Zinc in PDB 3rfn: Epitope Backbone Grafting By Computational Design For Improved Presentation of Linear Epitopes on Scaffold Proteins

The structure of Epitope Backbone Grafting By Computational Design For Improved Presentation of Linear Epitopes on Scaffold Proteins, PDB code: 3rfn was solved by M.L.Azoitei, Y.A.Ban, J.P.Julien, S.Bryson, A.Schroeter, O.Kalyuzhniy, J.R.Porter, Y.Adachi, D.Baker, E.Szabo, E.F.Pai, W.R.Schief, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.00 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	93.800, 36.100, 46.300, 90.00, 99.40, 90.00
R / Rfree (%)	21.9 / 23.7

The binding sites of Zinc atom in the Epitope Backbone Grafting By Computational Design For Improved Presentation of Linear Epitopes on Scaffold Proteins (pdb code 3rfn). 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 Epitope Backbone Grafting By Computational Design For Improved Presentation of Linear Epitopes on Scaffold Proteins, PDB code: 3rfn:

Zinc binding site 1 out of 1 in the Epitope Backbone Grafting By Computational Design For Improved Presentation of Linear Epitopes on Scaffold Proteins


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Epitope Backbone Grafting By Computational Design For Improved Presentation of Linear Epitopes on Scaffold Proteins within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:17.6 occ:0.50 NE2 A:HIS13 2.1 18.5 1.0 NE2 A:HIS9 2.2 28.8 1.0 NE2 A:HIS120 2.2 22.1 1.0 SG A:CYS116 2.4 25.1 1.0 CB A:CYS116 3.0 23.1 1.0 CE1 A:HIS120 3.0 21.3 1.0 CE1 A:HIS9 3.1 28.6 1.0 CE1 A:HIS13 3.1 19.4 1.0 CD2 A:HIS13 3.1 20.2 1.0 CD2 A:HIS9 3.2 27.1 1.0 CD2 A:HIS120 3.3 21.2 1.0 O A:HOH195 3.8 50.2 1.0 CG2 A:VAL106 4.1 20.7 1.0 ND1 A:HIS13 4.2 18.8 1.0 ND1 A:HIS9 4.2 27.4 1.0 CG A:HIS13 4.2 17.8 1.0 ND1 A:HIS120 4.2 22.1 1.0 CG A:HIS9 4.3 27.1 1.0 CG A:HIS120 4.4 23.4 1.0 OD1 A:ASN114 4.4 19.4 1.0 CA A:CYS116 4.5 22.2 1.0 CB A:LYS118 4.7 25.8 1.0 CB A:VAL106 4.8 19.4 1.0 O A:HIS9 4.9 20.4 1.0 C A:CYS116 4.9 23.3 1.0

M.L.Azoitei, Y.E.Ban, J.P.Julien, S.Bryson, A.Schroeter, O.Kalyuzhniy, J.R.Porter, Y.Adachi, D.Baker, E.F.Pai, W.R.Schief. Computational Design of High-Affinity Epitope Scaffolds By Backbone Grafting of A Linear Epitope. J.Mol.Biol. V. 415 175 2012.
ISSN: ISSN 0022-2836
PubMed: 22061265
DOI: 10.1016/J.JMB.2011.10.003