Zinc in PDB 6k5z: Structure of Uridylyltransferase

The structure of Structure of Uridylyltransferase, PDB code: 6k5z was solved by H.Sakuraba, T.Ohshida, K.Yoneda, T.Ohshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.33
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	73.194, 73.194, 126.036, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 25.5

The structure of Structure of Uridylyltransferase also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the Structure of Uridylyltransferase (pdb code 6k5z). 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 Uridylyltransferase, PDB code: 6k5z:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Uridylyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Uridylyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:48.9 occ:1.00 ND1 A:HIS86 2.1 34.4 1.0 ND1 A:HIS138 2.2 55.1 1.0 SG A:CYS30 2.2 48.6 1.0 SG A:CYS33 2.4 52.7 1.0 CE1 A:HIS86 3.0 35.0 1.0 CB A:CYS30 3.0 61.5 1.0 CG A:HIS138 3.1 50.6 1.0 CG A:HIS86 3.1 37.3 1.0 CE1 A:HIS138 3.1 55.5 1.0 CB A:HIS138 3.3 42.5 1.0 CB A:CYS33 3.4 53.7 1.0 CB A:HIS86 3.5 43.6 1.0 N A:CYS33 3.6 53.8 1.0 CA A:CYS33 3.7 52.9 1.0 CA A:HIS86 4.0 43.7 1.0 NE2 A:HIS86 4.1 37.3 1.0 CD2 A:HIS138 4.2 54.4 1.0 NE2 A:HIS138 4.2 53.5 1.0 CD2 A:HIS86 4.2 38.4 1.0 C A:PHE32 4.4 47.3 1.0 CA A:CYS30 4.5 54.1 1.0 CA A:HIS138 4.6 43.2 1.0 N A:HIS86 4.8 41.5 1.0 O A:PHE32 4.9 45.3 1.0 C A:CYS30 4.9 53.4 1.0 CB A:PHE32 5.0 43.7 1.0

Zinc binding site 2 out of 4 in the Structure of Uridylyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Uridylyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:45.6 occ:1.00 ND1 A:HIS211 2.1 39.3 1.0 ND1 A:HIS264 2.4 41.6 1.0 SG A:CYS173 2.4 48.8 1.0 SG A:CYS170 2.4 44.3 1.0 CE1 A:HIS211 3.0 41.5 1.0 CB A:CYS170 3.1 52.0 1.0 CG A:HIS264 3.2 39.2 1.0 CB A:CYS173 3.2 44.9 1.0 CG A:HIS211 3.2 41.2 1.0 CB A:HIS264 3.3 36.0 1.0 CE1 A:HIS264 3.4 39.4 1.0 N A:CYS173 3.4 44.9 1.0 CB A:HIS211 3.6 42.9 1.0 CA A:CYS173 3.7 47.9 1.0 NE2 A:HIS211 4.1 35.9 1.0 CA A:HIS211 4.2 43.0 1.0 CD2 A:HIS211 4.3 40.4 1.0 CB A:HIS172 4.3 38.5 1.0 C A:HIS172 4.3 40.9 1.0 CD2 A:HIS264 4.3 38.0 1.0 NE2 A:HIS264 4.4 38.3 1.0 CA A:HIS264 4.5 37.8 1.0 CA A:CYS170 4.5 48.5 1.0 O A:HOH1121 4.7 45.8 1.0 CA A:HIS172 4.8 40.2 1.0 C A:CYS170 4.9 45.7 1.0 O A:CYS170 5.0 47.9 1.0

Zinc binding site 3 out of 4 in the Structure of Uridylyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Uridylyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:44.9 occ:1.00 ND1 B:HIS138 2.2 49.5 1.0 SG B:CYS30 2.3 47.4 1.0 ND1 B:HIS86 2.3 47.8 1.0 SG B:CYS33 2.4 41.9 1.0 CG B:HIS138 3.1 46.8 1.0 CE1 B:HIS138 3.1 49.9 1.0 CB B:CYS30 3.2 49.9 1.0 CG B:HIS86 3.2 50.0 1.0 CE1 B:HIS86 3.3 50.3 1.0 CB B:HIS86 3.4 51.3 1.0 CB B:HIS138 3.4 43.0 1.0 CB B:CYS33 3.5 43.8 1.0 N B:CYS33 3.7 51.9 1.0 CA B:CYS33 3.8 46.6 1.0 CA B:HIS86 4.0 49.9 1.0 NE2 B:HIS138 4.2 56.4 1.0 CD2 B:HIS138 4.2 50.4 1.0 C B:PHE32 4.3 50.1 1.0 CD2 B:HIS86 4.4 49.6 1.0 NE2 B:HIS86 4.4 48.8 1.0 CA B:HIS138 4.6 43.8 1.0 CA B:CYS30 4.6 49.9 1.0 CB B:PHE32 4.8 47.3 1.0 N B:HIS86 4.8 46.6 1.0 CA B:PHE32 4.9 48.0 1.0 O B:PHE32 4.9 44.3 1.0 N B:PHE32 4.9 44.8 1.0

Zinc binding site 4 out of 4 in the Structure of Uridylyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Uridylyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:62.9 occ:1.00 ND1 B:HIS211 2.0 45.3 1.0 SG B:CYS173 2.3 65.0 1.0 SG B:CYS170 2.5 66.3 1.0 ND1 B:HIS264 2.7 56.5 1.0 CE1 B:HIS211 2.9 53.7 1.0 CG B:HIS211 3.0 54.9 1.0 CB B:CYS170 3.3 78.4 1.0 CG B:HIS264 3.3 53.1 1.0 CB B:HIS264 3.4 48.2 1.0 CB B:HIS211 3.5 56.4 1.0 N B:CYS173 3.5 60.3 1.0 CB B:CYS173 3.6 62.0 1.0 CE1 B:HIS264 3.6 61.0 1.0 CA B:CYS173 4.0 63.6 1.0 NE2 B:HIS211 4.0 58.7 1.0 CD2 B:HIS211 4.1 57.7 1.0 CA B:HIS211 4.1 60.4 1.0 CB B:HIS172 4.3 62.8 1.0 CD2 B:HIS264 4.4 59.6 1.0 NE2 B:HIS264 4.5 61.7 1.0 C B:HIS172 4.5 58.0 1.0 CA B:HIS264 4.6 51.6 1.0 CA B:CYS170 4.7 77.1 1.0 CA B:HIS172 4.8 62.2 1.0 O B:GLN261 4.9 66.3 1.0 O B:CYS170 4.9 68.2 1.0 C B:CYS170 5.0 71.2 1.0

T.Ohshida, J.Hayashi, K.Yoneda, T.Ohshima, H.Sakuraba. Unique Active Site Formation in A Novel Galactose 1-Phosphate Uridylyltransferase From the Hyperthermophilic Archaeon Pyrobaculum Aerophilum. Proteins 2019.
ISSN: ESSN 1097-0134
PubMed: 31693208
DOI: 10.1002/PROT.25848