Zinc in PDB 6ksn: Structure of A Zn-Bound Camelid Single Domain Antibody

The structure of Structure of A Zn-Bound Camelid Single Domain Antibody, PDB code: 6ksn was solved by S.Kumar, A.Athreya, A.Penmatsa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.28 / 2.15
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	106.880, 106.880, 70.580, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 23.2

The structure of Structure of A Zn-Bound Camelid Single Domain Antibody also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the Structure of A Zn-Bound Camelid Single Domain Antibody (pdb code 6ksn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of A Zn-Bound Camelid Single Domain Antibody, PDB code: 6ksn:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of A Zn-Bound Camelid Single Domain Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Zn-Bound Camelid Single Domain Antibody within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:34.9 occ:1.00 OD1 A:ASP106 1.9 33.2 1.0 NE2 A:HIS109 2.1 37.4 1.0 ND1 A:HIS116 2.2 33.4 1.0 SG A:CYS40 2.2 34.7 1.0 CG A:ASP106 2.9 38.8 1.0 CE1 A:HIS116 3.1 32.5 1.0 CE1 A:HIS109 3.1 32.5 1.0 CB A:CYS40 3.1 36.1 1.0 CD2 A:HIS109 3.1 31.9 1.0 CG A:HIS116 3.2 37.0 1.0 OD2 A:ASP106 3.2 33.9 1.0 CB A:HIS116 3.6 34.3 1.0 N A:CYS40 3.7 36.9 1.0 N A:HIS116 4.0 35.0 1.0 CA A:CYS40 4.1 39.7 1.0 O A:HOH323 4.2 34.0 1.0 ND1 A:HIS109 4.2 31.9 1.0 NE2 A:HIS116 4.2 37.4 1.0 CG A:HIS109 4.3 32.1 1.0 CB A:ASP106 4.3 33.4 1.0 CD2 A:HIS116 4.3 40.0 1.0 C A:TYR39 4.5 39.4 1.0 CA A:HIS116 4.5 34.9 1.0 CA A:TYR39 4.6 38.5 1.0 O A:SER114 4.8 38.5 1.0 O A:PHE107 5.0 32.6 1.0 C A:VAL115 5.0 39.5 1.0

Zinc binding site 2 out of 2 in the Structure of A Zn-Bound Camelid Single Domain Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Zn-Bound Camelid Single Domain Antibody within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:43.5 occ:1.00 OD1 B:ASP106 1.9 40.9 1.0 ND1 B:HIS116 2.1 48.6 1.0 NE2 B:HIS109 2.1 41.9 1.0 SG B:CYS40 2.2 42.7 1.0 CE1 B:HIS116 2.9 48.2 1.0 CG B:ASP106 3.0 41.0 1.0 CE1 B:HIS109 3.0 42.5 1.0 CD2 B:HIS109 3.1 47.8 1.0 CB B:CYS40 3.1 46.2 1.0 CG B:HIS116 3.2 44.8 1.0 OD2 B:ASP106 3.4 41.6 1.0 N B:CYS40 3.6 42.5 1.0 CB B:HIS116 3.7 41.8 1.0 CA B:CYS40 4.0 42.6 1.0 NE2 B:HIS116 4.1 48.4 1.0 ND1 B:HIS109 4.1 44.5 1.0 CG B:HIS109 4.2 42.1 1.0 N B:HIS116 4.2 44.4 1.0 O B:HOH343 4.2 48.5 1.0 CD2 B:HIS116 4.2 47.7 1.0 CB B:ASP106 4.3 39.3 1.0 C B:TYR39 4.3 50.8 1.0 CA B:TYR39 4.5 43.2 1.0 CA B:HIS116 4.6 45.0 1.0 O B:SER114 4.9 45.0 1.0

S.Kumar, M.Ithayaraja, A.Athreya, R.Ranjan, A.Penmatsa. Isolation and Structural Characterization of A ZN2+-Bound Single-Domain Antibody Against Norc, A Putative Multi-Drug Efflux Transporter in Bacteria. J.Biol.Chem. 2019.
ISSN: ESSN 1083-351X
PubMed: 31699895
DOI: 10.1074/JBC.RA119.010902