Zinc in PDB 1gup: Structure of Nucleotidyltransferase Complexed with Udp- Galactose

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

The structure of Structure of Nucleotidyltransferase Complexed with Udp- Galactose, PDB code: 1gup 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 (°)	68.700, 57.700, 188.700, 90.00, 100.08, 90.00
R / Rfree (%)	n/a / n/a

The structure of Structure of Nucleotidyltransferase Complexed with Udp- Galactose 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- Galactose (pdb code 1gup). 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- Galactose, PDB code: 1gup:
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- Galactose


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- Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn350 b:21.0 occ:1.00 ND1 A:HIS164 1.9 12.9 1.0 ND1 A:HIS115 2.1 19.6 1.0 SG A:CYS55 2.2 18.5 1.0 SG A:CYS52 2.4 18.4 1.0 CE1 A:HIS164 2.8 11.8 1.0 CG A:HIS164 3.0 14.9 1.0 CB A:CYS52 3.0 12.9 1.0 CE1 A:HIS115 3.1 36.4 1.0 CG A:HIS115 3.1 18.4 1.0 CB A:HIS164 3.4 14.9 1.0 CB A:CYS55 3.4 19.7 1.0 CB A:HIS115 3.5 27.1 1.0 N A:CYS55 3.5 14.7 1.0 CA A:CYS55 3.7 25.8 1.0 NE2 A:HIS164 4.0 13.2 1.0 C A:LEU54 4.1 10.9 1.0 CD2 A:HIS164 4.1 13.1 1.0 CA A:HIS115 4.2 13.0 1.0 NE2 A:HIS115 4.2 19.1 1.0 CD2 A:HIS115 4.3 15.1 1.0 CA A:HIS164 4.3 18.7 1.0 O A:HOH687 4.3 79.0 1.0 CA A:CYS52 4.5 14.7 1.0 CB A:LEU54 4.5 19.7 1.0 CA A:LEU54 4.6 25.7 1.0 CB A:ASP49 4.6 18.8 1.0 O A:LEU54 4.7 18.9 1.0 N A:LEU54 4.7 24.6 1.0 O A:CYS52 4.8 19.3 1.0 C A:CYS52 4.8 14.8 1.0 N A:ASP49 4.9 17.6 1.0 O A:ASP49 4.9 22.8 1.0 N A:HIS164 4.9 17.1 1.0 N A:HIS115 5.0 20.3 1.0

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


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- Galactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn350 b:25.7 occ:1.00 ND1 B:HIS115 2.0 32.0 1.0 ND1 B:HIS164 2.1 14.4 1.0 SG B:CYS55 2.2 21.7 1.0 SG B:CYS52 2.3 23.5 1.0 CE1 B:HIS115 2.9 20.1 1.0 CB B:CYS52 3.1 21.3 1.0 CG B:HIS164 3.1 15.0 1.0 CG B:HIS115 3.1 21.5 1.0 CE1 B:HIS164 3.1 10.5 1.0 CB B:HIS164 3.3 18.9 1.0 CB B:CYS55 3.4 17.7 1.0 N B:CYS55 3.4 13.8 1.0 CB B:HIS115 3.5 28.6 1.0 CA B:CYS55 3.6 16.4 1.0 C B:LEU54 4.1 7.2 1.0 NE2 B:HIS115 4.1 23.3 1.0 CA B:HIS164 4.2 23.9 1.0 CA B:HIS115 4.2 39.3 1.0 CD2 B:HIS115 4.2 27.8 1.0 NE2 B:HIS164 4.2 16.1 1.0 CD2 B:HIS164 4.2 15.8 1.0 CB B:LEU54 4.4 30.1 1.0 CA B:CYS52 4.5 31.2 1.0 CB B:ASP49 4.5 25.7 1.0 CA B:LEU54 4.6 24.3 1.0 N B:HIS164 4.7 33.5 1.0 N B:LEU54 4.7 48.1 1.0 O B:LEU54 4.7 27.5 1.0 N B:ASP49 4.8 32.2 1.0 C B:CYS52 4.8 17.9 1.0 O B:ASP49 4.9 33.5 1.0 O B:HOH516 4.9 34.9 1.0 O B:CYS52 4.9 21.4 1.0

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


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- Galactose within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn350 b:25.3 occ:1.00 ND1 C:HIS115 2.1 19.5 1.0 SG C:CYS52 2.1 24.3 1.0 ND1 C:HIS164 2.3 23.3 1.0 SG C:CYS55 2.3 22.1 1.0 CE1 C:HIS115 2.8 18.8 1.0 CB C:CYS52 2.8 25.4 1.0 CG C:HIS164 3.2 24.9 1.0 CG C:HIS115 3.3 24.9 1.0 CB C:CYS55 3.3 17.2 1.0 CE1 C:HIS164 3.3 21.6 1.0 CB C:HIS164 3.4 28.0 1.0 N C:CYS55 3.6 24.8 1.0 CA C:CYS55 3.7 14.5 1.0 CB C:HIS115 3.8 25.2 1.0 NE2 C:HIS115 4.0 19.9 1.0 C C:LEU54 4.1 26.2 1.0 CA C:HIS115 4.2 23.6 1.0 CA C:CYS52 4.3 24.2 1.0 CD2 C:HIS115 4.3 23.3 1.0 CA C:HIS164 4.4 25.8 1.0 CD2 C:HIS164 4.4 29.5 1.0 NE2 C:HIS164 4.4 32.2 1.0 O C:LEU54 4.6 27.8 1.0 CB C:ASP49 4.6 28.0 1.0 C C:CYS52 4.8 20.6 1.0 N C:ASP49 4.8 26.9 1.0 CA C:LEU54 4.8 31.9 1.0 O C:ASP49 4.8 26.7 1.0 N C:LEU54 4.9 21.6 1.0 O C:CYS52 4.9 25.5 1.0 CB C:LEU54 4.9 30.9 1.0 N C:HIS115 5.0 22.2 1.0

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


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- Galactose within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn350 b:30.5 occ:1.00 ND1 D:HIS164 1.8 26.8 1.0 ND1 D:HIS115 2.0 34.9 1.0 SG D:CYS52 2.2 26.2 1.0 SG D:CYS55 2.3 31.4 1.0 CE1 D:HIS164 2.8 28.9 1.0 CE1 D:HIS115 2.8 16.2 1.0 CB D:CYS52 2.8 44.1 1.0 CG D:HIS164 2.9 40.2 1.0 CG D:HIS115 3.1 38.4 1.0 CB D:HIS164 3.3 27.9 1.0 CB D:CYS55 3.3 51.2 1.0 CB D:HIS115 3.5 24.5 1.0 N D:CYS55 3.6 30.9 1.0 CA D:CYS55 3.7 33.6 1.0 NE2 D:HIS164 3.9 24.9 1.0 CD2 D:HIS164 3.9 29.8 1.0 NE2 D:HIS115 4.0 43.1 1.0 C D:LEU54 4.0 25.2 1.0 CD2 D:HIS115 4.1 21.4 1.0 CB D:LEU54 4.2 31.5 1.0 CA D:HIS115 4.2 19.4 1.0 CA D:HIS164 4.3 32.7 1.0 CA D:CYS52 4.3 30.7 1.0 O D:LEU54 4.5 22.7 1.0 CA D:LEU54 4.6 34.7 1.0 CB D:ASP49 4.6 28.9 1.0 C D:CYS52 4.7 35.2 1.0 N D:LEU54 4.7 34.7 1.0 N D:HIS164 4.8 27.1 1.0 O D:CYS52 4.8 36.6 1.0 O D:HOH978 4.8 57.5 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