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Iron in PDB 7kdy: Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, Methionine, and (2R)- Pantetheinylated Carbapenam

Protein crystallography data

The structure of Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, Methionine, and (2R)- Pantetheinylated Carbapenam, PDB code: 7kdy 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) 44.19 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.503, 132.817, 155.509, 90, 90, 90
R / Rfree (%) 15.7 / 18.8

Other elements in 7kdy:

The structure of Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, Methionine, and (2R)- Pantetheinylated Carbapenam also contains other interesting chemical elements:

Potassium (K) 4 atoms
Cobalt (Co) 2 atoms

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 7kdy

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Iron binding site 1 out of 8 in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, Methionine, and (2R)- Pantetheinylated Carbapenam


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, Methionine, and (2R)- Pantetheinylated Carbapenam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:14.5
occ:1.00
FE1 A:SF4701 0.0 14.5 1.0
S4 A:SF4701 2.2 13.8 1.0
S3 A:SF4701 2.2 15.7 1.0
S2 A:SF4701 2.3 13.3 1.0
SG A:CYS210 2.5 17.3 1.0
FE2 A:SF4701 2.7 13.4 1.0
FE4 A:SF4701 2.7 14.6 1.0
FE3 A:SF4701 2.7 14.5 1.0
CB A:CYS210 3.2 15.5 1.0
NH1 A:ARG324 3.6 12.6 1.0
S1 A:SF4701 3.8 13.2 1.0
O A:MET703 3.9 13.3 1.0
N A:CYS210 4.1 16.2 1.0
CA A:CYS210 4.3 16.3 1.0
CB A:TYR208 4.6 17.3 1.0
CB A:CYS213 4.7 14.9 1.0
O A:HOH897 4.7 17.3 1.0
SG A:CYS206 4.8 14.0 1.0
N A:MET703 4.8 14.2 1.0
SG A:CYS213 4.9 14.7 1.0
CZ A:PHE212 4.9 16.8 1.0
CZ A:ARG324 4.9 16.6 1.0
CD A:LYS285 4.9 18.5 1.0
C A:MET703 5.0 16.2 1.0

Iron binding site 2 out of 8 in 7kdy

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


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, Methionine, and (2R)- Pantetheinylated Carbapenam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:13.4
occ:1.00
FE2 A:SF4701 0.0 13.4 1.0
S3 A:SF4701 2.2 15.7 1.0
S1 A:SF4701 2.3 13.2 1.0
S4 A:SF4701 2.3 13.8 1.0
SG A:CYS206 2.4 14.0 1.0
FE1 A:SF4701 2.7 14.5 1.0
FE4 A:SF4701 2.7 14.6 1.0
FE3 A:SF4701 2.8 14.5 1.0
CB A:CYS206 3.4 13.9 1.0
S2 A:SF4701 3.8 13.3 1.0
N A:MET703 4.1 14.2 1.0
CB A:TYR208 4.2 17.3 1.0
CD2 A:TYR208 4.4 12.8 1.0
ND2 A:ASN252 4.5 10.1 1.0
CA A:CYS206 4.8 11.0 1.0
O A:MET703 4.8 13.3 1.0
CG A:TYR208 4.8 15.1 1.0
CB A:ALA251 4.8 11.9 1.0
N A:TYR208 4.9 18.3 1.0
CA A:TYR208 4.9 19.8 1.0
C A:TYR208 4.9 16.3 1.0
SG A:CYS213 4.9 14.7 1.0
CG2 A:THR219 4.9 13.7 1.0
SG A:CYS210 4.9 17.3 1.0

Iron binding site 3 out of 8 in 7kdy

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Iron binding site 3 out of 8 in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, Methionine, and (2R)- Pantetheinylated Carbapenam


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, Methionine, and (2R)- Pantetheinylated Carbapenam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:14.5
occ:1.00
FE3 A:SF4701 0.0 14.5 1.0
S2 A:SF4701 2.3 13.3 1.0
S1 A:SF4701 2.3 13.2 1.0
S4 A:SF4701 2.3 13.8 1.0
O A:MET703 2.4 13.3 1.0
N A:MET703 2.4 14.2 1.0
FE1 A:SF4701 2.7 14.5 1.0
SD A:MET703 2.8 13.2 1.0
FE4 A:SF4701 2.8 14.6 1.0
FE2 A:SF4701 2.8 13.4 1.0
C A:MET703 3.2 16.2 1.0
CA A:MET703 3.3 13.4 1.0
CE A:MET703 3.7 11.6 1.0
CG A:MET703 3.7 9.0 1.0
S3 A:SF4701 3.9 15.7 1.0
CB A:MET703 3.9 12.2 1.0
NH1 A:ARG324 4.2 12.6 1.0
OXT A:MET703 4.3 15.4 1.0
O A:ALA251 4.8 11.3 1.0
SG A:CYS206 4.8 14.0 1.0
OD1 A:ASN252 5.0 13.3 1.0

Iron binding site 4 out of 8 in 7kdy

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Iron binding site 4 out of 8 in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, Methionine, and (2R)- Pantetheinylated Carbapenam


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, Methionine, and (2R)- Pantetheinylated Carbapenam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:14.6
occ:1.00
FE4 A:SF4701 0.0 14.6 1.0
S1 A:SF4701 2.2 13.2 1.0
S3 A:SF4701 2.3 15.7 1.0
S2 A:SF4701 2.3 13.3 1.0
SG A:CYS213 2.5 14.7 1.0
FE2 A:SF4701 2.7 13.4 1.0
FE1 A:SF4701 2.7 14.5 1.0
FE3 A:SF4701 2.8 14.5 1.0
CB A:CYS213 3.2 14.9 1.0
S4 A:SF4701 3.8 13.8 1.0
SD A:MET703 4.2 13.2 1.0
CB A:TRP215 4.3 10.6 1.0
CG2 A:THR219 4.6 13.7 1.0
CB A:CYS210 4.6 15.5 1.0
CA A:CYS213 4.7 15.8 1.0
CE A:MET703 4.8 11.6 1.0
SG A:CYS210 4.9 17.3 1.0
CE3 A:TRP215 4.9 13.9 1.0
CG A:TRP215 4.9 12.4 1.0
O A:MET703 4.9 13.3 1.0
SG A:CYS206 4.9 14.0 1.0
CE1 A:PHE212 4.9 14.8 1.0
N A:MET703 5.0 14.2 1.0

Iron binding site 5 out of 8 in 7kdy

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


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, Methionine, and (2R)- Pantetheinylated Carbapenam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:12.3
occ:1.00
FE1 B:SF4701 0.0 12.3 1.0
S3 B:SF4701 2.2 10.6 1.0
S2 B:SF4701 2.3 12.2 1.0
S4 B:SF4701 2.3 10.4 1.0
SG B:CYS210 2.5 12.3 1.0
FE4 B:SF4701 2.7 11.4 1.0
FE3 B:SF4701 2.7 11.7 1.0
FE2 B:SF4701 2.8 11.2 1.0
CB B:CYS210 3.2 11.1 1.0
NH1 B:ARG324 3.6 9.3 1.0
S1 B:SF4701 3.9 10.1 1.0
OXT B:MET703 3.9 12.1 1.0
N B:CYS210 4.1 13.0 1.0
CA B:CYS210 4.3 11.7 1.0
CB B:TYR208 4.6 11.7 1.0
CB B:CYS213 4.6 9.7 1.0
O B:HOH932 4.7 11.6 1.0
SG B:CYS213 4.8 12.4 1.0
SG B:CYS206 4.9 11.0 1.0
CZ B:ARG324 4.9 10.2 1.0
N B:MET703 4.9 10.8 1.0
CZ B:PHE212 4.9 14.1 1.0
CD B:LYS285 4.9 14.0 1.0

Iron binding site 6 out of 8 in 7kdy

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Iron binding site 6 out of 8 in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, Methionine, and (2R)- Pantetheinylated Carbapenam


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, Methionine, and (2R)- Pantetheinylated Carbapenam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:11.2
occ:1.00
FE2 B:SF4701 0.0 11.2 1.0
S4 B:SF4701 2.3 10.4 1.0
S1 B:SF4701 2.3 10.1 1.0
S3 B:SF4701 2.4 10.6 1.0
OXT B:MET703 2.4 12.1 1.0
N B:MET703 2.5 10.8 1.0
SD B:MET703 2.8 11.7 1.0
FE3 B:SF4701 2.8 11.7 1.0
FE1 B:SF4701 2.8 12.3 1.0
FE4 B:SF4701 2.8 11.4 1.0
C B:MET703 3.2 13.6 1.0
CA B:MET703 3.3 9.3 1.0
CE B:MET703 3.7 9.1 1.0
CG B:MET703 3.7 8.4 1.0
CB B:MET703 3.9 8.6 1.0
S2 B:SF4701 3.9 12.2 1.0
NH1 B:ARG324 4.2 9.3 1.0
O B:MET703 4.4 13.6 1.0
O B:ALA251 4.7 10.1 1.0
SG B:CYS206 4.9 11.0 1.0
OD1 B:ASN252 4.9 9.8 1.0

Iron binding site 7 out of 8 in 7kdy

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Iron binding site 7 out of 8 in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, Methionine, and (2R)- Pantetheinylated Carbapenam


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, Methionine, and (2R)- Pantetheinylated Carbapenam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:11.7
occ:1.00
FE3 B:SF4701 0.0 11.7 1.0
S1 B:SF4701 2.2 10.1 1.0
S2 B:SF4701 2.3 12.2 1.0
S4 B:SF4701 2.3 10.4 1.0
SG B:CYS213 2.5 12.4 1.0
FE4 B:SF4701 2.7 11.4 1.0
FE1 B:SF4701 2.7 12.3 1.0
FE2 B:SF4701 2.8 11.2 1.0
CB B:CYS213 3.2 9.7 1.0
S3 B:SF4701 3.8 10.6 1.0
SD B:MET703 4.2 11.7 1.0
CB B:TRP215 4.3 8.0 1.0
CG2 B:THR219 4.6 10.9 1.0
CA B:CYS213 4.7 10.8 1.0
CB B:CYS210 4.7 11.1 1.0
CE3 B:TRP215 4.8 11.9 1.0
SG B:CYS210 4.8 12.3 1.0
CE B:MET703 4.8 9.1 1.0
CG B:TRP215 4.9 8.1 1.0
SG B:CYS206 4.9 11.0 1.0
OXT B:MET703 4.9 12.1 1.0
CE1 B:PHE212 4.9 16.1 1.0

Iron binding site 8 out of 8 in 7kdy

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


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, Methionine, and (2R)- Pantetheinylated Carbapenam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:11.4
occ:1.00
FE4 B:SF4701 0.0 11.4 1.0
S2 B:SF4701 2.2 12.2 1.0
S3 B:SF4701 2.3 10.6 1.0
S1 B:SF4701 2.3 10.1 1.0
SG B:CYS206 2.4 11.0 1.0
FE1 B:SF4701 2.7 12.3 1.0
FE3 B:SF4701 2.7 11.7 1.0
FE2 B:SF4701 2.8 11.2 1.0
CB B:CYS206 3.4 11.5 1.0
S4 B:SF4701 3.9 10.4 1.0
N B:MET703 4.2 10.8 1.0
CB B:TYR208 4.2 11.7 1.0
CD2 B:TYR208 4.4 11.7 1.0
ND2 B:ASN252 4.5 7.7 1.0
CG2 B:THR219 4.8 10.9 1.0
CB B:ALA251 4.8 7.4 1.0
CA B:CYS206 4.8 9.7 1.0
CG B:TYR208 4.8 11.9 1.0
N B:TYR208 4.9 9.8 1.0
OXT B:MET703 4.9 12.1 1.0
CA B:TYR208 4.9 12.3 1.0
SG B:CYS213 4.9 12.4 1.0
C B:TYR208 4.9 13.7 1.0
SG B:CYS210 4.9 12.3 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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