Atomistry » Iron » PDB 5cne-5da5 » 5cnv
Atomistry »
  Iron »
    PDB 5cne-5da5 »
      5cnv »

Iron in PDB 5cnv: Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution

Enzymatic activity of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution

All present enzymatic activity of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution:
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution, PDB code: 5cnv was solved by P.Y.-T.Chen, C.M.Zimanyi, 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) 49.73 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 274.776, 157.753, 165.768, 90.00, 119.49, 90.00
R / Rfree (%) 19 / 21.9

Other elements in 5cnv:

The structure of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution (pdb code 5cnv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution, PDB code: 5cnv:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 5cnv

Go back to Iron Binding Sites List in 5cnv
Iron binding site 1 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:81.3
occ:1.00
 FE1 E:FEO501 0.0 81.3 1.0
O E:FEO501 1.8 75.4 1.0
O E:HOH601 2.0 75.9 1.0
OE1 E:GLU115 2.1 75.1 1.0
OD1 E:ASP84 2.1 77.7 1.0
OD2 E:ASP84 2.1 76.8 1.0
ND1 E:HIS118 2.3 72.9 1.0
CG E:ASP84 2.4 77.6 1.0
CE1 E:HIS118 3.1 73.1 1.0
FE2 E:FEO501 3.2 73.5 1.0
CD E:GLU115 3.2 74.0 1.0
OE1 E:GLU238 3.2 74.7 1.0
O E:HOH603 3.2 77.5 1.0
CG E:HIS118 3.5 72.8 1.0
OE2 E:GLU115 3.6 74.3 1.0
CB E:ASP84 3.9 77.0 1.0
CB E:HIS118 3.9 72.8 1.0
CZ E:PHE208 4.2 79.0 1.0
CE2 E:PHE208 4.3 79.2 1.0
CG2 E:ILE234 4.3 72.4 1.0
NE2 E:HIS118 4.3 72.2 1.0
CD E:GLU238 4.4 75.2 1.0
CG E:GLU115 4.5 71.9 1.0
CD2 E:HIS118 4.5 72.0 1.0
CE1 E:HIS241 4.6 73.1 1.0
CA E:GLU115 4.6 71.2 1.0
CB E:GLU115 4.7 72.0 1.0
CA E:ASP84 4.7 78.7 1.0
ND1 E:HIS241 4.7 72.8 1.0
OH E:TYR122 4.9 76.1 1.0
CE1 E:PHE208 4.9 77.9 1.0
CD2 E:PHE208 5.0 79.3 1.0

Iron binding site 2 out of 8 in 5cnv

Go back to Iron Binding Sites List in 5cnv
Iron binding site 2 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:73.5
occ:1.00
 FE2 E:FEO501 0.0 73.5 1.0
O E:FEO501 1.8 75.4 1.0
O E:HOH603 2.0 77.5 1.0
OE2 E:GLU115 2.0 74.3 1.0
OE1 E:GLU238 2.1 74.7 1.0
OE1 E:GLU204 2.1 75.0 1.0
ND1 E:HIS241 2.2 72.8 1.0
OE2 E:GLU238 2.4 76.3 1.0
CD E:GLU238 2.6 75.2 1.0
CD E:GLU115 2.9 74.0 1.0
CE1 E:HIS241 2.9 73.1 1.0
OE1 E:GLU115 3.0 75.1 1.0
FE1 E:FEO501 3.2 81.3 1.0
CD E:GLU204 3.2 75.3 1.0
CG E:HIS241 3.4 73.2 1.0
O E:HOH601 3.5 75.9 1.0
CG E:GLU204 3.7 77.5 1.0
CB E:HIS241 3.9 73.4 1.0
OD1 E:ASP84 4.0 77.7 1.0
CG E:GLU238 4.1 74.9 1.0
NE2 E:HIS241 4.2 72.7 1.0
OE2 E:GLU204 4.2 73.4 1.0
CG E:GLU115 4.3 71.9 1.0
NE1 E:TRP111 4.3 72.0 1.0
CD2 E:HIS241 4.4 73.1 1.0
CB E:GLU204 4.5 77.5 1.0
CA E:GLU238 4.5 73.7 1.0
CE1 E:HIS118 4.6 73.1 1.0
ND1 E:HIS118 4.7 72.9 1.0
CB E:GLU238 4.7 74.4 1.0
NE2 E:GLN87 4.8 75.5 1.0
CD1 E:TRP111 4.9 72.9 1.0

Iron binding site 3 out of 8 in 5cnv

Go back to Iron Binding Sites List in 5cnv
Iron binding site 3 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:49.9
occ:1.00
 FE1 F:FEO501 0.0 49.9 1.0
O F:FEO501 1.8 47.0 1.0
O F:HOH601 2.0 47.1 1.0
OE1 F:GLU115 2.0 44.2 1.0
OD1 F:ASP84 2.1 49.2 1.0
OD2 F:ASP84 2.1 47.6 1.0
ND1 F:HIS118 2.2 44.0 1.0
CG F:ASP84 2.4 48.8 1.0
CE1 F:HIS118 3.0 43.5 1.0
CD F:GLU115 3.1 43.8 1.0
O F:HOH602 3.1 46.6 1.0
FE2 F:FEO501 3.2 47.6 1.0
OE1 F:GLU238 3.3 48.6 1.0
CG F:HIS118 3.3 44.6 1.0
OE2 F:GLU115 3.4 44.6 1.0
CB F:HIS118 3.8 44.9 1.0
CB F:ASP84 3.9 47.0 1.0
NE2 F:HIS118 4.2 43.7 1.0
CZ F:PHE208 4.2 51.1 1.0
CE2 F:PHE208 4.2 51.4 1.0
CD2 F:HIS118 4.4 43.9 1.0
CE1 F:HIS241 4.4 44.5 1.0
CG F:GLU115 4.4 43.5 1.0
CG2 F:ILE234 4.5 42.6 1.0
CD F:GLU238 4.5 48.5 1.0
ND1 F:HIS241 4.6 44.8 1.0
CA F:GLU115 4.6 43.6 1.0
CB F:GLU115 4.7 43.4 1.0
CA F:ASP84 4.7 46.2 1.0
CE1 F:PHE208 4.9 49.4 1.0
CD2 F:PHE208 4.9 50.8 1.0

Iron binding site 4 out of 8 in 5cnv

Go back to Iron Binding Sites List in 5cnv
Iron binding site 4 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:47.6
occ:1.00
 FE2 F:FEO501 0.0 47.6 1.0
O F:FEO501 1.8 47.0 1.0
O F:HOH602 2.0 46.6 1.0
OE1 F:GLU204 2.0 44.2 1.0
OE2 F:GLU115 2.0 44.6 1.0
OE1 F:GLU238 2.1 48.6 1.0
ND1 F:HIS241 2.2 44.8 1.0
OE2 F:GLU238 2.5 48.6 1.0
CD F:GLU238 2.6 48.5 1.0
CE1 F:HIS241 2.9 44.5 1.0
CD F:GLU115 3.0 43.8 1.0
CD F:GLU204 3.1 46.9 1.0
FE1 F:FEO501 3.2 49.9 1.0
OE1 F:GLU115 3.2 44.2 1.0
CG F:HIS241 3.4 45.6 1.0
O F:HOH601 3.6 47.1 1.0
CG F:GLU204 3.7 46.4 1.0
CB F:HIS241 3.9 45.1 1.0
OD1 F:ASP84 3.9 49.2 1.0
CG F:GLU238 4.1 47.1 1.0
OE2 F:GLU204 4.2 48.6 1.0
NE2 F:HIS241 4.2 43.6 1.0
NE1 F:TRP111 4.3 42.3 1.0
CG F:GLU115 4.3 43.5 1.0
CD2 F:HIS241 4.4 44.8 1.0
CB F:GLU204 4.5 46.1 1.0
NE2 F:GLN87 4.6 44.1 1.0
CE1 F:HIS118 4.6 43.5 1.0
CA F:GLU238 4.6 45.0 1.0
ND1 F:HIS118 4.6 44.0 1.0
CB F:GLU238 4.8 44.5 1.0
CG F:GLN87 4.8 44.8 1.0
CD1 F:TRP111 4.9 43.3 1.0
CG F:ASP84 5.0 48.8 1.0

Iron binding site 5 out of 8 in 5cnv

Go back to Iron Binding Sites List in 5cnv
Iron binding site 5 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe501

b:47.6
occ:1.00
 FE1 G:FEO501 0.0 47.6 1.0
O G:FEO501 1.8 43.9 1.0
O G:HOH601 2.0 44.3 1.0
OE1 G:GLU115 2.0 44.3 1.0
OD2 G:ASP84 2.1 47.2 1.0
OD1 G:ASP84 2.1 47.3 1.0
ND1 G:HIS118 2.3 44.0 1.0
CG G:ASP84 2.4 47.5 1.0
OE1 G:GLU238 3.0 44.5 1.0
CE1 G:HIS118 3.0 44.6 1.0
CD G:GLU115 3.1 43.7 1.0
FE2 G:FEO501 3.2 45.6 1.0
O G:HOH603 3.2 44.3 1.0
OE2 G:GLU115 3.4 43.7 1.0
CG G:HIS118 3.4 44.2 1.0
CB G:ASP84 3.9 46.8 1.0
CB G:HIS118 3.9 45.1 1.0
CD G:GLU238 4.2 44.3 1.0
NE2 G:HIS118 4.2 44.3 1.0
CG G:GLU115 4.4 42.7 1.0
CE1 G:HIS241 4.4 42.3 1.0
CZ G:PHE208 4.4 47.9 1.0
CE2 G:PHE208 4.4 47.4 1.0
CD2 G:HIS118 4.5 44.3 1.0
ND1 G:HIS241 4.5 42.8 1.0
CG2 G:ILE234 4.5 44.6 1.0
CA G:GLU115 4.7 43.6 1.0
CB G:GLU115 4.7 43.2 1.0
CA G:ASP84 4.8 46.7 1.0
OE2 G:GLU238 4.8 44.9 1.0

Iron binding site 6 out of 8 in 5cnv

Go back to Iron Binding Sites List in 5cnv
Iron binding site 6 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe501

b:45.6
occ:1.00
 FE2 G:FEO501 0.0 45.6 1.0
O G:FEO501 1.8 43.9 1.0
O G:HOH603 2.0 44.3 1.0
OE2 G:GLU115 2.0 43.7 1.0
OE1 G:GLU204 2.1 41.5 1.0
OE1 G:GLU238 2.1 44.5 1.0
ND1 G:HIS241 2.3 42.8 1.0
OE2 G:GLU238 2.3 44.9 1.0
CD G:GLU238 2.5 44.3 1.0
CD G:GLU115 3.0 43.7 1.0
CE1 G:HIS241 3.1 42.3 1.0
CD G:GLU204 3.1 42.9 1.0
FE1 G:FEO501 3.2 47.6 1.0
OE1 G:GLU115 3.3 44.3 1.0
CG G:HIS241 3.4 43.1 1.0
CG G:GLU204 3.7 44.3 1.0
CB G:HIS241 3.8 42.5 1.0
O G:HOH601 3.8 44.3 1.0
OD1 G:ASP84 3.9 47.3 1.0
CG G:GLU238 4.0 43.2 1.0
NE1 G:TRP111 4.2 41.1 1.0
OE2 G:GLU204 4.2 43.7 1.0
NE2 G:HIS241 4.3 41.0 1.0
CG G:GLU115 4.3 42.7 1.0
CD2 G:HIS241 4.4 42.5 1.0
CA G:GLU238 4.5 42.4 1.0
CB G:GLU204 4.5 42.8 1.0
NE2 G:GLN87 4.6 42.7 1.0
CB G:GLU238 4.7 42.9 1.0
CE1 G:HIS118 4.8 44.6 1.0
ND1 G:HIS118 4.8 44.0 1.0
CD1 G:TRP111 4.8 40.6 1.0
CG G:GLN87 4.8 44.7 1.0
CG G:ASP84 4.9 47.5 1.0

Iron binding site 7 out of 8 in 5cnv

Go back to Iron Binding Sites List in 5cnv
Iron binding site 7 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe501

b:63.3
occ:1.00
 FE1 H:FEO501 0.0 63.3 1.0
O H:FEO501 1.8 63.0 1.0
O H:HOH603 2.0 62.3 1.0
OE1 H:GLU115 2.1 64.7 1.0
OD1 H:ASP84 2.1 64.8 1.0
OD2 H:ASP84 2.1 63.5 1.0
ND1 H:HIS118 2.3 62.6 1.0
CG H:ASP84 2.4 64.1 1.0
O H:HOH606 3.0 63.7 1.0
CE1 H:HIS118 3.1 63.2 1.0
FE2 H:FEO501 3.2 62.8 1.0
CD H:GLU115 3.2 64.2 1.0
OE1 H:GLU238 3.3 64.1 1.0
CG H:HIS118 3.4 63.0 1.0
OE2 H:GLU115 3.6 64.6 1.0
CB H:HIS118 3.8 62.9 1.0
CB H:ASP84 3.9 63.1 1.0
CZ H:PHE208 4.2 63.9 1.0
CE2 H:PHE208 4.3 62.8 1.0
NE2 H:HIS118 4.3 62.8 1.0
CG H:GLU115 4.4 63.0 1.0
CG2 H:ILE234 4.5 59.6 1.0
CD2 H:HIS118 4.5 63.1 1.0
CD H:GLU238 4.5 62.9 1.0
CA H:GLU115 4.6 64.8 1.0
CE1 H:HIS241 4.6 62.2 1.0
CB H:GLU115 4.6 65.0 1.0
CA H:ASP84 4.7 64.5 1.0
ND1 H:HIS241 4.8 62.8 1.0
CE1 H:PHE208 4.8 63.4 1.0
CD2 H:PHE208 5.0 63.0 1.0
O H:GLU115 5.0 64.0 1.0

Iron binding site 8 out of 8 in 5cnv

Go back to Iron Binding Sites List in 5cnv
Iron binding site 8 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Gdp and Ttp at 3.20 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe501

b:62.8
occ:1.00
 FE2 H:FEO501 0.0 62.8 1.0
O H:FEO501 1.8 63.0 1.0
O H:HOH606 2.0 63.7 1.0
OE2 H:GLU115 2.0 64.6 1.0
OE1 H:GLU204 2.1 61.4 1.0
OE1 H:GLU238 2.1 64.1 1.0
ND1 H:HIS241 2.3 62.8 1.0
OE2 H:GLU238 2.6 64.2 1.0
CD H:GLU238 2.7 62.9 1.0
CD H:GLU115 2.9 64.2 1.0
CE1 H:HIS241 2.9 62.2 1.0
OE1 H:GLU115 3.0 64.7 1.0
FE1 H:FEO501 3.2 63.3 1.0
CD H:GLU204 3.2 63.0 1.0
CG H:HIS241 3.5 64.2 1.0
O H:HOH603 3.6 62.3 1.0
CG H:GLU204 3.7 63.7 1.0
CB H:HIS241 4.0 63.3 1.0
OD1 H:ASP84 4.0 64.8 1.0
CG H:GLU238 4.1 60.8 1.0
NE2 H:HIS241 4.2 61.9 1.0
OE2 H:GLU204 4.2 63.1 1.0
CG H:GLU115 4.3 63.0 1.0
NE1 H:TRP111 4.3 63.1 1.0
CD2 H:HIS241 4.4 63.6 1.0
CE1 H:HIS118 4.5 63.2 1.0
ND1 H:HIS118 4.6 62.6 1.0
CB H:GLU204 4.6 64.4 1.0
CA H:GLU238 4.6 61.3 1.0
NE2 H:GLN87 4.7 66.0 1.0
CB H:GLU238 4.8 61.2 1.0
CD1 H:TRP111 4.9 62.8 1.0
CG H:GLN87 5.0 65.4 1.0
CG H:ASP84 5.0 64.1 1.0

Reference:

C.M.Zimanyi, P.Y.Chen, G.Kang, M.A.Funk, C.L.Drennan. Molecular Basis For Allosteric Specificity Regulation in Class Ia Ribonucleotide Reductase From Escherichia Coli. Elife V. 5 07141 2016.
ISSN: ESSN 2050-084X
PubMed: 26754917
DOI: 10.7554/ELIFE.07141
Page generated: Mon Aug 5 21:34:12 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy