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Iron in PDB 6bxm: Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam

Protein crystallography data

The structure of Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam, PDB code: 6bxm 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) 49.81 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.887, 64.080, 158.368, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 22.7

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 6bxm

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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 Sam/Cleaved 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 Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:22.1
occ:1.00
FE1 A:SF4401 0.0 22.1 1.0
S4 A:SF4401 2.2 20.4 1.0
S2 A:SF4401 2.3 22.4 1.0
SG A:CYS61 2.3 25.0 1.0
S3 A:SF4401 2.3 22.1 1.0
FE3 A:SF4401 2.7 21.0 1.0
FE4 A:SF4401 2.7 32.6 1.0
FE2 A:SF4401 2.7 24.2 1.0
CB A:CYS61 3.2 19.8 1.0
S1 A:SF4401 3.8 26.2 1.0
NE2 A:GLN237 3.9 20.2 1.0
N A:SAM402 4.3 42.7 1.0
CA A:CYS61 4.5 18.5 1.0
N A:CYS61 4.6 20.6 1.0
SG A:CYS283 4.6 23.6 1.0
CD A:GLN237 4.7 22.5 1.0
SG A:CYS159 4.7 28.6 1.0
O A:PHE58 4.8 29.6 1.0
CG A:GLN237 4.8 22.9 1.0
CB A:CYS283 4.9 18.0 1.0

Iron binding site 2 out of 8 in 6bxm

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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 Sam/Cleaved 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 Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:24.2
occ:1.00
FE2 A:SF4401 0.0 24.2 1.0
SG A:CYS159 2.2 28.6 1.0
S3 A:SF4401 2.2 22.1 1.0
S1 A:SF4401 2.3 26.2 1.0
S4 A:SF4401 2.3 20.4 1.0
FE4 A:SF4401 2.7 32.6 1.0
FE1 A:SF4401 2.7 22.1 1.0
FE3 A:SF4401 2.8 21.0 1.0
CB A:CYS159 3.2 30.5 1.0
N A:CYS159 3.9 22.4 1.0
S2 A:SF4401 3.9 22.4 1.0
CA A:CYS159 4.2 25.0 1.0
CB A:LEU157 4.6 29.9 1.0
C A:GLY158 4.7 27.7 1.0
N A:GLY158 4.8 30.8 1.0
SG A:CYS61 4.8 25.0 1.0
CD A:PRO284 4.8 23.4 1.0
N A:SAM402 4.8 42.7 1.0
CB A:CYS61 4.9 19.8 1.0
SG A:CYS283 4.9 23.6 1.0
CG A:MET321 4.9 34.9 1.0

Iron binding site 3 out of 8 in 6bxm

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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 Sam/Cleaved 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 Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:21.0
occ:1.00
FE3 A:SF4401 0.0 21.0 1.0
S2 A:SF4401 2.2 22.4 1.0
SG A:CYS283 2.3 23.6 1.0
S4 A:SF4401 2.3 20.4 1.0
S1 A:SF4401 2.3 26.2 1.0
FE1 A:SF4401 2.7 22.1 1.0
FE4 A:SF4401 2.8 32.6 1.0
FE2 A:SF4401 2.8 24.2 1.0
CB A:CYS283 3.2 18.0 1.0
CA A:CYS283 3.8 21.4 1.0
S3 A:SF4401 3.9 22.1 1.0
C A:CYS283 4.4 23.1 1.0
CD A:PRO284 4.4 23.4 1.0
C8 A:SAM402 4.5 20.2 1.0
N A:PRO284 4.5 23.4 1.0
CG A:ARG285 4.6 40.2 1.0
CB A:ARG285 4.6 27.2 1.0
NE2 A:GLN237 4.6 20.2 1.0
N A:ARG285 4.7 21.4 1.0
SG A:CYS61 4.7 25.0 1.0
CG A:SAM402 4.7 42.1 1.0
SG A:CYS159 4.8 28.6 1.0
N A:SAM402 4.8 42.7 1.0
N7 A:SAM402 4.9 25.3 1.0
C5' A:SAM402 4.9 40.9 1.0
CD A:ARG285 5.0 37.1 1.0

Iron binding site 4 out of 8 in 6bxm

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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 Sam/Cleaved 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 Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:32.6
occ:1.00
FE4 A:SF4401 0.0 32.6 1.0
N A:SAM402 2.3 42.7 1.0
S1 A:SF4401 2.3 26.2 1.0
S3 A:SF4401 2.3 22.1 1.0
S2 A:SF4401 2.3 22.4 1.0
FE2 A:SF4401 2.7 24.2 1.0
FE1 A:SF4401 2.7 22.1 1.0
FE3 A:SF4401 2.8 21.0 1.0
CA A:SAM402 3.2 48.6 1.0
C A:SAM402 3.3 42.1 1.0
CG A:SAM402 3.4 42.1 1.0
OXT A:SAM402 3.5 49.1 1.0
O A:SAM402 3.9 41.2 1.0
S4 A:SF4401 3.9 20.4 1.0
CB A:SAM402 4.0 39.7 1.0
O A:PHE58 4.6 29.6 1.0
N A:GLY158 4.7 30.8 1.0
SG A:CYS159 4.7 28.6 1.0
O A:HOH572 4.8 35.2 1.0
SG A:CYS61 4.8 25.0 1.0
SD A:SAM402 4.8 59.8 1.0
SG A:CYS283 4.8 23.6 1.0
CD A:ARG285 4.8 37.1 1.0
CB A:LEU157 5.0 29.9 1.0

Iron binding site 5 out of 8 in 6bxm

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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 Sam/Cleaved 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 Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:24.7
occ:1.00
FE1 B:SF4401 0.0 24.7 1.0
S2 B:SF4401 2.2 24.8 1.0
S4 B:SF4401 2.2 17.2 1.0
SG B:CYS61 2.3 26.0 1.0
S3 B:SF4401 2.3 24.5 1.0
FE3 B:SF4401 2.6 19.3 1.0
FE4 B:SF4401 2.7 35.1 1.0
FE2 B:SF4401 2.8 21.1 1.0
CB B:CYS61 3.2 24.7 1.0
S1 B:SF4401 3.8 24.1 1.0
NE2 B:GLN237 3.9 19.5 1.0
CA B:CYS61 4.5 23.7 1.0
N B:CYS61 4.6 22.0 1.0
NH1 B:ARG149 4.7 42.1 1.0
SG B:CYS283 4.7 21.3 1.0
CD B:GLN237 4.8 20.4 1.0
SG B:CYS159 4.8 24.8 1.0
CG B:GLN237 4.8 20.4 1.0
O B:HOH577 4.8 40.2 1.0
O B:PHE58 5.0 25.9 1.0
CB B:CYS283 5.0 21.1 1.0
N B:ABA402 5.0 51.3 1.0

Iron binding site 6 out of 8 in 6bxm

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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 Sam/Cleaved 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 Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:21.1
occ:1.00
FE2 B:SF4401 0.0 21.1 1.0
S3 B:SF4401 2.3 24.5 1.0
SG B:CYS159 2.3 24.8 1.0
S1 B:SF4401 2.3 24.1 1.0
S4 B:SF4401 2.3 17.2 1.0
FE4 B:SF4401 2.7 35.1 1.0
FE3 B:SF4401 2.7 19.3 1.0
FE1 B:SF4401 2.8 24.7 1.0
CB B:CYS159 3.2 29.9 1.0
S2 B:SF4401 3.9 24.8 1.0
N B:CYS159 3.9 27.8 1.0
CA B:CYS159 4.2 28.1 1.0
NH1 B:ARG149 4.3 42.1 1.0
N B:ABA402 4.5 51.3 1.0
C B:GLY158 4.7 25.9 1.0
N B:GLY158 4.7 27.1 1.0
CB B:LEU157 4.7 23.1 1.0
CD B:PRO284 4.7 20.3 1.0
NE B:ARG149 4.8 52.6 1.0
SG B:CYS61 4.8 26.0 1.0
SG B:CYS283 4.8 21.3 1.0
CA B:GLY158 4.9 27.7 1.0

Iron binding site 7 out of 8 in 6bxm

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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 Sam/Cleaved 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 Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:19.3
occ:1.00
FE3 B:SF4401 0.0 19.3 1.0
S2 B:SF4401 2.2 24.8 1.0
S1 B:SF4401 2.2 24.1 1.0
S4 B:SF4401 2.3 17.2 1.0
SG B:CYS283 2.3 21.3 1.0
FE1 B:SF4401 2.6 24.7 1.0
FE2 B:SF4401 2.7 21.1 1.0
FE4 B:SF4401 2.8 35.1 1.0
CB B:CYS283 3.2 21.1 1.0
S3 B:SF4401 3.9 24.5 1.0
CA B:CYS283 3.9 21.8 1.0
CD B:PRO284 4.2 20.3 1.0
NE2 B:GLN237 4.4 19.5 1.0
C B:CYS283 4.6 19.7 1.0
CG B:ARG285 4.6 28.5 1.0
C5' B:MTA403 4.6 44.6 1.0
SG B:CYS61 4.6 26.0 1.0
C8 B:MTA403 4.6 19.9 1.0
N B:PRO284 4.7 24.6 1.0
CB B:ARG285 4.7 25.5 1.0
N B:ARG285 4.8 22.6 1.0
SG B:CYS159 4.8 24.8 1.0
N7 B:MTA403 4.9 16.9 1.0

Iron binding site 8 out of 8 in 6bxm

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Iron binding site 8 out of 8 in the Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved 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 Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam/Cleaved Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:35.1
occ:1.00
FE4 B:SF4401 0.0 35.1 1.0
S3 B:SF4401 2.3 24.5 1.0
S1 B:SF4401 2.3 24.1 1.0
S2 B:SF4401 2.3 24.8 1.0
N B:ABA402 2.7 51.3 1.0
FE2 B:SF4401 2.7 21.1 1.0
FE1 B:SF4401 2.7 24.7 1.0
FE3 B:SF4401 2.8 19.3 1.0
CB B:ABA402 3.0 41.6 1.0
CA B:ABA402 3.3 45.3 1.0
CG B:ABA402 3.4 46.5 1.0
C B:ABA402 3.8 38.5 1.0
S4 B:SF4401 3.9 17.2 1.0
O B:ABA402 4.1 42.3 1.0
OXT B:ABA402 4.4 45.6 1.0
O B:HOH577 4.5 40.2 1.0
SG B:CYS61 4.7 26.0 1.0
SG B:CYS159 4.7 24.8 1.0
S5' B:MTA403 4.7 63.5 1.0
N B:GLY158 4.8 27.1 1.0
SG B:CYS283 4.8 21.3 1.0
C5' B:MTA403 4.8 44.6 1.0
O B:PHE58 4.9 25.9 1.0
CD B:ARG285 5.0 38.5 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 14:40:42 2024

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