Zinc in PDB 8s6z: CD28 in Complex with the Antibody Fab Fragment AI3

The structure of CD28 in Complex with the Antibody Fab Fragment AI3, PDB code: 8s6z was solved by S.Majocchi, M.Giovanni, P.Malinge, N.Fischer, L.A.Svensson, V.Kelpsas, N.C.Rose, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	91.84 / 3.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.874, 117.939, 145.719, 90, 90, 90
R / Rfree (%)	19.8 / 25.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 26;

Binding sites:

The binding sites of Zinc atom in the CD28 in Complex with the Antibody Fab Fragment AI3 (pdb code 8s6z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 26 binding sites of Zinc where determined in the CD28 in Complex with the Antibody Fab Fragment AI3, PDB code: 8s6z:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 26 in the CD28 in Complex with the Antibody Fab Fragment AI3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of CD28 in Complex with the Antibody Fab Fragment AI3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:104.2 occ:1.00 OD2 A:ASP61 1.9 93.2 1.0 O A:HOH404 2.4 63.1 1.0 O A:HOH401 2.5 55.4 1.0 CG A:ASP61 3.0 92.7 1.0 OD1 A:ASP61 3.4 92.3 1.0 N B:ASP1 3.5 86.8 1.0 CB B:ASP1 3.8 74.1 1.0 CA B:ASP1 4.2 82.8 1.0 CB A:ASP61 4.3 95.6 1.0 CG B:PRO95 4.7 95.0 1.0 CD B:PRO95 4.7 85.1 1.0

Zinc binding site 2 out of 26 in the CD28 in Complex with the Antibody Fab Fragment AI3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of CD28 in Complex with the Antibody Fab Fragment AI3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:71.1 occ:0.37 N3 A:IMD301 3.1 136.3 1.0 C2 A:IMD301 3.1 138.0 1.0 OE2 A:GLU147 3.3 105.6 1.0 OE1 A:GLU147 3.4 109.8 1.0 N A:ALA167 3.7 79.7 1.0 CD A:GLU147 3.7 110.8 1.0 CA A:PRO166 4.2 80.2 1.0 CB A:ALA167 4.2 96.5 1.0 C4 A:IMD301 4.3 140.5 1.0 N1 A:IMD301 4.4 117.4 1.0 C A:PRO166 4.5 79.2 1.0 CA A:ALA167 4.6 86.6 1.0 CB A:PRO166 4.7 80.0 1.0 O A:ALA167 4.9 86.9 1.0 C5 A:IMD301 5.0 128.7 1.0

Zinc binding site 3 out of 26 in the CD28 in Complex with the Antibody Fab Fragment AI3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of CD28 in Complex with the Antibody Fab Fragment AI3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:121.1 occ:0.67 OE2 A:GLU46 2.7 125.1 1.0 CD A:GLU46 3.0 119.6 1.0 OE1 A:GLU46 3.0 106.5 1.0 CG A:GLU46 4.1 119.9 1.0 OG A:SER62 4.2 93.0 1.0 NH2 A:ARG38 4.2 95.7 1.0 CB A:SER62 4.6 85.9 1.0 CB A:GLU46 4.9 106.2 1.0

Zinc binding site 4 out of 26 in the CD28 in Complex with the Antibody Fab Fragment AI3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of CD28 in Complex with the Antibody Fab Fragment AI3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:84.6 occ:1.00 NE2 A:HIS163 2.0 106.8 1.0 OD1 B:ASN137 2.0 116.0 1.0 OD1 B:ASN138 2.1 93.0 1.0 OE1 D:GLU1 2.4 103.3 1.0 CD2 A:HIS163 2.6 94.8 1.0 OE2 D:GLU1 2.9 99.9 1.0 CG B:ASN137 2.9 98.0 1.0 CD D:GLU1 2.9 106.0 1.0 ND2 B:ASN137 3.1 88.3 1.0 CE1 A:HIS163 3.2 109.9 1.0 CG B:ASN138 3.4 99.5 1.0 OG1 A:THR182 3.4 89.6 1.0 CG A:HIS163 3.8 82.2 1.0 ND1 A:HIS163 4.1 92.2 1.0 ND2 B:ASN138 4.1 118.4 1.0 O A:GLY161 4.2 100.5 1.0 OG B:SER174 4.2 105.1 1.0 CG D:GLU1 4.3 102.8 1.0 CB B:ASN137 4.3 82.5 1.0 CB B:ASN138 4.4 97.2 1.0 C A:GLY161 4.7 99.0 1.0 CB D:GLU1 4.7 101.7 1.0 N B:ASN138 4.7 108.2 1.0 CB A:THR182 4.7 94.7 1.0 CA A:GLY161 4.8 108.5 1.0 CG2 A:THR182 4.8 106.0 1.0 CA B:ASN137 5.0 85.1 1.0 ZN B:ZN308 5.0 137.1 1.0

Zinc binding site 5 out of 26 in the CD28 in Complex with the Antibody Fab Fragment AI3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of CD28 in Complex with the Antibody Fab Fragment AI3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn305 b:101.5 occ:1.00 OE1 B:GLU55 2.5 117.1 1.0 OE2 B:GLU55 2.6 101.1 1.0 O B:HOH407 2.7 66.0 1.0 O A:HOH402 2.8 43.8 1.0 CD B:GLU55 2.8 104.3 1.0 O B:HOH404 2.9 34.1 1.0 OD2 A:ASP100 3.4 92.2 1.0 OG B:SER56 3.9 111.0 1.0 CB A:ASP100 4.2 80.2 1.0 CG A:ASP100 4.2 92.9 1.0 CG B:GLU55 4.3 92.3 1.0

Zinc binding site 6 out of 26 in the CD28 in Complex with the Antibody Fab Fragment AI3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of CD28 in Complex with the Antibody Fab Fragment AI3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn306 b:137.8 occ:0.91 OD2 B:ASP9 2.2 121.5 1.0 C2 B:IMD302 2.4 126.5 1.0 N1 B:IMD302 2.4 121.0 1.0 CG B:ASP9 2.9 109.4 1.0 OD1 B:ASP9 3.1 115.2 1.0 N3 B:IMD302 3.7 119.6 1.0 C5 B:IMD302 3.7 118.8 1.0 CB B:ASP9 4.2 95.1 1.0 C4 B:IMD302 4.3 124.2 1.0

Zinc binding site 7 out of 26 in the CD28 in Complex with the Antibody Fab Fragment AI3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of CD28 in Complex with the Antibody Fab Fragment AI3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn307 b:125.1 occ:1.00 NE2 B:HIS189 2.6 100.8 1.0 O B:HOH402 2.9 73.1 1.0 CD2 B:HIS189 2.9 94.6 1.0 NZ B:LYS188 3.1 133.2 1.0 CE1 B:HIS189 3.9 93.3 1.0 CE B:LYS188 4.2 134.7 1.0 OD1 B:ASP185 4.2 112.5 1.0 CG B:HIS189 4.3 92.2 1.0 O B:ASP185 4.4 110.1 1.0 CB B:ASP185 4.4 108.6 1.0 CD B:LYS188 4.5 127.2 1.0 CG B:ASP185 4.6 122.2 1.0 ND1 B:HIS189 4.7 85.7 1.0 CA B:ASP185 4.8 97.5 1.0

Zinc binding site 8 out of 26 in the CD28 in Complex with the Antibody Fab Fragment AI3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of CD28 in Complex with the Antibody Fab Fragment AI3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn308 b:137.1 occ:1.00 OD2 B:ASP167 2.7 123.0 1.0 OD1 B:ASP167 3.0 107.9 1.0 CG B:ASP167 3.1 113.3 1.0 OE2 D:GLU1 3.5 99.9 1.0 CE1 A:HIS163 3.9 109.9 1.0 O A:VAL162 4.4 96.3 1.0 CB B:ASP167 4.4 107.2 1.0 CA A:GLY161 4.4 108.5 1.0 N A:GLY161 4.4 107.9 1.0 NE2 A:HIS163 4.5 106.8 1.0 CE B:LYS169 4.5 149.0 1.0 CG B:LYS169 4.6 126.5 1.0 ND1 A:HIS163 4.6 92.2 1.0 CD D:GLU1 4.8 106.0 1.0 N A:VAL162 4.9 98.4 1.0 C A:GLY161 4.9 99.0 1.0 ZN B:ZN304 5.0 84.6 1.0

Zinc binding site 9 out of 26 in the CD28 in Complex with the Antibody Fab Fragment AI3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of CD28 in Complex with the Antibody Fab Fragment AI3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn309 b:116.5 occ:0.68 OE1 B:GLU81 1.8 139.4 1.0 OE2 B:GLU81 2.2 125.5 1.0 CD B:GLU81 2.2 145.3 1.0 OE1 B:GLN79 3.6 93.6 1.0 CG B:GLU81 3.7 123.1 1.0 NH2 E:ARG61 4.1 104.7 1.0 CB B:GLN79 4.3 100.7 1.0 N B:ALA80 4.3 85.0 1.0 CG E:PRO59 4.3 68.5 1.0 CD B:GLN79 4.5 93.6 1.0 N B:GLU81 4.5 81.1 1.0 CB B:ALA80 4.5 90.8 1.0 CG E:GLU81 4.6 89.3 1.0 CB B:GLU81 4.8 99.4 1.0 CG B:GLN79 4.8 98.5 1.0 CA B:ALA80 4.9 86.5 1.0 CA B:GLN79 5.0 89.8 1.0

Zinc binding site 10 out of 26 in the CD28 in Complex with the Antibody Fab Fragment AI3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of CD28 in Complex with the Antibody Fab Fragment AI3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn310 b:111.3 occ:0.74 OD1 B:ASP60 1.8 124.2 1.0 CG B:ASP60 2.4 115.9 1.0 OG E:SER77 2.9 109.5 1.0 OD2 B:ASP60 3.1 97.3 1.0 CB B:ASP60 3.3 102.5 1.0 N B:ASP60 3.4 89.8 1.0 NE2 E:GLN79 3.7 78.8 1.0 O B:HOH403 3.7 68.2 1.0 CA B:ASP60 3.9 88.8 1.0 CB E:SER77 4.0 103.1 1.0 CB B:PRO59 4.3 67.8 1.0 C B:PRO59 4.4 73.5 1.0 CA B:PRO59 4.5 65.7 1.0 N B:ARG61 4.6 79.2 1.0 CD E:GLN79 4.7 89.1 1.0 CA E:GLY16 4.7 95.5 1.0 C B:ASP60 4.7 81.5 1.0 OE1 E:GLN79 5.0 100.3 1.0

S.Majocchi, M.Giovanni, P.Malinge, N.Fischer, L.A.Svensson, V.Kelpsas. Ni-3201 Is A Bispecific Antibody Mediating Pd-L1-Dependent CD28 Costimulation on T Cells For Enhanced Tumor Control Cancer Immunology Research 2024.
DOI: 10.1158/2326-6066.CIR-24-0298