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Iron in PDB 6bxo: Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sah

Protein crystallography data

The structure of Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sah, PDB code: 6bxo was solved by M.K.Fenwick, A.T.Torelli, 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) 47.53 / 1.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 31.442, 128.031, 141.925, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.7

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 6bxo

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Iron binding site 1 out of 8 in the Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sah


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 Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe900

b:23.1
occ:1.00
FE1 A:SF4900 0.0 23.1 1.0
S3 A:SF4900 2.2 23.2 1.0
S4 A:SF4900 2.3 22.3 1.0
S2 A:SF4900 2.3 22.1 1.0
SG A:CYS61 2.3 21.5 1.0
FE2 A:SF4900 2.6 25.8 1.0
FE3 A:SF4900 2.6 23.4 1.0
FE4 A:SF4900 2.7 26.7 1.0
CB A:CYS61 3.3 23.9 1.0
S1 A:SF4900 3.8 24.8 1.0
NE2 A:GLN237 4.0 18.9 1.0
N A:SAH901 4.2 29.1 1.0
NH2 A:ARG149 4.5 33.0 1.0
CA A:CYS61 4.6 19.8 1.0
SG A:CYS159 4.8 25.8 1.0
N A:CYS61 4.8 21.4 1.0
CD A:GLN237 4.8 21.5 1.0
SG A:CYS283 4.8 21.0 1.0
CG A:GLN237 4.8 20.2 1.0
CA A:GLY59 4.9 31.4 1.0
O A:SAH901 4.9 31.2 1.0
O A:PHE58 5.0 26.9 1.0

Iron binding site 2 out of 8 in 6bxo

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Iron binding site 2 out of 8 in the Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sah


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 Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe900

b:25.8
occ:1.00
FE2 A:SF4900 0.0 25.8 1.0
S3 A:SF4900 2.3 23.2 1.0
S4 A:SF4900 2.3 22.3 1.0
S1 A:SF4900 2.3 24.8 1.0
SG A:CYS159 2.4 25.8 1.0
FE1 A:SF4900 2.6 23.1 1.0
FE3 A:SF4900 2.7 23.4 1.0
FE4 A:SF4900 2.7 26.7 1.0
CB A:CYS159 3.2 20.9 1.0
S2 A:SF4900 3.8 22.1 1.0
N A:CYS159 4.0 22.5 1.0
O A:SAH901 4.0 31.2 1.0
NH2 A:ARG149 4.1 33.0 1.0
CA A:CYS159 4.2 23.1 1.0
CB A:LEU157 4.6 28.0 1.0
N A:GLY158 4.7 23.7 1.0
C A:GLY158 4.7 27.2 1.0
CD A:PRO284 4.7 21.1 1.0
SD A:MET321 4.7 32.1 0.4
SG A:CYS61 4.8 21.5 1.0
SG A:CYS283 4.9 21.0 1.0
N A:SAH901 4.9 29.1 1.0
CA A:GLY158 5.0 26.8 1.0

Iron binding site 3 out of 8 in 6bxo

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Iron binding site 3 out of 8 in the Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sah


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 Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe900

b:23.4
occ:1.00
FE3 A:SF4900 0.0 23.4 1.0
S1 A:SF4900 2.2 24.8 1.0
S2 A:SF4900 2.2 22.1 1.0
S4 A:SF4900 2.3 22.3 1.0
SG A:CYS283 2.4 21.0 1.0
FE1 A:SF4900 2.6 23.1 1.0
FE2 A:SF4900 2.7 25.8 1.0
FE4 A:SF4900 2.8 26.7 1.0
CB A:CYS283 3.3 21.6 1.0
S3 A:SF4900 3.9 23.2 1.0
CA A:CYS283 3.9 18.8 1.0
CD A:PRO284 4.4 21.1 1.0
C8 A:SAH901 4.4 18.8 1.0
C5' A:SAH901 4.5 29.1 1.0
NE2 A:GLN237 4.5 18.9 1.0
C A:CYS283 4.5 18.0 1.0
N A:PRO284 4.6 20.0 1.0
N A:SAH901 4.7 29.1 1.0
N7 A:SAH901 4.7 18.0 1.0
CB A:ARG285 4.7 26.7 1.0
SG A:CYS61 4.7 21.5 1.0
N A:ARG285 4.8 23.1 1.0
O A:SAH901 4.8 31.2 1.0
SG A:CYS159 4.9 25.8 1.0

Iron binding site 4 out of 8 in 6bxo

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Iron binding site 4 out of 8 in the Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sah


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 Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe900

b:26.7
occ:1.00
FE4 A:SF4900 0.0 26.7 1.0
S3 A:SF4900 2.3 23.2 1.0
N A:SAH901 2.3 29.1 1.0
S1 A:SF4900 2.3 24.8 1.0
S2 A:SF4900 2.3 22.1 1.0
O A:SAH901 2.4 31.2 1.0
FE2 A:SF4900 2.7 25.8 1.0
FE1 A:SF4900 2.7 23.1 1.0
FE3 A:SF4900 2.8 23.4 1.0
CA A:SAH901 3.0 28.8 1.0
C A:SAH901 3.1 32.4 1.0
CB A:SAH901 3.4 40.3 1.0
S4 A:SF4900 3.9 22.3 1.0
OXT A:SAH901 4.3 31.1 1.0
N A:GLY158 4.5 23.7 1.0
C5' A:SAH901 4.6 29.1 1.0
SD A:SAH901 4.6 40.7 1.0
CG A:SAH901 4.7 43.8 1.0
O A:PHE58 4.7 26.9 1.0
SG A:CYS159 4.8 25.8 1.0
SG A:CYS61 4.8 21.5 1.0
CD2 A:LEU157 4.9 25.2 1.0
SG A:CYS283 4.9 21.0 1.0
CB A:LEU157 4.9 28.0 1.0

Iron binding site 5 out of 8 in 6bxo

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Iron binding site 5 out of 8 in the Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sah


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 Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe900

b:21.8
occ:1.00
FE1 B:SF4900 0.0 21.8 1.0
S2 B:SF4900 2.2 21.5 1.0
S4 B:SF4900 2.3 21.8 1.0
S3 B:SF4900 2.3 23.5 1.0
SG B:CYS61 2.3 21.1 1.0
FE3 B:SF4900 2.6 22.4 1.0
FE2 B:SF4900 2.6 23.4 1.0
FE4 B:SF4900 2.7 27.8 1.0
CB B:CYS61 3.2 19.7 1.0
S1 B:SF4900 3.8 23.0 1.0
NE2 B:GLN237 4.2 18.7 1.0
N B:SAH901 4.3 27.9 1.0
NH2 B:ARG149 4.4 38.1 1.0
CA B:CYS61 4.5 22.7 1.0
N B:CYS61 4.6 21.8 1.0
CA B:GLY59 4.7 24.6 1.0
SG B:CYS283 4.8 21.1 1.0
SG B:CYS159 4.8 24.5 1.0
CG B:GLN237 4.8 21.3 1.0
CD B:GLN237 4.9 21.8 1.0
O B:HOH1121 4.9 29.0 1.0
CB B:CYS283 4.9 22.1 1.0
OXT B:SAH901 4.9 34.4 1.0

Iron binding site 6 out of 8 in 6bxo

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Iron binding site 6 out of 8 in the Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sah


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 Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe900

b:23.4
occ:1.00
FE2 B:SF4900 0.0 23.4 1.0
S1 B:SF4900 2.3 23.0 1.0
S3 B:SF4900 2.3 23.5 1.0
S4 B:SF4900 2.3 21.8 1.0
SG B:CYS159 2.3 24.5 1.0
FE1 B:SF4900 2.6 21.8 1.0
FE3 B:SF4900 2.7 22.4 1.0
FE4 B:SF4900 2.7 27.8 1.0
CB B:CYS159 3.2 20.2 1.0
S2 B:SF4900 3.8 21.5 1.0
OXT B:SAH901 3.9 34.4 1.0
NH2 B:ARG149 4.0 38.1 1.0
N B:CYS159 4.0 20.6 1.0
CA B:CYS159 4.2 21.9 1.0
CB B:LEU157 4.6 24.0 1.0
SD B:MET321 4.6 29.8 0.4
N B:GLY158 4.7 26.2 1.0
CD B:PRO284 4.8 21.2 1.0
C B:GLY158 4.8 28.1 1.0
SG B:CYS61 4.8 21.1 1.0
NE B:ARG149 4.8 51.6 1.0
SG B:CYS283 4.9 21.1 1.0
N B:SAH901 4.9 27.9 1.0
CZ B:ARG149 4.9 41.2 1.0
CD1 B:LEU157 5.0 33.0 1.0

Iron binding site 7 out of 8 in 6bxo

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Iron binding site 7 out of 8 in the Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sah


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 Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe900

b:22.4
occ:1.00
FE3 B:SF4900 0.0 22.4 1.0
S2 B:SF4900 2.2 21.5 1.0
S4 B:SF4900 2.2 21.8 1.0
S1 B:SF4900 2.2 23.0 1.0
SG B:CYS283 2.4 21.1 1.0
FE1 B:SF4900 2.6 21.8 1.0
FE2 B:SF4900 2.7 23.4 1.0
FE4 B:SF4900 2.8 27.8 1.0
CB B:CYS283 3.2 22.1 1.0
S3 B:SF4900 3.9 23.5 1.0
CA B:CYS283 3.9 19.8 1.0
CD B:PRO284 4.3 21.2 1.0
C8 B:SAH901 4.5 19.7 1.0
C B:CYS283 4.6 18.2 1.0
C5' B:SAH901 4.6 49.7 1.0
SG B:CYS61 4.6 21.1 1.0
NE2 B:GLN237 4.6 18.7 1.0
CB B:SAH901 4.6 51.9 1.0
N B:PRO284 4.6 20.5 1.0
OXT B:SAH901 4.7 34.4 1.0
N B:SAH901 4.7 27.9 1.0
CB B:ARG285 4.8 23.5 1.0
N B:ARG285 4.8 20.0 1.0
SG B:CYS159 4.8 24.5 1.0
N7 B:SAH901 4.9 20.5 1.0
CG B:ARG285 4.9 37.5 1.0
CB B:CYS159 5.0 20.2 1.0

Iron binding site 8 out of 8 in 6bxo

Go back to Iron Binding Sites List in 6bxo
Iron binding site 8 out of 8 in the Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sah


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 Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe900

b:27.8
occ:1.00
FE4 B:SF4900 0.0 27.8 1.0
S3 B:SF4900 2.3 23.5 1.0
N B:SAH901 2.3 27.9 1.0
S1 B:SF4900 2.3 23.0 1.0
S2 B:SF4900 2.3 21.5 1.0
OXT B:SAH901 2.4 34.4 1.0
FE2 B:SF4900 2.7 23.4 1.0
FE1 B:SF4900 2.7 21.8 1.0
FE3 B:SF4900 2.8 22.4 1.0
CA B:SAH901 2.9 31.2 1.0
C B:SAH901 3.1 38.5 1.0
CB B:SAH901 3.1 51.9 1.0
S4 B:SF4900 3.9 21.8 1.0
O B:SAH901 4.3 33.7 1.0
O B:HOH1121 4.5 29.0 1.0
N B:GLY158 4.6 26.2 1.0
CG B:SAH901 4.6 64.4 1.0
O B:PHE58 4.6 24.9 1.0
SG B:CYS159 4.7 24.5 1.0
SG B:CYS61 4.8 21.1 1.0
C5' B:SAH901 4.9 49.7 1.0
CB B:LEU157 4.9 24.0 1.0
CD2 B:LEU157 4.9 24.1 1.0
SG B:CYS283 4.9 21.1 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 14:40:46 2024

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