Iron in PDB 3pdi: Precursor Bound Nifen

The structure of Precursor Bound Nifen, PDB code: 3pdi was solved by J.T.Kaiser, Y.Hu, J.A.Wiig, D.C.Rees, M.W.Ribbe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.83 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	146.070, 95.220, 149.980, 90.00, 95.50, 90.00
R / Rfree (%)	29.4 / 34.1

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 48;

Binding sites:

The binding sites of Iron atom in the Precursor Bound Nifen (pdb code 3pdi). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 48 binding sites of Iron where determined in the Precursor Bound Nifen, PDB code: 3pdi:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 48 in the Precursor Bound Nifen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Precursor Bound Nifen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:21.4 occ:1.00 FE1 A:SF4501 0.0 21.4 1.0 SG A:CYS37 2.1 30.7 1.0 S4 A:SF4501 2.2 22.9 1.0 S2 A:SF4501 2.3 22.7 1.0 S3 A:SF4501 2.4 20.7 1.0 FE3 A:SF4501 2.6 23.4 1.0 FE2 A:SF4501 2.7 17.9 1.0 FE4 A:SF4501 2.9 28.2 1.0 CB A:CYS37 3.2 27.3 1.0 S1 A:SF4501 3.8 18.3 1.0 CA A:GLY155 3.9 19.3 1.0 CA B:GLY43 4.1 34.8 1.0 N B:CYS44 4.3 36.9 1.0 C B:GLY43 4.3 44.0 1.0 N A:GLY155 4.3 27.0 1.0 CD1 A:PHE39 4.4 23.6 1.0 CB A:PHE39 4.5 20.0 1.0 CA A:CYS37 4.6 28.7 1.0 CE2 B:PHE47 4.6 14.1 1.0 N B:GLY43 4.7 24.0 1.0 N A:CYS37 4.7 31.2 1.0 SG A:CYS124 4.8 27.7 1.0 SG B:CYS44 4.8 22.8 1.0 CG A:PHE39 4.8 22.3 1.0 CD2 B:PHE47 4.9 19.5 1.0

Iron binding site 2 out of 48 in the Precursor Bound Nifen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Precursor Bound Nifen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:17.9 occ:1.00 FE2 A:SF4501 0.0 17.9 1.0 S3 A:SF4501 2.3 20.7 1.0 S1 A:SF4501 2.3 18.3 1.0 S4 A:SF4501 2.3 22.9 1.0 FE4 A:SF4501 2.6 28.2 1.0 FE1 A:SF4501 2.7 21.4 1.0 SG A:CYS62 2.8 13.2 1.0 FE3 A:SF4501 2.9 23.4 1.0 CG2 A:THR123 2.9 38.9 1.0 CB A:CYS62 3.2 25.1 1.0 CA A:CYS62 3.7 32.2 1.0 S2 A:SF4501 3.9 22.7 1.0 N A:CYS62 4.1 21.4 1.0 CB A:THR123 4.3 39.2 1.0 CD1 A:PHE39 4.6 23.6 1.0 SG B:CYS44 4.6 22.8 1.0 N A:CYS124 4.6 30.7 1.0 SG A:CYS37 4.7 30.7 1.0 C A:ALA61 4.9 26.6 1.0 CA A:THR123 4.9 19.0 1.0 SG A:CYS124 4.9 27.7 1.0 CG A:PHE39 5.0 22.3 1.0

Iron binding site 3 out of 48 in the Precursor Bound Nifen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Precursor Bound Nifen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:23.4 occ:1.00 FE3 A:SF4501 0.0 23.4 1.0 S4 A:SF4501 2.3 22.9 1.0 S2 A:SF4501 2.3 22.7 1.0 S1 A:SF4501 2.3 18.3 1.0 SG A:CYS124 2.5 27.7 1.0 FE1 A:SF4501 2.6 21.4 1.0 FE4 A:SF4501 2.7 28.2 1.0 FE2 A:SF4501 2.9 17.9 1.0 CB A:CYS124 3.4 34.7 1.0 CA A:GLY155 3.7 19.3 1.0 N A:GLY155 3.8 27.0 1.0 S3 A:SF4501 3.9 20.7 1.0 N A:CYS124 4.1 30.7 1.0 SG A:CYS37 4.2 30.7 1.0 SG B:CYS44 4.3 22.8 1.0 CA A:CYS124 4.4 20.4 1.0 CB B:SER41 4.4 24.3 1.0 N A:PHE156 4.5 27.2 1.0 C A:GLY155 4.6 32.1 1.0 CG2 A:THR123 4.7 38.9 1.0 CB A:CYS37 4.7 27.3 1.0

Iron binding site 4 out of 48 in the Precursor Bound Nifen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Precursor Bound Nifen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:28.2 occ:1.00 FE4 A:SF4501 0.0 28.2 1.0 SG B:CYS44 2.1 22.8 1.0 S1 A:SF4501 2.2 18.3 1.0 S2 A:SF4501 2.3 22.7 1.0 S3 A:SF4501 2.3 20.7 1.0 FE2 A:SF4501 2.6 17.9 1.0 FE3 A:SF4501 2.7 23.4 1.0 FE1 A:SF4501 2.9 21.4 1.0 CB B:CYS44 3.5 35.2 1.0 N B:CYS44 3.5 36.9 1.0 CA B:CYS44 3.6 34.9 1.0 S4 A:SF4501 3.9 22.9 1.0 CB A:ALA61 4.3 31.1 1.0 C B:GLY43 4.3 44.0 1.0 SG A:CYS62 4.5 13.2 1.0 SG A:CYS37 4.7 30.7 1.0 N A:CYS62 4.8 21.4 1.0 C A:ALA61 4.9 26.6 1.0 CA A:CYS62 4.9 32.2 1.0 CA B:GLY43 4.9 34.8 1.0

Iron binding site 5 out of 48 in the Precursor Bound Nifen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Precursor Bound Nifen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:44.9 occ:1.00 FE1 A:CZL502 0.0 44.9 1.0 S2A A:CZL502 2.3 52.3 1.0 S4A A:CZL502 2.3 45.0 1.0 S1A A:CZL502 2.3 54.6 1.0 FE4 A:CZL502 2.6 48.2 1.0 FE3 A:CZL502 2.7 46.3 1.0 FE2 A:CZL502 2.7 52.7 1.0 SG A:CYS25 3.9 85.0 1.0 CB A:ASN161 4.5 45.4 1.0 S5A A:CZL502 4.8 58.7 1.0 O A:GLY24 4.8 41.4 1.0 S2B A:CZL502 4.8 48.4 1.0 OG1 A:THR159 4.8 42.5 1.0 S3A A:CZL502 4.9 62.6 1.0 FE5 A:CZL502 4.9 40.4 1.0

Iron binding site 6 out of 48 in the Precursor Bound Nifen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Precursor Bound Nifen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:52.7 occ:1.00 FE2 A:CZL502 0.0 52.7 1.0 S2A A:CZL502 2.3 52.3 1.0 S2B A:CZL502 2.3 48.4 1.0 S1A A:CZL502 2.3 54.6 1.0 FE3 A:CZL502 2.6 46.3 1.0 FE4 A:CZL502 2.6 48.2 1.0 FE6 A:CZL502 2.7 47.6 1.0 FE1 A:CZL502 2.7 44.9 1.0 FE5 A:CZL502 3.5 40.4 1.0 FE7 A:CZL502 3.7 50.6 1.0 S4A A:CZL502 3.9 45.0 1.0 CG2 A:THR359 4.1 71.6 1.0 S1B A:CZL502 4.2 34.6 1.0 S3B A:CZL502 4.4 57.2 1.0 S3A A:CZL502 4.5 62.6 1.0 CA A:GLY24 4.5 64.6 1.0 S5A A:CZL502 4.5 58.7 1.0 O A:GLY24 4.6 41.4 1.0 C A:GLY24 4.8 64.4 1.0 CA A:THR359 4.9 71.3 1.0 CB A:THR359 4.9 73.4 1.0 FE8 A:CZL502 5.0 40.1 1.0

Iron binding site 7 out of 48 in the Precursor Bound Nifen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Precursor Bound Nifen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:46.3 occ:1.00 FE3 A:CZL502 0.0 46.3 1.0 S5A A:CZL502 2.3 58.7 1.0 S2A A:CZL502 2.3 52.3 1.0 S4A A:CZL502 2.3 45.0 1.0 FE2 A:CZL502 2.6 52.7 1.0 FE7 A:CZL502 2.6 50.6 1.0 FE1 A:CZL502 2.7 44.9 1.0 FE4 A:CZL502 2.7 48.2 1.0 FE5 A:CZL502 3.4 40.4 1.0 FE6 A:CZL502 3.8 47.6 1.0 S1A A:CZL502 3.9 54.6 1.0 CG2 A:THR359 3.9 71.6 1.0 S4B A:CZL502 4.1 26.6 1.0 S3A A:CZL502 4.3 62.6 1.0 CB A:ASN161 4.4 45.4 1.0 S3B A:CZL502 4.5 57.2 1.0 CG A:ASN161 4.5 45.1 1.0 S2B A:CZL502 4.5 48.4 1.0 OD1 A:ASN161 4.6 52.7 1.0 FE8 A:CZL502 5.0 40.1 1.0

Iron binding site 8 out of 48 in the Precursor Bound Nifen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Precursor Bound Nifen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:48.2 occ:1.00 FE4 A:CZL502 0.0 48.2 1.0 S3A A:CZL502 2.3 62.6 1.0 S1A A:CZL502 2.3 54.6 1.0 S4A A:CZL502 2.3 45.0 1.0 FE1 A:CZL502 2.6 44.9 1.0 FE2 A:CZL502 2.6 52.7 1.0 FE5 A:CZL502 2.7 40.4 1.0 FE3 A:CZL502 2.7 46.3 1.0 S2A A:CZL502 3.8 52.3 1.0 FE6 A:CZL502 4.0 47.6 1.0 FE7 A:CZL502 4.0 50.6 1.0 S1B A:CZL502 4.3 34.6 1.0 S4B A:CZL502 4.5 26.6 1.0 S2B A:CZL502 4.6 48.4 1.0 NH2 A:ARG165 4.7 54.0 1.0 S5A A:CZL502 4.7 58.7 1.0

Iron binding site 9 out of 48 in the Precursor Bound Nifen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Precursor Bound Nifen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:40.4 occ:1.00 FE5 A:CZL502 0.0 40.4 1.0 S4B A:CZL502 2.3 26.6 1.0 S3A A:CZL502 2.3 62.6 1.0 S1B A:CZL502 2.3 34.6 1.0 FE7 A:CZL502 2.6 50.6 1.0 FE6 A:CZL502 2.7 47.6 1.0 FE4 A:CZL502 2.7 48.2 1.0 FE8 A:CZL502 2.7 40.1 1.0 FE3 A:CZL502 3.4 46.3 1.0 FE2 A:CZL502 3.5 52.7 1.0 S3B A:CZL502 3.9 57.2 1.0 S4A A:CZL502 4.2 45.0 1.0 S1A A:CZL502 4.3 54.6 1.0 S5A A:CZL502 4.5 58.7 1.0 S2B A:CZL502 4.5 48.4 1.0 NH2 A:ARG165 4.5 54.0 1.0 NH1 A:ARG165 4.8 43.8 1.0 FE1 A:CZL502 4.9 44.9 1.0

Iron binding site 10 out of 48 in the Precursor Bound Nifen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Precursor Bound Nifen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:47.6 occ:1.00 FE6 A:CZL502 0.0 47.6 1.0 S1B A:CZL502 2.3 34.6 1.0 S2B A:CZL502 2.3 48.4 1.0 S3B A:CZL502 2.3 57.2 1.0 FE7 A:CZL502 2.6 50.6 1.0 FE8 A:CZL502 2.6 40.1 1.0 FE5 A:CZL502 2.7 40.4 1.0 FE2 A:CZL502 2.7 52.7 1.0 FE3 A:CZL502 3.8 46.3 1.0 S4B A:CZL502 3.8 26.6 1.0 FE4 A:CZL502 4.0 48.2 1.0 N A:GLU360 4.2 67.9 1.0 S2A A:CZL502 4.3 52.3 1.0 CG2 A:THR359 4.3 71.6 1.0 CB A:GLU360 4.5 84.0 1.0 S1A A:CZL502 4.5 54.6 1.0 S5A A:CZL502 4.6 58.7 1.0 CB A:THR359 4.6 73.4 1.0 CG A:GLU360 4.6 86.7 1.0 S3A A:CZL502 4.7 62.6 1.0 CA A:THR359 4.9 71.3 1.0 CA A:GLU360 4.9 76.8 1.0

J.T.Kaiser, Y.Hu, J.A.Wiig, D.C.Rees, M.W.Ribbe. Structure of Precursor-Bound Nifen: A Nitrogenase Femo Cofactor Maturase/Insertase. Science V. 331 91 2011.
ISSN: ISSN 0036-8075
PubMed: 21212358
DOI: 10.1126/SCIENCE.1196954