Zinc in PDB 6k9z: Structure of Uridylyltransferase Mutant

The structure of Structure of Uridylyltransferase Mutant, PDB code: 6k9z 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)	47.76 / 1.78
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	62.188, 62.188, 308.594, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 19.6

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

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the Structure of Uridylyltransferase Mutant (pdb code 6k9z). 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 Mutant, PDB code: 6k9z:
Jump to Zinc binding site number: 1; 2; 3; 4;

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


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 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:24.2 occ:1.00 ND1 A:HIS86 1.9 35.8 1.0 ND1 A:HIS138 2.1 24.4 1.0 SG A:CYS30 2.3 26.3 1.0 SG A:CYS33 2.3 27.7 1.0 CE1 A:HIS86 2.9 35.7 1.0 CG A:HIS86 3.0 35.7 1.0 CB A:CYS30 3.1 27.8 1.0 CE1 A:HIS138 3.1 24.8 1.0 CG A:HIS138 3.1 24.8 1.0 CB A:HIS86 3.4 36.2 1.0 CB A:HIS138 3.4 25.6 1.0 CB A:CYS33 3.4 29.0 1.0 N A:CYS33 3.4 28.2 1.0 CA A:CYS33 3.6 29.3 1.0 NE2 A:HIS86 4.0 36.6 1.0 CD2 A:HIS86 4.1 37.1 1.0 CA A:HIS86 4.1 35.1 1.0 C A:PHE32 4.2 28.0 1.0 CD2 A:HIS138 4.2 22.9 1.0 NE2 A:HIS138 4.2 23.1 1.0 CA A:CYS30 4.5 28.7 1.0 CA A:HIS138 4.5 25.8 1.0 O A:HOH626 4.6 32.9 1.0 CB A:PHE32 4.7 27.5 1.0 CA A:PHE32 4.8 27.5 1.0 N A:PHE32 4.8 27.7 1.0 C A:CYS30 4.9 27.6 1.0 N A:HIS86 4.9 34.5 1.0 O A:PHE32 4.9 28.8 1.0 O A:CYS30 5.0 27.6 1.0

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


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 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:18.4 occ:1.00 ND1 A:HIS211 2.1 18.5 1.0 SG A:CYS173 2.3 21.6 1.0 ND1 A:HIS264 2.3 17.5 1.0 SG A:CYS170 2.3 20.9 1.0 CE1 A:HIS211 3.0 18.1 1.0 CB A:CYS170 3.2 24.3 1.0 CG A:HIS211 3.2 18.6 1.0 CE1 A:HIS264 3.2 17.3 1.0 CG A:HIS264 3.3 16.5 1.0 CB A:CYS173 3.4 23.5 1.0 N A:CYS173 3.5 20.8 1.0 CB A:HIS264 3.5 16.9 1.0 CB A:HIS211 3.6 19.0 1.0 CA A:CYS173 3.7 22.5 1.0 O A:HOH651 4.0 28.9 1.0 NE2 A:HIS211 4.2 18.2 1.0 CA A:HIS211 4.2 18.6 1.0 CB A:HIS172 4.3 17.9 1.0 CD2 A:HIS211 4.3 18.5 1.0 NE2 A:HIS264 4.3 16.7 1.0 C A:HIS172 4.4 19.7 1.0 CD2 A:HIS264 4.4 15.8 1.0 CA A:CYS170 4.6 26.4 1.0 CA A:HIS264 4.6 15.9 1.0 O A:CYS170 4.8 28.9 1.0 CA A:HIS172 4.8 18.5 1.0 C A:CYS170 4.8 26.6 1.0 O A:HOH577 5.0 26.0 1.0 N A:HIS172 5.0 20.0 1.0

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


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 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:39.3 occ:1.00 ND1 B:HIS86 2.1 44.8 1.0 ND1 B:HIS138 2.2 35.6 1.0 SG B:CYS30 2.3 56.9 1.0 SG B:CYS33 2.6 67.5 1.0 CE1 B:HIS86 3.0 46.8 1.0 CG B:HIS138 3.1 34.9 1.0 CG B:HIS86 3.2 47.6 1.0 CE1 B:HIS138 3.2 36.3 1.0 CB B:CYS30 3.2 60.2 1.0 CB B:HIS138 3.4 35.1 1.0 CB B:CYS33 3.6 67.3 1.0 CB B:HIS86 3.6 47.8 1.0 N B:CYS33 3.6 61.9 1.0 CA B:CYS33 3.8 64.9 1.0 C B:PHE32 4.1 59.4 1.0 CA B:HIS86 4.1 45.3 1.0 NE2 B:HIS86 4.1 48.3 1.0 CD2 B:HIS86 4.3 49.3 1.0 CD2 B:HIS138 4.3 32.7 1.0 NE2 B:HIS138 4.3 33.5 1.0 CA B:HIS138 4.5 34.0 1.0 O B:PHE32 4.6 60.0 1.0 CA B:CYS30 4.7 60.4 1.0 CA B:PHE32 4.8 57.8 1.0 N B:PHE32 4.8 58.9 1.0 CB B:PHE32 4.8 54.1 1.0 N B:HIS86 5.0 44.2 1.0

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


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 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:20.1 occ:1.00 ND1 B:HIS211 2.0 21.4 1.0 ND1 B:HIS264 2.1 17.4 1.0 SG B:CYS173 2.3 21.3 1.0 SG B:CYS170 2.3 20.5 1.0 CE1 B:HIS211 2.9 22.4 1.0 CE1 B:HIS264 3.0 17.8 1.0 CB B:CYS170 3.1 23.0 1.0 CG B:HIS264 3.1 17.1 1.0 CG B:HIS211 3.1 21.2 1.0 CB B:CYS173 3.3 22.0 1.0 CB B:HIS264 3.4 17.0 1.0 N B:CYS173 3.4 20.2 1.0 CB B:HIS211 3.5 21.0 1.0 CA B:CYS173 3.8 20.9 1.0 CA B:HIS211 4.1 20.1 1.0 NE2 B:HIS211 4.1 21.7 1.0 NE2 B:HIS264 4.2 16.8 1.0 CD2 B:HIS264 4.2 16.9 1.0 CD2 B:HIS211 4.2 21.8 1.0 CB B:HIS172 4.3 17.8 1.0 C B:HIS172 4.4 18.8 1.0 CA B:CYS170 4.5 24.1 1.0 CA B:HIS264 4.7 16.6 1.0 CA B:HIS172 4.8 18.8 1.0 O B:HOH1140 4.8 33.2 1.0 O B:CYS170 4.8 23.0 1.0 C B:CYS170 4.9 23.6 1.0 N B:HIS172 5.0 19.7 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