Nickel in PDB 6yjd: Lamin A COIL2 Dimer Stabilized By N-Terminal Capping

The structure of Lamin A COIL2 Dimer Stabilized By N-Terminal Capping, PDB code: 6yjd was solved by A.V.Lilina, G.Stalmans, S.V.Strelkov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.62 / 2.90
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	117.25, 117.25, 93.156, 90, 90, 120
R / Rfree (%)	25.3 / 30.4

The structure of Lamin A COIL2 Dimer Stabilized By N-Terminal Capping also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Nickel atom in the Lamin A COIL2 Dimer Stabilized By N-Terminal Capping (pdb code 6yjd). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Lamin A COIL2 Dimer Stabilized By N-Terminal Capping, PDB code: 6yjd:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Lamin A COIL2 Dimer Stabilized By N-Terminal Capping


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Lamin A COIL2 Dimer Stabilized By N-Terminal Capping within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:104.9 occ:0.33 NE2 A:HIS285 2.5 113.8 1.0 CD2 A:HIS285 3.0 126.4 1.0 CE1 A:HIS285 3.7 121.5 1.0 CB A:TYR313 3.8 102.4 1.0 CG A:LEU309 4.0 135.0 1.0 O A:LEU309 4.0 117.3 1.0 CD1 A:TYR313 4.1 121.8 1.0 CG A:HIS285 4.3 97.0 1.0 CG A:TYR313 4.3 100.9 1.0 CA A:TYR313 4.4 105.3 1.0 CD1 A:LEU309 4.4 130.5 1.0 C A:LEU309 4.5 111.3 1.0 N A:TYR313 4.5 100.1 1.0 ND1 A:HIS285 4.6 111.5 1.0 CD2 A:LEU309 4.7 134.4 1.0 CA A:LEU309 4.7 121.5 1.0 CB A:LEU309 4.9 132.7 1.0 ND2 A:ASN312 4.9 132.7 1.0

Nickel binding site 2 out of 2 in the Lamin A COIL2 Dimer Stabilized By N-Terminal Capping


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Lamin A COIL2 Dimer Stabilized By N-Terminal Capping within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni502 b:176.7 occ:1.00 CB A:GLN308 4.2 113.0 1.0 CG1 A:VAL311 4.4 146.6 1.0 CG A:GLN308 4.4 119.2 1.0 O A:GLN308 4.6 107.4 1.0 CA A:GLN308 4.6 115.8 1.0 CD1 A:LEU280 4.7 115.4 1.0 NE2 A:GLN308 4.9 116.7 1.0

G.Stalmans, A.V.Lilina, P.J.Vermeire, J.Fiala, P.Novak, S.V.Strelkov. Addressing the Molecular Mechanism of Longitudinal Lamin Assembly Using Chimeric Fusions. Cells V. 9 2020.
ISSN: ESSN 2073-4409
PubMed: 32645958
DOI: 10.3390/CELLS9071633