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Iron in PDB 5ci1: Ribonucleotide Reductase Y122 2,3-F2Y Variant

Enzymatic activity of Ribonucleotide Reductase Y122 2,3-F2Y Variant

All present enzymatic activity of Ribonucleotide Reductase Y122 2,3-F2Y Variant:
1.17.4.1;

Protein crystallography data

The structure of Ribonucleotide Reductase Y122 2,3-F2Y Variant, PDB code: 5ci1 was solved by M.A.Funk, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.00 / 1.95
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 90.589, 90.589, 209.468, 90.00, 90.00, 120.00
R / Rfree (%) 15.4 / 18.3

Other elements in 5ci1:

The structure of Ribonucleotide Reductase Y122 2,3-F2Y Variant also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Ribonucleotide Reductase Y122 2,3-F2Y Variant (pdb code 5ci1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Ribonucleotide Reductase Y122 2,3-F2Y Variant, PDB code: 5ci1:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 5ci1

Go back to Iron Binding Sites List in 5ci1
Iron binding site 1 out of 2 in the Ribonucleotide Reductase Y122 2,3-F2Y Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ribonucleotide Reductase Y122 2,3-F2Y Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:29.8
occ:1.00
FE1 A:FEO401 0.0 29.8 1.0
O A:FEO401 1.9 23.4 1.0
OE1 A:GLU204 2.1 29.4 1.0
OE1 A:GLU238 2.1 32.6 1.0
OE2 A:GLU115 2.2 35.4 1.0
O A:HOH547 2.2 35.1 1.0
ND1 A:HIS241 2.2 31.4 1.0
CD A:GLU238 3.0 35.0 1.0
HG2 A:GLU204 3.0 43.8 1.0
CD A:GLU115 3.1 33.4 1.0
CD A:GLU204 3.1 33.4 1.0
CE1 A:HIS241 3.1 33.7 1.0
HE1 A:HIS241 3.2 40.5 1.0
OE2 A:GLU238 3.3 43.1 1.0
HE1 A:TRP111 3.3 32.0 1.0
FE2 A:FEO401 3.3 29.7 1.0
OE1 A:GLU115 3.3 29.2 1.0
CG A:HIS241 3.3 30.2 1.0
HB2 A:HIS241 3.5 33.7 1.0
CG A:GLU204 3.5 36.5 1.0
HB3 A:HIS241 3.6 33.7 1.0
HA A:GLU238 3.6 34.3 1.0
CB A:HIS241 3.7 28.1 1.0
HE21 A:GLN87 3.7 49.9 1.0
NE1 A:TRP111 4.0 26.7 1.0
OE2 A:GLU204 4.1 36.6 1.0
HG3 A:GLU204 4.2 43.8 1.0
HE1 A:HIS118 4.3 27.7 1.0
NE2 A:HIS241 4.3 27.5 1.0
HB3 A:GLU204 4.3 37.7 1.0
O A:HOH591 4.3 35.5 1.0
OD1 A:ASP84 4.3 36.0 1.0
CG A:GLU238 4.3 31.4 1.0
HD1 A:TRP111 4.4 30.3 1.0
HG3 A:GLN87 4.4 40.3 1.0
CD2 A:HIS241 4.4 29.6 1.0
CG A:GLU115 4.4 21.9 1.0
CA A:GLU238 4.5 28.6 1.0
HB3 A:GLN87 4.5 39.5 1.0
CB A:GLU204 4.5 31.4 1.0
NE2 A:GLN87 4.6 41.6 1.0
HB2 A:GLU238 4.6 35.5 1.0
HG3 A:GLU238 4.6 37.6 1.0
HG2 A:GLU115 4.6 26.3 1.0
CD1 A:TRP111 4.6 25.2 1.0
HG3 A:GLU115 4.6 26.3 1.0
CB A:GLU238 4.7 29.6 1.0
ND1 A:HIS118 4.8 25.1 1.0
OD2 A:ASP84 4.8 29.0 1.0
CE1 A:HIS118 4.8 23.1 1.0
HA A:GLU204 4.9 39.4 1.0

Iron binding site 2 out of 2 in 5ci1

Go back to Iron Binding Sites List in 5ci1
Iron binding site 2 out of 2 in the Ribonucleotide Reductase Y122 2,3-F2Y Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ribonucleotide Reductase Y122 2,3-F2Y Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:29.7
occ:1.00
FE2 A:FEO401 0.0 29.7 1.0
OD2 A:ASP84 1.9 29.0 1.0
O A:FEO401 1.9 23.4 1.0
OE1 A:GLU115 2.1 29.2 1.0
ND1 A:HIS118 2.2 25.1 1.0
O A:HOH591 2.4 35.5 1.0
CG A:ASP84 2.7 34.4 1.0
OD1 A:ASP84 2.9 36.0 1.0
O A:HOH547 3.0 35.1 1.0
CE1 A:HIS118 3.0 23.1 1.0
HE1 A:HIS118 3.1 27.7 1.0
CD A:GLU115 3.1 33.4 1.0
FE1 A:FEO401 3.3 29.8 1.0
CG A:HIS118 3.3 23.0 1.0
OE2 A:GLU115 3.5 35.4 1.0
HB2 A:HIS118 3.5 32.4 1.0
HG23 A:ILE234 3.6 30.1 1.0
HB3 A:HIS118 3.7 32.4 1.0
HA A:GLU115 3.7 34.0 1.0
CB A:HIS118 3.8 27.0 1.0
HE1 A:HIS241 3.8 40.5 1.0
OE2 A:GLU238 3.9 43.1 1.0
CB A:ASP84 4.1 24.9 1.0
NE2 A:HIS118 4.2 22.8 1.0
HB3 A:ASP84 4.3 29.9 1.0
CD2 A:HIS118 4.4 26.8 1.0
CG2 A:ILE234 4.4 25.1 1.0
HZ A:PHE208 4.4 39.7 1.0
HG21 A:ILE234 4.4 30.1 1.0
CE1 A:HIS241 4.4 33.7 1.0
CZ A:PHE208 4.4 33.1 1.0
OH A:FY2122 4.4 37.9 0.3
CG A:GLU115 4.4 21.9 1.0
HB3 A:GLU115 4.5 29.3 1.0
HH A:FY2122 4.5 45.4 0.3
CD A:GLU238 4.5 35.0 1.0
ND1 A:HIS241 4.5 31.4 1.0
HB2 A:ASP84 4.5 29.9 1.0
OE1 A:GLU238 4.5 32.6 1.0
CE2 A:PHE208 4.6 35.9 1.0
CA A:GLU115 4.6 28.3 1.0
HE2 A:PHE208 4.6 43.1 1.0
HG22 A:ILE234 4.7 30.1 1.0
F3 A:FY2122 4.7 42.1 0.7
HH A:FY2122 4.7 32.6 0.7
CB A:GLU115 4.7 24.4 1.0
HB2 A:GLN87 4.8 39.5 1.0
HA A:ASP84 4.9 40.9 1.0
CE1 A:PHE208 4.9 32.8 1.0
HG2 A:GLU115 4.9 26.3 1.0

Reference:

P.H.Oyala, K.R.Ravichandran, M.A.Funk, P.A.Stucky, T.A.Stich, C.L.Drennan, R.D.Britt, J.Stubbe. Biophysical Characterization of Fluorotyrosine Probes Site-Specifically Incorporated Into Enzymes: E. Coli Ribonucleotide Reductase As An Example. J.Am.Chem.Soc. V. 138 7951 2016.
ISSN: ESSN 1520-5126
PubMed: 27276098
DOI: 10.1021/JACS.6B03605
Page generated: Mon Aug 5 20:58:46 2024

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