Atomistry » Iron » PDB 4egn-4f2n » 4erp
Atomistry »
  Iron »
    PDB 4egn-4f2n »
      4erp »

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

Go back to Iron Binding Sites List in 4erp
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

Go back to Iron Binding Sites List in 4erp
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

Go back to Iron Binding Sites List in 4erp
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

Go back to Iron Binding Sites List in 4erp
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

Go back to Iron Binding Sites List in 4erp
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

Go back to Iron Binding Sites List in 4erp
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

Go back to Iron Binding Sites List in 4erp
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

Go back to Iron Binding Sites List in 4erp
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

Last articles

Ca in 5NGQ
Ca in 5NH5
Ca in 5NGY
Ca in 5NG1
Ca in 5NFZ
Ca in 5NF3
Ca in 5NF2
Ca in 5NF0
Ca in 5NEY
Ca in 5NES
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy