Nickel in PDB 8drd: Ni(II)-Bound B2 Dimer (H60/H100/H104)

The structure of Ni(II)-Bound B2 Dimer (H60/H100/H104), PDB code: 8drd was solved by T.S.Choi, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.70 / 1.89
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.09, 55.43, 101.97, 90, 90, 90
R / Rfree (%)	18.9 / 21.6

The structure of Ni(II)-Bound B2 Dimer (H60/H100/H104) also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Nickel atom in the Ni(II)-Bound B2 Dimer (H60/H100/H104) (pdb code 8drd). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Ni(II)-Bound B2 Dimer (H60/H100/H104), PDB code: 8drd:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Ni(II)-Bound B2 Dimer (H60/H100/H104)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Ni(II)-Bound B2 Dimer (H60/H100/H104) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni202 b:11.7 occ:1.00 NE2 A:HIS60 2.1 10.5 1.0 NE2 A:HIS104 2.1 11.3 1.0 O B:HOH319 2.1 12.4 1.0 O A:HOH334 2.1 13.0 1.0 NE2 B:HIS100 2.1 11.2 1.0 NE2 B:HIS104 2.1 11.4 1.0 CE1 A:HIS104 3.0 15.4 1.0 CE1 A:HIS60 3.0 10.3 1.0 CE1 B:HIS104 3.1 11.7 1.0 CD2 A:HIS60 3.1 13.7 1.0 CE1 B:HIS100 3.1 11.0 1.0 CD2 B:HIS100 3.1 10.8 1.0 CD2 A:HIS104 3.2 12.1 1.0 CD2 B:HIS104 3.2 14.3 1.0 ND1 A:HIS60 4.2 11.2 1.0 ND1 A:HIS104 4.2 11.8 1.0 ND1 B:HIS104 4.2 10.1 1.0 CG A:HIS60 4.2 11.2 1.0 ND1 B:HIS100 4.2 12.3 1.0 CG A:HIS104 4.3 12.5 1.0 O A:HOH349 4.3 7.6 1.0 CG B:HIS100 4.3 13.2 1.0 CG B:HIS104 4.3 11.4 1.0 O A:HOH342 4.5 14.8 1.0 O A:HIS100 4.5 12.5 1.0 OE1 B:GLN103 4.7 21.6 1.0 CB A:HIS100 4.8 12.7 1.0 O2 B:MPD201 4.9 22.9 1.0 C A:HIS100 5.0 11.1 1.0

Nickel binding site 2 out of 2 in the Ni(II)-Bound B2 Dimer (H60/H100/H104)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Ni(II)-Bound B2 Dimer (H60/H100/H104) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni203 b:38.7 occ:1.00 OD2 B:ASP2 2.1 20.4 1.0 CG B:ASP2 3.1 21.9 1.0 OD1 B:ASP2 3.4 20.7 1.0 OD1 B:ASP5 4.1 21.3 1.0 OE1 B:GLU4 4.2 35.9 1.0 OD2 B:ASP5 4.3 25.7 1.0 CG B:ASP5 4.4 24.9 1.0 CB B:ASP2 4.4 15.8 1.0 CD B:GLU4 4.7 35.5 1.0 O B:HOH303 4.7 17.2 1.0 CB B:GLU4 4.7 22.7 1.0 O B:HOH318 4.9 22.5 1.0

T.S.Choi, F.A.Tezcan. Design of A Flexible, Zn-Selective Protein Scaffold That Displays Anti-Irving-Williams Behavior. J.Am.Chem.Soc. V. 144 18090 2022.
ISSN: ESSN 1520-5126
PubMed: 36154053
DOI: 10.1021/JACS.2C08050