Zinc in PDB 8drm: Zn(II)-Bound B2 Dimer (H60/H100/H104) Formed in Zn(II)//Cu(II) (M1 // M2) Condition

The structure of Zn(II)-Bound B2 Dimer (H60/H100/H104) Formed in Zn(II)//Cu(II) (M1 // M2) Condition, PDB code: 8drm 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)	39.26 / 1.55
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.26, 51.32, 58.82, 90, 90, 90
R / Rfree (%)	19.3 / 22.9

The structure of Zn(II)-Bound B2 Dimer (H60/H100/H104) Formed in Zn(II)//Cu(II) (M1 // M2) Condition 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) Formed in Zn(II)//Cu(II) (M1 // M2) Condition (pdb code 8drm). 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) Formed in Zn(II)//Cu(II) (M1 // M2) Condition, PDB code: 8drm:
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) Formed in Zn(II)//Cu(II) (M1 // M2) Condition


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) Formed in Zn(II)//Cu(II) (M1 // M2) Condition within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:21.7 occ:0.50 NE2 A:HIS60 2.0 16.9 1.0 O A:HOH395 2.6 19.0 1.0 CD2 A:HIS60 3.0 18.7 1.0 CE1 A:HIS60 3.0 19.2 1.0 NE2 A:HIS100 3.4 38.3 1.0 ND1 A:HIS60 4.1 17.9 1.0 CG A:HIS60 4.1 18.9 1.0 CD2 A:HIS100 4.2 32.6 1.0 O A:HOH329 4.4 29.1 1.0 CE1 A:HIS100 4.4 32.4 1.0

Zinc binding site 2 out of 3 in the Zn(II)-Bound B2 Dimer (H60/H100/H104) Formed in Zn(II)//Cu(II) (M1 // M2) Condition


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) Formed in Zn(II)//Cu(II) (M1 // M2) Condition within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:22.6 occ:1.00 NE2 A:HIS63 2.1 18.4 1.0 CD2 A:HIS63 3.1 19.0 1.0 CE1 A:HIS63 3.1 20.2 1.0 ND1 A:HIS63 4.2 18.6 1.0 CG A:HIS63 4.2 16.9 1.0 CD1 A:ILE67 4.4 18.3 1.0 CH2 A:TRP59 4.6 20.2 1.0

Zinc binding site 3 out of 3 in the Zn(II)-Bound B2 Dimer (H60/H100/H104) Formed in Zn(II)//Cu(II) (M1 // M2) Condition


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) Formed in Zn(II)//Cu(II) (M1 // M2) Condition within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:23.5 occ:0.99 O1A A:HEC201 1.9 22.0 1.0 OE1 A:GLU8 2.0 17.8 1.0 OE1 A:GLU4 2.0 24.4 1.0 CD A:GLU4 2.8 22.1 1.0 CGA A:HEC201 2.9 21.7 1.0 CD A:GLU8 2.9 19.9 1.0 OE2 A:GLU4 3.1 22.9 1.0 CBA A:HEC201 3.2 20.7 1.0 CG A:GLU8 3.3 19.8 1.0 OE2 A:GLU8 4.0 19.1 1.0 O2A A:HEC201 4.0 22.9 1.0 O A:HOH360 4.1 35.5 1.0 CG A:GLU4 4.2 25.1 1.0 CAA A:HEC201 4.5 21.5 1.0 CB A:GLU8 4.8 19.5 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