Zinc in PDB 3kj4: Structure of Rat Nogo Receptor Bound to 1D9 Antagonist Antibody

The structure of Structure of Rat Nogo Receptor Bound to 1D9 Antagonist Antibody, PDB code: 3kj4 was solved by L.F.Silvian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.04 / 3.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	188.664, 125.488, 90.575, 90.00, 90.00, 90.00
R / Rfree (%)	25.3 / 31.8

The binding sites of Zinc atom in the Structure of Rat Nogo Receptor Bound to 1D9 Antagonist Antibody (pdb code 3kj4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Rat Nogo Receptor Bound to 1D9 Antagonist Antibody, PDB code: 3kj4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Rat Nogo Receptor Bound to 1D9 Antagonist Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Rat Nogo Receptor Bound to 1D9 Antagonist Antibody within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn221 b:62.2 occ:1.00 CD1 H:TRP106 2.7 22.3 1.0 CE2 H:TYR102 2.8 9.6 1.0 CB H:TRP106 3.3 17.6 1.0 CG H:TRP106 3.4 19.8 1.0 OH H:TYR102 3.5 10.3 1.0 CZ H:TYR102 3.6 9.2 1.0 CD2 H:TYR102 3.7 13.2 1.0 OG L:SER97 3.7 19.3 1.0 CB L:SER97 3.8 20.5 1.0 NE1 H:TRP106 3.9 25.6 1.0 CA H:TRP106 4.1 18.4 1.0 CE2 L:PHE101 4.5 13.7 1.0 CE L:MET95 4.7 23.0 1.0 CD2 H:TRP106 4.7 23.6 1.0 N H:TRP106 4.7 20.2 1.0 CE1 H:TYR102 4.9 9.8 1.0 CE2 H:TRP106 5.0 24.9 1.0 CG H:TYR102 5.0 11.6 1.0

Zinc binding site 2 out of 2 in the Structure of Rat Nogo Receptor Bound to 1D9 Antagonist Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Rat Nogo Receptor Bound to 1D9 Antagonist Antibody within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn221 b:65.0 occ:1.00 CE1 C:TYR102 2.9 3.7 1.0 CB C:TRP106 3.2 11.3 1.0 CD1 C:TRP106 3.3 15.4 1.0 CA C:TRP106 3.5 11.4 1.0 CG C:TRP106 3.6 13.4 1.0 OH C:TYR102 3.7 4.3 1.0 CD1 C:TYR102 3.7 7.7 1.0 CZ C:TYR102 3.7 3.1 1.0 OG B:SER97 3.8 18.4 1.0 CB B:SER97 4.0 15.8 1.0 N C:TRP106 4.2 13.8 1.0 NE1 C:TRP106 4.5 13.8 1.0 O C:ALA105 4.7 17.7 1.0 C C:ALA105 4.8 17.0 1.0 CE2 B:PHE101 4.9 15.2 1.0 C C:TRP106 4.9 12.0 1.0 CE B:MET95 4.9 23.0 1.0 CD2 C:TRP106 4.9 13.5 1.0

P.H.Weinreb, D.Wen, F.Qian, C.P.Wildes, E.A.Garber, L.Walus, M.Y.Jung, J.Wang, J.K.Relton, J.Amatucci, R.Wang, F.Porreca, L.Silvian, W.Meier, R.B.Pepinsky, D.H.Lee. Resolution of Disulfide Heterogeneity in Nogo Receptor 1 Fusion Proteins By Molecular Engineering. Biotechnol Appl Biochem V. 57 31 2010.
PubMed: 20815818
DOI: 10.1042/BA20100061