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

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

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

Protein crystallography data

The structure of Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Mta, PDB code: 6bxk 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) 40.48 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.509, 80.458, 161.920, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 25

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 6bxk

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


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 Mta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:0.5
occ:0.60
 FE1 A:SF4403 0.0 0.5 0.6
S4 A:SF4403 2.2 0.2 0.6
S2 A:SF4403 2.3 0.5 0.6
S3 A:SF4403 2.3 87.5 0.6
SG A:CYS59 2.3 69.3 1.0
FE4 A:SF4403 2.7 0.9 0.6
FE2 A:SF4403 2.8 0.2 0.6
FE3 A:SF4403 2.8 0.3 0.6
CB A:CYS59 3.5 58.8 1.0
NE2 A:GLN241 3.9 55.8 1.0
S1 A:SF4403 3.9 1.0 0.6
NH2 A:ARG153 4.2 68.3 1.0
O4 A:SO4402 4.7 72.9 0.6
CA A:CYS59 4.7 54.2 1.0
CD A:GLN241 4.7 70.5 1.0
SG A:CYS163 4.7 85.5 1.0
SG A:CYS287 4.7 75.9 1.0
CA A:GLY57 4.7 55.0 1.0
N A:CYS59 4.8 53.2 1.0
O A:TYR56 4.8 67.6 1.0
CG A:GLN241 4.8 69.1 1.0

Iron binding site 2 out of 8 in 6bxk

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


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 Mta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:0.2
occ:0.60
 FE2 A:SF4403 0.0 0.2 0.6
SG A:CYS163 2.3 85.5 1.0
S3 A:SF4403 2.3 87.5 0.6
S4 A:SF4403 2.3 0.2 0.6
S1 A:SF4403 2.3 1.0 0.6
FE3 A:SF4403 2.8 0.3 0.6
FE4 A:SF4403 2.8 0.9 0.6
FE1 A:SF4403 2.8 0.5 0.6
CB A:CYS163 3.7 71.6 1.0
NH2 A:ARG153 3.8 68.3 1.0
S2 A:SF4403 3.9 0.5 0.6
N A:CYS163 4.1 52.8 1.0
CD1 A:LEU161 4.2 46.2 1.0
CB A:LEU161 4.3 47.4 1.0
O4 A:SO4402 4.3 72.9 0.6
CA A:CYS163 4.5 62.4 1.0
CG A:LEU161 4.7 51.1 1.0
SG A:CYS59 4.8 69.3 1.0
O2 A:SO4402 4.8 74.1 0.6
CZ A:ARG153 4.9 73.7 1.0
N A:GLY162 4.9 55.4 1.0
SG A:CYS287 4.9 75.9 1.0
NE A:ARG153 5.0 77.9 1.0

Iron binding site 3 out of 8 in 6bxk

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


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 Mta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:0.3
occ:0.60
 FE3 A:SF4403 0.0 0.3 0.6
S2 A:SF4403 2.2 0.5 0.6
S1 A:SF4403 2.2 1.0 0.6
S4 A:SF4403 2.3 0.2 0.6
SG A:CYS287 2.3 75.9 1.0
FE2 A:SF4403 2.8 0.2 0.6
FE4 A:SF4403 2.8 0.9 0.6
FE1 A:SF4403 2.8 0.5 0.6
CB A:CYS287 3.4 66.1 1.0
SG A:CYS163 3.6 85.5 1.0
S3 A:SF4403 3.9 87.5 0.6
CB A:CYS163 4.2 71.6 1.0
CA A:CYS287 4.2 62.5 1.0
C5' A:MTA401 4.5 90.9 0.6
C8 A:MTA401 4.6 78.0 0.6
NE2 A:GLN241 4.7 55.8 1.0
N7 A:MTA401 4.7 77.1 0.6
SG A:CYS59 4.9 69.3 1.0
S5' A:MTA401 4.9 95.4 0.6
CD A:PRO288 4.9 67.2 1.0
O2 A:SO4402 5.0 74.1 0.6

Iron binding site 4 out of 8 in 6bxk

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


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 Mta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:0.9
occ:0.60
 FE4 A:SF4403 0.0 0.9 0.6
S1 A:SF4403 2.2 1.0 0.6
S3 A:SF4403 2.3 87.5 0.6
O4 A:SO4402 2.3 72.9 0.6
S2 A:SF4403 2.3 0.5 0.6
FE1 A:SF4403 2.7 0.5 0.6
FE3 A:SF4403 2.8 0.3 0.6
FE2 A:SF4403 2.8 0.2 0.6
O2 A:SO4402 3.1 74.1 0.6
S A:SO4402 3.3 70.4 0.6
S5' A:MTA401 3.4 95.4 0.6
S4 A:SF4403 3.8 0.2 0.6
C5' A:MTA401 4.0 90.9 0.6
O3 A:SO4402 4.2 65.1 0.6
O A:TYR56 4.3 67.6 1.0
O1 A:SO4402 4.3 66.7 0.6
CS A:MTA401 4.6 95.0 0.6
SG A:CYS287 4.7 75.9 1.0
SG A:CYS163 4.7 85.5 1.0
SG A:CYS59 4.9 69.3 1.0

Iron binding site 5 out of 8 in 6bxk

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


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 Mta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe403

b:0.7
occ:0.60
 FE1 B:SF4403 0.0 0.7 0.6
S4 B:SF4403 2.2 95.7 0.6
S2 B:SF4403 2.3 91.5 0.6
S3 B:SF4403 2.3 79.5 0.6
SG B:CYS59 2.3 69.0 1.0
FE4 B:SF4403 2.7 0.1 0.6
FE3 B:SF4403 2.8 0.7 0.6
FE2 B:SF4403 2.8 0.4 0.6
NE2 B:GLN241 3.5 83.5 1.0
CB B:CYS59 3.7 59.2 1.0
S1 B:SF4403 3.9 0.6 0.6
SG B:CYS287 4.5 80.6 1.0
O B:TYR56 4.5 70.0 1.0
CD B:GLN241 4.5 80.6 1.0
CG B:GLN241 4.6 76.4 1.0
CA B:GLY57 4.7 56.3 1.0
CB B:CYS287 4.8 68.9 1.0
SG B:CYS163 4.8 90.7 1.0
CA B:CYS59 4.9 58.9 1.0
O3 B:SO4402 4.9 85.1 0.6
N B:CYS59 5.0 58.0 1.0

Iron binding site 6 out of 8 in 6bxk

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


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 Mta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe403

b:0.4
occ:0.60
 FE2 B:SF4403 0.0 0.4 0.6
SG B:CYS163 2.3 90.7 1.0
S3 B:SF4403 2.3 79.5 0.6
S4 B:SF4403 2.3 95.7 0.6
S1 B:SF4403 2.3 0.6 0.6
FE3 B:SF4403 2.8 0.7 0.6
FE4 B:SF4403 2.8 0.1 0.6
FE1 B:SF4403 2.8 0.7 0.6
CB B:CYS163 3.2 80.7 1.0
S2 B:SF4403 3.9 91.5 0.6
O3 B:SO4402 4.0 85.1 0.6
N B:CYS163 4.0 69.8 1.0
CA B:CYS163 4.2 66.2 1.0
NH2 B:ARG153 4.5 79.3 1.0
CB B:LEU161 4.5 56.2 1.0
CD1 B:LEU161 4.6 44.2 1.0
SG B:CYS59 4.6 69.0 1.0
SG B:CYS287 4.8 80.6 1.0
C B:GLY162 4.9 68.3 1.0
N B:GLY162 4.9 55.5 1.0

Iron binding site 7 out of 8 in 6bxk

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


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 Mta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe403

b:0.7
occ:0.60
 FE3 B:SF4403 0.0 0.7 0.6
S2 B:SF4403 2.2 91.5 0.6
S1 B:SF4403 2.2 0.6 0.6
SG B:CYS287 2.2 80.6 1.0
S4 B:SF4403 2.3 95.7 0.6
FE4 B:SF4403 2.7 0.1 0.6
FE2 B:SF4403 2.8 0.4 0.6
FE1 B:SF4403 2.8 0.7 0.6
CB B:CYS287 3.4 68.9 1.0
S3 B:SF4403 3.9 79.5 0.6
CA B:CYS287 4.3 66.0 1.0
CB B:CYS163 4.3 80.7 1.0
SG B:CYS163 4.4 90.7 1.0
NE2 B:GLN241 4.5 83.5 1.0
CB B:ARG289 4.5 66.2 1.0
O3 B:SO4402 4.5 85.1 0.6
CD B:PRO288 4.7 76.1 1.0
C5' B:MTA401 4.8 88.1 0.6
C8 B:MTA401 4.8 78.4 0.6
C B:CYS287 4.8 63.3 1.0
CD B:ARG289 4.8 89.7 1.0
N7 B:MTA401 4.9 77.3 0.6

Iron binding site 8 out of 8 in 6bxk

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


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 Mta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe403

b:0.1
occ:0.60
 FE4 B:SF4403 0.0 0.1 0.6
S1 B:SF4403 2.2 0.6 0.6
S3 B:SF4403 2.3 79.5 0.6
O3 B:SO4402 2.3 85.1 0.6
S2 B:SF4403 2.3 91.5 0.6
FE3 B:SF4403 2.7 0.7 0.6
FE1 B:SF4403 2.7 0.7 0.6
FE2 B:SF4403 2.8 0.4 0.6
S B:SO4402 3.5 79.2 0.6
O4 B:SO4402 3.7 81.4 0.6
S4 B:SF4403 3.8 95.7 0.6
O B:TYR56 3.9 70.0 1.0
O1 B:SO4402 4.1 77.1 0.6
S5' B:MTA401 4.1 93.9 0.6
C5' B:MTA401 4.5 88.1 0.6
O2 B:SO4402 4.6 73.9 0.6
SG B:CYS59 4.7 69.0 1.0
SG B:CYS287 4.8 80.6 1.0
N B:GLY162 4.9 55.5 1.0
SG B:CYS163 4.9 90.7 1.0
CA B:GLY57 5.0 56.3 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: Tue Aug 6 14:39:06 2024

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