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Iron in PDB 4erm: Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex at 4 Angstroms Resolution

Enzymatic activity of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex at 4 Angstroms Resolution

All present enzymatic activity of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex at 4 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 at 4 Angstroms Resolution, PDB code: 4erm was solved by C.M.Zimanyi, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 280.471, 155.744, 166.919, 90.00, 119.07, 90.00
R / Rfree (%) 25.9 / 28.4

Other elements in 4erm:

The structure of Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex at 4 Angstroms Resolution also contains other interesting chemical elements:

Magnesium (Mg) 4 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 at 4 Angstroms Resolution (pdb code 4erm). 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 at 4 Angstroms Resolution, PDB code: 4erm:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4erm

Go back to Iron Binding Sites List in 4erm
Iron binding site 1 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex at 4 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 at 4 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:89.4
occ:1.00
 FE1 E:FEO501 0.0 89.4 1.0
O E:FEO501 2.0 89.4 1.0
OD2 E:ASP84 2.0 95.4 1.0
O E:HOH602 2.0 0.9 1.0
OE1 E:GLU115 2.0 90.2 1.0
ND1 E:HIS118 2.2 0.3 1.0
OD1 E:ASP84 2.4 95.4 1.0
CG E:ASP84 2.5 95.4 1.0
CE1 E:HIS118 3.1 0.3 1.0
O E:HOH601 3.1 0.7 1.0
CD E:GLU115 3.1 90.2 1.0
CG E:HIS118 3.3 0.3 1.0
FE2 E:FEO501 3.4 89.4 1.0
OE2 E:GLU115 3.5 90.2 1.0
CB E:HIS118 3.6 0.3 1.0
OE1 E:GLU238 3.7 95.3 1.0
CZ E:PHE208 3.9 0.9 1.0
CB E:ASP84 4.0 95.4 1.0
CE2 E:PHE208 4.0 0.9 1.0
CG2 E:ILE234 4.1 96.7 1.0
NE2 E:HIS118 4.2 0.3 1.0
CD2 E:HIS118 4.3 0.3 1.0
CD E:GLU238 4.4 95.3 1.0
CE1 E:HIS241 4.4 93.9 1.0
CA E:GLU115 4.4 92.8 1.0
CG E:GLU115 4.4 90.2 1.0
OE2 E:GLU238 4.5 95.3 1.0
ND1 E:HIS241 4.6 93.9 1.0
CB E:GLU115 4.7 90.2 1.0
CE1 E:PHE208 4.7 0.9 1.0
CA E:ASP84 4.9 0.1 1.0
CD2 E:PHE208 4.9 0.9 1.0
O E:GLU115 4.9 92.8 1.0

Iron binding site 2 out of 8 in 4erm

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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 at 4 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 at 4 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:89.4
occ:1.00
 FE2 E:FEO501 0.0 89.4 1.0
OE2 E:GLU204 2.0 0.6 1.0
O E:FEO501 2.0 89.4 1.0
OE2 E:GLU238 2.0 95.3 1.0
OE2 E:GLU115 2.1 90.2 1.0
ND1 E:HIS241 2.2 93.9 1.0
O E:HOH601 2.3 0.7 1.0
CD E:GLU238 2.9 95.3 1.0
CD E:GLU115 3.0 90.2 1.0
CD E:GLU204 3.0 0.6 1.0
CE1 E:HIS241 3.1 93.9 1.0
CG E:HIS241 3.3 93.9 1.0
OE1 E:GLU115 3.3 90.2 1.0
OE1 E:GLU238 3.3 95.3 1.0
FE1 E:FEO501 3.4 89.4 1.0
CG E:GLU204 3.5 0.6 1.0
CB E:HIS241 3.6 93.9 1.0
OE1 E:GLU204 4.1 0.6 1.0
NE1 E:TRP111 4.2 99.7 1.0
OD1 E:ASP84 4.2 95.4 1.0
CG E:GLU238 4.2 95.3 1.0
NE2 E:HIS241 4.2 93.9 1.0
O E:HOH602 4.2 0.9 1.0
CG E:GLU115 4.3 90.2 1.0
CD2 E:HIS241 4.3 93.9 1.0
CB E:GLU204 4.4 0.6 1.0
CA E:GLU238 4.5 94.8 1.0
CE2 E:PHE208 4.6 0.9 1.0
CB E:GLU238 4.7 95.3 1.0
CD2 E:PHE208 4.8 0.9 1.0
CD1 E:TRP111 4.9 99.7 1.0
ND1 E:HIS118 4.9 0.3 1.0
CE1 E:HIS118 4.9 0.3 1.0
O E:GLU238 4.9 94.8 1.0

Iron binding site 3 out of 8 in 4erm

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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 at 4 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 at 4 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:61.2
occ:1.00
 FE1 F:FEO501 0.0 61.2 1.0
O F:FEO501 2.0 61.2 1.0
OD2 F:ASP84 2.0 73.1 1.0
OE1 F:GLU115 2.0 65.2 1.0
OD1 F:ASP84 2.1 73.1 1.0
O F:HOH602 2.1 54.5 1.0
ND1 F:HIS118 2.2 65.4 1.0
CG F:ASP84 2.3 73.1 1.0
O F:HOH601 3.1 33.9 1.0
CE1 F:HIS118 3.1 65.4 1.0
CD F:GLU115 3.1 65.2 1.0
CG F:HIS118 3.3 65.4 1.0
FE2 F:FEO501 3.4 61.2 1.0
OE2 F:GLU115 3.5 65.2 1.0
CB F:HIS118 3.6 65.4 1.0
CB F:ASP84 3.8 73.1 1.0
CZ F:PHE208 3.9 54.8 1.0
OE1 F:GLU238 4.0 84.0 1.0
CE2 F:PHE208 4.0 54.8 1.0
CG2 F:ILE234 4.1 63.5 1.0
NE2 F:HIS118 4.2 65.4 1.0
OE2 F:GLU238 4.3 84.0 1.0
CD2 F:HIS118 4.3 65.4 1.0
CD F:GLU238 4.4 84.0 1.0
CE1 F:HIS241 4.4 60.6 1.0
CA F:GLU115 4.4 69.2 1.0
CG F:GLU115 4.4 65.2 1.0
ND1 F:HIS241 4.6 60.6 1.0
CA F:ASP84 4.6 78.9 1.0
CE1 F:PHE208 4.7 54.8 1.0
CB F:GLU115 4.7 65.2 1.0
CD2 F:PHE208 4.9 54.8 1.0
O F:GLU115 4.9 69.2 1.0

Iron binding site 4 out of 8 in 4erm

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

b:61.2
occ:1.00
 FE2 F:FEO501 0.0 61.2 1.0
O F:FEO501 2.0 61.2 1.0
OE1 F:GLU204 2.0 70.1 1.0
OE2 F:GLU115 2.0 65.2 1.0
OE2 F:GLU238 2.1 84.0 1.0
ND1 F:HIS241 2.2 60.6 1.0
O F:HOH601 2.2 33.9 1.0
CD F:GLU204 2.9 70.1 1.0
CD F:GLU115 3.0 65.2 1.0
CE1 F:HIS241 3.1 60.6 1.0
CD F:GLU238 3.1 84.0 1.0
CG F:HIS241 3.3 60.6 1.0
OE1 F:GLU115 3.3 65.2 1.0
FE1 F:FEO501 3.4 61.2 1.0
CG F:GLU204 3.4 70.1 1.0
OE1 F:GLU238 3.6 84.0 1.0
CB F:HIS241 3.6 60.6 1.0
OE2 F:GLU204 3.9 70.1 1.0
OD1 F:ASP84 4.1 73.1 1.0
NE1 F:TRP111 4.2 61.4 1.0
O F:HOH602 4.2 54.5 1.0
NE2 F:HIS241 4.2 60.6 1.0
CG F:GLU238 4.2 84.0 1.0
CG F:GLU115 4.3 65.2 1.0
CB F:GLU204 4.3 70.1 1.0
CD2 F:HIS241 4.3 60.6 1.0
CA F:GLU238 4.5 78.0 1.0
CE2 F:PHE208 4.6 54.8 1.0
CB F:GLU238 4.7 84.0 1.0
CD2 F:PHE208 4.8 54.8 1.0
CD1 F:TRP111 4.9 61.4 1.0
ND1 F:HIS118 4.9 65.4 1.0
O F:GLU238 4.9 78.0 1.0
CE1 F:HIS118 4.9 65.4 1.0

Iron binding site 5 out of 8 in 4erm

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

b:78.9
occ:1.00
 FE1 G:FEO501 0.0 78.9 1.0
OD2 G:ASP84 2.0 89.6 1.0
O G:HOH601 2.0 29.7 1.0
O G:FEO501 2.0 78.9 1.0
OE1 G:GLU115 2.0 78.4 1.0
ND1 G:HIS118 2.2 79.2 1.0
OD1 G:ASP84 2.3 89.6 1.0
CG G:ASP84 2.4 89.6 1.0
CE1 G:HIS118 3.1 79.2 1.0
CD G:GLU115 3.1 78.4 1.0
O G:HOH602 3.1 75.4 1.0
CG G:HIS118 3.3 79.2 1.0
FE2 G:FEO501 3.4 78.9 1.0
OE2 G:GLU115 3.5 78.4 1.0
CB G:HIS118 3.6 79.2 1.0
CZ G:PHE208 3.9 85.7 1.0
CB G:ASP84 3.9 89.6 1.0
OE1 G:GLU238 3.9 97.9 1.0
CE2 G:PHE208 4.0 85.7 1.0
CG2 G:ILE234 4.1 81.9 1.0
OE2 G:GLU238 4.1 97.9 1.0
NE2 G:HIS118 4.2 79.2 1.0
CD G:GLU238 4.3 97.9 1.0
CD2 G:HIS118 4.3 79.2 1.0
CE1 G:HIS241 4.4 84.3 1.0
CG G:GLU115 4.4 78.4 1.0
CA G:GLU115 4.4 74.3 1.0
ND1 G:HIS241 4.6 84.3 1.0
CE1 G:PHE208 4.7 85.7 1.0
CB G:GLU115 4.7 78.4 1.0
CA G:ASP84 4.8 86.0 1.0
CD2 G:PHE208 4.9 85.7 1.0
O G:GLU115 4.9 74.3 1.0

Iron binding site 6 out of 8 in 4erm

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Iron binding site 6 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex at 4 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 at 4 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe501

b:78.9
occ:1.00
 FE2 G:FEO501 0.0 78.9 1.0
OE1 G:GLU204 2.0 76.4 1.0
O G:FEO501 2.0 78.9 1.0
OE2 G:GLU238 2.1 97.9 1.0
OE2 G:GLU115 2.1 78.4 1.0
ND1 G:HIS241 2.2 84.3 1.0
O G:HOH602 2.2 75.4 1.0
CD G:GLU204 2.9 76.4 1.0
CD G:GLU115 3.0 78.4 1.0
CE1 G:HIS241 3.1 84.3 1.0
CD G:GLU238 3.1 97.9 1.0
CG G:HIS241 3.3 84.3 1.0
OE1 G:GLU115 3.3 78.4 1.0
CG G:GLU204 3.4 76.4 1.0
FE1 G:FEO501 3.4 78.9 1.0
CB G:HIS241 3.6 84.3 1.0
OE1 G:GLU238 3.8 97.9 1.0
OE2 G:GLU204 3.9 76.4 1.0
OD1 G:ASP84 4.1 89.6 1.0
NE1 G:TRP111 4.2 71.8 1.0
CG G:GLU238 4.2 97.9 1.0
NE2 G:HIS241 4.2 84.3 1.0
O G:HOH601 4.3 29.7 1.0
CB G:GLU204 4.3 76.4 1.0
CG G:GLU115 4.3 78.4 1.0
CD2 G:HIS241 4.3 84.3 1.0
CA G:GLU238 4.5 94.5 1.0
CG G:GLN87 4.6 81.1 1.0
CE2 G:PHE208 4.6 85.7 1.0
CB G:GLU238 4.7 97.9 1.0
OE1 G:GLN87 4.8 81.1 1.0
CD2 G:PHE208 4.8 85.7 1.0
CD1 G:TRP111 4.9 71.8 1.0
ND1 G:HIS118 4.9 79.2 1.0
O G:GLU238 4.9 94.5 1.0
CE1 G:HIS118 4.9 79.2 1.0
CB G:GLN87 4.9 81.1 1.0

Iron binding site 7 out of 8 in 4erm

Go back to Iron Binding Sites List in 4erm
Iron binding site 7 out of 8 in the Crystal Structure of the Datp Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex at 4 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 at 4 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe501

b:69.6
occ:1.00
 FE1 H:FEO501 0.0 69.6 1.0
O H:FEO501 2.0 69.6 1.0
OD2 H:ASP84 2.0 73.2 1.0
OE1 H:GLU115 2.0 63.7 1.0
O H:HOH601 2.1 18.2 1.0
ND1 H:HIS118 2.2 74.1 1.0
OD1 H:ASP84 2.3 73.2 1.0
CG H:ASP84 2.4 73.2 1.0
O H:HOH602 3.0 44.0 1.0
CE1 H:HIS118 3.1 74.1 1.0
CD H:GLU115 3.1 63.7 1.0
CG H:HIS118 3.3 74.1 1.0
FE2 H:FEO501 3.4 69.6 1.0
OE2 H:GLU115 3.5 63.7 1.0
CB H:HIS118 3.6 74.1 1.0
CZ H:PHE208 3.9 77.2 1.0
OE1 H:GLU238 3.9 86.3 1.0
CB H:ASP84 3.9 73.2 1.0
CE2 H:PHE208 4.0 77.2 1.0
CG2 H:ILE234 4.1 78.5 1.0
OE2 H:GLU238 4.2 86.3 1.0
NE2 H:HIS118 4.2 74.1 1.0
CD H:GLU238 4.3 86.3 1.0
CD2 H:HIS118 4.3 74.1 1.0
CE1 H:HIS241 4.4 78.8 1.0
CG H:GLU115 4.4 63.7 1.0
CA H:GLU115 4.4 67.0 1.0
ND1 H:HIS241 4.6 78.8 1.0
CE1 H:PHE208 4.7 77.2 1.0
CB H:GLU115 4.7 63.7 1.0
CA H:ASP84 4.8 76.5 1.0
CD2 H:PHE208 4.9 77.2 1.0
O H:GLU115 4.9 67.0 1.0

Iron binding site 8 out of 8 in 4erm

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

b:69.6
occ:1.00
 FE2 H:FEO501 0.0 69.6 1.0
O H:FEO501 2.0 69.6 1.0
OE1 H:GLU204 2.0 90.1 1.0
OE2 H:GLU238 2.0 86.3 1.0
OE2 H:GLU115 2.0 63.7 1.0
ND1 H:HIS241 2.2 78.8 1.0
O H:HOH602 2.3 44.0 1.0
CD H:GLU204 2.9 90.1 1.0
CD H:GLU115 3.0 63.7 1.0
CE1 H:HIS241 3.1 78.8 1.0
CD H:GLU238 3.1 86.3 1.0
CG H:HIS241 3.3 78.8 1.0
OE1 H:GLU115 3.3 63.7 1.0
FE1 H:FEO501 3.4 69.6 1.0
CG H:GLU204 3.4 90.1 1.0
CB H:HIS241 3.6 78.8 1.0
OE1 H:GLU238 3.7 86.3 1.0
OE2 H:GLU204 3.9 90.1 1.0
NE1 H:TRP111 4.0 88.1 1.0
OD1 H:ASP84 4.2 73.2 1.0
CG H:GLU238 4.2 86.3 1.0
NE2 H:HIS241 4.2 78.8 1.0
O H:HOH601 4.2 18.2 1.0
CG H:GLN87 4.3 82.2 1.0
CB H:GLU204 4.3 90.1 1.0
CG H:GLU115 4.3 63.7 1.0
CD2 H:HIS241 4.3 78.8 1.0
CA H:GLU238 4.5 81.5 1.0
CE2 H:PHE208 4.6 77.2 1.0
CB H:GLU238 4.7 86.3 1.0
CD1 H:TRP111 4.8 88.1 1.0
CD2 H:PHE208 4.8 77.2 1.0
ND1 H:HIS118 4.9 74.1 1.0
CE1 H:HIS118 4.9 74.1 1.0
O H:GLU238 4.9 81.5 1.0

Reference:

C.M.Zimanyi, N.Ando, E.J.Brignole, F.J.Asturias, J.Stubbe, C.L.Drennan. Tangled Up in Knots: Structures of Inactivated Forms of E. Coli Class Ia Ribonucleotide Reductase. Structure V. 20 1374 2012.
ISSN: ISSN 0969-2126
PubMed: 22727814
DOI: 10.1016/J.STR.2012.05.009
Page generated: Mon Aug 5 01:48:19 2024

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