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Iron in PDB 7mdi: Structure of the Neisseria Gonorrhoeae Ribonucleotide Reductase in the Inactive State

Enzymatic activity of Structure of the Neisseria Gonorrhoeae Ribonucleotide Reductase in the Inactive State

All present enzymatic activity of Structure of the Neisseria Gonorrhoeae Ribonucleotide Reductase in the Inactive State:
1.17.4.1;

Other elements in 7mdi:

The structure of Structure of the Neisseria Gonorrhoeae Ribonucleotide Reductase in the Inactive State also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of the Neisseria Gonorrhoeae Ribonucleotide Reductase in the Inactive State (pdb code 7mdi). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Structure of the Neisseria Gonorrhoeae Ribonucleotide Reductase in the Inactive State, PDB code: 7mdi:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 7mdi

Go back to Iron Binding Sites List in 7mdi
Iron binding site 1 out of 8 in the Structure of the Neisseria Gonorrhoeae Ribonucleotide Reductase in the Inactive State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Neisseria Gonorrhoeae Ribonucleotide Reductase in the Inactive State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:107.0
occ:1.00
FE1 E:FEO501 0.0 107.0 1.0
O E:FEO501 1.8 107.0 1.0
ND1 E:HIS119 2.3 87.5 1.0
OD2 E:ASP85 2.5 95.8 1.0
OE1 E:GLU116 2.7 94.0 1.0
CG E:ASP85 2.9 95.8 1.0
OD1 E:ASP85 3.1 95.8 1.0
CE1 E:HIS119 3.1 87.5 1.0
FE2 E:FEO501 3.1 107.0 1.0
CG E:HIS119 3.3 87.5 1.0
CD E:GLU116 3.5 94.0 1.0
CB E:HIS119 3.7 87.5 1.0
OE2 E:GLU116 3.9 94.0 1.0
CB E:ASP85 4.0 95.8 1.0
OE1 E:GLU239 4.2 98.0 1.0
NE2 E:HIS119 4.2 87.5 1.0
CD2 E:HIS119 4.4 87.5 1.0
CE1 E:HIS242 4.4 92.8 1.0
CA E:GLU116 4.5 94.0 1.0
ND1 E:HIS242 4.7 92.8 1.0
CG E:GLU116 4.8 94.0 1.0
CA E:ASP85 4.9 95.8 1.0
CB E:GLU116 4.9 94.0 1.0
CE2 E:PHE209 4.9 90.5 1.0

Iron binding site 2 out of 8 in 7mdi

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Iron binding site 2 out of 8 in the Structure of the Neisseria Gonorrhoeae Ribonucleotide Reductase in the Inactive State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Neisseria Gonorrhoeae Ribonucleotide Reductase in the Inactive State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:107.0
occ:1.00
FE2 E:FEO501 0.0 107.0 1.0
O E:FEO501 1.8 107.0 1.0
OE2 E:GLU116 2.2 94.0 1.0
ND1 E:HIS242 2.2 92.8 1.0
CE1 E:HIS242 2.6 92.8 1.0
OE1 E:GLU116 2.8 94.0 1.0
CD E:GLU116 2.8 94.0 1.0
OE1 E:GLU239 3.0 98.0 1.0
FE1 E:FEO501 3.1 107.0 1.0
CG E:HIS242 3.4 92.8 1.0
NE1 E:TRP112 3.6 91.9 1.0
NE2 E:HIS242 3.8 92.8 1.0
CD E:GLU239 4.1 98.0 1.0
CB E:HIS242 4.2 92.8 1.0
CD2 E:HIS242 4.2 92.8 1.0
CE1 E:HIS119 4.3 87.5 1.0
ND1 E:HIS119 4.3 87.5 1.0
CG E:GLU116 4.3 94.0 1.0
CD1 E:TRP112 4.4 91.9 1.0
OE2 E:GLU239 4.6 98.0 1.0
CE2 E:TRP112 4.7 91.9 1.0
CA E:GLU239 4.7 98.0 1.0
OD1 E:ASP85 5.0 95.8 1.0
CZ2 E:TRP112 5.0 91.9 1.0

Iron binding site 3 out of 8 in 7mdi

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Iron binding site 3 out of 8 in the Structure of the Neisseria Gonorrhoeae Ribonucleotide Reductase in the Inactive State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the Neisseria Gonorrhoeae Ribonucleotide Reductase in the Inactive State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe501

b:107.0
occ:1.00
FE1 G:FEO501 0.0 107.0 1.0
O G:FEO501 1.8 107.0 1.0
ND1 G:HIS119 2.3 87.5 1.0
OD2 G:ASP85 2.5 95.8 1.0
OE1 G:GLU116 2.7 94.0 1.0
CG G:ASP85 2.9 95.8 1.0
OD1 G:ASP85 3.1 95.8 1.0
CE1 G:HIS119 3.1 87.5 1.0
FE2 G:FEO501 3.1 107.0 1.0
CG G:HIS119 3.3 87.5 1.0
CD G:GLU116 3.5 94.0 1.0
CB G:HIS119 3.7 87.5 1.0
OE2 G:GLU116 3.9 94.0 1.0
CB G:ASP85 4.0 95.8 1.0
OE1 G:GLU239 4.2 98.0 1.0
NE2 G:HIS119 4.2 87.5 1.0
CD2 G:HIS119 4.4 87.5 1.0
CE1 G:HIS242 4.4 92.8 1.0
CA G:GLU116 4.5 94.0 1.0
ND1 G:HIS242 4.7 92.8 1.0
CG G:GLU116 4.8 94.0 1.0
CA G:ASP85 4.9 95.8 1.0
CB G:GLU116 4.9 94.0 1.0
CE2 G:PHE209 4.9 90.5 1.0

Iron binding site 4 out of 8 in 7mdi

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Iron binding site 4 out of 8 in the Structure of the Neisseria Gonorrhoeae Ribonucleotide Reductase in the Inactive State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the Neisseria Gonorrhoeae Ribonucleotide Reductase in the Inactive State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe501

b:107.0
occ:1.00
FE2 G:FEO501 0.0 107.0 1.0
O G:FEO501 1.8 107.0 1.0
OE2 G:GLU116 2.2 94.0 1.0
ND1 G:HIS242 2.2 92.8 1.0
CE1 G:HIS242 2.6 92.8 1.0
OE1 G:GLU116 2.8 94.0 1.0
CD G:GLU116 2.8 94.0 1.0
OE1 G:GLU239 3.0 98.0 1.0
FE1 G:FEO501 3.1 107.0 1.0
CG G:HIS242 3.4 92.8 1.0
NE1 G:TRP112 3.6 91.9 1.0
NE2 G:HIS242 3.8 92.8 1.0
CD G:GLU239 4.1 98.0 1.0
CB G:HIS242 4.2 92.8 1.0
CD2 G:HIS242 4.2 92.8 1.0
CE1 G:HIS119 4.3 87.5 1.0
ND1 G:HIS119 4.3 87.5 1.0
CG G:GLU116 4.3 94.0 1.0
CD1 G:TRP112 4.4 91.9 1.0
OE2 G:GLU239 4.6 98.0 1.0
CE2 G:TRP112 4.7 91.9 1.0
CA G:GLU239 4.7 98.0 1.0
OD1 G:ASP85 5.0 95.8 1.0
CZ2 G:TRP112 5.0 91.9 1.0

Iron binding site 5 out of 8 in 7mdi

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Iron binding site 5 out of 8 in the Structure of the Neisseria Gonorrhoeae Ribonucleotide Reductase in the Inactive State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of the Neisseria Gonorrhoeae Ribonucleotide Reductase in the Inactive State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:107.0
occ:1.00
FE1 F:FEO501 0.0 107.0 1.0
O F:FEO501 1.8 107.0 1.0
ND1 F:HIS119 2.3 87.5 1.0
OD2 F:ASP85 2.5 95.8 1.0
OE1 F:GLU116 2.7 94.0 1.0
CG F:ASP85 2.9 95.8 1.0
OD1 F:ASP85 3.1 95.8 1.0
CE1 F:HIS119 3.1 87.5 1.0
FE2 F:FEO501 3.1 107.0 1.0
CG F:HIS119 3.3 87.5 1.0
CD F:GLU116 3.5 94.0 1.0
CB F:HIS119 3.7 87.5 1.0
OE2 F:GLU116 3.9 94.0 1.0
CB F:ASP85 4.0 95.8 1.0
OE1 F:GLU239 4.2 98.0 1.0
NE2 F:HIS119 4.2 87.5 1.0
CD2 F:HIS119 4.4 87.5 1.0
CE1 F:HIS242 4.4 92.8 1.0
CA F:GLU116 4.5 94.0 1.0
ND1 F:HIS242 4.7 92.8 1.0
CG F:GLU116 4.8 94.0 1.0
CA F:ASP85 4.9 95.8 1.0
CB F:GLU116 4.9 94.0 1.0
CE2 F:PHE209 4.9 90.5 1.0

Iron binding site 6 out of 8 in 7mdi

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Iron binding site 6 out of 8 in the Structure of the Neisseria Gonorrhoeae Ribonucleotide Reductase in the Inactive State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of the Neisseria Gonorrhoeae Ribonucleotide Reductase in the Inactive State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:107.0
occ:1.00
FE2 F:FEO501 0.0 107.0 1.0
O F:FEO501 1.8 107.0 1.0
OE2 F:GLU116 2.2 94.0 1.0
ND1 F:HIS242 2.2 92.8 1.0
CE1 F:HIS242 2.6 92.8 1.0
OE1 F:GLU116 2.8 94.0 1.0
CD F:GLU116 2.8 94.0 1.0
OE1 F:GLU239 3.0 98.0 1.0
FE1 F:FEO501 3.1 107.0 1.0
CG F:HIS242 3.4 92.8 1.0
NE1 F:TRP112 3.6 91.9 1.0
NE2 F:HIS242 3.8 92.8 1.0
CD F:GLU239 4.1 98.0 1.0
CB F:HIS242 4.2 92.8 1.0
CD2 F:HIS242 4.2 92.8 1.0
CE1 F:HIS119 4.3 87.5 1.0
ND1 F:HIS119 4.3 87.5 1.0
CG F:GLU116 4.3 94.0 1.0
CD1 F:TRP112 4.4 91.9 1.0
OE2 F:GLU239 4.6 98.0 1.0
CE2 F:TRP112 4.7 91.9 1.0
CA F:GLU239 4.7 98.0 1.0
OD1 F:ASP85 5.0 95.8 1.0
CZ2 F:TRP112 5.0 91.9 1.0

Iron binding site 7 out of 8 in 7mdi

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Iron binding site 7 out of 8 in the Structure of the Neisseria Gonorrhoeae Ribonucleotide Reductase in the Inactive State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of the Neisseria Gonorrhoeae Ribonucleotide Reductase in the Inactive State within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe501

b:107.0
occ:1.00
FE1 H:FEO501 0.0 107.0 1.0
O H:FEO501 1.8 107.0 1.0
ND1 H:HIS119 2.3 87.5 1.0
OD2 H:ASP85 2.5 95.8 1.0
OE1 H:GLU116 2.7 94.0 1.0
CG H:ASP85 2.9 95.8 1.0
OD1 H:ASP85 3.1 95.8 1.0
CE1 H:HIS119 3.1 87.5 1.0
FE2 H:FEO501 3.1 107.0 1.0
CG H:HIS119 3.3 87.5 1.0
CD H:GLU116 3.5 94.0 1.0
CB H:HIS119 3.7 87.5 1.0
OE2 H:GLU116 3.9 94.0 1.0
CB H:ASP85 4.0 95.8 1.0
OE1 H:GLU239 4.2 98.0 1.0
NE2 H:HIS119 4.2 87.5 1.0
CD2 H:HIS119 4.4 87.5 1.0
CE1 H:HIS242 4.4 92.8 1.0
CA H:GLU116 4.5 94.0 1.0
ND1 H:HIS242 4.7 92.8 1.0
CG H:GLU116 4.8 94.0 1.0
CA H:ASP85 4.9 95.8 1.0
CB H:GLU116 4.9 94.0 1.0
CE2 H:PHE209 4.9 90.5 1.0

Iron binding site 8 out of 8 in 7mdi

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Iron binding site 8 out of 8 in the Structure of the Neisseria Gonorrhoeae Ribonucleotide Reductase in the Inactive State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of the Neisseria Gonorrhoeae Ribonucleotide Reductase in the Inactive State within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe501

b:107.0
occ:1.00
FE2 H:FEO501 0.0 107.0 1.0
O H:FEO501 1.8 107.0 1.0
OE2 H:GLU116 2.2 94.0 1.0
ND1 H:HIS242 2.2 92.8 1.0
CE1 H:HIS242 2.6 92.8 1.0
OE1 H:GLU116 2.8 94.0 1.0
CD H:GLU116 2.8 94.0 1.0
OE1 H:GLU239 3.0 98.0 1.0
FE1 H:FEO501 3.1 107.0 1.0
CG H:HIS242 3.4 92.8 1.0
NE1 H:TRP112 3.6 91.9 1.0
NE2 H:HIS242 3.8 92.8 1.0
CD H:GLU239 4.1 98.0 1.0
CB H:HIS242 4.2 92.8 1.0
CD2 H:HIS242 4.2 92.8 1.0
CE1 H:HIS119 4.3 87.5 1.0
ND1 H:HIS119 4.3 87.5 1.0
CG H:GLU116 4.3 94.0 1.0
CD1 H:TRP112 4.4 91.9 1.0
OE2 H:GLU239 4.6 98.0 1.0
CE2 H:TRP112 4.7 91.9 1.0
CA H:GLU239 4.7 98.0 1.0
OD1 H:ASP85 5.0 95.8 1.0
CZ2 H:TRP112 5.0 91.9 1.0

Reference:

T.S.Levitz, E.J.Brignole, I.Fong, M.C.Darrow, C.L.Drennan. Effects of Chameleon Dispense-to-Plunge Speed on Particle Concentration, Complex Formation, and Final Resolution: A Case Study Using the Neisseria Gonorrhoeae Ribonucleotide Reductase Inactive Complex. J.Struct.Biol. V. 214 07825 2021.
ISSN: ESSN 1095-8657
PubMed: 34906669
DOI: 10.1016/J.JSB.2021.107825
Page generated: Thu Mar 31 03:19:58 2022

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