Nickel in PDB 4zmv: Crystal Structure of Human P-Cadherin (Ss-X-Dimer Pocket I)

The structure of Crystal Structure of Human P-Cadherin (Ss-X-Dimer Pocket I), PDB code: 4zmv 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)	45.10 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	78.440, 98.910, 109.980, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 23.6

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

Calcium

(Ca)

4 atoms

The binding sites of Nickel atom in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer Pocket I) (pdb code 4zmv). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer Pocket I), PDB code: 4zmv:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer Pocket I)


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 (Ss-X-Dimer Pocket I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni303 b:53.8 occ:1.00 O3 A:SO4305 1.7 76.0 1.0 O3 A:SO4306 2.0 73.0 1.0 O2 A:SO4305 2.0 81.1 1.0 S A:SO4305 2.0 77.4 1.0 NE2 A:HIS104 2.1 44.0 1.0 O1 A:SO4305 2.6 53.6 1.0 O2 A:SO4306 2.6 67.1 1.0 S A:SO4306 2.8 95.6 1.0 CE1 A:HIS104 3.0 41.7 1.0 CD2 A:HIS104 3.2 42.9 1.0 O4 A:SO4305 3.4 71.7 1.0 O1 A:SO4306 3.6 90.0 1.0 OE2 A:GLU135 4.0 53.4 1.0 O4 A:SO4306 4.0 63.7 1.0 ND1 A:HIS104 4.2 41.2 1.0 OD2 A:ASP67 4.2 42.1 1.0 CG A:HIS104 4.3 42.6 1.0 OE1 A:GLU135 4.3 48.2 1.0 CD A:GLU135 4.5 47.5 1.0

Nickel binding site 2 out of 3 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer Pocket I)


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 (Ss-X-Dimer Pocket I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni304 b:48.8 occ:1.00 O A:MET0 2.0 51.0 1.0 O B:MET0 2.2 53.7 1.0 O B:HOH404 2.2 45.6 1.0 N B:MET0 2.2 56.4 1.0 N A:MET0 2.3 52.5 1.0 C A:MET0 2.8 53.8 1.0 C B:MET0 2.9 54.1 1.0 CA B:MET0 3.0 58.4 1.0 CA A:MET0 3.0 57.5 1.0 CB B:MET0 3.7 62.2 1.0 CB A:MET0 3.8 61.7 1.0 N A:ASP1 4.1 53.8 1.0 N B:ASP1 4.1 51.8 1.0 OD1 B:ASP1 4.2 54.8 1.0 OD2 A:ASP1 4.3 62.9 1.0 CG A:ASP1 4.5 59.6 1.0 OD1 A:ASP1 4.5 58.5 1.0 SD A:MET0 4.5 89.1 1.0 CG B:ASP1 4.6 54.5 1.0 CA A:ASP1 4.7 54.1 1.0 CG A:MET0 4.7 66.0 1.0 OD2 B:ASP1 4.8 55.0 1.0 CA B:ASP1 4.8 50.5 1.0 CG B:MET0 4.8 67.8 1.0

Nickel binding site 3 out of 3 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer Pocket I)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Human P-Cadherin (Ss-X-Dimer Pocket I) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni303 b:54.1 occ:1.00 O3 B:SO4305 1.7 71.4 1.0 O4 B:SO4304 1.9 77.2 1.0 NE2 B:HIS104 2.2 48.6 1.0 O2 B:SO4304 2.2 67.7 1.0 O2 B:SO4305 2.2 67.0 1.0 S B:SO4305 2.4 93.1 1.0 S B:SO4304 2.4 94.9 1.0 O B:HOH401 2.6 48.0 1.0 CD2 B:HIS104 3.1 48.3 1.0 CE1 B:HIS104 3.2 48.7 1.0 O1 B:SO4305 3.2 80.1 1.0 O1 B:SO4304 3.5 77.0 1.0 O3 B:SO4304 3.6 81.9 1.0 O4 B:SO4305 3.6 82.1 1.0 OE1 B:GLU135 3.9 46.8 1.0 OE2 B:GLU135 3.9 48.7 1.0 OD2 B:ASP67 4.1 48.1 1.0 CG B:HIS104 4.3 48.2 1.0 ND1 B:HIS104 4.3 45.6 1.0 CD B:GLU135 4.3 49.9 1.0 O B:HOH433 4.7 45.6 1.0 CB B:GLU69 4.9 46.3 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