Calcium in PDB 6jjd: Cryo-Em Structure of Giant Freshwater Prawn Macrobrachium Rosenbergii Nodavirus (Mrnv) Full Vlp

The binding sites of Calcium atom in the Cryo-Em Structure of Giant Freshwater Prawn Macrobrachium Rosenbergii Nodavirus (Mrnv) Full Vlp (pdb code 6jjd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Cryo-Em Structure of Giant Freshwater Prawn Macrobrachium Rosenbergii Nodavirus (Mrnv) Full Vlp, PDB code: 6jjd:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Cryo-Em Structure of Giant Freshwater Prawn Macrobrachium Rosenbergii Nodavirus (Mrnv) Full Vlp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Giant Freshwater Prawn Macrobrachium Rosenbergii Nodavirus (Mrnv) Full Vlp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:60.0 occ:1.00 OE1 A:GLU114 2.1 46.3 1.0 OD2 C:ASP147 2.4 50.7 1.0 OD2 C:ASP144 2.5 48.0 1.0 OE2 A:GLU114 2.6 46.3 1.0 OD1 A:ASN246 2.7 50.3 1.0 CD A:GLU114 2.7 46.3 1.0 OD1 C:ASP147 2.7 50.7 1.0 CG C:ASP147 2.9 50.7 1.0 HE22 A:GLN244 3.0 47.9 1.0 HE21 A:GLN244 3.2 47.9 1.0 CG A:ASN246 3.4 50.3 1.0 NE2 A:GLN244 3.4 47.9 1.0 HB3 C:ASP144 3.5 48.0 1.0 CG C:ASP144 3.6 48.0 1.0 HD21 A:ASN246 3.7 50.3 1.0 HB2 C:ASP144 3.9 48.0 1.0 ND2 A:ASN246 3.9 50.3 1.0 CB C:ASP144 3.9 48.0 1.0 HA A:GLU114 4.0 46.3 1.0 HA3 A:GLY193 4.0 50.8 1.0 HH21 C:ARG200 4.1 47.3 1.0 HB3 A:ASN246 4.2 50.3 1.0 CG A:GLU114 4.2 46.3 1.0 H A:GLY193 4.2 50.8 1.0 HZ1 A:LYS196 4.3 53.1 1.0 CB C:ASP147 4.4 50.7 1.0 CB A:ASN246 4.4 50.3 1.0 H A:THR192 4.4 45.7 1.0 O A:GLU114 4.5 46.3 1.0 N A:GLY193 4.5 50.8 1.0 HB3 A:TYR191 4.5 45.7 1.0 HD1 A:TYR191 4.5 45.7 1.0 HG2 A:GLU114 4.5 46.3 1.0 OG1 A:THR192 4.5 45.7 1.0 HD22 A:ASN246 4.6 50.3 1.0 HB2 C:ASP147 4.6 50.7 1.0 CA A:CA404 4.6 59.8 1.0 HH22 C:ARG200 4.6 47.3 1.0 CA A:GLY193 4.6 50.8 1.0 NH2 C:ARG200 4.7 47.3 1.0 OD1 C:ASP144 4.7 48.0 1.0 HZ2 A:LYS196 4.7 53.1 1.0 HZ3 A:LYS196 4.7 53.1 1.0 HG3 A:GLU114 4.7 46.3 1.0 CD A:GLN244 4.7 47.9 1.0 CA A:GLU114 4.8 46.3 1.0 HA2 A:GLY193 4.8 50.8 1.0 NZ A:LYS196 4.8 53.1 1.0 HB3 C:ASP147 4.9 50.7 1.0 CB A:GLU114 4.9 46.3 1.0 HG1 A:THR192 4.9 45.7 1.0 HA A:ASN246 4.9 50.3 1.0 HB2 A:GLU114 4.9 46.3 1.0

Calcium binding site 2 out of 7 in the Cryo-Em Structure of Giant Freshwater Prawn Macrobrachium Rosenbergii Nodavirus (Mrnv) Full Vlp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Giant Freshwater Prawn Macrobrachium Rosenbergii Nodavirus (Mrnv) Full Vlp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:57.5 occ:1.00 OE1 B:GLN244 1.9 44.9 1.0 OD1 A:ASP142 2.1 49.1 1.0 OD2 A:ASP142 2.3 49.1 1.0 OD2 A:ASP147 2.5 51.7 1.0 CG A:ASP142 2.5 49.1 1.0 OE2 B:GLU114 2.6 44.9 1.0 CD B:GLN244 2.8 44.9 1.0 HE22 B:GLN244 2.9 44.9 1.0 NE2 B:GLN244 3.2 44.9 1.0 HB2 A:ASP147 3.3 51.7 1.0 HB3 A:ASP147 3.3 51.7 1.0 CG A:ASP147 3.4 51.7 1.0 CB A:ASP147 3.5 51.7 1.0 CD B:GLU114 3.6 44.9 1.0 HB3 A:ASP144 3.7 48.8 1.0 HB2 B:GLN244 3.9 44.9 1.0 CB A:ASP142 4.0 49.1 1.0 HE21 B:GLN244 4.0 44.9 1.0 CG B:GLN244 4.1 44.9 1.0 HE21 A:GLN165 4.2 48.1 1.0 HG2 B:GLU114 4.2 44.9 1.0 OD1 B:ASN246 4.2 48.3 1.0 H A:ASP144 4.2 48.8 1.0 OE1 B:GLU114 4.3 44.9 1.0 HA A:ASP142 4.4 49.1 1.0 O B:ILE245 4.4 47.1 1.0 HB2 A:ASP142 4.4 49.1 1.0 CG B:GLU114 4.4 44.9 1.0 CB B:GLN244 4.5 44.9 1.0 HB3 A:ASP142 4.5 49.1 1.0 HE22 A:GLN165 4.5 48.1 1.0 HG3 B:GLN244 4.5 44.9 1.0 CB A:ASP144 4.6 48.8 1.0 OD1 A:ASP147 4.6 51.7 1.0 HB3 B:GLN244 4.6 44.9 1.0 NE2 A:GLN165 4.7 48.1 1.0 CA A:CA403 4.7 55.9 1.0 HA B:ASN246 4.7 48.3 1.0 HE2 A:TYR140 4.7 48.8 1.0 HG3 B:GLU114 4.7 44.9 1.0 HB2 A:ASP144 4.7 48.8 1.0 CA A:ASP142 4.8 49.1 1.0 HG2 B:GLN244 4.8 44.9 1.0 H A:THR143 4.8 47.3 1.0 HD3 B:PRO247 4.8 54.1 1.0 O A:ASP144 4.9 48.8 1.0 N A:ASP144 5.0 48.8 1.0

Calcium binding site 3 out of 7 in the Cryo-Em Structure of Giant Freshwater Prawn Macrobrachium Rosenbergii Nodavirus (Mrnv) Full Vlp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of Giant Freshwater Prawn Macrobrachium Rosenbergii Nodavirus (Mrnv) Full Vlp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:55.9 occ:1.00 OD2 A:ASP144 2.4 48.8 1.0 OD1 A:ASP147 2.5 51.7 1.0 OD2 A:ASP147 2.5 51.7 1.0 OD1 B:ASN246 2.6 48.3 1.0 CG A:ASP147 2.8 51.7 1.0 HE22 B:GLN244 2.8 44.9 1.0 OE1 B:GLU114 3.0 44.9 1.0 CG A:ASP144 3.5 48.8 1.0 CG B:ASN246 3.5 48.3 1.0 HB3 A:ASP144 3.5 48.8 1.0 HD22 B:ASN246 3.5 48.3 1.0 H B:GLY193 3.5 49.6 1.0 NE2 B:GLN244 3.6 44.9 1.0 HE21 B:GLN244 3.7 44.9 1.0 HA3 B:GLY193 3.7 49.6 1.0 CD B:GLU114 3.8 44.9 1.0 CB A:ASP144 3.9 48.8 1.0 ND2 B:ASN246 3.9 48.3 1.0 HB2 A:ASP144 3.9 48.8 1.0 HZ1 B:LYS196 4.0 53.2 1.0 HG1 B:THR192 4.0 44.5 1.0 HZ3 B:LYS196 4.0 53.2 1.0 HH21 A:ARG200 4.0 47.7 1.0 OE2 B:GLU114 4.1 44.9 1.0 HA B:GLU114 4.1 44.9 1.0 HB3 B:TYR191 4.2 44.5 1.0 N B:GLY193 4.2 49.6 1.0 HZ2 B:LYS196 4.2 53.2 1.0 HD1 B:TYR191 4.2 44.5 1.0 NZ B:LYS196 4.3 53.2 1.0 CB A:ASP147 4.3 51.7 1.0 CA B:GLY193 4.4 49.6 1.0 H B:THR192 4.5 44.5 1.0 OD1 A:ASP144 4.6 48.8 1.0 HB2 A:ASP147 4.6 51.7 1.0 HD21 B:ASN246 4.6 48.3 1.0 CA A:CA402 4.7 57.5 1.0 HH22 A:ARG200 4.7 47.7 1.0 NH2 A:ARG200 4.7 47.7 1.0 HB3 B:ASN246 4.7 48.3 1.0 OG1 B:THR192 4.7 44.5 1.0 CD B:GLN244 4.7 44.9 1.0 CB B:ASN246 4.7 48.3 1.0 O B:GLU114 4.7 44.9 1.0 HB3 A:ASP147 4.8 51.7 1.0 HA2 B:GLY193 4.9 49.6 1.0 H A:ASP147 4.9 51.7 1.0 HA B:ASN246 4.9 48.3 1.0 HA A:ASP147 4.9 51.7 1.0 CD1 B:TYR191 5.0 44.5 1.0

Calcium binding site 4 out of 7 in the Cryo-Em Structure of Giant Freshwater Prawn Macrobrachium Rosenbergii Nodavirus (Mrnv) Full Vlp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of Giant Freshwater Prawn Macrobrachium Rosenbergii Nodavirus (Mrnv) Full Vlp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:59.8 occ:1.00 OE1 A:GLN244 2.0 47.9 1.0 HE22 A:GLN244 2.2 47.9 1.0 OD1 C:ASP142 2.2 48.6 1.0 CD A:GLN244 2.4 47.9 1.0 NE2 A:GLN244 2.5 47.9 1.0 OD2 C:ASP142 2.5 48.6 1.0 CG C:ASP142 2.6 48.6 1.0 OD2 C:ASP147 2.7 50.7 1.0 HE21 A:GLN244 3.2 47.9 1.0 HB2 C:ASP147 3.5 50.7 1.0 CG C:ASP147 3.6 50.7 1.0 HB3 C:ASP147 3.6 50.7 1.0 HB3 C:ASP144 3.7 48.0 1.0 CG A:GLN244 3.7 47.9 1.0 CB C:ASP147 3.8 50.7 1.0 OE1 A:GLU114 3.9 46.3 1.0 HB2 A:GLN244 3.9 47.9 1.0 HG3 A:GLN244 3.9 47.9 1.0 HE22 C:GLN165 4.0 49.7 1.0 OD1 A:ASN246 4.0 50.3 1.0 HE21 C:GLN165 4.0 49.7 1.0 CB C:ASP142 4.1 48.6 1.0 HE21 C:GLN161 4.1 53.7 1.0 H C:ASP144 4.2 48.0 1.0 CB A:GLN244 4.3 47.9 1.0 HB2 C:ASP142 4.3 48.6 1.0 NE2 C:GLN165 4.4 49.7 1.0 HG2 A:GLU114 4.4 46.3 1.0 HG2 A:GLN244 4.4 47.9 1.0 HA C:ASP142 4.4 48.6 1.0 HB2 A:GLU114 4.4 46.3 1.0 HB3 A:GLN244 4.4 47.9 1.0 CD A:GLU114 4.5 46.3 1.0 CB C:ASP144 4.6 48.0 1.0 CA A:CA401 4.6 60.0 1.0 O A:ILE245 4.6 49.4 1.0 HB3 C:ASP142 4.7 48.6 1.0 HB2 C:ASP144 4.7 48.0 1.0 H C:THR143 4.7 47.8 1.0 OD1 C:ASP147 4.8 50.7 1.0 CA C:ASP142 4.8 48.6 1.0 HA A:ASN246 4.8 50.3 1.0 CG A:GLU114 4.9 46.3 1.0 O C:ASP144 4.9 48.0 1.0 HE2 C:TYR140 4.9 48.5 1.0 N C:ASP144 4.9 48.0 1.0 NE2 C:GLN161 4.9 53.7 1.0

Calcium binding site 5 out of 7 in the Cryo-Em Structure of Giant Freshwater Prawn Macrobrachium Rosenbergii Nodavirus (Mrnv) Full Vlp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cryo-Em Structure of Giant Freshwater Prawn Macrobrachium Rosenbergii Nodavirus (Mrnv) Full Vlp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:96.0 occ:1.00 OD1 B:ASP187 3.0 50.9 1.0 OD1 C:ASP187 3.3 52.7 1.0 O B:ASP186 3.4 49.7 1.0 O C:ASP186 3.4 52.6 1.0 HE22 C:GLN188 3.5 48.7 1.0 O A:ASP186 3.7 50.6 1.0 HB2 B:ASP186 3.7 49.7 1.0 OD1 A:ASP187 3.7 52.3 1.0 HA B:GLN188 3.8 48.1 1.0 NE2 C:GLN188 3.9 48.7 1.0 HB2 A:ASP186 4.0 50.6 1.0 HB2 A:GLN188 4.0 50.0 1.0 HA A:GLN188 4.1 50.0 1.0 HB2 B:GLN188 4.1 48.1 1.0 CG B:ASP187 4.1 50.9 1.0 HA C:GLN188 4.2 48.7 1.0 HE21 C:GLN188 4.2 48.7 1.0 HB2 C:ASP186 4.2 52.6 1.0 OD2 A:ASP186 4.3 50.6 1.0 C B:ASP186 4.4 49.7 1.0 O C:ASP187 4.4 52.7 1.0 N B:GLN188 4.4 48.1 1.0 CA B:GLN188 4.4 48.1 1.0 HG2 B:GLN188 4.4 48.1 1.0 CD C:GLN188 4.4 48.7 1.0 H B:GLN188 4.5 48.1 1.0 CG C:ASP187 4.6 52.7 1.0 OE1 C:GLN188 4.6 48.7 1.0 C C:ASP186 4.6 52.6 1.0 OD2 B:ASP187 4.6 50.9 1.0 CB B:ASP186 4.6 49.7 1.0 CB B:GLN188 4.6 48.1 1.0 CA A:GLN188 4.7 50.0 1.0 HB2 C:GLN188 4.7 48.7 1.0 HG3 B:GLN188 4.7 48.1 1.0 C B:ASP187 4.7 50.9 1.0 C A:ASP186 4.7 50.6 1.0 C C:ASP187 4.8 52.7 1.0 CB A:GLN188 4.8 50.0 1.0 OD2 B:ASP186 4.8 49.7 1.0 HG3 A:GLN188 4.8 50.0 1.0 N A:GLN188 4.8 50.0 1.0 CB A:ASP186 4.8 50.6 1.0 CG B:GLN188 4.8 48.1 1.0 CG A:ASP187 4.8 52.3 1.0 OD2 C:ASP186 4.8 52.6 1.0 CG A:ASP186 4.8 50.6 1.0 CA C:GLN188 4.9 48.7 1.0 H A:GLN188 4.9 50.0 1.0 CB C:ASP186 5.0 52.6 1.0 CG B:ASP186 5.0 49.7 1.0 N C:GLN188 5.0 48.7 1.0

Calcium binding site 6 out of 7 in the Cryo-Em Structure of Giant Freshwater Prawn Macrobrachium Rosenbergii Nodavirus (Mrnv) Full Vlp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cryo-Em Structure of Giant Freshwater Prawn Macrobrachium Rosenbergii Nodavirus (Mrnv) Full Vlp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:55.7 occ:1.00 OD1 B:ASP142 2.0 48.6 1.0 OE1 C:GLN244 2.1 47.3 1.0 OD2 B:ASP142 2.3 48.6 1.0 CG B:ASP142 2.4 48.6 1.0 HE22 C:GLN244 2.5 47.3 1.0 CD C:GLN244 2.5 47.3 1.0 OD2 B:ASP147 2.7 51.4 1.0 NE2 C:GLN244 2.7 47.3 1.0 OE1 C:GLU114 3.2 46.2 1.0 HE21 C:GLN244 3.5 47.3 1.0 HB2 B:ASP147 3.5 51.4 1.0 HB3 B:ASP144 3.5 48.8 1.0 HE21 B:GLN165 3.6 47.9 1.0 CG B:ASP147 3.6 51.4 1.0 HE22 B:GLN165 3.6 47.9 1.0 HB2 C:GLN244 3.7 47.3 1.0 HB3 B:ASP147 3.8 51.4 1.0 CG C:GLN244 3.8 47.3 1.0 CB B:ASP147 3.8 51.4 1.0 NE2 B:GLN165 3.9 47.9 1.0 CB B:ASP142 3.9 48.6 1.0 HG3 C:GLN244 3.9 47.3 1.0 H B:ASP144 4.0 48.8 1.0 CB C:GLN244 4.2 47.3 1.0 HA B:ASP142 4.2 48.6 1.0 HB2 B:ASP142 4.3 48.6 1.0 OD1 C:ASN246 4.4 48.3 1.0 HB3 C:GLN244 4.4 47.3 1.0 CD C:GLU114 4.4 46.2 1.0 HB3 B:ASP142 4.4 48.6 1.0 CB B:ASP144 4.4 48.8 1.0 HG2 C:GLN244 4.5 47.3 1.0 CA B:ASP142 4.6 48.6 1.0 O B:ASP144 4.6 48.8 1.0 OD1 B:ASP147 4.6 51.4 1.0 HB2 B:ASP144 4.6 48.8 1.0 HB2 C:GLU114 4.7 46.2 1.0 CA B:CA403 4.7 55.0 1.0 H B:THR143 4.7 47.7 1.0 HG2 C:GLU114 4.7 46.2 1.0 N B:ASP144 4.7 48.8 1.0 O C:ILE245 4.7 48.3 1.0 H C:ILE245 5.0 48.3 1.0

Calcium binding site 7 out of 7 in the Cryo-Em Structure of Giant Freshwater Prawn Macrobrachium Rosenbergii Nodavirus (Mrnv) Full Vlp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cryo-Em Structure of Giant Freshwater Prawn Macrobrachium Rosenbergii Nodavirus (Mrnv) Full Vlp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:55.0 occ:1.00 OD2 B:ASP144 2.2 48.8 1.0 OE2 C:GLU114 2.5 46.2 1.0 OE1 C:GLU114 2.6 46.2 1.0 OD1 B:ASP147 2.6 51.4 1.0 HE22 C:GLN244 2.7 47.3 1.0 CD C:GLU114 2.9 46.2 1.0 OD2 B:ASP147 2.9 51.4 1.0 OD1 C:ASN246 3.0 48.3 1.0 CG B:ASP147 3.1 51.4 1.0 CG B:ASP144 3.2 48.8 1.0 NE2 C:GLN244 3.3 47.3 1.0 HE21 C:GLN244 3.3 47.3 1.0 HB3 B:ASP144 3.3 48.8 1.0 CB B:ASP144 3.6 48.8 1.0 HB2 B:ASP144 3.7 48.8 1.0 CG C:ASN246 3.7 48.3 1.0 HD22 C:ASN246 3.8 48.3 1.0 HH21 B:ARG200 3.8 47.7 1.0 H C:GLY193 4.1 47.9 1.0 ND2 C:ASN246 4.1 48.3 1.0 HB3 C:TYR191 4.3 45.4 1.0 HD1 C:TYR191 4.3 45.4 1.0 HA3 C:GLY193 4.3 47.9 1.0 OD1 B:ASP144 4.3 48.8 1.0 HA C:GLU114 4.4 46.2 1.0 CG C:GLU114 4.4 46.2 1.0 CB B:ASP147 4.5 51.4 1.0 NH2 B:ARG200 4.5 47.7 1.0 CD C:GLN244 4.5 47.3 1.0 HE3 C:LYS196 4.5 53.2 1.0 HH22 B:ARG200 4.6 47.7 1.0 CA B:CA402 4.7 55.7 1.0 HB2 B:ASP147 4.7 51.4 1.0 H C:THR192 4.7 45.1 1.0 HG3 C:GLU114 4.7 46.2 1.0 N C:GLY193 4.8 47.9 1.0 HB3 C:ASN246 4.8 48.3 1.0 HZ3 C:LYS196 4.8 53.2 1.0 HG2 C:GLU114 4.8 46.2 1.0 HG1 C:THR192 4.8 45.1 1.0 HD21 C:ASN246 4.8 48.3 1.0 CD1 C:TYR191 4.8 45.4 1.0 CB C:ASN246 4.9 48.3 1.0 O C:GLU114 4.9 46.2 1.0

W.H.Chang, C.H.Wang, H.H.Lin, S.Y.Lin, S.C.Chong, Y.Y.Wu. Cryo-Em Structure of Giant Freshwater Prawn Macrobrachium Rosenbergii Nodavirus (Mrnv) Full Vlp To Be Published.