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Iron in PDB 7kdx: Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine

Protein crystallography data

The structure of Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine, PDB code: 7kdx was solved by H.L.Knox, S.J.Booker, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.35 / 1.79
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.644, 137.739, 77.914, 90, 90.47, 90
R / Rfree (%) 16.5 / 19.3

Other elements in 7kdx:

The structure of Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Cobalt (Co) 2 atoms
Potassium (K) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine (pdb code 7kdx). 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 Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine, PDB code: 7kdx:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 7kdx

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Iron binding site 1 out of 8 in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine


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 Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:13.4
occ:1.00
FE1 A:SF4701 0.0 13.4 1.0
S4 A:SF4701 2.3 13.0 1.0
S3 A:SF4701 2.3 14.6 1.0
SG A:CYS210 2.3 13.3 1.0
S2 A:SF4701 2.3 12.1 1.0
FE2 A:SF4701 2.7 13.7 1.0
FE4 A:SF4701 2.7 12.7 1.0
FE3 A:SF4701 2.8 12.3 1.0
CB A:CYS210 3.1 9.8 1.0
NH1 A:ARG324 3.6 10.8 1.0
S1 A:SF4701 3.9 11.7 1.0
O A:MET704 3.9 14.8 1.0
N A:CYS210 4.0 15.0 1.0
CA A:CYS210 4.2 14.6 1.0
O A:HOH834 4.5 18.2 1.0
CB A:CYS213 4.6 10.7 1.0
CB A:TYR208 4.6 11.6 1.0
SG A:CYS213 4.7 12.2 1.0
SG A:CYS206 4.7 12.2 1.0
N A:MET704 4.8 14.1 1.0
CZ A:ARG324 4.8 15.1 1.0
CZ A:PHE212 4.9 13.9 1.0
CD A:LYS285 5.0 16.8 1.0
C A:MET704 5.0 12.1 1.0
N A:SER209 5.0 15.3 1.0

Iron binding site 2 out of 8 in 7kdx

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Iron binding site 2 out of 8 in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine


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 Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:13.7
occ:1.00
FE2 A:SF4701 0.0 13.7 1.0
SG A:CYS206 2.2 12.2 1.0
S3 A:SF4701 2.3 14.6 1.0
S4 A:SF4701 2.3 13.0 1.0
S1 A:SF4701 2.3 11.7 1.0
FE1 A:SF4701 2.7 13.4 1.0
FE4 A:SF4701 2.7 12.7 1.0
FE3 A:SF4701 2.8 12.3 1.0
CB A:CYS206 3.3 10.8 1.0
S2 A:SF4701 3.9 12.1 1.0
N A:MET704 4.1 14.1 1.0
CB A:TYR208 4.2 11.6 1.0
CD2 A:TYR208 4.4 15.5 1.0
ND2 A:ASN252 4.4 9.6 1.0
SG A:CYS213 4.7 12.2 1.0
CA A:CYS206 4.7 11.7 1.0
CB A:ALA251 4.8 11.8 1.0
SG A:CYS210 4.8 13.3 1.0
CG A:TYR208 4.8 16.1 1.0
O A:MET704 4.8 14.8 1.0
CG2 A:THR219 4.9 11.4 1.0
N A:TYR208 4.9 16.8 1.0
CA A:TYR208 4.9 15.2 1.0
C A:TYR208 4.9 13.3 1.0

Iron binding site 3 out of 8 in 7kdx

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Iron binding site 3 out of 8 in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine


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 Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:12.3
occ:1.00
FE3 A:SF4701 0.0 12.3 1.0
S2 A:SF4701 2.3 12.1 1.0
S1 A:SF4701 2.3 11.7 1.0
N A:MET704 2.3 14.1 1.0
O A:MET704 2.4 14.8 1.0
S4 A:SF4701 2.4 13.0 1.0
SD A:MET704 2.7 12.0 1.0
FE4 A:SF4701 2.8 12.7 1.0
FE1 A:SF4701 2.8 13.4 1.0
FE2 A:SF4701 2.8 13.7 1.0
C A:MET704 3.1 12.1 1.0
CA A:MET704 3.2 8.1 1.0
CE A:MET704 3.7 11.0 1.0
CG A:MET704 3.7 11.4 1.0
CB A:MET704 3.9 9.3 1.0
S3 A:SF4701 4.0 14.6 1.0
NH1 A:ARG324 4.2 10.8 1.0
OXT A:MET704 4.3 14.4 1.0
SG A:CYS206 4.7 12.2 1.0
O A:ALA251 4.8 11.2 1.0
SG A:CYS213 4.9 12.2 1.0
SG A:CYS210 4.9 13.3 1.0
OD1 A:ASN252 4.9 13.6 1.0

Iron binding site 4 out of 8 in 7kdx

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Iron binding site 4 out of 8 in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine


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 Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:12.7
occ:1.00
FE4 A:SF4701 0.0 12.7 1.0
SG A:CYS213 2.3 12.2 1.0
S1 A:SF4701 2.3 11.7 1.0
S3 A:SF4701 2.3 14.6 1.0
S2 A:SF4701 2.3 12.1 1.0
FE2 A:SF4701 2.7 13.7 1.0
FE1 A:SF4701 2.7 13.4 1.0
FE3 A:SF4701 2.8 12.3 1.0
CB A:CYS213 3.1 10.7 1.0
S4 A:SF4701 3.9 13.0 1.0
SD A:MET704 4.2 12.0 1.0
CB A:TRP215 4.3 11.3 1.0
CG2 A:THR219 4.6 11.4 1.0
CB A:CYS210 4.6 9.8 1.0
CA A:CYS213 4.6 10.7 1.0
SG A:CYS210 4.7 13.3 1.0
SG A:CYS206 4.8 12.2 1.0
CE A:MET704 4.8 11.0 1.0
O A:MET704 4.9 14.8 1.0
CG A:TRP215 4.9 12.4 1.0
CE3 A:TRP215 4.9 14.3 1.0
N A:MET704 4.9 14.1 1.0
CE1 A:PHE212 5.0 13.3 1.0

Iron binding site 5 out of 8 in 7kdx

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Iron binding site 5 out of 8 in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine


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 Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1903

b:13.4
occ:1.00
FE1 B:SF41903 0.0 13.4 1.0
S3 B:SF41903 2.3 12.3 1.0
SG B:CYS210 2.3 13.7 1.0
S4 B:SF41903 2.3 11.1 1.0
S2 B:SF41903 2.3 13.7 1.0
FE4 B:SF41903 2.7 13.2 1.0
FE3 B:SF41903 2.7 12.8 1.0
FE2 B:SF41903 2.8 12.8 1.0
CB B:CYS210 3.1 13.8 1.0
NH1 B:ARG324 3.6 9.4 1.0
O B:MET1905 3.9 13.9 1.0
S1 B:SF41903 3.9 11.4 1.0
N B:CYS210 4.1 14.6 1.0
CA B:CYS210 4.2 14.9 1.0
O B:HOH2139 4.6 15.8 1.0
CB B:TYR208 4.6 12.5 1.0
CB B:CYS213 4.6 13.2 1.0
SG B:CYS213 4.7 12.9 1.0
SG B:CYS206 4.7 12.9 1.0
N B:MET1905 4.8 11.4 1.0
CZ B:ARG324 4.8 13.4 1.0
CZ B:PHE212 4.9 14.5 1.0
C B:MET1905 5.0 12.0 1.0

Iron binding site 6 out of 8 in 7kdx

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Iron binding site 6 out of 8 in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine


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 Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1903

b:12.8
occ:1.00
FE2 B:SF41903 0.0 12.8 1.0
S4 B:SF41903 2.3 11.1 1.0
O B:MET1905 2.3 13.9 1.0
S3 B:SF41903 2.4 12.3 1.0
N B:MET1905 2.4 11.4 1.0
S1 B:SF41903 2.4 11.4 1.0
SD B:MET1905 2.8 11.7 1.0
FE1 B:SF41903 2.8 13.4 1.0
FE3 B:SF41903 2.8 12.8 1.0
FE4 B:SF41903 2.8 13.2 1.0
C B:MET1905 3.1 12.0 1.0
CA B:MET1905 3.2 10.1 1.0
CG B:MET1905 3.7 9.8 1.0
CE B:MET1905 3.7 10.3 1.0
CB B:MET1905 3.9 10.6 1.0
S2 B:SF41903 4.0 13.7 1.0
NH1 B:ARG324 4.1 9.4 1.0
OXT B:MET1905 4.3 11.9 1.0
SG B:CYS206 4.7 12.9 1.0
O B:ALA251 4.8 8.8 1.0
SG B:CYS210 4.8 13.7 1.0
SG B:CYS213 4.9 12.9 1.0
OD1 B:ASN252 4.9 11.7 1.0

Iron binding site 7 out of 8 in 7kdx

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Iron binding site 7 out of 8 in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine


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 Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1903

b:12.8
occ:1.00
FE3 B:SF41903 0.0 12.8 1.0
S1 B:SF41903 2.3 11.4 1.0
S2 B:SF41903 2.3 13.7 1.0
SG B:CYS213 2.3 12.9 1.0
S4 B:SF41903 2.3 11.1 1.0
FE4 B:SF41903 2.7 13.2 1.0
FE1 B:SF41903 2.7 13.4 1.0
FE2 B:SF41903 2.8 12.8 1.0
CB B:CYS213 3.1 13.2 1.0
S3 B:SF41903 3.9 12.3 1.0
SD B:MET1905 4.2 11.7 1.0
CB B:TRP215 4.3 10.9 1.0
CG2 B:THR219 4.5 13.2 1.0
CB B:CYS210 4.6 13.8 1.0
CA B:CYS213 4.6 14.2 1.0
SG B:CYS210 4.7 13.7 1.0
SG B:CYS206 4.8 12.9 1.0
CE B:MET1905 4.8 10.3 1.0
O B:MET1905 4.9 13.9 1.0
CE1 B:PHE212 4.9 9.8 1.0
CG B:TRP215 4.9 9.7 1.0
CE3 B:TRP215 4.9 9.9 1.0
N B:MET1905 5.0 11.4 1.0

Iron binding site 8 out of 8 in 7kdx

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Iron binding site 8 out of 8 in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine


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 Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1903

b:13.2
occ:1.00
FE4 B:SF41903 0.0 13.2 1.0
SG B:CYS206 2.2 12.9 1.0
S2 B:SF41903 2.2 13.7 1.0
S1 B:SF41903 2.3 11.4 1.0
S3 B:SF41903 2.3 12.3 1.0
FE3 B:SF41903 2.7 12.8 1.0
FE1 B:SF41903 2.7 13.4 1.0
FE2 B:SF41903 2.8 12.8 1.0
CB B:CYS206 3.3 8.0 1.0
S4 B:SF41903 3.9 11.1 1.0
N B:MET1905 4.1 11.4 1.0
CB B:TYR208 4.2 12.5 1.0
CD2 B:TYR208 4.3 12.3 1.0
ND2 B:ASN252 4.5 10.2 1.0
CA B:CYS206 4.7 10.8 1.0
SG B:CYS213 4.8 12.9 1.0
CG B:TYR208 4.8 14.6 1.0
N B:TYR208 4.8 14.4 1.0
SG B:CYS210 4.8 13.7 1.0
O B:MET1905 4.8 13.9 1.0
CA B:TYR208 4.8 13.2 1.0
CB B:ALA251 4.9 10.2 1.0
CG2 B:THR219 4.9 13.2 1.0
C B:TYR208 4.9 16.5 1.0

Reference:

H.L.Knox, E.K.Sinner, C.A.Townsend, A.K.Boal, S.J.Booker. Structure of A B 12 -Dependent Radical Sam Enzyme in Carbapenem Biosynthesis. Nature V. 602 343 2022.
ISSN: ESSN 1476-4687
PubMed: 35110734
DOI: 10.1038/S41586-021-04392-4
Page generated: Wed Apr 5 02:56:37 2023

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