Zinc in PDB 1dvb: Rubrerythrin

The structure of Rubrerythrin, PDB code: 1dvb was solved by L.C.Sieker, M.Holmes, I.Le Trong, S.Turley, M.Y.Liu, J.Legall, R.E.Stenkamp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.90
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	50.630, 81.550, 100.260, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 27

The structure of Rubrerythrin also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the Rubrerythrin (pdb code 1dvb). 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 Rubrerythrin, PDB code: 1dvb:

Zinc binding site 1 out of 1 in the Rubrerythrin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rubrerythrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn194 b:20.6 occ:1.00 OE2 A:GLU128 2.1 38.3 1.0 OE2 A:GLU20 2.1 50.9 1.0 OE1 A:GLU53 2.1 28.6 1.0 ND1 A:HIS56 2.2 16.3 1.0 CD A:GLU128 2.8 31.0 1.0 OE1 A:GLU128 2.8 26.2 1.0 CD A:GLU20 2.8 47.9 1.0 OE1 A:GLU20 2.8 61.0 1.0 CE1 A:HIS56 3.0 15.5 1.0 CD A:GLU53 3.0 25.2 1.0 OE2 A:GLU53 3.2 30.2 1.0 O A:HOH196 3.3 30.6 1.0 CG A:HIS56 3.3 13.7 1.0 FE A:FE193 3.7 35.3 1.0 CB A:HIS56 3.8 10.9 1.0 CG2 A:ILE124 4.1 21.1 1.0 CG A:GLU20 4.2 33.4 1.0 CG A:GLU128 4.2 22.2 1.0 NE2 A:HIS56 4.2 13.6 1.0 CG A:GLU53 4.3 15.4 1.0 CA A:GLU53 4.4 9.2 1.0 CD2 A:HIS56 4.4 15.1 1.0 O A:HOH347 4.6 47.5 0.7 CB A:GLU53 4.6 10.4 1.0 CE1 A:HIS131 4.7 18.8 1.0 OE1 A:GLU97 4.7 37.7 1.0 ND1 A:HIS131 4.9 18.4 1.0 CB A:GLU20 4.9 19.0 1.0 OH A:TYR102 4.9 56.4 1.0

L.C.Sieker, M.Holmes, I.Le Trong, S.Turley, M.Y.Liu, J.Legall, R.E.Stenkamp. The 1.9 A Crystal Structure of the "As Isolated" Rubrerythrin From Desulfovibrio Vulgaris: Some Surprising Results. J.Biol.Inorg.Chem. V. 5 505 2000.
ISSN: ISSN 0949-8257
PubMed: 10968622
DOI: 10.1007/S007750050011