Zinc in PDB 8yj7: 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: 8yj7 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)	48.27 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.591, 129.272, 245.588, 90, 90, 90
R / Rfree (%)	22.2 / 27.6

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 8yj7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 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: 8yj7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 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 B:Zn301 b:67.5 occ:1.00 CE1 B:HIS37 1.9 64.0 1.0 OD2 B:ASP250 2.0 41.4 1.0 NE2 B:HIS109 2.3 33.4 1.0 NE2 B:HIS37 2.4 68.5 1.0 OE2 B:GLU175 2.6 36.4 1.0 OE1 B:GLU175 2.6 36.2 1.0 CG B:ASP250 2.8 31.5 1.0 CD B:GLU175 2.9 35.0 1.0 OD1 B:ASP250 3.0 29.7 1.0 ND1 B:HIS37 3.2 63.8 1.0 CD2 B:HIS109 3.2 28.6 1.0 CE1 B:HIS109 3.3 31.2 1.0 ND2 B:ASN196 3.4 34.8 1.0 CD2 B:HIS37 3.7 67.2 1.0 CG B:HIS37 4.0 57.6 1.0 CB B:ASP250 4.2 25.3 1.0 CG B:ASN196 4.2 35.6 1.0 CG B:HIS109 4.4 27.0 1.0 ND1 B:HIS109 4.4 29.0 1.0 CG B:GLU175 4.4 32.3 1.0 OD1 B:ASP35 4.4 44.0 1.0 CD1 B:LEU62 4.6 28.6 1.0 CB B:ASN196 4.7 46.4 1.0 N B:ASN196 4.9 40.1 1.0 CB B:CYS177 4.9 28.6 1.0

Zinc binding site 2 out of 4 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 D:Zn301 b:84.7 occ:1.00 CE1 D:HIS37 1.9 92.2 1.0 NE2 D:HIS109 2.3 46.2 1.0 OE2 D:GLU175 2.3 48.9 1.0 NE2 D:HIS37 2.4 90.1 1.0 OE1 D:GLU175 2.6 48.3 1.0 OD1 D:ASP250 2.7 43.7 1.0 OD2 D:ASP250 2.7 53.8 1.0 CD D:GLU175 2.8 47.1 1.0 CG D:ASP250 3.0 47.0 1.0 CE1 D:HIS109 3.1 51.0 1.0 ND1 D:HIS37 3.2 84.3 1.0 CD2 D:HIS109 3.3 40.5 1.0 ND2 D:ASN196 3.6 45.1 1.0 CD2 D:HIS37 3.7 77.1 1.0 CG D:HIS37 4.1 80.5 1.0 CG D:ASN196 4.1 48.7 1.0 CG D:GLU175 4.3 47.0 1.0 ND1 D:HIS109 4.3 45.5 1.0 OD1 D:ASP35 4.3 59.9 1.0 CB D:ASP250 4.3 36.3 1.0 CG D:HIS109 4.4 39.8 1.0 OD1 D:ASN196 4.6 37.4 1.0 CD1 D:LEU62 4.6 46.7 1.0 CB D:ASN196 4.6 58.9 1.0 CG1 D:ILE195 4.8 52.2 1.0 N D:ASN196 4.9 51.7 1.0 CB D:CYS177 4.9 46.2 1.0

Zinc binding site 3 out of 4 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 3 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:61.5 occ:1.00 OE1 A:GLU175 2.2 36.6 1.0 NE2 A:HIS109 2.3 37.4 1.0 OD2 A:ASP250 2.3 41.9 1.0 CE1 A:HIS37 2.4 51.7 1.0 OE2 A:GLU175 2.5 36.9 1.0 CD A:GLU175 2.6 34.5 1.0 OD1 A:ASP250 2.8 35.2 1.0 CG A:ASP250 2.8 34.7 1.0 NE2 A:HIS37 3.1 54.0 1.0 CD2 A:HIS109 3.1 32.8 1.0 CE1 A:HIS109 3.3 38.2 1.0 ND1 A:HIS37 3.5 65.1 1.0 ND2 A:ASN196 3.7 32.9 1.0 CG A:ASN196 4.1 38.0 1.0 CG A:GLU175 4.1 32.8 1.0 CG A:HIS109 4.3 32.5 1.0 CB A:ASP250 4.3 32.6 1.0 CD2 A:HIS37 4.3 59.0 1.0 ND1 A:HIS109 4.4 34.5 1.0 OD1 A:ASP35 4.5 39.7 1.0 CG A:HIS37 4.5 61.6 1.0 OD1 A:ASN196 4.6 39.6 1.0 CB A:CYS177 4.6 34.4 1.0 CB A:ASN196 4.7 38.9 1.0 CB A:GLU175 4.9 29.3 1.0 CD1 A:LEU62 4.9 33.2 1.0 N A:ASN196 4.9 37.4 1.0

Zinc binding site 4 out of 4 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 4 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 C:Zn301 b:91.7 occ:1.00 CE1 C:HIS37 1.8 84.7 1.0 OE2 C:GLU175 2.3 69.8 1.0 NE2 C:HIS109 2.3 64.6 1.0 NE2 C:HIS37 2.4 93.7 1.0 OE1 C:GLU175 2.5 73.3 1.0 OD2 C:ASP250 2.5 62.0 1.0 CD C:GLU175 2.7 68.3 1.0 OD1 C:ASP250 2.9 48.5 1.0 ND1 C:HIS37 3.0 70.9 1.0 CG C:ASP250 3.0 54.2 1.0 ND2 C:ASN196 3.2 57.7 1.0 CD2 C:HIS109 3.2 57.2 1.0 CE1 C:HIS109 3.3 68.4 1.0 CD2 C:HIS37 3.6 79.7 1.0 CG C:HIS37 3.9 70.8 1.0 CG C:ASN196 4.0 63.4 1.0 CG C:GLU175 4.2 61.6 1.0 CG C:HIS109 4.4 57.2 1.0 ND1 C:HIS109 4.4 64.7 1.0 CB C:ASP250 4.4 49.8 1.0 CB C:ASN196 4.4 70.5 1.0 CD1 C:LEU62 4.6 48.3 1.0 N C:ASN196 4.7 65.0 1.0 OD1 C:ASP35 4.7 56.9 1.0 CD1 C:ILE195 4.9 68.2 1.0 OD1 C:ASN196 4.9 63.7 1.0 CB C:CYS177 4.9 61.1 1.0 CG1 C:ILE195 5.0 67.4 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