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

Protein crystallography data

The structure of Crystal Structure of Candidatus Methanoperedens Nitroreducens DPH2 with 4FE-4S Cluster and Sam, PDB code: 6bxn 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) 44.49 / 2.08
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 31.476, 127.190, 142.462, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 26

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 6bxn

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe900

b:27.5
occ:1.00
FE1 A:SF4900 0.0 27.5 1.0
SG A:CYS61 2.2 28.2 1.0
S2 A:SF4900 2.2 26.2 1.0
S4 A:SF4900 2.3 27.2 1.0
S3 A:SF4900 2.3 31.6 1.0
FE4 A:SF4900 2.7 38.1 1.0
FE3 A:SF4900 2.8 26.7 1.0
FE2 A:SF4900 2.8 33.6 1.0
CB A:CYS61 3.2 28.2 1.0
S1 A:SF4900 3.9 30.6 1.0
NE2 A:GLN237 4.1 23.3 1.0
N A:SAM901 4.2 54.6 1.0
CA A:CYS61 4.5 25.4 1.0
O A:HOH1075 4.7 41.0 1.0
O A:PHE58 4.7 30.5 1.0
N A:CYS61 4.7 28.3 1.0
SG A:CYS283 4.7 29.7 1.0
SG A:CYS159 4.8 30.4 1.0
CD A:GLN237 4.9 28.5 1.0
CG A:GLN237 4.9 25.2 1.0
CA A:GLY59 4.9 30.9 1.0
CB A:CYS283 4.9 25.0 1.0

Iron binding site 2 out of 8 in 6bxn

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe900

b:33.6
occ:1.00
FE2 A:SF4900 0.0 33.6 1.0
SG A:CYS159 2.3 30.4 1.0
S3 A:SF4900 2.3 31.6 1.0
S4 A:SF4900 2.3 27.2 1.0
S1 A:SF4900 2.3 30.6 1.0
FE4 A:SF4900 2.7 38.1 1.0
FE3 A:SF4900 2.8 26.7 1.0
FE1 A:SF4900 2.8 27.5 1.0
CB A:CYS159 3.1 27.6 1.0
S2 A:SF4900 3.9 26.2 1.0
N A:CYS159 3.9 32.6 1.0
CA A:CYS159 4.1 35.6 1.0
O A:SAM901 4.4 54.1 1.0
CD A:PRO284 4.7 28.8 1.0
C A:GLY158 4.7 31.3 1.0
CB A:LEU157 4.7 28.1 1.0
N A:GLY158 4.8 27.5 1.0
SG A:CYS61 4.8 28.2 1.0
SG A:CYS283 4.8 29.7 1.0

Iron binding site 3 out of 8 in 6bxn

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe900

b:26.7
occ:1.00
FE3 A:SF4900 0.0 26.7 1.0
S1 A:SF4900 2.2 30.6 1.0
S2 A:SF4900 2.2 26.2 1.0
S4 A:SF4900 2.2 27.2 1.0
SG A:CYS283 2.3 29.7 1.0
FE2 A:SF4900 2.8 33.6 1.0
FE1 A:SF4900 2.8 27.5 1.0
FE4 A:SF4900 2.8 38.1 1.0
CB A:CYS283 3.2 25.0 1.0
S3 A:SF4900 3.9 31.6 1.0
CA A:CYS283 4.0 24.8 1.0
CD A:PRO284 4.2 28.8 1.0
C8 A:SAM901 4.5 21.0 1.0
C A:CYS283 4.5 22.4 1.0
N A:PRO284 4.6 23.2 1.0
N A:SAM901 4.6 54.6 1.0
C5' A:SAM901 4.7 35.3 1.0
CB A:ARG285 4.7 31.2 1.0
SG A:CYS61 4.7 28.2 1.0
N A:ARG285 4.7 23.8 1.0
NE2 A:GLN237 4.8 23.3 1.0
N7 A:SAM901 4.8 22.2 1.0
SG A:CYS159 4.9 30.4 1.0
CB A:CYS159 4.9 27.6 1.0
CG A:ARG285 5.0 37.5 1.0

Iron binding site 4 out of 8 in 6bxn

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe900

b:38.1
occ:1.00
FE4 A:SF4900 0.0 38.1 1.0
S3 A:SF4900 2.3 31.6 1.0
S1 A:SF4900 2.3 30.6 1.0
S2 A:SF4900 2.3 26.2 1.0
N A:SAM901 2.3 54.6 1.0
O A:SAM901 2.7 54.1 1.0
FE1 A:SF4900 2.7 27.5 1.0
FE2 A:SF4900 2.7 33.6 1.0
FE3 A:SF4900 2.8 26.7 1.0
C A:SAM901 3.1 56.5 1.0
CA A:SAM901 3.2 57.4 1.0
S4 A:SF4900 3.8 27.2 1.0
OXT A:SAM901 4.0 57.5 1.0
CG A:SAM901 4.3 48.5 1.0
CB A:SAM901 4.3 55.6 1.0
O A:PHE58 4.6 30.5 1.0
O A:HOH1075 4.6 41.0 1.0
N A:GLY158 4.7 27.5 1.0
SD A:SAM901 4.7 42.6 1.0
SG A:CYS159 4.7 30.4 1.0
SG A:CYS61 4.8 28.2 1.0
SG A:CYS283 4.8 29.7 1.0
CD2 A:LEU157 4.9 44.5 1.0
C5' A:SAM901 4.9 35.3 1.0

Iron binding site 5 out of 8 in 6bxn

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe900

b:26.3
occ:1.00
FE1 B:SF4900 0.0 26.3 1.0
S2 B:SF4900 2.2 21.9 1.0
S4 B:SF4900 2.3 25.1 1.0
SG B:CYS61 2.3 28.9 1.0
S3 B:SF4900 2.3 27.4 1.0
FE4 B:SF4900 2.7 39.5 1.0
FE3 B:SF4900 2.7 24.8 1.0
FE2 B:SF4900 2.8 27.4 1.0
CB B:CYS61 3.3 28.6 1.0
S1 B:SF4900 3.9 25.0 1.0
NH1 B:ARG149 4.1 60.5 1.0
N B:SAM901 4.1 59.1 1.0
NE2 B:GLN237 4.3 25.3 1.0
CA B:CYS61 4.6 28.9 1.0
O B:HOH1095 4.6 50.4 1.0
N B:CYS61 4.7 26.6 1.0
SG B:CYS283 4.7 28.3 1.0
SG B:CYS159 4.8 28.9 1.0
O B:PHE58 4.9 31.3 1.0
CD B:GLN237 4.9 25.1 1.0
CB B:CYS283 4.9 21.0 1.0
CG B:GLN237 4.9 25.7 1.0

Iron binding site 6 out of 8 in 6bxn

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe900

b:27.4
occ:1.00
FE2 B:SF4900 0.0 27.4 1.0
SG B:CYS159 2.3 28.9 1.0
S3 B:SF4900 2.3 27.4 1.0
S1 B:SF4900 2.3 25.0 1.0
S4 B:SF4900 2.3 25.1 1.0
FE4 B:SF4900 2.7 39.5 1.0
FE3 B:SF4900 2.8 24.8 1.0
FE1 B:SF4900 2.8 26.3 1.0
CB B:CYS159 3.1 21.9 1.0
NH1 B:ARG149 3.6 60.5 1.0
N B:CYS159 3.8 28.3 1.0
S2 B:SF4900 3.9 21.9 1.0
CA B:CYS159 4.1 31.0 1.0
O B:SAM901 4.5 56.1 1.0
C B:GLY158 4.7 26.8 1.0
CZ B:ARG149 4.7 55.6 1.0
N B:GLY158 4.7 32.4 1.0
CD B:PRO284 4.7 25.6 1.0
CB B:LEU157 4.7 28.3 1.0
NE B:ARG149 4.8 64.5 1.0
SG B:CYS283 4.8 28.3 1.0
N B:SAM901 4.8 59.1 1.0
SG B:CYS61 4.8 28.9 1.0
CA B:GLY158 4.9 29.9 1.0

Iron binding site 7 out of 8 in 6bxn

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe900

b:24.8
occ:1.00
FE3 B:SF4900 0.0 24.8 1.0
S1 B:SF4900 2.2 25.0 1.0
S4 B:SF4900 2.2 25.1 1.0
S2 B:SF4900 2.2 21.9 1.0
SG B:CYS283 2.2 28.3 1.0
FE1 B:SF4900 2.7 26.3 1.0
FE2 B:SF4900 2.8 27.4 1.0
FE4 B:SF4900 2.8 39.5 1.0
CB B:CYS283 3.1 21.0 1.0
CA B:CYS283 3.9 23.7 1.0
S3 B:SF4900 3.9 27.4 1.0
CD B:PRO284 4.3 25.6 1.0
C B:CYS283 4.4 19.2 1.0
C8 B:SAM901 4.5 20.3 1.0
N B:PRO284 4.6 22.8 1.0
C5' B:SAM901 4.7 41.4 1.0
N B:ARG285 4.7 19.1 1.0
CB B:ARG285 4.7 23.2 1.0
SG B:CYS61 4.7 28.9 1.0
N B:SAM901 4.9 59.1 1.0
SG B:CYS159 4.9 28.9 1.0
N7 B:SAM901 4.9 19.4 0.8
NE2 B:GLN237 4.9 25.3 1.0
CG B:ARG285 4.9 31.7 1.0
CB B:CYS159 4.9 21.9 1.0

Iron binding site 8 out of 8 in 6bxn

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe900

b:39.5
occ:1.00
FE4 B:SF4900 0.0 39.5 1.0
S3 B:SF4900 2.2 27.4 1.0
S1 B:SF4900 2.3 25.0 1.0
N B:SAM901 2.3 59.1 1.0
S2 B:SF4900 2.3 21.9 1.0
FE2 B:SF4900 2.7 27.4 1.0
FE1 B:SF4900 2.7 26.3 1.0
O B:SAM901 2.8 56.1 1.0
FE3 B:SF4900 2.8 24.8 1.0
C B:SAM901 3.1 57.4 1.0
CA B:SAM901 3.2 56.5 1.0
CG B:SAM901 3.8 50.6 0.8
S4 B:SF4900 3.8 25.1 1.0
OXT B:SAM901 4.0 57.1 1.0
CB B:SAM901 4.0 52.1 1.0
O B:HOH1095 4.5 50.4 1.0
N B:GLY158 4.6 32.4 1.0
SG B:CYS159 4.7 28.9 1.0
SG B:CYS61 4.8 28.9 1.0
SG B:CYS283 4.9 28.3 1.0
O B:PHE58 4.9 31.3 1.0
CD2 B:LEU157 4.9 34.6 1.0
C5' B:SAM901 4.9 41.4 1.0
SD B:SAM901 5.0 45.8 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 04:17:09 2025

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