Iron in PDB 3lzd: Crystal Structure of DPH2 From Pyrococcus Horikoshii with 4FE-4S Cluster

The structure of Crystal Structure of DPH2 From Pyrococcus Horikoshii with 4FE-4S Cluster, PDB code: 3lzd was solved by A.T.Torelli, Y.Zhang, X.Zhu, M.Lee, B.Dzikovski, R.M.Koralewski, E.Wang, J.Freed, C.Krebs, H.Lin, S.E.Ealick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.695, 80.525, 162.142, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 25.2

The binding sites of Iron atom in the Crystal Structure of DPH2 From Pyrococcus Horikoshii with 4FE-4S Cluster (pdb code 3lzd). 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 DPH2 From Pyrococcus Horikoshii with 4FE-4S Cluster, PDB code: 3lzd:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Crystal Structure of DPH2 From Pyrococcus Horikoshii with 4FE-4S Cluster


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 DPH2 From Pyrococcus Horikoshii with 4FE-4S Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe343 b:71.2 occ:1.00 FE1 A:SF4343 0.0 71.2 1.0 S2 A:SF4343 2.2 72.0 1.0 S3 A:SF4343 2.3 72.9 1.0 SG A:CYS287 2.3 54.2 1.0 S4 A:SF4343 2.4 71.6 1.0 FE3 A:SF4343 2.8 75.7 1.0 FE4 A:SF4343 2.8 69.6 1.0 FE2 A:SF4343 2.8 92.3 1.0 CB A:CYS287 3.3 45.5 1.0 S1 A:SF4343 4.0 73.3 1.0 CA A:CYS287 4.3 42.1 1.0 NE2 A:GLN241 4.4 46.1 1.0 SG A:CYS163 4.6 60.9 1.0 O A:HOH396 4.6 60.7 1.0 O A:HOH398 4.6 68.2 1.0 CB A:CYS163 4.6 45.5 1.0 SG A:CYS59 4.9 45.6 1.0 CD A:ARG289 4.9 56.8 1.0 CB A:ARG289 4.9 41.6 1.0 CD A:GLN241 4.9 46.9 1.0 C A:CYS287 5.0 38.3 1.0

Iron binding site 2 out of 8 in the Crystal Structure of DPH2 From Pyrococcus Horikoshii with 4FE-4S Cluster


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 DPH2 From Pyrococcus Horikoshii with 4FE-4S Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe343 b:92.3 occ:1.00 FE2 A:SF4343 0.0 92.3 1.0 S1 A:SF4343 2.3 73.3 1.0 S3 A:SF4343 2.3 72.9 1.0 S4 A:SF4343 2.3 71.6 1.0 FE3 A:SF4343 2.7 75.7 1.0 FE4 A:SF4343 2.7 69.6 1.0 O4 A:SO4344 2.8 88.2 1.0 FE1 A:SF4343 2.8 71.2 1.0 O1 A:SO4344 3.0 88.8 1.0 S A:SO4344 3.4 86.7 1.0 O A:HOH398 3.5 68.2 1.0 S2 A:SF4343 3.9 72.0 1.0 O3 A:SO4344 4.0 89.0 1.0 O A:TYR56 4.4 45.3 1.0 O2 A:SO4344 4.7 83.9 1.0 SG A:CYS59 4.9 45.6 1.0 SG A:CYS287 4.9 54.2 1.0 N A:GLY162 4.9 29.0 1.0 SG A:CYS163 5.0 60.9 1.0

Iron binding site 3 out of 8 in the Crystal Structure of DPH2 From Pyrococcus Horikoshii with 4FE-4S Cluster


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 DPH2 From Pyrococcus Horikoshii with 4FE-4S Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe343 b:75.7 occ:1.00 FE3 A:SF4343 0.0 75.7 1.0 S4 A:SF4343 2.2 71.6 1.0 S2 A:SF4343 2.3 72.0 1.0 S1 A:SF4343 2.3 73.3 1.0 SG A:CYS163 2.4 60.9 1.0 FE2 A:SF4343 2.7 92.3 1.0 FE1 A:SF4343 2.8 71.2 1.0 FE4 A:SF4343 2.8 69.6 1.0 CB A:CYS163 3.3 45.5 1.0 S3 A:SF4343 3.9 72.9 1.0 O4 A:SO4344 3.9 88.2 1.0 NH2 A:ARG153 4.0 43.2 1.0 N A:CYS163 4.0 35.1 1.0 CA A:CYS163 4.3 36.9 1.0 NE A:ARG153 4.4 54.5 1.0 CB A:LEU161 4.6 28.1 1.0 CZ A:ARG153 4.7 53.1 1.0 SG A:CYS287 4.7 54.2 1.0 CD1 A:LEU161 4.8 34.1 1.0 N A:GLY162 4.9 29.0 1.0 C A:GLY162 5.0 33.0 1.0 SG A:CYS59 5.0 45.6 1.0

Iron binding site 4 out of 8 in the Crystal Structure of DPH2 From Pyrococcus Horikoshii with 4FE-4S Cluster


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 DPH2 From Pyrococcus Horikoshii with 4FE-4S Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe343 b:69.6 occ:1.00 FE4 A:SF4343 0.0 69.6 1.0 S3 A:SF4343 2.3 72.9 1.0 S2 A:SF4343 2.3 72.0 1.0 S1 A:SF4343 2.3 73.3 1.0 SG A:CYS59 2.4 45.6 1.0 FE2 A:SF4343 2.7 92.3 1.0 FE1 A:SF4343 2.8 71.2 1.0 FE3 A:SF4343 2.8 75.7 1.0 CB A:CYS59 3.4 34.4 1.0 NE2 A:GLN241 3.7 46.1 1.0 S4 A:SF4343 4.0 71.6 1.0 NH2 A:ARG153 4.2 43.2 1.0 CD A:GLN241 4.7 46.9 1.0 CA A:CYS59 4.7 31.8 1.0 CG A:GLN241 4.7 44.6 1.0 N A:CYS59 4.9 32.7 1.0 CA A:GLY57 4.9 32.1 1.0 SG A:CYS287 4.9 54.2 1.0 O A:HOH396 4.9 60.7 1.0 SG A:CYS163 5.0 60.9 1.0

Iron binding site 5 out of 8 in the Crystal Structure of DPH2 From Pyrococcus Horikoshii with 4FE-4S Cluster


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 DPH2 From Pyrococcus Horikoshii with 4FE-4S Cluster within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe343 b:62.6 occ:1.00 FE1 B:SF4343 0.0 62.6 1.0 S2 B:SF4343 2.3 60.6 1.0 S3 B:SF4343 2.3 64.3 1.0 SG B:CYS287 2.3 54.4 1.0 S4 B:SF4343 2.4 66.3 1.0 FE4 B:SF4343 2.8 70.3 1.0 FE3 B:SF4343 2.8 69.1 1.0 FE2 B:SF4343 2.8 82.3 1.0 CB B:CYS287 3.3 43.1 1.0 S1 B:SF4343 4.0 67.2 1.0 CA B:CYS287 4.2 43.4 1.0 CB B:CYS163 4.6 36.4 1.0 SG B:CYS163 4.7 54.0 1.0 CD B:ARG289 4.8 49.5 1.0 CB B:ARG289 4.8 47.1 1.0 CD B:PRO288 4.9 41.1 1.0 SG B:CYS59 4.9 50.5 1.0 C B:CYS287 4.9 39.0 1.0 NE2 B:GLN241 5.0 59.9 1.0 CG B:ARG289 5.0 54.0 1.0

Iron binding site 6 out of 8 in the Crystal Structure of DPH2 From Pyrococcus Horikoshii with 4FE-4S Cluster


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 DPH2 From Pyrococcus Horikoshii with 4FE-4S Cluster within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe343 b:82.3 occ:1.00 FE2 B:SF4343 0.0 82.3 1.0 S1 B:SF4343 2.3 67.2 1.0 S4 B:SF4343 2.3 66.3 1.0 S3 B:SF4343 2.3 64.3 1.0 O4 B:SO4344 2.7 98.3 1.0 FE3 B:SF4343 2.7 69.1 1.0 FE4 B:SF4343 2.7 70.3 1.0 FE1 B:SF4343 2.8 62.6 1.0 O3 B:SO4344 3.4 97.3 1.0 S B:SO4344 3.5 99.0 1.0 S2 B:SF4343 3.9 60.6 1.0 O1 B:SO4344 4.1 0.1 1.0 O B:TYR56 4.2 50.0 1.0 O2 B:SO4344 4.8 100.0 1.0 SG B:CYS59 4.8 50.5 1.0 N B:GLY162 4.9 30.1 1.0 SG B:CYS163 4.9 54.0 1.0 NE B:ARG289 5.0 53.5 1.0 SG B:CYS287 5.0 54.4 1.0

Iron binding site 7 out of 8 in the Crystal Structure of DPH2 From Pyrococcus Horikoshii with 4FE-4S Cluster


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 DPH2 From Pyrococcus Horikoshii with 4FE-4S Cluster within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe343 b:69.1 occ:1.00 FE3 B:SF4343 0.0 69.1 1.0 S4 B:SF4343 2.2 66.3 1.0 S1 B:SF4343 2.3 67.2 1.0 S2 B:SF4343 2.3 60.6 1.0 SG B:CYS163 2.3 54.0 1.0 FE2 B:SF4343 2.7 82.3 1.0 FE1 B:SF4343 2.8 62.6 1.0 FE4 B:SF4343 2.8 70.3 1.0 CB B:CYS163 3.2 36.4 1.0 NH2 B:ARG153 3.9 51.8 1.0 S3 B:SF4343 3.9 64.3 1.0 N B:CYS163 4.0 34.9 1.0 CA B:CYS163 4.2 38.3 1.0 O4 B:SO4344 4.5 98.3 1.0 CB B:LEU161 4.6 28.3 1.0 SG B:CYS287 4.8 54.4 1.0 CD1 B:LEU161 4.8 40.2 1.0 SG B:CYS59 4.9 50.5 1.0 N B:GLY162 4.9 30.1 1.0 C B:CYS163 5.0 34.9 1.0

Iron binding site 8 out of 8 in the Crystal Structure of DPH2 From Pyrococcus Horikoshii with 4FE-4S Cluster


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 DPH2 From Pyrococcus Horikoshii with 4FE-4S Cluster within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe343 b:70.3 occ:1.00 FE4 B:SF4343 0.0 70.3 1.0 S3 B:SF4343 2.3 64.3 1.0 S2 B:SF4343 2.3 60.6 1.0 S1 B:SF4343 2.3 67.2 1.0 SG B:CYS59 2.3 50.5 1.0 FE2 B:SF4343 2.7 82.3 1.0 FE1 B:SF4343 2.8 62.6 1.0 FE3 B:SF4343 2.8 69.1 1.0 CB B:CYS59 3.4 38.3 1.0 S4 B:SF4343 3.9 66.3 1.0 NE2 B:GLN241 4.3 59.9 1.0 NH2 B:ARG153 4.6 51.8 1.0 CA B:CYS59 4.7 36.9 1.0 CA B:GLY57 4.7 36.3 1.0 CG B:GLN241 4.7 57.8 1.0 N B:CYS59 4.7 36.5 1.0 O B:TYR56 4.8 50.0 1.0 CD B:GLN241 4.8 62.4 1.0 SG B:CYS287 4.8 54.4 1.0 SG B:CYS163 4.9 54.0 1.0

Y.Zhang, X.Zhu, A.T.Torelli, M.Lee, B.Dzikovski, R.M.Koralewski, E.Wang, J.Freed, C.Krebs, S.E.Ealick, H.Lin. Diphthamide Biosynthesis Requires An Organic Radical Generated By An Iron-Sulphur Enzyme. Nature V. 465 891 2010.
ISSN: ISSN 0028-0836
PubMed: 20559380
DOI: 10.1038/NATURE09138