Iron 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:

Nickel

(Ni)

2 atoms

The binding sites of Iron 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 Iron atom.
In total 2 binding sites of Iron where determined in the Ni(II)-Bound B2 Dimer (H60/H100/H104), PDB code: 8drd:
Jump to Iron binding site number: 1; 2;

Iron 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 Iron with other atoms in the Fe 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:Fe201 b:11.0 occ:1.00 FE A:HEC201 0.0 11.0 1.0 ND A:HEC201 2.0 8.7 1.0 NC A:HEC201 2.0 8.8 1.0 NB A:HEC201 2.0 8.4 1.0 NA A:HEC201 2.0 12.0 1.0 NE2 A:HIS102 2.1 8.7 1.0 SD A:MET7 2.4 11.4 1.0 C1C A:HEC201 3.0 9.6 1.0 C4B A:HEC201 3.0 9.8 1.0 C1D A:HEC201 3.0 11.2 1.0 CD2 A:HIS102 3.0 7.3 1.0 C4D A:HEC201 3.1 10.9 1.0 C1A A:HEC201 3.1 11.4 1.0 C4A A:HEC201 3.1 9.6 1.0 C4C A:HEC201 3.1 8.0 1.0 C1B A:HEC201 3.1 8.0 1.0 CE1 A:HIS102 3.1 10.4 1.0 CHC A:HEC201 3.4 10.5 1.0 CHA A:HEC201 3.4 12.6 1.0 CHD A:HEC201 3.4 11.2 1.0 CE A:MET7 3.4 9.5 1.0 CG A:MET7 3.4 9.9 1.0 CHB A:HEC201 3.5 11.8 1.0 CG A:HIS102 4.2 9.3 1.0 ND1 A:HIS102 4.2 10.4 1.0 CB A:MET7 4.2 9.9 1.0 C2C A:HEC201 4.2 9.2 1.0 C2D A:HEC201 4.3 10.7 1.0 C3D A:HEC201 4.3 11.8 1.0 C3B A:HEC201 4.3 8.9 1.0 C2B A:HEC201 4.3 9.8 1.0 C3A A:HEC201 4.3 11.5 1.0 C2A A:HEC201 4.3 9.7 1.0 C3C A:HEC201 4.3 8.6 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe202 b:15.7 occ:1.00 FE B:HEC202 0.0 15.7 1.0 ND B:HEC202 2.0 15.2 1.0 NC B:HEC202 2.0 12.0 1.0 NA B:HEC202 2.0 15.0 1.0 NB B:HEC202 2.1 12.1 1.0 NE2 B:HIS102 2.2 14.5 1.0 SD B:MET7 2.5 17.0 1.0 C1D B:HEC202 3.0 15.3 1.0 C4C B:HEC202 3.0 13.8 1.0 C4D B:HEC202 3.1 14.5 1.0 C4A B:HEC202 3.1 17.3 1.0 C1A B:HEC202 3.1 18.5 1.0 C1C B:HEC202 3.1 16.0 1.0 C1B B:HEC202 3.1 17.1 1.0 CD2 B:HIS102 3.1 14.6 1.0 C4B B:HEC202 3.1 16.9 1.0 CE1 B:HIS102 3.2 13.8 1.0 CE B:MET7 3.3 14.9 1.0 CHD B:HEC202 3.4 13.8 1.0 CG B:MET7 3.4 14.4 1.0 CHA B:HEC202 3.4 14.3 1.0 CHB B:HEC202 3.4 17.5 1.0 CHC B:HEC202 3.5 14.7 1.0 C2D B:HEC202 4.3 15.9 1.0 C3D B:HEC202 4.3 14.7 1.0 CG B:HIS102 4.3 16.0 1.0 C3C B:HEC202 4.3 12.8 1.0 CB B:MET7 4.3 16.6 1.0 C2C B:HEC202 4.3 13.1 1.0 C3A B:HEC202 4.3 20.6 1.0 ND1 B:HIS102 4.3 13.5 1.0 C2A B:HEC202 4.3 16.7 1.0 C2B B:HEC202 4.3 17.8 1.0 C3B B:HEC202 4.3 14.2 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