Calcium in PDB 9u8g: Crystal Structure of TMPRSS2 in Complex with NANOBODY77_10

The structure of Crystal Structure of TMPRSS2 in Complex with NANOBODY77_10, PDB code: 9u8g was solved by Y.Duan, Z.Zhao, X.Liu, H.Wang, H.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.29 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	67.616, 69.827, 82.192, 104.97, 112.85, 102.1
R / Rfree (%)	19.3 / 23

The binding sites of Calcium atom in the Crystal Structure of TMPRSS2 in Complex with NANOBODY77_10 (pdb code 9u8g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of TMPRSS2 in Complex with NANOBODY77_10, PDB code: 9u8g:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of TMPRSS2 in Complex with NANOBODY77_10


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of TMPRSS2 in Complex with NANOBODY77_10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:29.7 occ:1.00 O A:VAL136 2.2 30.2 1.0 OE2 A:GLU145 2.3 31.8 1.0 O A:ASN131 2.3 28.4 1.0 OD2 A:ASP144 2.3 30.4 1.0 OD1 A:ASP134 2.3 33.4 1.0 ND1 A:HIS138 2.6 30.2 1.0 CG A:ASP134 3.3 35.9 1.0 CE1 A:HIS138 3.3 29.8 1.0 CD A:GLU145 3.4 29.6 1.0 CG A:ASP144 3.4 26.2 1.0 C A:VAL136 3.4 31.5 1.0 C A:ASN131 3.5 30.8 1.0 CG A:HIS138 3.7 28.8 1.0 OD2 A:ASP134 3.8 36.2 1.0 CG A:GLU145 3.9 27.9 1.0 N A:HIS138 3.9 29.0 1.0 CB A:ASP144 4.0 26.1 1.0 N A:ASP134 4.1 33.8 1.0 CB A:ASN131 4.2 30.6 1.0 CB A:HIS138 4.2 27.2 1.0 CA A:ASN131 4.2 33.8 1.0 N A:VAL136 4.2 36.3 1.0 CA A:VAL136 4.3 36.3 1.0 OE1 A:GLU145 4.3 30.0 1.0 OD1 A:ASP144 4.4 28.4 1.0 N A:SER137 4.4 33.0 0.7 N A:SER137 4.4 33.0 0.3 N A:CYS133 4.4 32.9 1.0 CB A:ASP134 4.4 36.4 1.0 N A:TRP132 4.5 31.4 1.0 CA A:SER137 4.5 33.9 0.3 CA A:SER137 4.5 33.9 0.7 NE2 A:HIS138 4.5 33.9 1.0 CD1 A:ILE127 4.6 36.8 1.0 CA A:TRP132 4.6 29.5 1.0 C A:SER137 4.6 33.3 0.3 C A:SER137 4.6 33.3 0.7 CB A:VAL136 4.7 41.0 1.0 CA A:ASP134 4.7 34.0 1.0 CA A:HIS138 4.7 31.8 1.0 CD2 A:HIS138 4.8 32.1 1.0 O A:ASP144 4.8 27.4 1.0 C A:TRP132 4.8 31.9 1.0 N A:GLY135 4.8 36.5 1.0 C A:ASP134 4.9 36.8 1.0 C A:ASP144 5.0 26.1 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of TMPRSS2 in Complex with NANOBODY77_10


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of TMPRSS2 in Complex with NANOBODY77_10 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:30.4 occ:1.00 O C:VAL136 2.1 24.5 1.0 O C:ASN131 2.3 27.9 1.0 OD2 C:ASP144 2.3 33.0 1.0 OE2 C:GLU145 2.3 27.1 1.0 OD1 C:ASP134 2.3 29.0 1.0 ND1 C:HIS138 2.5 34.9 1.0 CE1 C:HIS138 3.3 33.9 1.0 CG C:ASP134 3.3 39.1 1.0 C C:VAL136 3.4 31.6 1.0 CD C:GLU145 3.4 30.0 1.0 CG C:ASP144 3.4 31.7 1.0 C C:ASN131 3.4 33.6 1.0 CG C:HIS138 3.7 34.4 1.0 OD2 C:ASP134 3.9 39.8 1.0 N C:HIS138 3.9 29.5 1.0 CG C:GLU145 4.0 32.0 1.0 CB C:ASP144 4.0 31.5 1.0 CB C:HIS138 4.1 32.7 1.0 N C:VAL136 4.1 34.9 1.0 CA C:ASN131 4.1 36.3 1.0 N C:ASP134 4.2 31.0 1.0 CB C:ASN131 4.2 29.7 1.0 CA C:VAL136 4.2 31.4 1.0 N C:SER137 4.3 32.4 0.7 N C:SER137 4.3 32.4 0.3 OD1 C:ASP144 4.4 33.2 1.0 CA C:SER137 4.4 31.6 0.7 OE1 C:GLU145 4.4 32.8 1.0 CA C:SER137 4.4 31.6 0.3 N C:CYS133 4.5 33.2 1.0 N C:TRP132 4.5 30.3 1.0 NE2 C:HIS138 4.5 31.8 1.0 CB C:ASP134 4.5 33.8 1.0 C C:SER137 4.5 31.4 0.3 C C:SER137 4.5 30.9 0.7 CD1 C:ILE127 4.6 32.4 1.0 CB C:VAL136 4.6 33.8 1.0 CA C:TRP132 4.6 30.4 1.0 CA C:HIS138 4.7 34.6 1.0 CD2 C:HIS138 4.7 34.3 1.0 CA C:ASP134 4.7 32.5 1.0 N C:GLY135 4.8 30.3 1.0 C C:TRP132 4.8 36.0 1.0 C C:ASP134 4.9 33.9 1.0 O C:ASP144 4.9 33.6 1.0

Z.Zhao, Q.Yang, X.Liu, M.Li, Y.Duan, M.Du, A.Zhou, H.Liu, Y.He, W.Wang, Y.Lu, X.Zhang, H.Wang, X.Yang, H.Zhang, X.Chen, Z.Rao, H.Yang. The Crystal Structure of Coronavirus Rbd-TMPRSS2 Complex Provides Basis For the Discovery of Therapeutic Antibodies. Nat Commun V. 16 6636 2025.
ISSN: ESSN 2041-1723
PubMed: 40681508
DOI: 10.1038/S41467-025-62023-2