Iron in PDB 7jmb: Crystal Structure of Nitrogenase Iron-Molybdenum Cofactor Biosynthesis Enzyme Nifb From Methanothermobacter Thermautotrophicus with Three FE4S4 Clusters

The structure of Crystal Structure of Nitrogenase Iron-Molybdenum Cofactor Biosynthesis Enzyme Nifb From Methanothermobacter Thermautotrophicus with Three FE4S4 Clusters, PDB code: 7jmb was solved by W.Kang, L.Rettberg, M.W.Ribbe, Y.Hu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.70 / 3.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	121.870, 77.640, 90.800, 90.00, 128.85, 90.00
R / Rfree (%)	26.2 / 31.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Nitrogenase Iron-Molybdenum Cofactor Biosynthesis Enzyme Nifb From Methanothermobacter Thermautotrophicus with Three FE4S4 Clusters (pdb code 7jmb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Crystal Structure of Nitrogenase Iron-Molybdenum Cofactor Biosynthesis Enzyme Nifb From Methanothermobacter Thermautotrophicus with Three FE4S4 Clusters, PDB code: 7jmb:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in the Crystal Structure of Nitrogenase Iron-Molybdenum Cofactor Biosynthesis Enzyme Nifb From Methanothermobacter Thermautotrophicus with Three FE4S4 Clusters


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 Nitrogenase Iron-Molybdenum Cofactor Biosynthesis Enzyme Nifb From Methanothermobacter Thermautotrophicus with Three FE4S4 Clusters within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:60.6 occ:0.51 FE1 A:SF4301 0.0 60.6 0.5 S4 A:SF4301 2.2 58.1 0.5 S2 A:SF4301 2.2 65.1 0.5 S3 A:SF4301 2.2 52.8 0.5 SG A:CYS38 2.3 94.3 1.0 CB A:CYS38 3.0 82.2 1.0 FE4 A:SF4301 3.1 57.3 0.5 FE2 A:SF4301 3.1 48.2 0.5 FE3 A:SF4301 3.1 61.8 0.5 S1 A:SF4301 3.8 55.7 0.5 CG1 A:ILE40 3.9 74.1 1.0 O A:ILE40 4.2 67.6 1.0 CA A:CYS38 4.4 73.0 1.0 CD1 A:ILE40 4.4 78.5 1.0 N A:ASP91 4.6 59.2 1.0 C A:ILE40 4.7 71.2 1.0 CA A:GLY90 4.8 65.0 1.0 C A:GLY90 4.9 65.6 1.0 N A:ILE40 4.9 74.0 1.0 O A:PRO89 4.9 39.0 1.0 SG A:CYS42 5.0 81.1 1.0

Iron binding site 2 out of 24 in the Crystal Structure of Nitrogenase Iron-Molybdenum Cofactor Biosynthesis Enzyme Nifb From Methanothermobacter Thermautotrophicus with Three FE4S4 Clusters


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 Nitrogenase Iron-Molybdenum Cofactor Biosynthesis Enzyme Nifb From Methanothermobacter Thermautotrophicus with Three FE4S4 Clusters within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:48.2 occ:0.51 FE2 A:SF4301 0.0 48.2 0.5 S3 A:SF4301 2.2 52.8 0.5 S4 A:SF4301 2.2 58.1 0.5 S1 A:SF4301 2.2 55.7 0.5 SG A:CYS45 2.3 0.2 1.0 CB A:CYS45 2.9 0.8 1.0 FE4 A:SF4301 3.1 57.3 0.5 FE3 A:SF4301 3.1 61.8 0.5 FE1 A:SF4301 3.1 60.6 0.5 S2 A:SF4301 3.8 65.1 0.5 CA A:CYS45 4.0 0.3 1.0 NE A:ARG47 4.4 56.3 1.0 CD A:ARG47 4.7 41.0 1.0 O A:PRO89 4.7 39.0 1.0 CG A:ARG47 4.8 39.3 1.0 CB A:CYS42 4.9 77.0 1.0 N A:CYS45 5.0 0.2 1.0 N A:CYS42 5.0 58.7 1.0 SG A:CYS42 5.0 81.1 1.0

Iron binding site 3 out of 24 in the Crystal Structure of Nitrogenase Iron-Molybdenum Cofactor Biosynthesis Enzyme Nifb From Methanothermobacter Thermautotrophicus with Three FE4S4 Clusters


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 Nitrogenase Iron-Molybdenum Cofactor Biosynthesis Enzyme Nifb From Methanothermobacter Thermautotrophicus with Three FE4S4 Clusters within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:61.8 occ:0.51 FE3 A:SF4301 0.0 61.8 0.5 S2 A:SF4301 2.2 65.1 0.5 S1 A:SF4301 2.2 55.7 0.5 S4 A:SF4301 2.2 58.1 0.5 FE2 A:SF4301 3.1 48.2 0.5 FE4 A:SF4301 3.1 57.3 0.5 FE1 A:SF4301 3.1 60.6 0.5 S3 A:SF4301 3.8 52.8 0.5 O A:PRO89 3.9 39.0 1.0

Iron binding site 4 out of 24 in the Crystal Structure of Nitrogenase Iron-Molybdenum Cofactor Biosynthesis Enzyme Nifb From Methanothermobacter Thermautotrophicus with Three FE4S4 Clusters


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 Nitrogenase Iron-Molybdenum Cofactor Biosynthesis Enzyme Nifb From Methanothermobacter Thermautotrophicus with Three FE4S4 Clusters within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:57.3 occ:0.51 FE4 A:SF4301 0.0 57.3 0.5 S1 A:SF4301 2.2 55.7 0.5 S3 A:SF4301 2.2 52.8 0.5 S2 A:SF4301 2.2 65.1 0.5 SG A:CYS42 2.3 81.1 1.0 FE2 A:SF4301 3.1 48.2 0.5 FE1 A:SF4301 3.1 60.6 0.5 FE3 A:SF4301 3.1 61.8 0.5 CB A:CYS42 3.2 77.0 1.0 S4 A:SF4301 3.8 58.1 0.5 N A:CYS42 4.0 58.7 1.0 CA A:CYS42 4.2 70.7 1.0 CD1 A:ILE40 4.2 78.5 1.0 CG1 A:ILE40 4.5 74.1 1.0 CB A:CYS45 4.8 0.8 1.0

Iron binding site 5 out of 24 in the Crystal Structure of Nitrogenase Iron-Molybdenum Cofactor Biosynthesis Enzyme Nifb From Methanothermobacter Thermautotrophicus with Three FE4S4 Clusters


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 Nitrogenase Iron-Molybdenum Cofactor Biosynthesis Enzyme Nifb From Methanothermobacter Thermautotrophicus with Three FE4S4 Clusters within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:88.0 occ:0.87 FE1 A:SF4302 0.0 88.0 0.9 S2 A:SF4302 2.2 65.2 0.9 S4 A:SF4302 2.2 82.4 0.9 S3 A:SF4302 2.2 73.7 0.9 NE2 A:HIS31 2.8 44.8 1.0 FE2 A:SF4302 3.1 85.9 0.9 FE4 A:SF4302 3.1 83.5 0.9 FE3 A:SF4302 3.1 70.5 0.9 CD2 A:HIS31 3.3 44.7 1.0 S1 A:SF4302 3.8 74.4 0.9 CA A:GLY85 3.9 41.6 1.0 CE1 A:HIS31 3.9 47.5 1.0 CB A:ALA87 3.9 64.7 1.0 C A:GLY85 4.2 38.8 1.0 CG A:HIS31 4.4 51.6 1.0 O A:GLY85 4.5 43.3 1.0 N A:ALA87 4.6 48.5 1.0 ND1 A:HIS31 4.7 50.0 1.0 N A:GLY85 4.7 46.6 1.0 N A:VAL86 4.8 38.2 1.0 CB A:CYS115 4.8 68.7 1.0 CA A:ALA87 4.9 49.9 1.0 SG A:CYS115 4.9 87.3 1.0 FE1 A:SF4303 5.0 57.2 0.8

Iron binding site 6 out of 24 in the Crystal Structure of Nitrogenase Iron-Molybdenum Cofactor Biosynthesis Enzyme Nifb From Methanothermobacter Thermautotrophicus with Three FE4S4 Clusters


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 Nitrogenase Iron-Molybdenum Cofactor Biosynthesis Enzyme Nifb From Methanothermobacter Thermautotrophicus with Three FE4S4 Clusters within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:85.9 occ:0.87 FE2 A:SF4302 0.0 85.9 0.9 S3 A:SF4302 2.2 73.7 0.9 S1 A:SF4302 2.2 74.4 0.9 S4 A:SF4302 2.2 82.4 0.9 SG A:CYS115 2.3 87.3 1.0 FE3 A:SF4302 3.1 70.5 0.9 FE1 A:SF4302 3.1 88.0 0.9 FE4 A:SF4302 3.1 83.5 0.9 CB A:CYS115 3.1 68.7 1.0 S2 A:SF4302 3.8 65.2 0.9 N A:MET116 4.0 56.9 1.0 O A:MET116 4.2 59.1 1.0 CA A:CYS115 4.3 63.3 1.0 CG2 A:THR139 4.3 41.3 1.0 CE1 A:HIS16 4.3 87.2 1.0 C A:CYS115 4.4 72.9 1.0 SG A:CYS18 4.4 65.7 1.0 NE2 A:HIS16 4.5 84.0 1.0 C A:MET116 4.5 52.2 1.0 CA A:MET116 4.8 51.4 1.0 CB A:CYS18 4.9 68.0 1.0

Iron binding site 7 out of 24 in the Crystal Structure of Nitrogenase Iron-Molybdenum Cofactor Biosynthesis Enzyme Nifb From Methanothermobacter Thermautotrophicus with Three FE4S4 Clusters


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 Nitrogenase Iron-Molybdenum Cofactor Biosynthesis Enzyme Nifb From Methanothermobacter Thermautotrophicus with Three FE4S4 Clusters within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:70.5 occ:0.87 FE3 A:SF4302 0.0 70.5 0.9 S2 A:SF4302 2.2 65.2 0.9 S1 A:SF4302 2.2 74.4 0.9 S4 A:SF4302 2.2 82.4 0.9 FE1 A:SF4303 2.8 57.2 0.8 FE2 A:SF4302 3.1 85.9 0.9 FE4 A:SF4302 3.1 83.5 0.9 FE1 A:SF4302 3.1 88.0 0.9 S3 A:SF4302 3.8 73.7 0.9 CG2 A:THR139 3.9 41.3 1.0 CB A:SER117 4.3 57.5 1.0 S3 A:SF4303 4.4 66.5 0.8 S4 A:SF4303 4.5 66.2 0.8 S2 A:SF4303 4.5 60.3 0.8 SG A:CYS18 4.6 65.7 1.0 NE2 A:HIS31 4.7 44.8 1.0 CB A:ALA87 4.8 64.7 1.0

Iron binding site 8 out of 24 in the Crystal Structure of Nitrogenase Iron-Molybdenum Cofactor Biosynthesis Enzyme Nifb From Methanothermobacter Thermautotrophicus with Three FE4S4 Clusters


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 Nitrogenase Iron-Molybdenum Cofactor Biosynthesis Enzyme Nifb From Methanothermobacter Thermautotrophicus with Three FE4S4 Clusters within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:83.5 occ:0.87 FE4 A:SF4302 0.0 83.5 0.9 S3 A:SF4302 2.2 73.7 0.9 S2 A:SF4302 2.2 65.2 0.9 S1 A:SF4302 2.2 74.4 0.9 SG A:CYS18 2.3 65.7 1.0 FE3 A:SF4302 3.1 70.5 0.9 FE2 A:SF4302 3.1 85.9 0.9 FE1 A:SF4302 3.1 88.0 0.9 S3 A:SF4303 3.2 66.5 0.8 FE1 A:SF4303 3.4 57.2 0.8 CB A:CYS18 3.7 68.0 1.0 S4 A:SF4302 3.8 82.4 0.9 NE2 A:HIS31 4.0 44.8 1.0 NH1 A:ARG29 4.2 53.7 1.0 FE2 A:SF4303 4.5 83.2 0.8 S4 A:SF4303 4.6 66.2 0.8 NE2 A:HIS16 4.7 84.0 1.0 CD A:ARG29 4.8 43.1 1.0 CE1 A:HIS31 4.8 47.5 1.0 CD2 A:HIS31 4.9 44.7 1.0 CA A:CYS18 5.0 65.4 1.0

Iron binding site 9 out of 24 in the Crystal Structure of Nitrogenase Iron-Molybdenum Cofactor Biosynthesis Enzyme Nifb From Methanothermobacter Thermautotrophicus with Three FE4S4 Clusters


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Nitrogenase Iron-Molybdenum Cofactor Biosynthesis Enzyme Nifb From Methanothermobacter Thermautotrophicus with Three FE4S4 Clusters within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe303 b:57.2 occ:0.84 FE1 A:SF4303 0.0 57.2 0.8 S4 A:SF4303 2.2 66.2 0.8 S2 A:SF4303 2.2 60.3 0.8 S3 A:SF4303 2.2 66.5 0.8 FE3 A:SF4302 2.8 70.5 0.9 S2 A:SF4302 2.9 65.2 0.9 FE3 A:SF4303 3.1 51.5 0.8 FE2 A:SF4303 3.1 83.2 0.8 FE4 A:SF4303 3.1 74.5 0.8 S1 A:SF4302 3.3 74.4 0.9 FE4 A:SF4302 3.4 83.5 0.9 S1 A:SF4303 3.8 67.3 0.8 SG A:CYS18 3.8 65.7 1.0 NH1 A:ARG29 4.8 53.7 1.0 S4 A:SF4302 4.9 82.4 0.9 CB A:CYS18 5.0 68.0 1.0 FE1 A:SF4302 5.0 88.0 0.9

Iron binding site 10 out of 24 in the Crystal Structure of Nitrogenase Iron-Molybdenum Cofactor Biosynthesis Enzyme Nifb From Methanothermobacter Thermautotrophicus with Three FE4S4 Clusters


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Nitrogenase Iron-Molybdenum Cofactor Biosynthesis Enzyme Nifb From Methanothermobacter Thermautotrophicus with Three FE4S4 Clusters within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe303 b:83.2 occ:0.84 FE2 A:SF4303 0.0 83.2 0.8 S3 A:SF4303 2.2 66.5 0.8 S1 A:SF4303 2.2 67.3 0.8 S4 A:SF4303 2.2 66.2 0.8 FE4 A:SF4303 3.1 74.5 0.8 FE1 A:SF4303 3.1 57.2 0.8 FE3 A:SF4303 3.1 51.5 0.8 SG A:CYS18 3.4 65.7 1.0 NE2 A:HIS24 3.5 0.5 1.0 S2 A:SF4303 3.8 60.3 0.8 CE1 A:HIS24 4.2 0.8 1.0 CB A:CYS18 4.2 68.0 1.0 CE2 A:PHE257 4.2 52.2 1.0 CA A:CYS18 4.2 65.4 1.0 CD2 A:HIS24 4.4 0.7 1.0 NH1 A:ARG29 4.5 53.7 1.0 FE4 A:SF4302 4.5 83.5 0.9 CZ A:PHE257 4.5 47.8 1.0 SG A:CYS263 4.7 0.3 1.0 O A:ALA259 4.7 76.8 1.0 CA A:CYS260 4.9 72.1 1.0 S1 A:SF4302 5.0 74.4 0.9

W.Kang, L.A.Rettberg, M.T.Stiebritz, A.J.Jasniewski, K.Tanifuji, C.C.Lee, M.W.Ribbe, Y.Hu. X-Ray Crystallographic Analysis of Nifb with A Full Complement of Clusters: Structural Insights Into the Radical Sam-Dependent Carbide Insertion During Nitrogenase Cofactor Assembly. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 33035363
DOI: 10.1002/ANIE.202011367