Zinc in PDB 1xer: Structure of Ferredoxin

The structure of Structure of Ferredoxin, PDB code: 1xer was solved by T.Fujii, Y.Hata, H.Moriyama, T.Wakagi, N.Tanaka, T.Oshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	50.120, 50.120, 69.520, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 24.4

The structure of Structure of Ferredoxin also contains other interesting chemical elements:

Iron

(Fe)

6 atoms

The binding sites of Zinc atom in the Structure of Ferredoxin (pdb code 1xer). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Structure of Ferredoxin, PDB code: 1xer:

Zinc binding site 1 out of 1 in the Structure of Ferredoxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Ferredoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn106 b:12.0 occ:1.00 OD1 A:ASP76 1.9 8.2 1.0 NE2 A:HIS19 2.0 6.3 1.0 ND1 A:HIS34 2.0 7.7 1.0 ND1 A:HIS16 2.1 4.9 1.0 CE1 A:HIS19 2.8 6.3 1.0 CG A:ASP76 2.8 4.7 1.0 CE1 A:HIS34 2.9 5.6 1.0 CE1 A:HIS16 2.9 5.0 1.0 OD2 A:ASP76 3.0 4.5 1.0 CG A:HIS34 3.1 7.7 1.0 CD2 A:HIS19 3.1 3.8 1.0 CG A:HIS16 3.2 5.3 1.0 CB A:HIS34 3.5 6.9 1.0 CB A:HIS16 3.6 7.0 1.0 ND1 A:HIS19 4.0 8.6 1.0 O A:HIS16 4.1 11.1 1.0 NE2 A:HIS34 4.1 9.9 1.0 NE2 A:HIS16 4.1 7.0 1.0 CB A:ASP76 4.2 5.4 1.0 CD2 A:HIS34 4.2 7.8 1.0 CG A:HIS19 4.2 6.3 1.0 CD2 A:HIS16 4.3 5.3 1.0 CZ A:PHE42 4.4 7.3 1.0 C A:HIS16 4.5 6.8 1.0 CD A:PRO77 4.6 4.3 1.0 CA A:HIS16 4.7 6.6 1.0 CE2 A:PHE42 4.7 6.0 1.0 CA A:HIS34 4.8 7.7 1.0 CA A:ASP76 4.9 4.9 1.0

T.Fujii, Y.Hata, T.Wakagi, N.Tanaka, T.Oshima. Novel Zinc-Binding Centre in Thermoacidophilic Archaeal Ferredoxins. Nat.Struct.Biol. V. 3 834 1996.
ISSN: ISSN 1072-8368
PubMed: 8836097
DOI: 10.1038/NSB1096-834