Zinc in PDB 8t59: Crystal Structure of Para.09 Bound to TREM2

The structure of Crystal Structure of Para.09 Bound to TREM2, PDB code: 8t59 was solved by H.Wallweber, P.L.Hsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.78 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.17, 68.16, 254.796, 90, 90, 90
R / Rfree (%)	20 / 23.7

The binding sites of Zinc atom in the Crystal Structure of Para.09 Bound to TREM2 (pdb code 8t59). 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 Para.09 Bound to TREM2, PDB code: 8t59:
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 Para.09 Bound to TREM2


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 Para.09 Bound to TREM2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:33.0 occ:1.00 OD1 B:ASN142 2.0 28.9 1.0 NE2 A:HIS166 2.1 28.4 1.0 OD1 B:ASN143 2.1 27.9 1.0 O A:HOH409 2.2 28.1 1.0 O C:HOH414 2.2 30.1 1.0 OE1 C:GLU1 2.2 25.9 1.0 CG B:ASN142 2.9 29.5 1.0 CD2 A:HIS166 3.0 29.7 1.0 CG B:ASN143 3.1 29.5 1.0 CD C:GLU1 3.1 29.4 1.0 CE1 A:HIS166 3.1 29.1 1.0 ND2 B:ASN142 3.2 27.9 1.0 OE2 C:GLU1 3.3 28.4 1.0 ND2 B:ASN143 3.5 31.6 1.0 OG B:SER179 4.1 28.7 1.0 CG A:HIS166 4.2 27.5 1.0 ND1 A:HIS166 4.2 31.8 1.0 O A:GLY164 4.2 30.2 1.0 CB B:ASN142 4.3 29.9 1.0 OG1 A:THR185 4.3 30.5 1.0 CB B:ASN143 4.4 29.5 1.0 O A:HOH480 4.4 33.5 1.0 CG C:GLU1 4.5 26.8 1.0 N B:ASN143 4.6 27.4 1.0 O B:HOH450 4.7 29.0 1.0 CG2 A:THR185 4.7 29.2 1.0 CA A:GLY164 4.8 31.7 1.0 CA B:ASN142 4.8 28.5 1.0 C A:GLY164 4.8 29.8 1.0 C B:ASN142 5.0 30.3 1.0

Zinc binding site 2 out of 7 in the Crystal Structure of Para.09 Bound to TREM2


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 Para.09 Bound to TREM2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:43.0 occ:1.00 ND1 B:HIS194 2.1 43.1 1.0 OD2 B:ASP156 2.1 37.3 1.0 CE1 B:HIS194 3.0 44.8 1.0 CG B:ASP156 3.0 39.4 1.0 CG B:HIS194 3.2 44.6 1.0 CB B:ASP156 3.3 36.5 1.0 CB B:HIS194 3.6 43.6 1.0 CA B:HIS194 3.8 39.2 1.0 NE2 B:HIS194 4.1 46.1 1.0 O B:LYS193 4.1 38.6 1.0 OD1 B:ASP156 4.2 39.3 1.0 CD2 B:HIS194 4.2 46.0 1.0 C B:LYS193 4.7 45.6 1.0 N B:HIS194 4.7 43.2 1.0 N B:LYS195 4.7 40.0 1.0 CA B:ASP156 4.7 37.5 1.0 C B:HIS194 4.9 42.8 1.0

Zinc binding site 3 out of 7 in the Crystal Structure of Para.09 Bound to TREM2


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 Para.09 Bound to TREM2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn307 b:36.1 occ:1.00 OE2 D:GLU86 1.8 35.8 1.0 OE2 B:GLU86 1.9 35.6 1.0 OE1 D:GLU84 2.0 33.8 1.0 OE1 B:GLU84 2.0 29.8 1.0 CD B:GLU86 2.8 35.6 1.0 CD D:GLU86 2.8 34.1 1.0 OE1 B:GLU86 3.0 31.9 1.0 CD D:GLU84 3.1 32.8 1.0 OE1 D:GLU86 3.1 30.9 1.0 CD B:GLU84 3.2 38.2 1.0 NH2 D:ARG66 3.5 28.4 1.0 NH2 B:ARG66 3.6 33.6 1.0 OE2 D:GLU84 3.8 32.9 1.0 CB B:GLU84 3.8 32.9 1.0 CB D:GLU84 3.9 31.1 1.0 OE2 B:GLU84 4.0 32.1 1.0 O D:HOH463 4.0 36.9 1.0 CG D:GLU84 4.0 31.6 1.0 CG B:GLU84 4.1 35.4 1.0 CG D:GLU86 4.2 35.2 1.0 CG B:GLU86 4.2 36.8 1.0 CZ D:ARG66 4.3 29.0 1.0 CZ B:ARG66 4.4 33.8 1.0 NE D:ARG66 4.5 27.8 1.0 NE B:ARG66 4.5 32.5 1.0

Zinc binding site 4 out of 7 in the Crystal Structure of Para.09 Bound to TREM2


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 Para.09 Bound to TREM2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:37.5 occ:1.00 O A:HOH404 2.1 32.1 1.0 OE1 A:GLU1 2.2 34.9 1.0 NE2 C:HIS166 2.2 32.5 1.0 OD1 D:ASN143 2.2 33.7 1.0 OD1 D:ASN142 2.3 31.1 1.0 O C:HOH415 2.3 31.2 1.0 CD2 C:HIS166 3.0 30.7 1.0 CD A:GLU1 3.1 36.2 1.0 CG D:ASN142 3.1 31.2 1.0 CG D:ASN143 3.2 34.1 1.0 CE1 C:HIS166 3.3 31.0 1.0 OE2 A:GLU1 3.3 32.6 1.0 ND2 D:ASN142 3.3 32.8 1.0 ND2 D:ASN143 3.6 37.0 1.0 OG D:SER179 4.0 26.1 1.0 O C:HOH501 4.2 42.4 1.0 CG C:HIS166 4.2 31.9 1.0 O C:GLY164 4.2 29.2 1.0 ND1 C:HIS166 4.3 28.6 1.0 OG1 C:THR185 4.3 28.8 1.0 O D:HOH446 4.4 28.7 1.0 CB D:ASN143 4.5 33.9 1.0 CG A:GLU1 4.5 34.2 1.0 CG2 C:THR185 4.6 30.1 1.0 CB D:ASN142 4.6 27.1 1.0 N D:ASN143 4.7 28.6 1.0 C C:GLY164 4.9 34.2 1.0 CA C:GLY164 4.9 34.7 1.0

Zinc binding site 5 out of 7 in the Crystal Structure of Para.09 Bound to TREM2


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 Para.09 Bound to TREM2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn303 b:33.1 occ:1.00 OD1 D:ASP190 1.9 32.8 1.0 O D:HOH517 2.0 30.2 1.0 NE2 D:HIS194 2.0 31.0 1.0 CD2 D:HIS194 2.9 27.1 1.0 CG D:ASP190 2.9 31.1 1.0 CE1 D:HIS194 3.1 31.9 1.0 OD2 D:ASP190 3.2 30.2 1.0 O D:HOH540 3.5 74.2 1.0 CG D:HIS194 4.1 27.5 1.0 O D:ASP190 4.1 32.1 1.0 ND1 D:HIS194 4.2 30.3 1.0 CB D:ASP190 4.2 34.1 1.0 CA D:ASP190 4.5 31.1 1.0 C D:ASP190 4.6 33.1 1.0 CB D:LYS193 4.8 31.9 1.0 CD2 D:LEU186 4.8 31.7 1.0 CD D:LYS193 4.8 35.7 1.0

Zinc binding site 6 out of 7 in the Crystal Structure of Para.09 Bound to TREM2


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 Para.09 Bound to TREM2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn201 b:50.6 occ:1.00 O E:HOH304 1.9 38.8 1.0 O A:HOH423 1.9 41.2 1.0 NE2 E:HIS157 2.2 41.4 1.0 O E:HOH312 2.2 46.5 1.0 O A:HOH447 2.3 43.5 1.0 O A:HOH477 2.4 53.2 1.0 CD2 E:HIS157 3.1 35.5 1.0 CE1 E:HIS157 3.3 37.2 1.0 O E:HOH314 3.9 44.9 1.0 OD1 A:ASP56 4.1 44.7 1.0 OD2 A:ASP56 4.2 40.9 1.0 CG E:HIS157 4.3 33.1 1.0 OG A:SER55 4.3 59.5 1.0 ND1 E:HIS157 4.3 34.7 1.0 OD1 A:ASN31 4.6 52.1 1.0 CG A:ASP56 4.6 43.1 1.0 NE1 A:TRP33 4.8 33.2 1.0 CZ2 A:TRP33 4.9 36.9 1.0 CB A:SER55 5.0 50.9 1.0

Zinc binding site 7 out of 7 in the Crystal Structure of Para.09 Bound to TREM2


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 Para.09 Bound to TREM2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn201 b:42.9 occ:1.00 O C:HOH410 1.7 35.7 1.0 NE2 F:HIS157 2.1 31.5 1.0 O C:HOH404 2.1 36.2 1.0 O C:HOH418 2.1 35.6 1.0 O F:HOH308 2.2 37.9 1.0 O C:HOH545 2.5 37.0 1.0 CD2 F:HIS157 3.0 30.4 1.0 CE1 F:HIS157 3.1 34.5 1.0 ND2 C:ASN31 3.9 36.8 1.0 OD1 C:ASP56 4.0 38.7 1.0 O F:HOH311 4.1 41.1 1.0 OD1 C:ASN31 4.1 39.3 1.0 CG F:HIS157 4.2 31.5 1.0 ND1 F:HIS157 4.2 31.1 1.0 OD2 C:ASP56 4.2 35.2 1.0 O F:HOH313 4.4 45.9 1.0 CG C:ASN31 4.4 42.4 1.0 CG C:ASP56 4.5 38.1 1.0 CZ2 C:TRP33 4.6 30.7 1.0 NE1 C:TRP33 4.9 30.9 1.0 CB C:SER55 5.0 41.5 1.0

Y.Hsiao, Z.Lin, C.Du, A.Echeverria, H.Wallweber, T.Aung, R.G.Alberstein, Y.Shang, F.Seeger, A.Watkins, D.Seshasayee, D.V.Hansen, C.Bolen, P.L.Hsu, I.Hotzel. Rapid Affinity Optimization of An Anti-TREM2 Clinical Lead Antibody By Cross-Lineage Immune Repertoire Mining To Be Published.