Zinc in PDB 8yj8: Characerization of A Novel Format Scfvxvhh Single-Chain Biparatopic Antibody Against A Metal Binding Protein, Mtsa

The structure of Characerization of A Novel Format Scfvxvhh Single-Chain Biparatopic Antibody Against A Metal Binding Protein, Mtsa, PDB code: 8yj8 was solved by S.Ito, S.Nagatoishi, M.Nakakido, K.Tsumoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.57 / 1.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	292.931, 58.083, 50.76, 90, 91.24, 90
R / Rfree (%)	18.8 / 22.8

The binding sites of Zinc atom in the Characerization of A Novel Format Scfvxvhh Single-Chain Biparatopic Antibody Against A Metal Binding Protein, Mtsa (pdb code 8yj8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Characerization of A Novel Format Scfvxvhh Single-Chain Biparatopic Antibody Against A Metal Binding Protein, Mtsa, PDB code: 8yj8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Characerization of A Novel Format Scfvxvhh Single-Chain Biparatopic Antibody Against A Metal Binding Protein, Mtsa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Characerization of A Novel Format Scfvxvhh Single-Chain Biparatopic Antibody Against A Metal Binding Protein, Mtsa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:38.5 occ:1.00 CE1 A:HIS52 2.0 30.3 1.0 OD2 A:ASP265 2.2 33.5 1.0 NE2 A:HIS124 2.2 28.2 1.0 OE1 A:GLU190 2.3 28.4 1.0 NE2 A:HIS52 2.4 31.0 1.0 OE2 A:GLU190 2.6 31.3 1.0 CD A:GLU190 2.7 27.9 1.0 OD1 A:ASP265 2.7 35.5 1.0 CG A:ASP265 2.8 34.9 1.0 CD2 A:HIS124 3.2 29.1 1.0 ND1 A:HIS52 3.2 35.0 1.0 CE1 A:HIS124 3.3 31.1 1.0 CD2 A:HIS52 3.7 32.9 1.0 ND2 A:ASN211 3.9 31.4 1.0 CG A:HIS52 4.1 28.6 1.0 CG A:ASN211 4.2 32.1 1.0 CG A:GLU190 4.2 25.7 1.0 CB A:ASP265 4.2 26.2 1.0 O A:HOH405 4.3 35.0 1.0 CG A:HIS124 4.3 25.6 1.0 ND1 A:HIS124 4.3 28.8 1.0 O A:HOH511 4.4 33.1 1.0 CB A:CYS192 4.6 33.4 1.0 OD1 A:ASN211 4.6 33.2 1.0 CB A:ASN211 4.6 33.7 1.0 CD1 A:LEU77 4.7 24.7 1.0 CB A:GLU190 5.0 28.2 1.0

Zinc binding site 2 out of 2 in the Characerization of A Novel Format Scfvxvhh Single-Chain Biparatopic Antibody Against A Metal Binding Protein, Mtsa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Characerization of A Novel Format Scfvxvhh Single-Chain Biparatopic Antibody Against A Metal Binding Protein, Mtsa within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:32.9 occ:1.00 CE1 B:HIS52 2.0 23.8 1.0 OD2 B:ASP265 2.1 25.9 1.0 NE2 B:HIS124 2.2 27.4 1.0 OE1 B:GLU190 2.2 27.0 1.0 NE2 B:HIS52 2.4 30.8 1.0 OE2 B:GLU190 2.5 27.4 1.0 CD B:GLU190 2.7 26.8 1.0 OD1 B:ASP265 2.7 32.6 1.0 CG B:ASP265 2.7 26.7 1.0 CD2 B:HIS124 3.1 28.6 1.0 ND1 B:HIS52 3.2 32.1 1.0 CE1 B:HIS124 3.2 26.4 1.0 CD2 B:HIS52 3.8 27.5 1.0 ND2 B:ASN211 3.8 30.2 1.0 CG B:HIS52 4.1 29.4 1.0 O B:HOH419 4.2 29.3 1.0 CG B:ASN211 4.2 29.8 1.0 CG B:GLU190 4.2 23.5 1.0 CB B:ASP265 4.2 24.5 1.0 O B:HOH446 4.2 27.3 1.0 CG B:HIS124 4.3 22.9 1.0 ND1 B:HIS124 4.3 24.1 1.0 CB B:CYS192 4.5 23.3 1.0 CB B:ASN211 4.6 27.4 1.0 OD1 B:ASN211 4.7 29.4 1.0 CD1 B:LEU77 4.7 25.6 1.0 CB B:GLU190 5.0 26.3 1.0

R.Asano, M.Takeuchi, M.Nakakido, S.Ito, C.Aikawa, T.Yokoyama, A.Senoo, G.Ueno, S.Nagatoishi, Y.Tanaka, I.Nakagawa, K.Tsumoto. Characterization of A Novel Format Scfv×Vhh Single-Chain Biparatopic Antibody Against Metal Binding Protein Mtsa. Protein Sci. V. 33 E5017 2024.
ISSN: ESSN 1469-896X
PubMed: 38747382
DOI: 10.1002/PRO.5017