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Iron in PDB 6k5z: Structure of Uridylyltransferase

Protein crystallography data

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

Other elements in 6k5z:

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

Zinc (Zn) 4 atoms

Iron Binding Sites:

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 6k5z

Go back to Iron Binding Sites List in 6k5z
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 6k5z

Go back to Iron Binding Sites List in 6k5z
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

Reference:

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
Page generated: Sun Dec 13 16:36:20 2020

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