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Iron in PDB 6bxl: Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam

Enzymatic activity of Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam

All present enzymatic activity of Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam:
2.5.1.108;

Protein crystallography data

The structure of Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam, PDB code: 6bxl was solved by A.T.Torelli, M.K.Fenwick, Y.Zhang, M.Dong, V.Kathiresan, J.D.Carantoa, B.Dzikovski, K.M.Lancaster, J.H.Freed, B.M.Hoffman, H.Lin, S.E.Ealick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.54 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.035, 80.904, 161.058, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 24.9

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam (pdb code 6bxl). 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 Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam, PDB code: 6bxl:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6bxl

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Iron binding site 1 out of 8 in the Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam


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 Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:86.4
occ:0.80
 FE1 A:SF4402 0.0 86.4 0.8
S4 A:SF4402 2.2 80.9 0.8
SG A:CYS59 2.3 53.4 1.0
S2 A:SF4402 2.3 91.6 0.8
S3 A:SF4402 2.3 89.7 0.8
FE4 A:SF4402 2.7 0.9 0.8
FE3 A:SF4402 2.8 94.9 0.8
FE2 A:SF4402 2.8 87.8 0.8
CB A:CYS59 3.5 41.8 1.0
NE2 A:GLN241 3.8 47.6 1.0
S1 A:SF4402 3.9 90.2 0.8
N A:SAM401 4.1 82.8 0.8
O A:TYR56 4.6 50.6 0.5
CA A:GLY57 4.7 44.6 1.0
CD A:GLN241 4.7 77.2 1.0
CA A:CYS59 4.7 45.4 1.0
N A:CYS59 4.7 42.8 1.0
NH2 A:ARG153 4.8 59.2 1.0
CG A:GLN241 4.8 69.8 1.0
CB A:CYS287 4.9 76.0 1.0
SG A:CYS287 4.9 87.2 1.0
SG A:CYS163 5.0 81.3 1.0

Iron binding site 2 out of 8 in 6bxl

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Iron binding site 2 out of 8 in the Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam


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 Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:87.8
occ:0.80
 FE2 A:SF4402 0.0 87.8 0.8
S3 A:SF4402 2.3 89.7 0.8
SG A:CYS163 2.3 81.3 1.0
S4 A:SF4402 2.3 80.9 0.8
S1 A:SF4402 2.3 90.2 0.8
FE4 A:SF4402 2.8 0.9 0.8
FE3 A:SF4402 2.8 94.9 0.8
FE1 A:SF4402 2.8 86.4 0.8
CB A:CYS163 3.2 70.3 1.0
N A:CYS163 3.8 43.9 1.0
S2 A:SF4402 3.9 91.6 0.8
NH2 A:ARG153 4.0 59.2 1.0
CA A:CYS163 4.1 57.8 1.0
N A:SAM401 4.5 82.8 0.8
O A:SAM401 4.6 70.3 0.8
SG A:CYS59 4.7 53.4 1.0
C A:GLY162 4.8 44.7 1.0
N A:GLY162 4.8 47.1 1.0
CB A:LEU161 4.8 48.4 1.0
CD1 A:ILE323 4.9 61.9 1.0
CD1 A:LEU161 4.9 45.5 1.0
SG A:CYS287 4.9 87.2 1.0

Iron binding site 3 out of 8 in 6bxl

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Iron binding site 3 out of 8 in the Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam


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 Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:94.9
occ:0.80
 FE3 A:SF4402 0.0 94.9 0.8
S2 A:SF4402 2.2 91.6 0.8
S1 A:SF4402 2.2 90.2 0.8
S4 A:SF4402 2.3 80.9 0.8
SG A:CYS287 2.4 87.2 1.0
FE4 A:SF4402 2.8 0.9 0.8
FE2 A:SF4402 2.8 87.8 0.8
FE1 A:SF4402 2.8 86.4 0.8
CB A:CYS287 3.1 76.0 1.0
S3 A:SF4402 3.9 89.7 0.8
CA A:CYS287 4.0 71.4 1.0
C8 A:SAM401 4.0 73.8 0.8
NE2 A:GLN241 4.4 47.6 1.0
N7 A:SAM401 4.4 74.8 0.8
CD A:PRO288 4.6 80.0 1.0
C A:CYS287 4.7 76.0 1.0
CG A:SAM401 4.7 83.8 0.8
CB A:ARG289 4.7 58.0 1.0
CB A:CYS163 4.8 70.3 1.0
SG A:CYS59 4.8 53.4 1.0
SG A:CYS163 4.8 81.3 1.0
N A:PRO288 4.9 79.9 1.0

Iron binding site 4 out of 8 in 6bxl

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Iron binding site 4 out of 8 in the Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam


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 Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:0.9
occ:0.80
 FE4 A:SF4402 0.0 0.9 0.8
S1 A:SF4402 2.2 90.2 0.8
S3 A:SF4402 2.3 89.7 0.8
N A:SAM401 2.3 82.8 0.8
S2 A:SF4402 2.3 91.6 0.8
FE1 A:SF4402 2.7 86.4 0.8
FE2 A:SF4402 2.8 87.8 0.8
FE3 A:SF4402 2.8 94.9 0.8
CG A:SAM401 3.0 83.8 0.8
O A:SAM401 3.1 70.3 0.8
CA A:SAM401 3.1 79.8 0.8
C A:SAM401 3.4 71.8 0.8
CB A:SAM401 3.5 82.7 0.8
S4 A:SF4402 3.8 80.9 0.8
O A:TYR56 4.3 50.6 0.5
SD A:SAM401 4.3 90.9 0.8
OXT A:SAM401 4.3 69.8 0.8
N A:GLY162 4.6 47.1 1.0
SG A:CYS59 4.8 53.4 1.0
SG A:CYS163 4.9 81.3 1.0
CA A:GLY162 5.0 42.5 1.0

Iron binding site 5 out of 8 in 6bxl

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Iron binding site 5 out of 8 in the Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam


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 Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:94.5
occ:0.80
 FE1 B:SF4402 0.0 94.5 0.8
S4 B:SF4402 2.2 75.4 0.8
S2 B:SF4402 2.3 75.7 0.8
S3 B:SF4402 2.3 98.5 0.8
SG B:CYS59 2.3 60.3 1.0
FE4 B:SF4402 2.7 0.8 0.8
FE3 B:SF4402 2.8 90.2 0.8
FE2 B:SF4402 2.8 98.7 0.8
CB B:CYS59 3.4 52.6 1.0
NE2 B:GLN241 3.7 73.5 1.0
S1 B:SF4402 3.9 0.3 0.8
N B:SAM401 4.5 78.4 0.8
CA B:GLY57 4.6 49.2 1.0
NH2 B:ARG153 4.6 69.7 1.0
O B:TYR56 4.6 61.8 1.0
CA B:CYS59 4.6 53.9 1.0
CD B:GLN241 4.7 73.9 1.0
CG B:GLN241 4.7 66.0 1.0
N B:CYS59 4.7 52.4 1.0
SG B:CYS163 4.7 81.0 1.0
SG B:CYS287 4.8 79.3 1.0

Iron binding site 6 out of 8 in 6bxl

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Iron binding site 6 out of 8 in the Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam


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 Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:98.7
occ:0.80
 FE2 B:SF4402 0.0 98.7 0.8
S3 B:SF4402 2.3 98.5 0.8
SG B:CYS163 2.3 81.0 1.0
S4 B:SF4402 2.3 75.4 0.8
S1 B:SF4402 2.3 0.3 0.8
FE4 B:SF4402 2.8 0.8 0.8
FE3 B:SF4402 2.8 90.2 0.8
FE1 B:SF4402 2.8 94.5 0.8
CB B:CYS163 3.1 77.0 1.0
N B:CYS163 3.7 57.9 1.0
S2 B:SF4402 3.9 75.7 0.8
CA B:CYS163 4.0 62.2 1.0
NH2 B:ARG153 4.1 69.7 1.0
CB B:LEU161 4.4 62.0 1.0
CD1 B:LEU161 4.4 52.9 1.0
O B:SAM401 4.4 68.8 0.8
N B:GLY162 4.5 59.1 1.0
N B:SAM401 4.6 78.4 0.8
C B:GLY162 4.6 62.5 1.0
CA B:GLY162 4.9 47.7 1.0
CG B:LEU161 4.9 66.3 1.0
SG B:CYS59 4.9 60.3 1.0
SG B:CYS287 5.0 79.3 1.0

Iron binding site 7 out of 8 in 6bxl

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Iron binding site 7 out of 8 in the Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam


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 Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:90.2
occ:0.80
 FE3 B:SF4402 0.0 90.2 0.8
S2 B:SF4402 2.2 75.7 0.8
S1 B:SF4402 2.2 0.3 0.8
S4 B:SF4402 2.3 75.4 0.8
SG B:CYS287 2.3 79.3 1.0
FE4 B:SF4402 2.8 0.8 0.8
FE2 B:SF4402 2.8 98.7 0.8
FE1 B:SF4402 2.8 94.5 0.8
CB B:CYS287 3.3 73.3 1.0
S3 B:SF4402 3.9 98.5 0.8
CA B:CYS287 4.0 67.2 1.0
C8 B:SAM401 4.3 70.5 0.8
NE2 B:GLN241 4.4 73.5 1.0
C5' B:SAM401 4.5 71.2 0.8
CD B:PRO288 4.5 85.7 1.0
CG B:ARG289 4.5 92.5 1.0
CB B:CYS163 4.6 77.0 1.0
N7 B:SAM401 4.6 65.0 0.8
C B:CYS287 4.7 66.2 1.0
SG B:CYS163 4.7 81.0 1.0
CD B:ARG289 4.8 96.4 1.0
CB B:ARG289 4.8 85.3 1.0
N B:PRO288 4.9 79.7 1.0
SG B:CYS59 5.0 60.3 1.0

Iron binding site 8 out of 8 in 6bxl

Go back to Iron Binding Sites List in 6bxl
Iron binding site 8 out of 8 in the Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam


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 Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:0.8
occ:0.80
 FE4 B:SF4402 0.0 0.8 0.8
S1 B:SF4402 2.2 0.3 0.8
S3 B:SF4402 2.3 98.5 0.8
N B:SAM401 2.3 78.4 0.8
S2 B:SF4402 2.3 75.7 0.8
FE1 B:SF4402 2.7 94.5 0.8
FE2 B:SF4402 2.8 98.7 0.8
FE3 B:SF4402 2.8 90.2 0.8
CA B:SAM401 3.4 78.0 0.8
O B:SAM401 3.4 68.8 0.8
C B:SAM401 3.5 71.7 0.8
S4 B:SF4402 3.8 75.4 0.8
O B:TYR56 3.8 61.8 1.0
CG B:SAM401 4.0 86.5 0.8
SD B:SAM401 4.0 77.7 0.8
CB B:SAM401 4.1 83.2 0.8
C5' B:SAM401 4.3 71.2 0.8
OXT B:SAM401 4.4 73.9 0.8
SG B:CYS59 4.7 60.3 1.0
SG B:CYS287 4.8 79.3 1.0
C B:TYR56 4.9 60.5 1.0
CA B:GLY57 4.9 49.2 1.0
N B:GLY162 4.9 59.1 1.0
SG B:CYS163 5.0 81.0 1.0

Reference:

M.Dong, V.Kathiresan, M.K.Fenwick, A.T.Torelli, Y.Zhang, J.D.Caranto, B.Dzikovski, A.Sharma, K.M.Lancaster, J.H.Freed, S.E.Ealick, B.M.Hoffman, H.Lin. Organometallic and Radical Intermediates Reveal Mechanism of Diphthamide Biosynthesis. Science V. 359 1247 2018.
ISSN: ESSN 1095-9203
PubMed: 29590073
DOI: 10.1126/SCIENCE.AAO6595
Page generated: Wed Aug 6 04:14:57 2025

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