Nickel in PDB 6vfu: Crystal Structure of Human Protocadherin 19 EC1-EC4

The structure of Crystal Structure of Human Protocadherin 19 EC1-EC4, PDB code: 6vfu was solved by O.J.Harrison, J.Brasch, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 3.50
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	108.971, 108.971, 309.663, 90.00, 90.00, 120.00
R / Rfree (%)	26.5 / 29.2

The structure of Crystal Structure of Human Protocadherin 19 EC1-EC4 also contains other interesting chemical elements:

Calcium	(Ca)	27 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Nickel atom in the Crystal Structure of Human Protocadherin 19 EC1-EC4 (pdb code 6vfu). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Human Protocadherin 19 EC1-EC4, PDB code: 6vfu:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Human Protocadherin 19 EC1-EC4


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Human Protocadherin 19 EC1-EC4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni515 b:0.1 occ:1.00 HD2 C:HIS428 1.5 0.1 1.0 CD2 C:HIS428 1.9 0.7 1.0 OE1 C:GLU336 2.0 0.8 1.0 NE2 C:HIS428 2.3 0.5 1.0 CG C:HIS428 3.0 0.7 1.0 CD C:GLU336 3.1 0.3 1.0 CE1 C:HIS428 3.4 0.9 1.0 OE2 C:GLU336 3.4 0.2 1.0 ND1 C:HIS428 3.8 0.3 1.0 HB3 C:HIS428 3.8 0.7 1.0 HB3 C:HIS426 3.9 0.0 1.0 CB C:HIS428 4.0 0.1 1.0 HB2 C:HIS426 4.0 0.0 1.0 HE1 C:HIS428 4.1 0.1 1.0 CG C:GLU336 4.4 0.3 1.0 CB C:HIS426 4.4 0.7 1.0 HB2 C:GLU336 4.4 0.8 1.0 HB2 C:HIS428 4.5 0.7 1.0 HG21 C:THR423 4.5 0.2 1.0 ND1 C:HIS426 4.5 0.7 1.0 HG3 C:GLU336 4.7 0.4 1.0 H C:HIS428 4.7 1.0 1.0 HB3 C:GLU336 4.8 0.8 1.0 CB C:GLU336 4.8 0.4 1.0 CG C:HIS426 4.9 0.3 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Human Protocadherin 19 EC1-EC4


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Human Protocadherin 19 EC1-EC4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni513 b:0.7 occ:1.00 NE2 A:HIS426 1.2 0.2 1.0 CE1 A:HIS426 1.9 0.4 1.0 OE2 A:GLU336 1.9 0.5 1.0 OE1 A:GLU336 2.0 0.9 1.0 HE1 A:HIS426 2.1 0.5 1.0 CD A:GLU336 2.1 0.9 1.0 CD2 A:HIS426 2.4 0.9 1.0 HD2 A:HIS426 2.9 0.7 1.0 ND1 A:HIS426 3.0 0.4 1.0 CG A:HIS426 3.2 0.6 1.0 CG A:GLU336 3.6 0.9 1.0 HD2 A:HIS428 3.7 0.9 1.0 HD1 A:HIS426 3.7 0.9 1.0 HG2 A:GLU336 3.9 0.5 1.0 HB3 A:GLU336 3.9 0.1 1.0 HG3 A:GLU336 4.2 0.5 1.0 CB A:GLU336 4.2 0.1 1.0 CD2 A:HIS428 4.2 0.2 1.0 HB2 A:GLU336 4.2 0.1 1.0 HG1 A:THR423 4.2 0.6 1.0 HD11 A:LEU421 4.3 0.7 1.0 NE2 A:HIS428 4.4 0.7 1.0 HG21 A:THR423 4.4 0.2 1.0 CB A:HIS426 4.7 0.6 1.0 HB3 A:HIS426 4.9 0.3 1.0

O.J.Harrison, J.Brasch, P.S.Katsamba, G.Ahlsen, A.J.Noble, H.Dan, R.V.Sampogna, C.S.Potter, B.Carragher, B.Honig, L.Shapiro. Family-Wide Structural and Biophysical Analysis of Binding Interactions Among Non-Clustered Delta-Protocadherins. Cell Rep V. 30 2655 2020.
ISSN: ESSN 2211-1247
PubMed: 32101743
DOI: 10.1016/J.CELREP.2020.02.003