Calcium in PDB 7xyd: Crystal Structure of TMPRSS2 in Complex with Nafamostat

The structure of Crystal Structure of TMPRSS2 in Complex with Nafamostat, PDB code: 7xyd was solved by H.Wang, X.Liu, Y.Duan, X.Liu, L.Sun, H.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.81 / 2.58
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.14, 93.203, 93.13, 90, 100.6, 90
R / Rfree (%)	21.1 / 24.8

The binding sites of Calcium atom in the Crystal Structure of TMPRSS2 in Complex with Nafamostat (pdb code 7xyd). 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 Nafamostat, PDB code: 7xyd:
Jump to Calcium binding site number: 1; 2;

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


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 Nafamostat within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:65.1 occ:1.00 O A:ASN131 2.2 60.7 1.0 OE2 A:GLU145 2.3 49.8 1.0 ND1 A:HIS138 2.3 64.8 1.0 OD1 A:ASP134 2.4 66.6 1.0 OD2 A:ASP144 2.4 46.3 1.0 O A:VAL136 2.5 59.0 1.0 CE1 A:HIS138 3.1 66.1 1.0 C A:ASN131 3.2 66.0 1.0 CG A:ASP134 3.4 67.3 1.0 CD A:GLU145 3.4 47.1 1.0 CG A:HIS138 3.5 60.2 1.0 CG A:ASP144 3.5 49.7 1.0 C A:VAL136 3.7 56.2 1.0 OD2 A:ASP134 3.9 65.3 1.0 CG A:GLU145 3.9 47.5 1.0 CB A:HIS138 4.0 57.3 1.0 CA A:ASN131 4.0 66.6 1.0 CB A:ASP144 4.0 52.6 1.0 N A:HIS138 4.1 57.0 1.0 N A:TRP132 4.1 62.7 1.0 CB A:ASN131 4.2 71.4 1.0 CA A:TRP132 4.3 56.6 1.0 N A:ASP134 4.3 58.4 1.0 NE2 A:HIS138 4.3 62.7 1.0 N A:VAL136 4.3 62.2 1.0 N A:CYS133 4.4 56.6 1.0 OE1 A:GLU145 4.4 47.9 1.0 CB A:ASP134 4.4 60.5 1.0 O A:ASP144 4.4 51.8 1.0 CA A:VAL136 4.5 60.8 1.0 CD2 A:HIS138 4.5 51.8 1.0 OD1 A:ASP144 4.6 51.0 1.0 C A:TRP132 4.6 56.1 1.0 N A:SER137 4.7 55.1 1.0 CA A:HIS138 4.7 56.3 1.0 CA A:SER137 4.8 53.6 1.0 C A:SER137 4.8 56.0 1.0 CA A:ASP134 4.8 54.7 1.0 C A:ASP144 4.8 45.8 1.0 CB A:VAL136 4.8 64.9 1.0 N A:GLY135 5.0 54.7 1.0

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


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 Nafamostat within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:67.2 occ:1.00 O B:ASN131 2.1 69.3 1.0 O B:VAL136 2.2 65.0 1.0 OD1 B:ASP134 2.3 69.2 1.0 ND1 B:HIS138 2.4 67.2 1.0 OD2 B:ASP144 2.5 65.0 1.0 OE2 B:GLU145 2.8 57.4 1.0 CE1 B:HIS138 3.0 67.7 1.0 CG B:ASP144 3.3 72.2 1.0 C B:ASN131 3.4 63.3 1.0 C B:VAL136 3.4 64.5 1.0 CG B:ASP134 3.5 62.9 1.0 CG B:HIS138 3.7 61.9 1.0 CD B:GLU145 3.8 66.5 1.0 OD1 B:ASP144 4.0 76.7 1.0 CG B:GLU145 4.0 67.0 1.0 CB B:ASP144 4.0 70.5 1.0 OD2 B:ASP134 4.0 57.5 1.0 N B:HIS138 4.0 72.5 1.0 N B:VAL136 4.2 69.3 1.0 CA B:ASN131 4.2 63.6 1.0 NE2 B:HIS138 4.2 53.5 1.0 N B:TRP132 4.3 59.4 1.0 CA B:VAL136 4.3 65.0 1.0 N B:ASP134 4.3 61.1 1.0 CB B:HIS138 4.3 63.4 1.0 CB B:ASN131 4.3 66.7 1.0 N B:CYS133 4.3 60.6 1.0 CA B:TRP132 4.4 61.4 1.0 N B:SER137 4.4 71.6 1.0 CA B:SER137 4.5 74.9 1.0 O B:ASP144 4.6 70.1 1.0 C B:SER137 4.6 74.3 1.0 CB B:ASP134 4.6 60.2 1.0 CD2 B:HIS138 4.6 51.3 1.0 CB B:VAL136 4.7 66.8 1.0 C B:TRP132 4.7 57.2 1.0 CA B:HIS138 4.8 70.8 1.0 C B:ASP144 4.9 67.1 1.0 N B:GLY135 4.9 66.4 1.0 OE1 B:GLU145 4.9 68.0 1.0 CA B:ASP134 4.9 64.8 1.0

H.Wang, Y.Duan, X.Liu, L.Sun, H.Yang. Crystal Structure of TMPRSS2 in Complex with Nafamostat To Be Published.