Calcium in PDB 3noi: Crystal Structure of Natural Killer Cell Cytotoxicity Receptor NKP30 (NCR3)

The structure of Crystal Structure of Natural Killer Cell Cytotoxicity Receptor NKP30 (NCR3), PDB code: 3noi was solved by M.G.Joyce, P.D.Sun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.81 / 1.84
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.100, 53.020, 51.952, 90.00, 107.73, 90.00
R / Rfree (%)	16.4 / 20.4

The binding sites of Calcium atom in the Crystal Structure of Natural Killer Cell Cytotoxicity Receptor NKP30 (NCR3) (pdb code 3noi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of Natural Killer Cell Cytotoxicity Receptor NKP30 (NCR3), PDB code: 3noi:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Crystal Structure of Natural Killer Cell Cytotoxicity Receptor NKP30 (NCR3)


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 Natural Killer Cell Cytotoxicity Receptor NKP30 (NCR3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca131 b:92.2 occ:1.00 HA A:LYS64 3.4 42.4 1.0 HB3 A:ARG57 3.6 39.1 1.0 O A:GLU65 3.7 35.8 1.0 O A:LYS64 3.8 32.2 1.0 HH22 A:ARG67 4.0 47.7 0.6 C A:LYS64 4.0 32.3 1.0 HD3 A:ARG57 4.0 41.3 1.0 CA A:LYS64 4.1 35.3 1.0 HG22 A:THR70 4.2 85.8 1.0 HD3 A:LYS64 4.2 72.0 1.0 HE2 A:PHE73 4.3 47.7 1.0 O A:GLY63 4.3 39.6 1.0 HA A:VAL66 4.3 38.8 1.0 HG21 A:VAL66 4.4 44.2 1.0 C A:GLU65 4.4 37.1 1.0 CB A:ARG57 4.4 32.6 1.0 HB2 A:ARG57 4.4 39.1 1.0 OE1 A:GLU72 4.5 20.0 1.0 HD2 A:ARG57 4.5 41.3 1.0 NH2 A:ARG67 4.5 39.8 0.6 HB A:THR70 4.5 84.5 1.0 HH12 A:ARG67 4.6 73.5 0.6 CD A:ARG57 4.6 34.4 1.0 HD2 A:LYS64 4.7 72.0 1.0 N A:GLU65 4.7 36.1 1.0 HB3 A:LYS64 4.7 45.3 1.0 H A:ARG57 4.7 30.4 1.0 HG23 A:THR70 4.7 85.8 1.0 CG2 A:THR70 4.8 71.5 1.0 CD A:LYS64 4.9 60.0 1.0 HH21 A:ARG67 4.9 47.7 0.6 N A:VAL66 4.9 28.5 1.0 CB A:LYS64 5.0 37.7 1.0

Calcium binding site 2 out of 7 in the Crystal Structure of Natural Killer Cell Cytotoxicity Receptor NKP30 (NCR3)


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 Natural Killer Cell Cytotoxicity Receptor NKP30 (NCR3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca132 b:80.0 occ:1.00 HH12 A:ARG124 3.4 75.6 0.7 O A:GLY122 3.8 32.0 1.0 HD12 A:ILE105 3.9 60.9 1.0 NH1 A:ARG124 4.0 63.0 0.7 HA A:PRO25 4.0 30.1 1.0 O A:PRO25 4.0 26.9 1.0 HH11 A:ARG124 4.1 75.6 0.7 O A:ASN121 4.1 33.0 1.0 HB2 A:ARG124 4.2 27.9 0.7 O A:HOH233 4.3 51.8 1.0 HB3 A:PRO25 4.3 34.9 1.0 C A:GLY122 4.3 34.2 1.0 HD13 A:ILE105 4.3 60.9 1.0 H A:ARG124 4.3 24.5 0.3 HB2 A:ARG124 4.3 38.2 0.3 H A:ARG124 4.3 24.5 0.7 HA A:THR123 4.4 31.3 0.3 HG12 A:ILE105 4.4 53.0 1.0 HA A:THR123 4.5 31.9 0.7 O A:HOH260 4.5 68.2 1.0 CD1 A:ILE105 4.5 50.8 1.0 HA3 A:GLY122 4.5 32.0 1.0 HG23 A:ILE105 4.6 37.5 1.0 HD22 A:ASN121 4.6 25.9 0.6 N A:ARG124 4.7 20.4 1.0 CA A:PRO25 4.7 25.1 1.0 HH22 A:ARG124 4.8 74.5 0.7 HG21 A:ILE105 4.8 37.5 1.0 C A:PRO25 4.9 24.7 1.0 CZ A:ARG124 4.9 63.0 0.7 N A:THR123 4.9 26.7 1.0 CA A:GLY122 4.9 26.6 1.0 CA A:THR123 5.0 26.1 0.3

Calcium binding site 3 out of 7 in the Crystal Structure of Natural Killer Cell Cytotoxicity Receptor NKP30 (NCR3)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Natural Killer Cell Cytotoxicity Receptor NKP30 (NCR3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca134 b:74.2 occ:1.00 O A:HOH250 2.6 43.8 1.0 HB3 A:SER22 3.6 40.1 1.0 HD3 A:PRO24 3.7 31.8 1.0 HB2 A:SER22 3.9 40.1 1.0 CA A:CA133 4.0 88.0 1.0 N A:PRO24 4.1 23.5 1.0 C A:GLN23 4.1 22.4 1.0 CB A:SER22 4.2 33.4 1.0 HA A:PRO24 4.2 27.6 1.0 HA A:GLN23 4.2 26.4 1.0 CD A:PRO24 4.3 26.5 1.0 C A:SER22 4.4 26.5 1.0 O A:SER22 4.4 21.8 1.0 N A:GLN23 4.4 20.6 1.0 CA A:GLN23 4.5 22.0 1.0 O A:GLN23 4.5 24.8 1.0 HB3 A:PRO24 4.5 30.2 1.0 CA A:PRO24 4.6 23.0 1.0 HG A:SER40 4.7 49.3 1.0 O A:HOH218 4.8 36.6 1.0 H A:GLN23 4.8 24.7 1.0 HG3 A:PRO24 4.8 36.3 1.0 HB2 A:SER40 4.8 32.0 1.0 CB A:PRO24 4.9 25.1 1.0 O A:HOH227 5.0 31.7 1.0 CA A:SER22 5.0 25.1 1.0 CG A:PRO24 5.0 30.3 1.0 OG A:SER40 5.0 41.1 1.0

Calcium binding site 4 out of 7 in the Crystal Structure of Natural Killer Cell Cytotoxicity Receptor NKP30 (NCR3)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Natural Killer Cell Cytotoxicity Receptor NKP30 (NCR3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca133 b:88.0 occ:1.00 HB3 A:SER22 3.8 40.1 1.0 HD3 A:PRO25 3.8 37.9 1.0 O A:GLN23 3.8 24.8 1.0 CA A:CA134 4.0 74.2 1.0 HA A:PRO24 4.1 27.6 1.0 H A:GLN23 4.6 24.7 1.0 C A:GLN23 4.6 22.4 1.0 HD21 A:ASN121 4.6 25.9 0.6 CB A:SER22 4.7 33.4 1.0 CD A:PRO25 4.8 31.6 1.0 N A:GLN23 5.0 20.6 1.0 HG3 A:PRO25 5.0 51.0 1.0 CA A:PRO24 5.0 23.0 1.0

Calcium binding site 5 out of 7 in the Crystal Structure of Natural Killer Cell Cytotoxicity Receptor NKP30 (NCR3)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Natural Killer Cell Cytotoxicity Receptor NKP30 (NCR3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca135 b:95.7 occ:1.00 O A:HOH261 2.9 66.8 1.0 NE1 A:TRP20 3.6 60.3 1.0 CD1 A:TRP20 3.6 52.5 1.0 CE2 A:TRP20 3.7 58.7 1.0 CG A:TRP20 3.7 44.5 1.0 CD2 A:TRP20 3.7 31.4 1.0 HE1 A:TRP20 4.0 72.4 1.0 HD1 A:TRP20 4.0 63.0 1.0 HB3 A:TRP20 4.1 32.3 1.0 CZ2 A:TRP20 4.3 51.4 1.0 CE3 A:TRP20 4.4 28.8 1.0 CB A:TRP20 4.4 26.9 1.0 HA A:TRP20 4.5 26.1 1.0 O A:HOH215 4.6 33.0 1.0 HZ2 A:TRP20 4.7 61.6 1.0 HG A:SER22 4.8 64.6 1.0 HE3 A:TRP20 4.8 34.6 1.0 CH2 A:TRP20 4.9 43.0 1.0 CZ3 A:TRP20 4.9 33.5 1.0 H A:VAL21 4.9 25.6 1.0 CA A:TRP20 5.0 21.7 1.0

Calcium binding site 6 out of 7 in the Crystal Structure of Natural Killer Cell Cytotoxicity Receptor NKP30 (NCR3)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Natural Killer Cell Cytotoxicity Receptor NKP30 (NCR3) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca131 b:73.4 occ:1.00 H B:THR119 2.6 31.2 1.0 O B:HOH255 3.0 43.0 1.0 HA2 B:GLY118 3.1 31.8 1.0 O B:HOH268 3.3 35.8 1.0 N B:THR119 3.4 26.0 1.0 O B:HOH265 3.4 67.2 1.0 O B:HOH212 3.6 30.0 1.0 O B:THR119 3.9 26.8 1.0 CA B:GLY118 3.9 26.5 1.0 HB B:THR119 4.0 50.5 1.0 HA3 B:GLY118 4.1 31.8 1.0 HA3 B:GLY17 4.1 46.6 1.0 C B:GLY118 4.1 29.7 1.0 H B:GLY17 4.2 53.8 1.0 O B:HOH269 4.2 61.8 1.0 O B:LEU19 4.2 31.8 1.0 CA B:THR119 4.4 22.5 1.0 HZ B:PHE15 4.4 59.8 1.0 O B:HOH234 4.4 59.1 1.0 HE2 B:PHE15 4.5 59.0 1.0 CZ B:PHE15 4.5 49.8 1.0 CB B:THR119 4.5 42.1 1.0 CE2 B:PHE15 4.6 49.1 1.0 C B:THR119 4.6 21.8 1.0 O B:VAL117 4.7 29.8 1.0 N B:GLY17 4.8 44.9 1.0 OG1 B:THR119 4.8 37.6 1.0 CA B:GLY17 4.9 38.9 1.0 O B:PHE15 4.9 35.5 1.0 HA B:TRP20 5.0 32.5 1.0

Calcium binding site 7 out of 7 in the Crystal Structure of Natural Killer Cell Cytotoxicity Receptor NKP30 (NCR3)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Natural Killer Cell Cytotoxicity Receptor NKP30 (NCR3) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca132 b:94.2 occ:1.00 H B:SER44 2.1 31.1 1.0 O B:HOH229 2.6 62.3 1.0 HB1 B:ALA43 2.9 32.4 1.0 HD11 B:LEU115 2.9 49.7 1.0 N B:SER44 3.0 25.9 1.0 HD2 B:ARG47 3.0 81.2 1.0 HA B:ALA43 3.2 28.7 1.0 HB2 B:ARG47 3.4 39.8 1.0 HB2 B:SER44 3.5 37.2 1.0 HG B:SER44 3.6 55.0 1.0 CB B:ALA43 3.7 27.0 1.0 CA B:ALA43 3.7 23.9 1.0 OG B:SER44 3.7 45.8 1.0 C B:ALA43 3.8 28.5 1.0 CD1 B:LEU115 3.8 41.4 1.0 CB B:SER44 3.9 31.0 1.0 CD B:ARG47 3.9 67.6 1.0 CA B:SER44 4.0 25.9 1.0 HB3 B:ARG47 4.0 39.8 1.0 HD12 B:LEU115 4.0 49.7 1.0 CB B:ARG47 4.1 33.2 1.0 HB2 B:ALA43 4.1 32.4 1.0 HE B:ARG47 4.2 90.4 1.0 HD23 B:LEU115 4.3 48.6 1.0 HD13 B:LEU115 4.4 49.7 1.0 HB3 B:ALA43 4.4 32.4 1.0 HD3 B:ARG47 4.5 81.2 1.0 O B:SER44 4.5 30.6 1.0 HG B:LEU115 4.5 55.3 1.0 CG B:ARG47 4.5 54.2 1.0 NE B:ARG47 4.6 75.3 1.0 HG3 B:ARG47 4.6 65.0 1.0 CG B:LEU115 4.7 46.1 1.0 HA B:SER44 4.7 31.1 1.0 C B:SER44 4.8 28.9 1.0 HG11 B:VAL112 4.8 33.4 1.0 HB3 B:SER44 4.9 37.2 1.0 CD2 B:LEU115 4.9 40.5 1.0 O B:ALA43 5.0 29.9 1.0 O B:LEU48 5.0 37.3 1.0

M.G.Joyce, P.Tran, M.A.Zhuravleva, J.Jaw, M.Colonna, P.D.Sun. Structure of the Natural Killer Cell Activating Receptor NKP30 and Dissection of Ligand Binding Site Proc.Natl.Acad.Sci.Usa 2011.
ISSN: ESSN 1091-6490