Iron in PDB 6c8v: X-Ray Structure of Pqqe From Methylobacterium Extorquens

The structure of X-Ray Structure of Pqqe From Methylobacterium Extorquens, PDB code: 6c8v was solved by A.S.Gizzi, T.L.Grove, J.B.Bonanno, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.75 / 3.20
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	97.570, 97.570, 86.417, 90.00, 90.00, 120.00
R / Rfree (%)	20.5 / 24.2

The binding sites of Iron atom in the X-Ray Structure of Pqqe From Methylobacterium Extorquens (pdb code 6c8v). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the X-Ray Structure of Pqqe From Methylobacterium Extorquens, PDB code: 6c8v:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the X-Ray Structure of Pqqe From Methylobacterium Extorquens


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Structure of Pqqe From Methylobacterium Extorquens within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:35.7 occ:1.00 FE1 A:FES501 0.0 35.7 1.0 S1 A:FES501 2.2 33.2 1.0 S2 A:FES501 2.2 35.1 1.0 SG A:CYS248 2.6 37.4 1.0 SG A:CYS323 2.7 37.7 1.0 FE2 A:FES501 3.0 37.8 1.0 CB A:CYS323 3.2 37.8 1.0 CB A:CYS248 3.3 37.7 1.0 CA A:CYS323 3.7 37.3 1.0 O A:ALA199 3.9 48.7 1.0 N A:ALA199 4.1 46.2 1.0 N A:ARG324 4.1 36.6 1.0 C A:CYS323 4.3 37.9 1.0 C A:ALA199 4.4 49.0 1.0 N A:CYS325 4.4 38.2 1.0 CA A:ALA199 4.6 47.8 1.0 CB A:CYS325 4.7 38.5 1.0 CB A:TRP198 4.7 45.3 1.0 CA A:CYS248 4.8 37.5 1.0 CB A:ALA199 4.8 47.4 1.0 SG A:CYS325 4.9 36.9 1.0 CD1 A:TRP198 4.9 41.5 1.0 N A:CYS323 5.0 37.6 1.0 C A:TRP198 5.0 47.3 1.0

Iron binding site 2 out of 6 in the X-Ray Structure of Pqqe From Methylobacterium Extorquens


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Structure of Pqqe From Methylobacterium Extorquens within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:37.8 occ:1.00 FE2 A:FES501 0.0 37.8 1.0 S1 A:FES501 2.2 33.2 1.0 S2 A:FES501 2.2 35.1 1.0 SG A:CYS268 2.6 36.1 1.0 SG A:CYS325 2.7 36.9 1.0 FE1 A:FES501 3.0 35.7 1.0 CB A:CYS325 3.6 38.5 1.0 CB A:CYS268 3.6 35.5 1.0 N A:CYS325 4.1 38.2 1.0 CZ3 A:TRP252 4.3 33.6 1.0 CA A:CYS325 4.5 39.2 1.0 SG A:CYS323 4.6 37.7 1.0 CB A:ALA270 4.6 38.1 1.0 CE3 A:TRP252 4.7 33.1 1.0 C A:ALA270 4.8 36.9 1.0 N A:ALA271 4.8 36.0 1.0 SG A:CYS248 4.8 37.4 1.0 N A:ARG324 4.9 36.6 1.0 N A:ALA270 4.9 36.8 1.0 CA A:CYS268 5.0 34.7 1.0

Iron binding site 3 out of 6 in the X-Ray Structure of Pqqe From Methylobacterium Extorquens


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Structure of Pqqe From Methylobacterium Extorquens within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:35.6 occ:1.00 FE1 A:SF4502 0.0 35.6 1.0 S2 A:SF4502 2.2 35.3 1.0 S4 A:SF4502 2.2 35.0 1.0 S3 A:SF4502 2.2 35.2 1.0 OD1 A:ASP319 2.4 38.4 1.0 OD2 A:ASP319 2.5 39.8 1.0 CG A:ASP319 2.7 38.5 1.0 FE3 A:SF4502 3.1 36.4 1.0 FE4 A:SF4502 3.1 36.7 1.0 FE2 A:SF4502 3.1 36.8 1.0 S1 A:SF4502 3.8 35.1 1.0 CD A:PRO245 4.0 38.7 1.0 O A:ARG315 4.1 37.8 1.0 CG A:PRO245 4.1 37.5 1.0 NH1 A:ARG315 4.2 41.5 1.0 CB A:ASP319 4.2 37.6 1.0 N A:GLY321 4.2 37.1 1.0 CA A:GLY321 4.3 37.9 1.0 CB A:ARG315 4.4 40.9 1.0 C A:ARG315 4.6 38.8 1.0 C A:GLY321 4.7 37.9 1.0 N A:GLY322 4.9 37.7 1.0

Iron binding site 4 out of 6 in the X-Ray Structure of Pqqe From Methylobacterium Extorquens


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of X-Ray Structure of Pqqe From Methylobacterium Extorquens within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:36.8 occ:1.00 FE2 A:SF4502 0.0 36.8 1.0 S4 A:SF4502 2.2 35.0 1.0 S1 A:SF4502 2.2 35.1 1.0 S3 A:SF4502 2.2 35.2 1.0 SG A:CYS310 2.4 39.2 1.0 CB A:CYS310 3.1 39.3 1.0 FE3 A:SF4502 3.1 36.4 1.0 FE1 A:SF4502 3.1 35.6 1.0 FE4 A:SF4502 3.1 36.7 1.0 CA A:CYS310 3.4 41.1 1.0 S2 A:SF4502 3.8 35.3 1.0 CG2 A:THR337 3.9 41.6 1.0 CA A:GLY321 3.9 37.9 1.0 N A:CYS310 4.0 43.0 1.0 OG1 A:THR337 4.3 42.1 1.0 N A:GLY321 4.6 37.1 1.0 OD1 A:ASP319 4.7 38.4 1.0 C A:GLY321 4.7 37.9 1.0 CB A:THR337 4.7 42.0 1.0 C A:PRO309 4.8 41.0 1.0 C A:CYS310 4.8 41.1 1.0 O A:GLY321 4.8 39.3 1.0

Iron binding site 5 out of 6 in the X-Ray Structure of Pqqe From Methylobacterium Extorquens


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of X-Ray Structure of Pqqe From Methylobacterium Extorquens within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:36.4 occ:1.00 FE3 A:SF4502 0.0 36.4 1.0 S1 A:SF4502 2.2 35.1 1.0 S4 A:SF4502 2.2 35.0 1.0 S2 A:SF4502 2.2 35.3 1.0 SG A:CYS313 2.4 42.0 1.0 FE1 A:SF4502 3.1 35.6 1.0 FE2 A:SF4502 3.1 36.8 1.0 FE4 A:SF4502 3.1 36.7 1.0 CB A:CYS313 3.2 42.2 1.0 S3 A:SF4502 3.8 35.2 1.0 CB A:ARG315 4.3 40.9 1.0 CD1 A:LEU343 4.3 44.6 1.0 CA A:CYS310 4.6 41.1 1.0 N A:ARG315 4.6 41.2 1.0 C A:ARG315 4.6 38.8 1.0 CA A:CYS313 4.6 43.4 1.0 CA A:ARG315 4.7 40.0 1.0 N A:ARG316 4.7 40.7 1.0 CG A:ARG315 4.9 42.7 1.0 O A:PRO309 4.9 41.5 1.0 O A:ARG315 4.9 37.8 1.0 OD2 A:ASP319 5.0 39.8 1.0

Iron binding site 6 out of 6 in the X-Ray Structure of Pqqe From Methylobacterium Extorquens


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of X-Ray Structure of Pqqe From Methylobacterium Extorquens within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:36.7 occ:1.00 FE4 A:SF4502 0.0 36.7 1.0 S1 A:SF4502 2.2 35.1 1.0 S3 A:SF4502 2.2 35.2 1.0 S2 A:SF4502 2.2 35.3 1.0 SG A:CYS341 2.4 44.0 1.0 FE1 A:SF4502 3.1 35.6 1.0 FE3 A:SF4502 3.1 36.4 1.0 FE2 A:SF4502 3.1 36.8 1.0 CB A:CYS341 3.2 43.5 1.0 S4 A:SF4502 3.8 35.0 1.0 CD A:PRO245 3.9 38.7 1.0 CG2 A:THR337 4.2 41.6 1.0 CD1 A:LEU343 4.3 44.6 1.0 CB A:LEU343 4.4 46.1 1.0 CG A:PRO245 4.5 37.5 1.0 CG A:LEU343 4.6 45.9 1.0 CA A:CYS341 4.6 44.4 1.0 CD1 A:TYR244 4.6 40.8 1.0 OD2 A:ASP319 5.0 39.8 1.0

I.Barr, T.A.Stich, A.S.Gizzi, T.L.Grove, J.B.Bonanno, J.A.Latham, T.Chung, C.M.Wilmot, R.D.Britt, S.C.Almo, J.P.Klinman. X-Ray and Epr Characterization of the Auxiliary Fe-S Clusters in the Radical Sam Enzyme Pqqe. Biochemistry V. 57 1306 2018.
ISSN: ISSN 1520-4995
PubMed: 29405700
DOI: 10.1021/ACS.BIOCHEM.7B01097