Zinc in PDB 8drf: Zn(II)-Bound B2 Dimer (H60/H100/H104)

The structure of Zn(II)-Bound B2 Dimer (H60/H100/H104), PDB code: 8drf 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)	38.92 / 1.70
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.5, 52.12, 58.51, 90, 90, 90
R / Rfree (%)	21.2 / 24.2

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

Iron

(Fe)

1 atom

The binding sites of Zinc atom in the Zn(II)-Bound B2 Dimer (H60/H100/H104) (pdb code 8drf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Zn(II)-Bound B2 Dimer (H60/H100/H104), PDB code: 8drf:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Zn(II)-Bound B2 Dimer (H60/H100/H104)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zn(II)-Bound B2 Dimer (H60/H100/H104) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:15.3 occ:0.76 NE2 A:HIS63 2.2 13.8 1.0 CD2 A:HIS63 3.0 18.2 1.0 CE1 A:HIS63 3.2 19.2 1.0 CG A:HIS63 4.2 13.6 1.0 ND1 A:HIS63 4.3 17.8 1.0 CD1 A:ILE67 4.3 22.3 1.0 CH2 A:TRP59 4.6 16.0 1.0

Zinc binding site 2 out of 3 in the Zn(II)-Bound B2 Dimer (H60/H100/H104)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zn(II)-Bound B2 Dimer (H60/H100/H104) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:18.0 occ:1.00 OE1 A:GLU8 2.0 16.0 1.0 OE1 A:GLU4 2.0 16.1 1.0 O1A A:HEC201 2.0 16.0 1.0 CD A:GLU4 2.8 16.2 1.0 CGA A:HEC201 2.9 16.1 1.0 CD A:GLU8 2.9 16.1 1.0 OE2 A:GLU4 3.1 16.5 1.0 CBA A:HEC201 3.2 16.2 1.0 CG A:GLU8 3.3 20.5 1.0 OE2 A:GLU8 4.0 16.0 1.0 O2A A:HEC201 4.0 16.7 1.0 CG A:GLU4 4.3 13.5 1.0 CAA A:HEC201 4.4 16.7 1.0 CB A:GLU8 4.9 14.8 1.0

Zinc binding site 3 out of 3 in the Zn(II)-Bound B2 Dimer (H60/H100/H104)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zn(II)-Bound B2 Dimer (H60/H100/H104) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:20.6 occ:0.50 NE2 A:HIS60 2.0 12.4 1.0 O A:HOH365 2.7 29.4 1.0 CD2 A:HIS60 2.9 11.4 1.0 CE1 A:HIS60 3.0 18.7 1.0 NE2 A:HIS100 3.3 31.4 1.0 CG A:HIS60 4.1 18.3 1.0 ND1 A:HIS60 4.1 10.4 1.0 CD2 A:HIS100 4.1 25.0 1.0 CE1 A:HIS100 4.4 23.1 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