Zinc in PDB 3na9: Crystal Structure of FAB15

The structure of Crystal Structure of FAB15, PDB code: 3na9 was solved by J.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.97 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.431, 74.568, 64.628, 90.00, 103.32, 90.00
R / Rfree (%)	16.8 / 19.7

The binding sites of Zinc atom in the Crystal Structure of FAB15 (pdb code 3na9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of FAB15, PDB code: 3na9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Crystal Structure of FAB15


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of FAB15 within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn215 b:22.2 occ:1.00 OD2 L:ASP151 1.9 20.7 1.0 OXT L:ACT218 2.0 27.0 1.0 ND1 L:HIS189 2.1 23.0 1.0 O L:ACT218 2.7 29.1 1.0 C L:ACT218 2.7 22.4 1.0 CG L:ASP151 2.9 20.2 1.0 CE1 L:HIS189 3.0 28.7 1.0 CG L:HIS189 3.2 22.1 1.0 CB L:ASP151 3.4 19.0 1.0 CB L:HIS189 3.6 19.5 1.0 CA L:HIS189 3.8 19.8 1.0 OD1 L:ASP151 4.0 21.1 1.0 NE2 L:HIS189 4.1 24.3 1.0 CH3 L:ACT218 4.2 31.1 1.0 O L:HOH225 4.2 25.6 1.0 O L:LYS188 4.2 18.9 0.4 O L:LYS188 4.3 19.0 0.4 CD2 L:HIS189 4.3 24.6 1.0 N L:HIS189 4.5 19.6 1.0 C L:LYS188 4.6 18.7 0.4 C L:LYS188 4.6 18.7 0.4 CA L:ASP151 4.8 16.7 1.0 C L:HIS189 5.0 19.8 1.0 N L:LYS190 5.0 20.9 1.0

Zinc binding site 2 out of 7 in the Crystal Structure of FAB15


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of FAB15 within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn216 b:26.4 occ:0.40 OD1 L:ASN137 2.1 38.8 1.0 O H:HOH340 2.2 31.8 1.0 O H:HOH236 2.3 36.0 1.0 NE2 H:HIS164 2.3 27.4 1.0 ND2 L:ASN138 2.3 26.5 1.0 CD2 H:HIS164 2.8 29.6 1.0 CG L:ASN137 2.9 31.8 1.0 ND2 L:ASN137 3.0 38.9 1.0 CG L:ASN138 3.3 35.1 1.0 CE1 H:HIS164 3.5 29.6 1.0 OD1 L:ASN138 3.7 48.4 1.0 CG H:HIS164 4.1 23.6 1.0 O L:HOH457 4.1 43.0 1.0 OG L:SER174 4.1 18.5 1.0 CB L:ASN137 4.3 21.5 1.0 OG1 H:THR183 4.3 37.0 1.0 O H:GLY162 4.4 29.2 1.0 CB L:ASN138 4.4 24.9 1.0 ND1 H:HIS164 4.4 27.6 1.0 N L:ASN138 4.5 18.5 1.0 CA L:ASN137 4.8 17.5 1.0 CG2 H:THR183 4.8 33.9 1.0 O L:HOH227 4.9 21.2 1.0 C L:ASN137 4.9 21.1 1.0 CA L:ASN138 5.0 19.4 1.0 C H:GLY162 5.0 30.8 1.0

Zinc binding site 3 out of 7 in the Crystal Structure of FAB15


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of FAB15 within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn217 b:21.4 occ:0.44 OE1 L:GLU123 2.1 33.2 1.0 OXT L:ACT219 2.1 33.8 1.0 NE2 H:HIS212 2.1 27.4 0.6 O L:HOH403 2.3 44.9 1.0 O L:ACT219 2.8 31.5 1.0 C L:ACT219 2.9 43.5 1.0 CD L:GLU123 2.9 39.5 1.0 CD2 H:HIS212 3.0 29.4 0.6 OE2 L:GLU123 3.1 34.5 1.0 CE1 H:HIS212 3.2 25.2 0.6 CG H:HIS212 4.2 25.3 0.6 ND1 H:HIS212 4.2 23.3 0.6 N L:ASP122 4.2 20.1 1.0 CG H:PRO123 4.3 19.2 1.0 CH3 L:ACT219 4.4 46.4 1.0 CG L:GLU123 4.4 38.1 1.0 N L:GLU123 4.4 25.2 1.0 CB L:ASP122 4.4 32.0 1.0 O L:HOH424 4.6 51.6 1.0 CB L:SER121 4.6 25.9 1.0 OD2 L:ASP122 4.7 48.2 1.0 O H:HIS212 4.8 28.5 0.4 CA L:ASP122 4.8 22.3 1.0 CB L:GLU123 4.9 38.5 1.0 CD H:PRO123 5.0 17.4 1.0

Zinc binding site 4 out of 7 in the Crystal Structure of FAB15


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of FAB15 within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn218 b:31.3 occ:1.00 O L:CYS214 2.0 32.6 1.0 NE2 H:HIS213 2.1 26.2 1.0 NE2 H:HIS217 2.1 32.6 1.0 OXT H:ACT222 2.2 34.2 1.0 O H:ACT222 2.6 46.3 1.0 OXT L:CYS214 2.7 32.6 1.0 C L:CYS214 2.7 34.4 1.0 C H:ACT222 2.8 44.5 1.0 CD2 H:HIS213 3.0 31.1 1.0 CE1 H:HIS217 3.1 35.8 1.0 CE1 H:HIS213 3.1 24.9 1.0 CD2 H:HIS217 3.1 35.8 1.0 O H:HIS214 3.5 32.9 1.0 ND1 H:HIS213 4.2 28.2 1.0 OG H:SER128 4.2 40.0 1.0 CG H:HIS213 4.2 27.4 1.0 O L:HOH226 4.2 52.9 1.0 CA L:CYS214 4.2 32.4 1.0 ND1 H:HIS217 4.2 34.3 1.0 CG H:HIS217 4.2 36.0 1.0 CH3 H:ACT222 4.3 48.3 1.0 C H:HIS214 4.7 26.3 1.0 SG L:CYS214 4.7 39.4 1.0 N L:CYS214 4.8 31.9 1.0 CB L:CYS214 4.8 36.9 1.0 N H:SER128 4.9 34.1 1.0 CA H:HIS215 5.0 33.5 1.0

Zinc binding site 5 out of 7 in the Crystal Structure of FAB15


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of FAB15 within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn219 b:35.2 occ:1.00 NE2 H:HIS216 1.9 36.0 1.0 NE2 H:HIS214 2.2 35.5 1.0 CD2 H:HIS216 2.8 39.0 1.0 CE1 H:HIS216 2.9 46.1 1.0 CD2 H:HIS214 3.2 35.9 1.0 CE1 H:HIS214 3.2 36.3 1.0 CG H:HIS216 4.0 42.6 1.0 ND1 H:HIS216 4.0 42.0 1.0 ND1 H:HIS214 4.3 34.2 1.0 CG H:HIS214 4.3 35.6 1.0 O H:HOH279 4.8 47.0 1.0

Zinc binding site 6 out of 7 in the Crystal Structure of FAB15


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of FAB15 within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn220 b:28.4 occ:0.41 NE2 H:HIS215 2.0 42.2 1.0 O H:HOH230 2.2 48.8 1.0 O H:HOH407 2.2 37.6 1.0 CE1 H:HIS215 3.0 46.2 1.0 CD2 H:HIS215 3.1 41.8 1.0 NE2 H:HIS212 3.8 51.0 0.4 O H:HIS213 4.0 30.1 1.0 OG H:SER128 4.0 40.0 1.0 ND1 H:HIS215 4.1 41.0 1.0 O H:HOH443 4.1 40.0 1.0 CG H:HIS215 4.2 38.0 1.0 CD2 H:HIS212 4.5 41.1 0.4 OXT H:ACT223 4.6 65.3 1.0 CB H:SER128 4.6 39.4 1.0 CE1 H:HIS212 4.8 48.2 0.4 CA H:SER128 4.9 39.5 1.0

Zinc binding site 7 out of 7 in the Crystal Structure of FAB15


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of FAB15 within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn221 b:80.9 occ:0.69 OD1 H:ASP72 2.4 53.5 1.0 OG H:SER74 2.5 46.0 1.0 O H:HOH321 2.5 57.2 1.0 CG H:ASP72 3.1 54.9 1.0 OD2 H:ASP72 3.2 60.7 1.0 CB H:SER74 3.6 52.5 1.0 CB H:ASP72 4.5 46.2 1.0 N H:SER74 4.5 55.3 1.0 CA H:SER74 4.6 58.0 1.0 CA H:ASP72 4.8 47.2 1.0

J.Luo, Y.Feng, G.L.Gilliland. Co-Evolution of Antibody Stability and Vk Cdr-L3 Canonical Structure To Be Published.