19.6 1.0 CA C:LEU54 4.7 25.8 1.0 N C:LEU54 4.7 13.2 1.0 CB C:LEU54 4.7 21.1 1.0 C C:CYS52 4.8 29.2 1.0 N C:ASP49 4.8 31.5 1.0 N C:HIS164 4.9 12.4 1.0

Zinc binding site 4 out of 4 in the Structure of Nucleotidyltransferase Complexed with Udp-Glucose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Nucleotidyltransferase Complexed with Udp-Glucose within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn350 b:25.7 occ:1.00 ND1 D:HIS115 2.0 35.0 1.0 ND1 D:HIS164 2.0 26.2 1.0 SG D:CYS52 2.2 21.6 1.0 SG D:CYS55 2.5 23.9 1.0 CE1 D:HIS115 2.7 31.2 1.0 CG D:HIS164 3.0 54.8 1.0 CB D:CYS52 3.0 21.5 1.0 CE1 D:HIS164 3.1 18.4 1.0 CG D:HIS115 3.2 27.9 1.0 CB D:HIS164 3.3 21.7 1.0 CB D:CYS55 3.4 22.2 1.0 N D:CYS55 3.5 23.7 1.0 CA D:CYS55 3.6 21.9 1.0 CB D:HIS115 3.7 16.1 1.0 NE2 D:HIS115 3.9 35.4 1.0 C D:LEU54 4.0 42.7 1.0 CD2 D:HIS164 4.1 32.9 1.0 CA D:HIS164 4.2 20.9 1.0 NE2 D:HIS164 4.2 17.3 1.0 CD2 D:HIS115 4.2 18.1 1.0 CA D:HIS115 4.3 22.2 1.0 CA D:CYS52 4.4 22.5 1.0 CB D:LEU54 4.5 25.6 1.0 O D:LEU54 4.6 23.0 1.0 O D:HOH1109 4.6 32.4 1.0 CA D:LEU54 4.6 29.7 1.0 N D:LEU54 4.6 19.7 1.0 C D:CYS52 4.7 31.2 1.0 O D:CYS52 4.7 21.9 1.0 N D:HIS164 4.8 21.8 1.0 CB D:ASP49 4.9 33.9 1.0

J.B.Thoden, F.J.Ruzicka, P.A.Frey, I.Rayment, H.M.Holden. Structural Analysis of the H166G Site-Directed Mutant of Galactose-1-Phosphate Uridylyltransferase Complexed with Either Udp-Glucose or Udp-Galactose: Detailed Description of the Nucleotide Sugar Binding Site. Biochemistry V. 36 1212 1997.
ISSN: ISSN 0006-2960
PubMed: 9063869
DOI: 10.1021/BI9626517