Iron 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:

Zinc

(Zn)

4 atoms

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

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1003 b:48.2 occ:1.00 OE2 A:GLU156 2.2 34.4 1.0 OE2 A:GLU268 2.2 35.1 1.0 NE2 A:HIS266 2.3 28.4 1.0 ND1 A:HIS252 2.3 35.1 1.0 O A:HOH1120 2.4 32.7 1.0 OE1 A:GLU156 2.5 36.5 1.0 CD A:GLU156 2.6 38.5 1.0 CD A:GLU268 3.0 35.5 1.0 CE1 A:HIS252 3.1 31.3 1.0 CE1 A:HIS266 3.2 31.5 1.0 CD2 A:HIS266 3.3 31.3 1.0 CG A:HIS252 3.5 37.2 1.0 OE1 A:GLU268 3.7 35.3 1.0 CG A:GLU268 3.9 34.1 1.0 CB A:HIS252 4.0 36.3 1.0 O B:HOH1120 4.0 44.2 1.0 CG A:GLU156 4.1 37.6 1.0 NE2 A:HIS252 4.3 32.0 1.0 OH A:TYR263 4.3 34.9 1.0 ND1 A:HIS266 4.4 34.9 1.0 O A:HOH1102 4.4 33.0 1.0 CG A:HIS266 4.5 33.8 1.0 CD2 A:HIS252 4.5 34.4 1.0 CE1 A:HIS205 4.8 37.1 1.0 CB A:GLU156 5.0 38.2 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1003 b:58.3 occ:1.00 OE2 B:GLU156 2.2 53.7 1.0 OE2 B:GLU268 2.3 37.1 1.0 OE1 B:GLU156 2.4 46.6 1.0 NE2 B:HIS266 2.4 41.0 1.0 ND1 B:HIS252 2.5 46.0 1.0 O B:HOH1121 2.5 54.9 1.0 CD B:GLU156 2.6 50.6 1.0 CD B:GLU268 3.1 37.1 1.0 CE1 B:HIS252 3.2 39.6 1.0 CD2 B:HIS266 3.2 39.5 1.0 CE1 B:HIS266 3.5 41.2 1.0 CG B:HIS252 3.6 46.7 1.0 OE1 B:GLU268 3.6 40.5 1.0 CG B:GLU268 4.0 38.2 1.0 CB B:HIS252 4.1 40.1 1.0 CG B:GLU156 4.1 48.3 1.0 CG B:HIS266 4.4 42.6 1.0 NE2 B:HIS252 4.4 36.0 1.0 OH B:TYR263 4.5 53.5 1.0 ND1 B:HIS266 4.5 44.6 1.0 CE1 B:HIS205 4.5 55.3 1.0 CD2 B:HIS252 4.6 41.6 1.0 ND1 B:HIS205 4.9 55.8 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