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Iron in PDB 6zjk: Ribonucleotide Reductase R2 Subunit From Clostridium Botulinum

Enzymatic activity of Ribonucleotide Reductase R2 Subunit From Clostridium Botulinum

All present enzymatic activity of Ribonucleotide Reductase R2 Subunit From Clostridium Botulinum:
1.17.4.1;

Protein crystallography data

The structure of Ribonucleotide Reductase R2 Subunit From Clostridium Botulinum, PDB code: 6zjk was solved by M.Martinez-Carranza, P.Stenmark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 83.67 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 210.827, 61.854, 154.342, 90.00, 127.46, 90.00
R / Rfree (%) 22.2 / 23.7

Iron Binding Sites:

The binding sites of Iron atom in the Ribonucleotide Reductase R2 Subunit From Clostridium Botulinum (pdb code 6zjk). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Ribonucleotide Reductase R2 Subunit From Clostridium Botulinum, PDB code: 6zjk:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6zjk

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Iron binding site 1 out of 8 in the Ribonucleotide Reductase R2 Subunit From Clostridium Botulinum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ribonucleotide Reductase R2 Subunit From Clostridium Botulinum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe403

b:43.1
occ:1.00
 OE2 C:GLU182 2.1 42.9 1.0
O C:HOH557 2.2 38.5 0.7
OE2 C:GLU115 2.2 44.5 1.0
ND1 C:HIS219 2.4 40.0 1.0
OE2 C:GLU216 2.5 45.8 1.0
CD C:GLU115 3.0 43.7 1.0
OE1 C:GLU115 3.1 43.5 1.0
CE1 C:HIS219 3.1 42.0 1.0
CD C:GLU182 3.2 45.2 1.0
FE C:FE404 3.3 48.1 0.8
CD C:GLU216 3.3 49.1 1.0
OE1 C:GLU216 3.4 50.8 1.0
CG C:HIS219 3.5 41.5 1.0
CB C:HIS219 3.9 39.1 1.0
OE1 C:GLU182 4.0 46.2 1.0
CG C:GLU182 4.0 50.4 1.0
NE2 C:GLN111 4.3 45.1 1.0
NE2 C:HIS219 4.3 40.3 1.0
CG C:GLU115 4.5 35.9 1.0
CD2 C:HIS219 4.5 38.2 1.0
CG C:GLU216 4.6 34.4 1.0
CB C:GLU182 4.7 44.4 1.0
NE2 C:GLN88 4.7 46.4 1.0
OD1 C:ASP85 4.7 45.1 1.0
CA C:GLU216 4.8 37.1 1.0
ND1 C:HIS118 4.9 39.8 1.0
CE1 C:HIS118 5.0 39.6 1.0

Iron binding site 2 out of 8 in 6zjk

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Iron binding site 2 out of 8 in the Ribonucleotide Reductase R2 Subunit From Clostridium Botulinum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ribonucleotide Reductase R2 Subunit From Clostridium Botulinum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe404

b:48.1
occ:0.76
 OE1 C:GLU115 2.2 43.5 1.0
OD1 C:ASP85 2.2 45.1 1.0
ND1 C:HIS118 2.4 39.8 1.0
O C:HOH557 2.4 38.5 0.7
CD C:GLU115 3.2 43.7 1.0
CE1 C:HIS118 3.2 39.6 1.0
CG C:ASP85 3.2 48.1 1.0
FE C:FE403 3.3 43.1 1.0
CG C:HIS118 3.5 41.7 1.0
OD2 C:ASP85 3.5 46.1 1.0
OE2 C:GLU115 3.5 44.5 1.0
CB C:HIS118 3.9 35.1 1.0
OE1 C:GLU216 4.0 50.8 1.0
CZ C:PHE186 4.2 41.4 1.0
NE2 C:HIS118 4.3 34.7 1.0
CG C:GLU115 4.4 35.9 1.0
CE2 C:PHE186 4.4 40.6 1.0
CA C:GLU115 4.5 35.3 1.0
CD2 C:HIS118 4.5 36.3 1.0
CB C:ASP85 4.5 38.9 1.0
CG2 C:ILE212 4.5 33.0 1.0
CE1 C:PHE186 4.6 46.1 1.0
CB C:GLU115 4.7 36.1 1.0
CE1 C:HIS219 4.7 42.0 1.0
CD C:GLU216 4.7 49.1 1.0
OE2 C:GLU216 4.8 45.8 1.0
ND1 C:HIS219 4.9 40.0 1.0

Iron binding site 3 out of 8 in 6zjk

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Iron binding site 3 out of 8 in the Ribonucleotide Reductase R2 Subunit From Clostridium Botulinum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ribonucleotide Reductase R2 Subunit From Clostridium Botulinum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:46.8
occ:0.88
 OE2 A:GLU115 2.2 54.5 1.0
OE1 A:GLU182 2.2 54.8 1.0
ND1 A:HIS219 2.4 49.2 1.0
O A:HOH524 2.5 54.2 0.7
OE2 A:GLU216 2.7 59.5 1.0
CD A:GLU182 2.9 58.6 1.0
CD A:GLU115 3.0 47.2 1.0
OE1 A:GLU115 3.0 46.7 1.0
CE1 A:HIS219 3.1 39.0 1.0
OE2 A:GLU182 3.1 58.6 1.0
FE A:FE403 3.2 48.6 0.7
OE1 A:GLU216 3.2 61.8 1.0
CD A:GLU216 3.4 58.8 1.0
CG A:HIS219 3.5 47.1 1.0
CB A:HIS219 4.0 41.1 1.0
CG A:GLU182 4.2 49.5 1.0
NE2 A:HIS219 4.3 41.2 1.0
CG A:GLU115 4.4 45.2 1.0
CD2 A:HIS219 4.5 41.1 1.0
NE2 A:GLN111 4.5 42.8 1.0
CB A:GLU182 4.5 47.1 1.0
OD1 A:ASP85 4.8 44.1 1.0
CG A:GLU216 4.8 53.1 1.0
CE1 A:HIS118 4.8 39.4 1.0
ND1 A:HIS118 4.8 41.0 1.0
CE2 A:PHE186 4.9 49.4 1.0
NE2 A:GLN88 5.0 39.0 1.0
CA A:GLU216 5.0 42.8 1.0

Iron binding site 4 out of 8 in 6zjk

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Iron binding site 4 out of 8 in the Ribonucleotide Reductase R2 Subunit From Clostridium Botulinum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ribonucleotide Reductase R2 Subunit From Clostridium Botulinum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:48.6
occ:0.69
 O A:HOH524 2.2 54.2 0.7
OD1 A:ASP85 2.2 44.1 1.0
OE1 A:GLU115 2.2 46.7 1.0
ND1 A:HIS118 2.4 41.0 1.0
CD A:GLU115 3.1 47.2 1.0
CG A:ASP85 3.2 43.6 1.0
FE A:FE402 3.2 46.8 0.9
CE1 A:HIS118 3.2 39.4 1.0
OD2 A:ASP85 3.4 46.4 1.0
CG A:HIS118 3.5 37.7 1.0
OE2 A:GLU115 3.5 54.5 1.0
OE1 A:GLU216 3.9 61.8 1.0
CB A:HIS118 3.9 39.1 1.0
CZ A:PHE186 3.9 42.4 1.0
CE2 A:PHE186 4.2 49.4 1.0
NE2 A:HIS118 4.4 42.3 1.0
CG A:GLU115 4.4 45.2 1.0
CE1 A:PHE186 4.5 47.2 1.0
CA A:GLU115 4.5 34.2 1.0
CB A:ASP85 4.5 37.4 1.0
CD2 A:HIS118 4.5 42.7 1.0
CB A:GLU115 4.6 36.1 1.0
CD A:GLU216 4.6 58.8 1.0
OE2 A:GLU216 4.7 59.5 1.0
CE1 A:HIS219 4.7 39.0 1.0
ND1 A:HIS219 4.8 49.2 1.0
CG2 A:ILE212 4.8 39.0 1.0
CD2 A:PHE186 4.9 50.3 1.0

Iron binding site 5 out of 8 in 6zjk

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Iron binding site 5 out of 8 in the Ribonucleotide Reductase R2 Subunit From Clostridium Botulinum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Ribonucleotide Reductase R2 Subunit From Clostridium Botulinum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:58.5
occ:0.70
 OE1 D:GLU115 2.2 54.6 1.0
ND1 D:HIS118 2.2 47.5 1.0
OD1 D:ASP85 2.4 52.2 1.0
OE1 D:GLU216 2.8 59.4 1.0
CE1 D:HIS118 2.9 45.8 1.0
CD D:GLU115 3.2 51.7 1.0
CG D:ASP85 3.3 55.3 1.0
FE D:FE402 3.3 52.4 0.9
CG D:HIS118 3.3 46.9 1.0
OE2 D:GLU216 3.5 62.2 1.0
CD D:GLU216 3.5 60.1 1.0
OD2 D:ASP85 3.6 53.6 1.0
OE2 D:GLU115 3.6 57.2 1.0
CB D:HIS118 3.9 39.2 1.0
CZ D:PHE186 4.1 52.9 1.0
NE2 D:HIS118 4.1 45.6 1.0
CD2 D:HIS118 4.3 41.7 1.0
CE2 D:PHE186 4.4 50.9 1.0
CG D:GLU115 4.4 44.2 1.0
CA D:GLU115 4.4 40.7 1.0
CG2 D:ILE212 4.5 41.3 1.0
CE1 D:PHE186 4.5 53.0 1.0
CB D:ASP85 4.6 43.6 1.0
CB D:GLU115 4.6 41.6 1.0
CE1 D:HIS219 4.6 41.5 1.0
ND1 D:HIS219 4.8 45.6 1.0
CG D:GLU216 5.0 53.4 1.0

Iron binding site 6 out of 8 in 6zjk

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Iron binding site 6 out of 8 in the Ribonucleotide Reductase R2 Subunit From Clostridium Botulinum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Ribonucleotide Reductase R2 Subunit From Clostridium Botulinum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe402

b:52.4
occ:0.90
 OE1 D:GLU216 2.1 59.4 1.0
OE2 D:GLU182 2.2 57.6 1.0
OE2 D:GLU115 2.3 57.2 1.0
ND1 D:HIS219 2.4 45.6 1.0
OE1 D:GLU182 2.6 62.9 1.0
CD D:GLU216 2.7 60.1 1.0
CD D:GLU182 2.7 58.9 1.0
OE1 D:GLU115 3.0 54.6 1.0
OE2 D:GLU216 3.0 62.2 1.0
CD D:GLU115 3.0 51.7 1.0
CE1 D:HIS219 3.2 41.5 1.0
FE D:FE401 3.3 58.5 0.7
CG D:HIS219 3.5 44.6 1.0
CG D:GLU216 3.6 53.4 1.0
CB D:HIS219 3.9 43.5 1.0
NE2 D:GLN111 4.1 49.0 1.0
CG D:GLU182 4.2 59.0 1.0
NE2 D:HIS219 4.4 47.6 1.0
CG D:GLU115 4.5 44.2 1.0
CD2 D:HIS219 4.6 46.8 1.0
NE2 D:GLN88 4.7 46.8 1.0
CB D:GLU216 4.8 50.9 1.0
OD1 D:ASP85 4.8 52.2 1.0
CE1 D:HIS118 4.9 45.8 1.0
CA D:GLU216 4.9 41.9 1.0
ND1 D:HIS118 4.9 47.5 1.0

Iron binding site 7 out of 8 in 6zjk

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Iron binding site 7 out of 8 in the Ribonucleotide Reductase R2 Subunit From Clostridium Botulinum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Ribonucleotide Reductase R2 Subunit From Clostridium Botulinum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:52.1
occ:0.70
 O B:HOH519 2.2 50.7 0.7
OE1 B:GLU182 2.2 72.2 1.0
OE2 B:GLU182 2.2 59.6 1.0
OE2 B:GLU216 2.5 54.8 1.0
CD B:GLU182 2.5 60.4 1.0
OE1 B:GLU115 2.5 53.0 1.0
ND1 B:HIS219 2.5 47.8 1.0
OE2 B:GLU115 3.2 56.6 1.0
CD B:GLU115 3.2 51.2 1.0
CE1 B:HIS219 3.3 43.4 1.0
CD B:GLU216 3.4 62.3 1.0
FE B:FE403 3.5 57.9 0.5
CG B:HIS219 3.6 50.0 1.0
OE1 B:GLU216 3.8 60.3 1.0
CB B:HIS219 3.9 44.9 1.0
CG B:GLU182 4.0 59.0 1.0
NE2 B:GLN111 4.0 46.5 1.0
NE2 B:HIS219 4.5 46.8 1.0
CB B:GLU182 4.6 55.1 1.0
CD2 B:HIS219 4.7 49.0 1.0
CG B:GLU115 4.7 47.9 1.0
CG B:GLU216 4.7 45.0 1.0
NE2 B:GLN88 4.7 51.7 1.0
OD2 B:ASP85 5.0 53.8 1.0
CA B:GLU216 5.0 47.5 1.0

Iron binding site 8 out of 8 in 6zjk

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Iron binding site 8 out of 8 in the Ribonucleotide Reductase R2 Subunit From Clostridium Botulinum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Ribonucleotide Reductase R2 Subunit From Clostridium Botulinum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe403

b:57.9
occ:0.54
 O B:HOH519 2.2 50.7 0.7
OD2 B:ASP85 2.2 53.8 1.0
OE2 B:GLU115 2.3 56.6 1.0
ND1 B:HIS118 2.5 43.9 1.0
CG B:ASP85 3.2 55.9 1.0
CE1 B:HIS118 3.3 45.2 1.0
CD B:GLU115 3.3 51.2 1.0
OD1 B:ASP85 3.4 60.7 1.0
FE B:FE402 3.5 52.1 0.7
CG B:HIS118 3.6 48.1 1.0
CZ B:PHE186 3.7 55.6 1.0
OE1 B:GLU115 3.8 53.0 1.0
OE1 B:GLU216 3.9 60.3 1.0
CB B:HIS118 4.0 43.0 1.0
CE1 B:PHE186 4.1 60.9 1.0
CE2 B:PHE186 4.2 53.6 1.0
CA B:GLU115 4.4 40.4 1.0
NE2 B:HIS118 4.5 43.6 1.0
OE2 B:GLU216 4.5 54.8 1.0
CG B:GLU115 4.5 47.9 1.0
CB B:GLU115 4.5 42.1 1.0
CB B:ASP85 4.5 43.6 1.0
CG2 B:ILE212 4.6 42.9 1.0
CD B:GLU216 4.6 62.3 1.0
CD2 B:HIS118 4.6 42.2 1.0
OE1 B:GLU182 4.7 72.2 1.0
CD1 B:PHE186 4.9 59.7 1.0
CD2 B:PHE186 4.9 58.7 1.0
CE1 B:HIS219 5.0 43.4 1.0

Reference:

M.Martinez-Carranza, R.J.Venkateswara, D.Lundin, M.Sahlin, L.A.Carlson, N.Jemal, M.Hogbom, B.M.Sjoberg, P.Stenmark, A.Hofer. Clostridium Botulinum Ribonucleotide Reductase and Overall Activity Regulation Mechanisms in Class I Enzymes To Be Published.
Page generated: Wed Aug 7 18:42:02 2024

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