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Iron in PDB 4erp: Crystal Structure of A Gemcitabine-Diphosphate Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex

Enzymatic activity of Crystal Structure of A Gemcitabine-Diphosphate Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex

All present enzymatic activity of Crystal Structure of A Gemcitabine-Diphosphate Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex:
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of A Gemcitabine-Diphosphate Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex, PDB code: 4erp 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) 50.00 / 4.45
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 128.669, 398.906, 319.437, 90.00, 90.00, 90.00
R / Rfree (%) 23.3 / 26.7

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of A Gemcitabine-Diphosphate Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex (pdb code 4erp). 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 A Gemcitabine-Diphosphate Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex, PDB code: 4erp:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4erp

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Iron binding site 1 out of 8 in the Crystal Structure of A Gemcitabine-Diphosphate Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex


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 A Gemcitabine-Diphosphate Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:0.7
occ:1.00
 FE1 E:FEO501 0.0 0.7 1.0
OE1 E:GLU115 1.8 0.2 1.0
O E:FEO501 2.0 0.7 1.0
OD2 E:ASP84 2.0 0.7 1.0
ND1 E:HIS118 2.1 0.9 1.0
CG E:ASP84 2.4 0.7 1.0
OD1 E:ASP84 2.6 0.7 1.0
O E:HOH601 2.6 58.7 1.0
CE1 E:HIS118 2.9 0.9 1.0
CD E:GLU115 2.9 0.2 1.0
CG E:HIS118 3.2 0.9 1.0
FE2 E:FEO501 3.4 0.7 1.0
O E:HOH602 3.4 0.6 1.0
OE2 E:GLU115 3.5 0.2 1.0
CB E:HIS118 3.7 0.9 1.0
CB E:ASP84 3.7 0.7 1.0
NE2 E:HIS118 4.0 0.9 1.0
CA E:GLU115 4.1 1.0 1.0
CG E:GLU115 4.2 0.2 1.0
CD2 E:HIS118 4.2 0.9 1.0
CE2 E:PHE208 4.2 0.6 1.0
CB E:GLU115 4.3 0.2 1.0
OE2 E:GLU238 4.3 0.2 1.0
CZ E:PHE208 4.5 0.6 1.0
OE1 E:GLU238 4.5 0.2 1.0
CG2 E:ILE234 4.5 0.8 1.0
OH E:TYR122 4.6 0.0 1.0
CD E:GLU238 4.7 0.2 1.0
O E:GLU115 4.7 1.0 1.0
CA E:ASP84 4.7 0.7 1.0
CD2 E:PHE208 5.0 0.6 1.0
C E:GLU115 5.0 1.0 1.0

Iron binding site 2 out of 8 in 4erp

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Iron binding site 2 out of 8 in the Crystal Structure of A Gemcitabine-Diphosphate Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex


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 A Gemcitabine-Diphosphate Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:0.7
occ:1.00
 FE2 E:FEO501 0.0 0.7 1.0
OE2 E:GLU115 1.8 0.2 1.0
OE1 E:GLU238 1.9 0.2 1.0
O E:FEO501 2.0 0.7 1.0
OE1 E:GLU204 2.0 0.2 1.0
ND1 E:HIS241 2.2 0.3 1.0
O E:HOH602 2.4 0.6 1.0
CD E:GLU115 2.7 0.2 1.0
CE1 E:HIS241 2.8 0.3 1.0
CD E:GLU204 2.9 0.2 1.0
CD E:GLU238 2.9 0.2 1.0
OE1 E:GLU115 3.0 0.2 1.0
CG E:GLU204 3.1 0.2 1.0
OE2 E:GLU238 3.2 0.2 1.0
FE1 E:FEO501 3.4 0.7 1.0
CG E:HIS241 3.4 0.3 1.0
CB E:HIS241 4.0 0.3 1.0
CG E:GLU115 4.0 0.2 1.0
NE2 E:HIS241 4.1 0.3 1.0
OE2 E:GLU204 4.1 0.2 1.0
NE1 E:TRP111 4.2 0.6 1.0
O E:HOH601 4.2 58.7 1.0
CG E:GLU238 4.3 0.2 1.0
OD1 E:ASP84 4.3 0.7 1.0
CD2 E:HIS241 4.4 0.3 1.0
CA E:GLU238 4.5 0.4 1.0
CB E:GLU204 4.6 0.2 1.0
CE1 E:HIS118 4.6 0.9 1.0
CB E:GLU238 4.7 0.2 1.0
CD1 E:TRP111 4.8 0.6 1.0
ND1 E:HIS118 4.8 0.9 1.0

Iron binding site 3 out of 8 in 4erp

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Iron binding site 3 out of 8 in the Crystal Structure of A Gemcitabine-Diphosphate Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex


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 A Gemcitabine-Diphosphate Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:0.7
occ:1.00
 FE1 F:FEO501 0.0 0.7 1.0
OD2 F:ASP84 2.0 0.2 1.0
O F:FEO501 2.0 0.7 1.0
OE1 F:GLU115 2.1 0.1 1.0
ND1 F:HIS118 2.2 0.3 1.0
CG F:ASP84 2.4 0.2 1.0
O F:HOH601 2.5 0.3 1.0
OD1 F:ASP84 2.5 0.2 1.0
CE1 F:HIS118 2.9 0.3 1.0
CD F:GLU115 3.0 0.1 1.0
CG F:HIS118 3.2 0.3 1.0
FE2 F:FEO501 3.4 0.7 1.0
OE2 F:GLU115 3.5 0.1 1.0
O F:HOH602 3.5 52.8 1.0
CB F:ASP84 3.6 0.2 1.0
CB F:HIS118 3.7 0.3 1.0
NE2 F:HIS118 4.1 0.3 1.0
CA F:GLU115 4.1 0.2 1.0
CG F:GLU115 4.2 0.1 1.0
CD2 F:HIS118 4.2 0.3 1.0
CE2 F:PHE208 4.2 0.7 1.0
CB F:GLU115 4.3 0.1 1.0
OE2 F:GLU238 4.3 0.9 1.0
CZ F:PHE208 4.5 0.7 1.0
OE1 F:GLU238 4.5 0.9 1.0
CG2 F:ILE234 4.5 0.9 1.0
OH F:TYR122 4.6 0.4 1.0
CD F:GLU238 4.7 0.9 1.0
CA F:ASP84 4.7 0.9 1.0
O F:GLU115 4.7 0.2 1.0
C F:GLU115 5.0 0.2 1.0
CD2 F:PHE208 5.0 0.7 1.0

Iron binding site 4 out of 8 in 4erp

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Iron binding site 4 out of 8 in the Crystal Structure of A Gemcitabine-Diphosphate Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex


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 A Gemcitabine-Diphosphate Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:0.7
occ:1.00
 FE2 F:FEO501 0.0 0.7 1.0
OE2 F:GLU115 1.8 0.1 1.0
OE1 F:GLU238 2.0 0.9 1.0
OE1 F:GLU204 2.0 0.4 1.0
O F:FEO501 2.0 0.7 1.0
ND1 F:HIS241 2.2 0.4 1.0
O F:HOH602 2.6 52.8 1.0
CD F:GLU115 2.7 0.1 1.0
CE1 F:HIS241 2.8 0.4 1.0
CD F:GLU204 2.9 0.4 1.0
CD F:GLU238 2.9 0.9 1.0
OE1 F:GLU115 3.0 0.1 1.0
CG F:GLU204 3.1 0.4 1.0
OE2 F:GLU238 3.2 0.9 1.0
FE1 F:FEO501 3.4 0.7 1.0
CG F:HIS241 3.5 0.4 1.0
OE2 F:GLU204 4.0 0.4 1.0
CB F:HIS241 4.1 0.4 1.0
NE2 F:HIS241 4.1 0.4 1.0
CG F:GLU115 4.1 0.1 1.0
NE1 F:TRP111 4.1 0.9 1.0
O F:HOH601 4.1 0.3 1.0
OD1 F:ASP84 4.3 0.2 1.0
CG F:GLU238 4.3 0.9 1.0
CD2 F:HIS241 4.4 0.4 1.0
CA F:GLU238 4.6 0.3 1.0
CB F:GLU204 4.6 0.4 1.0
CE1 F:HIS118 4.7 0.3 1.0
CD1 F:TRP111 4.7 0.9 1.0
CB F:GLU238 4.8 0.9 1.0
ND1 F:HIS118 4.9 0.3 1.0

Iron binding site 5 out of 8 in 4erp

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Iron binding site 5 out of 8 in the Crystal Structure of A Gemcitabine-Diphosphate Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex


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 A Gemcitabine-Diphosphate Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe501

b:0.5
occ:1.00
 FE1 G:FEO501 0.0 0.5 1.0
OE1 G:GLU115 1.8 0.1 1.0
OD2 G:ASP84 2.0 0.1 1.0
O G:FEO501 2.0 0.5 1.0
ND1 G:HIS118 2.2 0.1 1.0
CG G:ASP84 2.4 0.1 1.0
OD1 G:ASP84 2.5 0.1 1.0
O G:HOH602 2.7 0.5 1.0
CE1 G:HIS118 3.0 0.1 1.0
CD G:GLU115 3.0 0.1 1.0
CG G:HIS118 3.2 0.1 1.0
FE2 G:FEO501 3.4 0.5 1.0
O G:HOH601 3.5 61.4 1.0
CB G:ASP84 3.6 0.1 1.0
CB G:HIS118 3.7 0.1 1.0
OE2 G:GLU115 3.7 0.1 1.0
CA G:GLU115 4.0 0.3 1.0
NE2 G:HIS118 4.1 0.1 1.0
CG G:GLU115 4.1 0.1 1.0
CB G:GLU115 4.2 0.1 1.0
CD2 G:HIS118 4.2 0.1 1.0
CE2 G:PHE208 4.3 0.7 1.0
OE2 G:GLU238 4.4 0.1 1.0
CZ G:PHE208 4.5 0.7 1.0
OE1 G:GLU238 4.5 0.1 1.0
CG2 G:ILE234 4.6 0.9 1.0
O G:GLU115 4.7 0.3 1.0
OH G:TYR122 4.7 0.0 1.0
CA G:ASP84 4.7 0.4 1.0
CD G:GLU238 4.7 0.1 1.0
C G:GLU115 4.9 0.3 1.0
N G:GLU115 5.0 0.3 1.0
CE1 G:HIS241 5.0 0.8 1.0

Iron binding site 6 out of 8 in 4erp

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Iron binding site 6 out of 8 in the Crystal Structure of A Gemcitabine-Diphosphate Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex


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 A Gemcitabine-Diphosphate Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe501

b:0.5
occ:1.00
 FE2 G:FEO501 0.0 0.5 1.0
OE1 G:GLU204 2.0 0.6 1.0
O G:FEO501 2.0 0.5 1.0
OE1 G:GLU238 2.0 0.1 1.0
OE2 G:GLU115 2.2 0.1 1.0
ND1 G:HIS241 2.2 0.8 1.0
O G:HOH601 2.4 61.4 1.0
CD G:GLU115 2.7 0.1 1.0
CE1 G:HIS241 2.8 0.8 1.0
CD G:GLU204 2.9 0.6 1.0
OE1 G:GLU115 2.9 0.1 1.0
CD G:GLU238 3.0 0.1 1.0
CG G:GLU204 3.2 0.6 1.0
OE2 G:GLU238 3.3 0.1 1.0
FE1 G:FEO501 3.4 0.5 1.0
CG G:HIS241 3.4 0.8 1.0
CG G:GLU115 4.0 0.1 1.0
NE2 G:HIS241 4.0 0.8 1.0
OE2 G:GLU204 4.1 0.6 1.0
CB G:HIS241 4.1 0.8 1.0
NE1 G:TRP111 4.1 0.2 1.0
O G:HOH602 4.2 0.5 1.0
OD1 G:ASP84 4.3 0.1 1.0
CD2 G:HIS241 4.4 0.8 1.0
CG G:GLU238 4.4 0.1 1.0
CA G:GLU238 4.6 1.0 1.0
CE1 G:HIS118 4.7 0.1 1.0
CB G:GLU204 4.7 0.6 1.0
CD1 G:TRP111 4.7 0.2 1.0
CB G:GLU238 4.8 0.1 1.0
ND1 G:HIS118 4.9 0.1 1.0

Iron binding site 7 out of 8 in 4erp

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Iron binding site 7 out of 8 in the Crystal Structure of A Gemcitabine-Diphosphate Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex


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 A Gemcitabine-Diphosphate Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe501

b:0.1
occ:1.00
 FE1 H:FEO501 0.0 0.1 1.0
OE1 H:GLU115 1.8 0.3 1.0
OD2 H:ASP84 2.0 0.8 1.0
O H:FEO501 2.0 0.1 1.0
ND1 H:HIS118 2.2 0.3 1.0
CG H:ASP84 2.4 0.8 1.0
OD1 H:ASP84 2.5 0.8 1.0
O H:HOH602 2.7 47.9 1.0
CD H:GLU115 2.9 0.3 1.0
CE1 H:HIS118 3.0 0.3 1.0
CG H:HIS118 3.2 0.3 1.0
OE2 H:GLU115 3.4 0.3 1.0
FE2 H:FEO501 3.4 0.1 1.0
O H:HOH601 3.5 34.6 1.0
CB H:ASP84 3.6 0.8 1.0
CB H:HIS118 3.7 0.3 1.0
CA H:GLU115 4.0 0.9 1.0
NE2 H:HIS118 4.1 0.3 1.0
CG H:GLU115 4.1 0.3 1.0
CB H:GLU115 4.1 0.3 1.0
CD2 H:HIS118 4.2 0.3 1.0
CE2 H:PHE208 4.3 0.8 1.0
OE2 H:GLU238 4.4 0.8 1.0
OE1 H:GLU238 4.5 0.8 1.0
CZ H:PHE208 4.5 0.8 1.0
CG2 H:ILE234 4.6 0.7 1.0
O H:GLU115 4.7 0.9 1.0
OH H:TYR122 4.7 0.4 1.0
CA H:ASP84 4.7 0.7 1.0
CD H:GLU238 4.8 0.8 1.0
C H:GLU115 4.9 0.9 1.0
N H:GLU115 5.0 0.9 1.0
CE1 H:HIS241 5.0 0.6 1.0

Iron binding site 8 out of 8 in 4erp

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Iron binding site 8 out of 8 in the Crystal Structure of A Gemcitabine-Diphosphate Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex


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 A Gemcitabine-Diphosphate Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe501

b:0.1
occ:1.00
 FE2 H:FEO501 0.0 0.1 1.0
OE2 H:GLU115 1.7 0.3 1.0
OE1 H:GLU204 2.0 0.2 1.0
O H:FEO501 2.0 0.1 1.0
OE1 H:GLU238 2.0 0.8 1.0
ND1 H:HIS241 2.2 0.6 1.0
O H:HOH601 2.4 34.6 1.0
CD H:GLU115 2.6 0.3 1.0
CE1 H:HIS241 2.8 0.6 1.0
OE1 H:GLU115 2.9 0.3 1.0
CD H:GLU238 3.0 0.8 1.0
CD H:GLU204 3.1 0.2 1.0
OE2 H:GLU238 3.3 0.8 1.0
FE1 H:FEO501 3.4 0.1 1.0
CG H:HIS241 3.4 0.6 1.0
NE1 H:TRP111 3.9 0.1 1.0
OE2 H:GLU204 3.9 0.2 1.0
CG H:GLU115 4.0 0.3 1.0
CG H:GLU204 4.0 0.2 1.0
NE2 H:HIS241 4.0 0.6 1.0
CB H:HIS241 4.1 0.6 1.0
O H:HOH602 4.2 47.9 1.0
OD1 H:ASP84 4.3 0.8 1.0
CD2 H:HIS241 4.4 0.6 1.0
CG H:GLU238 4.4 0.8 1.0
CD1 H:TRP111 4.6 0.1 1.0
CA H:GLU238 4.7 0.6 1.0
CE1 H:HIS118 4.7 0.3 1.0
CB H:GLU204 4.7 0.2 1.0
CB H:GLU238 4.8 0.8 1.0
ND1 H:HIS118 4.9 0.3 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 01:48:35 2024

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