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Iron in PDB 5cns: Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Cdp and Datp at 2.97 Angstroms Resolution

Enzymatic activity of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Cdp and Datp at 2.97 Angstroms Resolution

All present enzymatic activity of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Cdp and Datp at 2.97 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 Cdp and Datp at 2.97 Angstroms Resolution, PDB code: 5cns 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) 49.48 / 2.98
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 274.154, 157.830, 164.251, 90.00, 118.82, 90.00
R / Rfree (%) 19 / 21.4

Other elements in 5cns:

The structure of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Cdp and Datp at 2.97 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 Cdp and Datp at 2.97 Angstroms Resolution (pdb code 5cns). 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 Cdp and Datp at 2.97 Angstroms Resolution, PDB code: 5cns:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 5cns

Go back to Iron Binding Sites List in 5cns
Iron binding site 1 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Cdp and Datp at 2.97 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 Cdp and Datp at 2.97 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:62.4
occ:1.00
 FE1 E:FEO501 0.0 62.4 1.0
O E:FEO501 1.8 59.2 1.0
O E:HOH602 2.0 57.9 1.0
OE1 E:GLU115 2.1 57.9 1.0
OD2 E:ASP84 2.1 61.5 1.0
OD1 E:ASP84 2.1 61.3 1.0
ND1 E:HIS118 2.3 56.0 1.0
CG E:ASP84 2.4 61.7 1.0
CE1 E:HIS118 3.1 56.5 1.0
FE2 E:FEO501 3.1 56.0 1.0
CD E:GLU115 3.2 57.4 1.0
O E:HOH606 3.2 59.1 1.0
OE1 E:GLU238 3.2 60.6 1.0
CG E:HIS118 3.4 55.8 1.0
OE2 E:GLU115 3.6 57.4 1.0
CB E:HIS118 3.8 56.5 1.0
CB E:ASP84 3.9 60.6 1.0
CZ E:PHE208 4.2 64.0 1.0
CE2 E:PHE208 4.3 63.8 1.0
NE2 E:HIS118 4.3 55.6 1.0
CG2 E:ILE234 4.4 55.7 1.0
CG E:GLU115 4.5 56.6 1.0
CD2 E:HIS118 4.5 55.1 1.0
CD E:GLU238 4.5 60.2 1.0
CE1 E:HIS241 4.5 57.0 1.0
CA E:GLU115 4.6 54.7 1.0
ND1 E:HIS241 4.6 57.2 1.0
CB E:GLU115 4.7 56.7 1.0
CA E:ASP84 4.7 62.0 1.0
CE1 E:PHE208 4.8 61.6 1.0
CD2 E:PHE208 5.0 63.5 1.0

Iron binding site 2 out of 8 in 5cns

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Iron binding site 2 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Cdp and Datp at 2.97 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 Cdp and Datp at 2.97 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:56.0
occ:1.00
 FE2 E:FEO501 0.0 56.0 1.0
O E:FEO501 1.8 59.2 1.0
O E:HOH606 2.0 59.1 1.0
OE2 E:GLU115 2.0 57.4 1.0
OE1 E:GLU204 2.1 57.8 1.0
OE1 E:GLU238 2.1 60.6 1.0
ND1 E:HIS241 2.2 57.2 1.0
OE2 E:GLU238 2.7 61.7 1.0
CD E:GLU238 2.7 60.2 1.0
CD E:GLU115 2.8 57.4 1.0
OE1 E:GLU115 3.0 57.9 1.0
CE1 E:HIS241 3.1 57.0 1.0
CD E:GLU204 3.1 59.5 1.0
FE1 E:FEO501 3.1 62.4 1.0
CG E:HIS241 3.4 57.3 1.0
O E:HOH602 3.6 57.9 1.0
CG E:GLU204 3.7 61.0 1.0
CB E:HIS241 3.8 56.2 1.0
OD1 E:ASP84 3.9 61.3 1.0
OE2 E:GLU204 4.1 59.1 1.0
NE1 E:TRP111 4.2 55.9 1.0
CG E:GLU238 4.2 58.1 1.0
NE2 E:HIS241 4.2 56.0 1.0
CG E:GLU115 4.3 56.6 1.0
CD2 E:HIS241 4.4 56.4 1.0
CB E:GLU204 4.6 59.4 1.0
CE1 E:HIS118 4.6 56.5 1.0
ND1 E:HIS118 4.6 56.0 1.0
CA E:GLU238 4.6 58.1 1.0
NE2 E:GLN87 4.7 59.1 1.0
CD1 E:TRP111 4.8 55.6 1.0
CB E:GLU238 4.8 59.1 1.0
CG E:GLN87 4.9 60.8 1.0
CG E:ASP84 4.9 61.7 1.0
CE2 E:PHE208 5.0 63.8 1.0

Iron binding site 3 out of 8 in 5cns

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Iron binding site 3 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Cdp and Datp at 2.97 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 Cdp and Datp at 2.97 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:36.5
occ:1.00
 FE1 F:FEO501 0.0 36.5 1.0
O F:FEO501 1.8 35.9 1.0
O F:HOH603 2.0 35.2 1.0
OE1 F:GLU115 2.0 34.0 1.0
OD1 F:ASP84 2.1 37.9 1.0
OD2 F:ASP84 2.1 37.7 1.0
ND1 F:HIS118 2.2 32.9 1.0
CG F:ASP84 2.4 37.4 1.0
CE1 F:HIS118 3.0 32.2 1.0
CD F:GLU115 3.1 33.2 1.0
O F:HOH602 3.2 34.5 1.0
FE2 F:FEO501 3.2 37.9 1.0
OE1 F:GLU238 3.3 37.0 1.0
CG F:HIS118 3.3 33.7 1.0
OE2 F:GLU115 3.5 32.8 1.0
CB F:HIS118 3.8 34.6 1.0
CB F:ASP84 3.9 35.5 1.0
NE2 F:HIS118 4.2 33.5 1.0
CZ F:PHE208 4.2 38.4 1.0
CE2 F:PHE208 4.3 39.2 1.0
CD2 F:HIS118 4.4 33.0 1.0
CG F:GLU115 4.4 33.7 1.0
CE1 F:HIS241 4.4 32.4 1.0
CG2 F:ILE234 4.5 31.4 1.0
CD F:GLU238 4.5 37.1 1.0
ND1 F:HIS241 4.6 32.5 1.0
CA F:GLU115 4.6 33.2 1.0
CB F:GLU115 4.7 32.6 1.0
CA F:ASP84 4.7 35.5 1.0
CE1 F:PHE208 4.9 38.4 1.0

Iron binding site 4 out of 8 in 5cns

Go back to Iron Binding Sites List in 5cns
Iron binding site 4 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Cdp and Datp at 2.97 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 Cdp and Datp at 2.97 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:37.9
occ:1.00
 FE2 F:FEO501 0.0 37.9 1.0
O F:FEO501 1.8 35.9 1.0
O F:HOH602 2.0 34.5 1.0
OE1 F:GLU204 2.0 32.7 1.0
OE2 F:GLU115 2.0 32.8 1.0
OE1 F:GLU238 2.1 37.0 1.0
ND1 F:HIS241 2.2 32.5 1.0
OE2 F:GLU238 2.7 37.4 1.0
CD F:GLU238 2.7 37.1 1.0
CD F:GLU115 3.0 33.2 1.0
CE1 F:HIS241 3.0 32.4 1.0
CD F:GLU204 3.1 35.8 1.0
FE1 F:FEO501 3.2 36.5 1.0
OE1 F:GLU115 3.2 34.0 1.0
CG F:HIS241 3.3 33.6 1.0
CB F:HIS241 3.8 32.9 1.0
O F:HOH603 3.8 35.2 1.0
CG F:GLU204 3.8 36.2 1.0
OD1 F:ASP84 4.0 37.9 1.0
NE1 F:TRP111 4.1 30.2 1.0
OE2 F:GLU204 4.1 37.2 1.0
NE2 F:HIS241 4.2 32.3 1.0
CG F:GLU238 4.2 35.5 1.0
CG F:GLU115 4.3 33.7 1.0
CD2 F:HIS241 4.3 32.7 1.0
CE1 F:HIS118 4.6 32.2 1.0
CA F:GLU238 4.6 32.4 1.0
NE2 F:GLN87 4.6 33.4 1.0
ND1 F:HIS118 4.6 32.9 1.0
CB F:GLU204 4.7 33.9 1.0
CD1 F:TRP111 4.7 31.0 1.0
CB F:GLU238 4.8 33.8 1.0
CG F:GLN87 4.9 34.9 1.0

Iron binding site 5 out of 8 in 5cns

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Iron binding site 5 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Cdp and Datp at 2.97 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 Cdp and Datp at 2.97 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe501

b:38.7
occ:1.00
 FE1 G:FEO501 0.0 38.7 1.0
O G:FEO501 1.8 37.2 1.0
O G:HOH605 2.0 38.8 1.0
OE1 G:GLU115 2.0 36.3 1.0
OD1 G:ASP84 2.1 39.7 1.0
OD2 G:ASP84 2.1 40.5 1.0
ND1 G:HIS118 2.2 35.4 1.0
CG G:ASP84 2.4 39.2 1.0
CE1 G:HIS118 3.0 35.9 1.0
CD G:GLU115 3.0 35.8 1.0
OE1 G:GLU238 3.2 38.3 1.0
FE2 G:FEO501 3.2 35.9 1.0
O G:HOH602 3.2 37.2 1.0
OE2 G:GLU115 3.4 36.1 1.0
CG G:HIS118 3.4 36.1 1.0
CB G:HIS118 3.9 36.3 1.0
CB G:ASP84 3.9 37.2 1.0
NE2 G:HIS118 4.2 35.9 1.0
CZ G:PHE208 4.3 40.6 1.0
CE2 G:PHE208 4.4 41.1 1.0
CD G:GLU238 4.4 38.9 1.0
CG G:GLU115 4.4 35.0 1.0
CD2 G:HIS118 4.4 35.9 1.0
CE1 G:HIS241 4.5 34.4 1.0
CG2 G:ILE234 4.5 37.2 1.0
ND1 G:HIS241 4.6 34.5 1.0
CA G:GLU115 4.7 35.2 1.0
CB G:GLU115 4.7 35.4 1.0
CA G:ASP84 4.8 37.8 1.0
CE1 G:PHE208 4.9 40.6 1.0
OE1 G:GLU204 5.0 33.8 1.0

Iron binding site 6 out of 8 in 5cns

Go back to Iron Binding Sites List in 5cns
Iron binding site 6 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Cdp and Datp at 2.97 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 Cdp and Datp at 2.97 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe501

b:35.9
occ:1.00
 FE2 G:FEO501 0.0 35.9 1.0
O G:FEO501 1.8 37.2 1.0
O G:HOH602 2.0 37.2 1.0
OE1 G:GLU204 2.0 33.8 1.0
OE2 G:GLU115 2.1 36.1 1.0
OE1 G:GLU238 2.1 38.3 1.0
ND1 G:HIS241 2.2 34.5 1.0
OE2 G:GLU238 2.6 40.0 1.0
CD G:GLU238 2.7 38.9 1.0
CD G:GLU115 3.0 35.8 1.0
CE1 G:HIS241 3.0 34.4 1.0
CD G:GLU204 3.1 37.0 1.0
FE1 G:FEO501 3.2 38.7 1.0
OE1 G:GLU115 3.3 36.3 1.0
CG G:HIS241 3.3 35.1 1.0
CB G:HIS241 3.8 34.8 1.0
CG G:GLU204 3.8 38.8 1.0
O G:HOH605 3.9 38.8 1.0
OD1 G:ASP84 4.0 39.7 1.0
NE1 G:TRP111 4.1 33.9 1.0
OE2 G:GLU204 4.1 39.4 1.0
CG G:GLU238 4.1 37.2 1.0
NE2 G:HIS241 4.2 34.2 1.0
CG G:GLU115 4.3 35.0 1.0
CD2 G:HIS241 4.4 34.4 1.0
CA G:GLU238 4.6 34.4 1.0
CE1 G:HIS118 4.6 35.9 1.0
NE2 G:GLN87 4.7 36.4 1.0
CB G:GLU204 4.7 35.8 1.0
ND1 G:HIS118 4.7 35.4 1.0
CD1 G:TRP111 4.7 33.3 1.0
CB G:GLU238 4.8 36.3 1.0
CG G:GLN87 4.9 36.2 1.0

Iron binding site 7 out of 8 in 5cns

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Iron binding site 7 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Cdp and Datp at 2.97 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 Cdp and Datp at 2.97 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe501

b:48.8
occ:1.00
 FE1 H:FEO501 0.0 48.8 1.0
O H:FEO501 1.8 50.2 1.0
O H:HOH604 2.0 49.3 1.0
OE1 H:GLU115 2.0 49.3 1.0
OD2 H:ASP84 2.1 51.7 1.0
OD1 H:ASP84 2.1 52.2 1.0
ND1 H:HIS118 2.2 47.9 1.0
CG H:ASP84 2.4 51.3 1.0
CE1 H:HIS118 3.0 49.7 1.0
O H:HOH605 3.1 50.7 1.0
CD H:GLU115 3.1 48.9 1.0
OE1 H:GLU238 3.2 52.5 1.0
FE2 H:FEO501 3.2 47.8 1.0
CG H:HIS118 3.3 49.3 1.0
OE2 H:GLU115 3.6 49.4 1.0
CB H:HIS118 3.8 49.3 1.0
CB H:ASP84 3.9 50.7 1.0
CZ H:PHE208 4.2 52.6 1.0
NE2 H:HIS118 4.2 50.0 1.0
CE2 H:PHE208 4.3 52.5 1.0
CD2 H:HIS118 4.4 50.2 1.0
CD H:GLU238 4.4 51.3 1.0
CG H:GLU115 4.4 49.1 1.0
CG2 H:ILE234 4.5 47.0 1.0
CA H:GLU115 4.6 49.4 1.0
CE1 H:HIS241 4.6 47.7 1.0
CB H:GLU115 4.6 50.2 1.0
ND1 H:HIS241 4.7 48.1 1.0
CA H:ASP84 4.7 52.6 1.0
CE1 H:PHE208 4.8 51.3 1.0

Iron binding site 8 out of 8 in 5cns

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Iron binding site 8 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex Bound to Cdp and Datp at 2.97 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 Cdp and Datp at 2.97 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe501

b:47.8
occ:1.00
 FE2 H:FEO501 0.0 47.8 1.0
O H:FEO501 1.8 50.2 1.0
O H:HOH605 2.0 50.7 1.0
OE2 H:GLU115 2.0 49.4 1.0
OE1 H:GLU204 2.1 46.7 1.0
OE1 H:GLU238 2.1 52.5 1.0
ND1 H:HIS241 2.2 48.1 1.0
OE2 H:GLU238 2.5 51.8 1.0
CD H:GLU238 2.6 51.3 1.0
CD H:GLU115 2.9 48.9 1.0
CE1 H:HIS241 3.0 47.7 1.0
OE1 H:GLU115 3.1 49.3 1.0
CD H:GLU204 3.2 49.5 1.0
FE1 H:FEO501 3.2 48.8 1.0
CG H:HIS241 3.4 48.6 1.0
O H:HOH604 3.6 49.3 1.0
CG H:GLU204 3.8 51.2 1.0
CB H:HIS241 3.8 48.7 1.0
OD1 H:ASP84 4.0 52.2 1.0
NE1 H:TRP111 4.1 48.0 1.0
CG H:GLU238 4.1 49.1 1.0
OE2 H:GLU204 4.1 49.2 1.0
NE2 H:HIS241 4.2 47.6 1.0
CG H:GLU115 4.3 49.1 1.0
CD2 H:HIS241 4.4 48.6 1.0
CE1 H:HIS118 4.5 49.7 1.0
ND1 H:HIS118 4.6 47.9 1.0
CA H:GLU238 4.6 47.9 1.0
CB H:GLU204 4.6 51.9 1.0
CD1 H:TRP111 4.7 48.2 1.0
NE2 H:GLN87 4.7 50.7 1.0
CB H:GLU238 4.8 48.8 1.0
CG H:GLN87 5.0 50.3 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 21:34:13 2024

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