Iron 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:

Zinc

(Zn)

4 atoms

The binding sites of Iron atom in the Structure of Uridylyltransferase Mutant (pdb code 6k9z). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Structure of Uridylyltransferase Mutant, PDB code: 6k9z:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Structure of Uridylyltransferase Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Uridylyltransferase Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe403 b:14.5 occ:1.00 NE2 A:HIS266 2.2 12.5 1.0 O A:HOH601 2.2 15.6 1.0 ND1 A:HIS252 2.2 13.5 1.0 OE1 A:GLU156 2.2 16.3 1.0 OE2 A:GLU156 2.3 16.6 1.0 OE1 A:GLU268 2.3 16.7 1.0 CD A:GLU156 2.6 16.2 1.0 CE1 A:HIS252 3.1 13.2 1.0 CD2 A:HIS266 3.1 12.6 1.0 CD A:GLU268 3.2 15.8 1.0 CE1 A:HIS266 3.3 13.8 1.0 CG A:HIS252 3.4 12.8 1.0 CB A:HIS252 3.8 12.8 1.0 OE2 A:GLU268 3.9 16.7 1.0 CG A:GLU268 4.0 14.8 1.0 CG A:GLU156 4.1 15.8 1.0 O B:HOH1227 4.2 31.2 1.0 OH A:TYR263 4.2 14.7 1.0 O A:HOH597 4.3 48.5 1.0 NE2 A:HIS252 4.3 12.9 1.0 CG A:HIS266 4.3 12.5 1.0 ND1 A:HIS266 4.3 12.4 1.0 O A:HOH531 4.4 14.6 1.0 CD2 A:HIS252 4.4 12.9 1.0 CE1 A:HIS205 4.9 14.4 1.0 CB A:GLU156 4.9 15.6 1.0

Iron binding site 2 out of 2 in the Structure of Uridylyltransferase Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Uridylyltransferase Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1004 b:14.9 occ:1.00 ND1 B:HIS252 2.2 13.9 1.0 NE2 B:HIS266 2.2 13.4 1.0 OE2 B:GLU156 2.2 15.3 1.0 OE1 B:GLU268 2.2 15.6 1.0 O B:HOH1215 2.2 15.5 1.0 OE1 B:GLU156 2.4 14.8 1.0 CD B:GLU156 2.6 15.5 1.0 CD2 B:HIS266 3.1 13.5 1.0 CE1 B:HIS252 3.1 13.9 1.0 CD B:GLU268 3.1 15.0 1.0 CE1 B:HIS266 3.3 14.1 1.0 CG B:HIS252 3.4 13.9 1.0 CB B:HIS252 3.8 13.9 1.0 OE2 B:GLU268 3.8 15.1 1.0 CG B:GLU268 3.9 14.4 1.0 O A:HOH540 4.0 39.3 1.0 CG B:GLU156 4.1 15.4 1.0 CG B:HIS266 4.3 13.4 1.0 NE2 B:HIS252 4.3 14.4 1.0 OH B:TYR263 4.3 17.1 1.0 O B:HOH1159 4.3 14.1 1.0 ND1 B:HIS266 4.4 13.8 1.0 CD2 B:HIS252 4.4 14.2 1.0 CE1 B:HIS205 4.9 14.2 1.0 CB B:GLU156 5.0 16.1 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