Zinc in PDB 3vk6: Crystal Structure of A Phosphotyrosine Binding Domain

The structure of Crystal Structure of A Phosphotyrosine Binding Domain, PDB code: 3vk6 was solved by J.Sivaraman, M.Mukherjee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.23 / 1.90
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	64.657, 64.657, 121.035, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 24.2

The binding sites of Zinc atom in the Crystal Structure of A Phosphotyrosine Binding Domain (pdb code 3vk6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of A Phosphotyrosine Binding Domain, PDB code: 3vk6:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of A Phosphotyrosine Binding Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Phosphotyrosine Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:29.1 occ:1.00 NE2 A:HIS80 2.1 31.2 1.0 NE2 A:HIS85 2.1 30.4 1.0 SG A:CYS67 2.3 30.0 1.0 CD2 A:HIS80 3.0 28.1 1.0 CD2 A:HIS85 3.1 29.3 1.0 CB A:CYS67 3.1 30.6 1.0 CE1 A:HIS80 3.1 29.6 1.0 CE1 A:HIS85 3.1 31.6 1.0 CG A:HIS80 4.2 29.1 1.0 ND1 A:HIS80 4.2 30.4 1.0 ND1 A:HIS85 4.2 29.4 1.0 CG A:HIS85 4.2 29.8 1.0 CA A:CYS67 4.6 26.0 1.0 O A:HOH166 4.7 37.5 1.0 CB A:ARG69 5.0 27.5 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of A Phosphotyrosine Binding Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Phosphotyrosine Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:32.1 occ:1.00 SG A:CYS7 2.3 31.7 1.0 SG A:CYS25 2.4 32.0 1.0 SG A:CYS4 2.4 31.1 1.0 SG A:CYS28 2.4 35.7 1.0 CB A:CYS25 3.1 31.9 1.0 CB A:CYS4 3.1 31.9 1.0 CB A:CYS7 3.2 33.6 1.0 CB A:CYS28 3.4 34.8 1.0 N A:CYS7 3.7 34.1 1.0 CA A:CYS7 4.0 34.5 1.0 N A:CYS28 4.2 37.0 1.0 CB A:LYS6 4.4 37.9 1.0 CA A:CYS28 4.4 38.4 1.0 CA A:CYS25 4.5 31.4 1.0 CA A:CYS4 4.6 32.0 1.0 O A:HOH172 4.7 34.0 1.0 C A:LYS6 4.7 39.2 1.0 C A:CYS7 4.9 35.8 1.0 N A:GLY8 4.9 31.7 1.0 CA A:LYS6 5.0 37.9 1.0 N A:LYS6 5.0 36.5 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of A Phosphotyrosine Binding Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Phosphotyrosine Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:30.6 occ:1.00 ND1 A:HIS22 2.0 30.3 1.0 SG A:CYS40 2.3 30.6 1.0 SG A:CYS20 2.3 33.1 1.0 SG A:CYS43 2.4 30.9 1.0 CE1 A:HIS22 2.9 30.6 1.0 CG A:HIS22 3.1 30.4 1.0 CB A:CYS40 3.1 33.3 1.0 CB A:CYS43 3.3 33.4 1.0 CB A:CYS20 3.3 34.0 1.0 CB A:HIS22 3.5 29.5 1.0 N A:CYS43 3.9 33.1 1.0 NE2 A:HIS22 4.0 29.2 1.0 CA A:CYS43 4.1 34.0 1.0 CD2 A:HIS22 4.1 31.0 1.0 N A:HIS22 4.5 27.9 1.0 CA A:CYS40 4.6 35.0 1.0 CA A:CYS20 4.6 35.2 1.0 CA A:HIS22 4.6 27.1 1.0 C A:CYS20 4.7 33.9 1.0 C A:CYS43 4.8 34.9 1.0 O A:CYS20 4.8 31.1 1.0 N A:SER44 4.8 30.8 1.0 C A:GLY42 4.9 34.9 1.0 O A:HOH112 4.9 39.0 1.0 CB A:ASP45 4.9 37.8 1.0 N A:ASP45 5.0 37.1 1.0

M.Mukherjee, S.Y.Chow, P.Yusoff, J.Seetharaman, C.Ng, S.Sinniah, X.W.Koh, N.F.Asgar, D.Li, D.Yim, R.A.Jackson, J.Yew, J.Qian, A.Iyu, Y.P.Lim, X.Zhou, S.K.Sze, G.R.Guy, J.Sivaraman. Structure of A Novel Phosphotyrosine-Binding Domain in Hakai That Targets E-Cadherin Embo J. V. 31 1308 2012.
ISSN: ISSN 0261-4189
PubMed: 22252131
DOI: 10.1038/EMBOJ.2011.496