Nickel in PDB 4zmw: Crystal Structure of Human P-Cadherin (Enc-X-Dimer)

The structure of Crystal Structure of Human P-Cadherin (Enc-X-Dimer), PDB code: 4zmw was solved by J.M.M.Caaveiro, S.Kudo, K.Tsumoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.02 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	94.369, 106.810, 77.579, 90.00, 94.86, 90.00
R / Rfree (%)	23 / 27.6

The structure of Crystal Structure of Human P-Cadherin (Enc-X-Dimer) also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Nickel atom in the Crystal Structure of Human P-Cadherin (Enc-X-Dimer) (pdb code 4zmw). 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 P-Cadherin (Enc-X-Dimer), PDB code: 4zmw:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Human P-Cadherin (Enc-X-Dimer)


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 P-Cadherin (Enc-X-Dimer) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni305 b:30.4 occ:1.00 O4 A:SO4304 1.8 41.8 1.0 O1 A:SO4303 1.9 69.7 1.0 O4 A:SO4303 2.0 71.7 1.0 NE2 A:HIS104 2.2 27.1 1.0 S A:SO4303 2.3 80.2 1.0 O3 A:SO4304 2.4 41.2 1.0 O A:HOH403 2.6 22.2 1.0 S A:SO4304 2.6 67.5 1.0 O2 A:SO4303 3.0 61.9 1.0 CE1 A:HIS104 3.0 24.9 1.0 CD2 A:HIS104 3.3 26.1 1.0 O3 A:SO4303 3.7 72.0 1.0 O1 A:SO4304 3.7 57.1 1.0 O2 A:SO4304 3.7 52.3 1.0 OE2 A:GLU135 4.1 29.7 1.0 ND1 A:HIS104 4.2 26.3 1.0 OD2 A:ASP67 4.2 27.1 1.0 CG A:HIS104 4.3 24.5 1.0 O A:HOH446 4.4 37.0 1.0 OE1 A:GLU135 4.5 27.4 1.0 CD A:GLU135 4.6 23.6 1.0 CB A:GLU69 4.7 23.6 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Human P-Cadherin (Enc-X-Dimer)


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 P-Cadherin (Enc-X-Dimer) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni308 b:34.4 occ:1.00 O2 B:SO4306 1.9 54.5 1.0 O1 B:SO4307 2.0 57.3 1.0 NE2 B:HIS104 2.1 27.9 1.0 O3 B:SO4307 2.2 61.8 1.0 S B:SO4307 2.3 82.6 1.0 O1 B:SO4306 2.5 62.3 1.0 O4 B:SO4307 2.7 76.5 1.0 S B:SO4306 2.7 81.2 1.0 CE1 B:HIS104 3.0 28.0 1.0 CD2 B:HIS104 3.2 26.9 1.0 O4 B:SO4306 3.6 67.9 1.0 O2 B:SO4307 3.7 71.1 1.0 O3 B:SO4306 3.9 69.4 1.0 OE1 B:GLU135 3.9 32.7 1.0 OD2 B:ASP67 4.1 37.1 1.0 ND1 B:HIS104 4.1 28.5 1.0 OE2 B:GLU135 4.2 33.8 1.0 CG B:HIS104 4.3 26.8 1.0 CD B:GLU135 4.4 32.1 1.0 CB B:GLU69 5.0 27.1 1.0

S.Kudo, J.M.Caaveiro, K.Tsumoto. Adhesive Dimerization of Human P-Cadherin Catalyzed By A Chaperone-Like Mechanism Structure V. 24 1523 2016.
ISSN: ISSN 0969-2126
PubMed: 27545624
DOI: 10.1016/J.STR.2016.07.002