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

The binding sites of Calcium atom in the Cryo-Em Structure of Giant Freshwater Prawn Macrobrachium Rosenbergii Nodavirus (Mrnv) Semi-Empty Vlp (pdb code 6jjc). 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) Semi-Empty Vlp, PDB code: 6jjc:
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) Semi-Empty 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) Semi-Empty Vlp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:48.8 occ:1.00 OE2 A:GLU114 2.2 29.6 1.0 OD2 C:ASP147 2.7 36.8 1.0 HE22 A:GLN244 2.8 31.2 1.0 OD2 C:ASP144 2.8 32.2 1.0 OD1 C:ASP147 3.1 36.8 1.0 OD1 A:ASN246 3.1 33.8 1.0 CG C:ASP147 3.2 36.8 1.0 CD A:GLU114 3.3 29.6 1.0 NE2 A:GLN244 3.4 31.2 1.0 HE21 A:GLN244 3.5 31.2 1.0 CG A:ASN246 3.7 33.8 1.0 HZ2 A:LYS196 3.8 38.1 1.0 HB3 C:ASP144 3.8 32.2 1.0 H A:GLY193 3.8 33.4 1.0 HA3 A:GLY193 3.8 33.4 1.0 OE1 A:GLU114 3.8 29.6 1.0 CG C:ASP144 3.8 32.2 1.0 HD2 A:TYR191 3.9 29.3 1.0 HA A:GLU114 4.0 29.6 1.0 HD22 A:ASN246 4.1 33.8 1.0 HB2 C:ASP144 4.1 32.2 1.0 HH21 C:ARG200 4.1 31.9 1.0 CB C:ASP144 4.2 32.2 1.0 ND2 A:ASN246 4.2 33.8 1.0 HG3 A:GLU114 4.3 29.6 1.0 HB3 A:ASN246 4.3 33.8 1.0 N A:GLY193 4.3 33.4 1.0 HB3 A:TYR191 4.4 29.3 1.0 CG A:GLU114 4.4 29.6 1.0 H A:THR192 4.4 29.0 1.0 HH22 C:ARG200 4.5 31.9 1.0 CA A:CA405 4.5 51.1 1.0 CA A:GLY193 4.5 33.4 1.0 O A:GLU114 4.6 29.6 1.0 NH2 C:ARG200 4.6 31.9 1.0 CB A:ASN246 4.6 33.8 1.0 NZ A:LYS196 4.6 38.1 1.0 CD A:GLN244 4.7 31.2 1.0 CD2 A:TYR191 4.7 29.3 1.0 CB C:ASP147 4.7 36.8 1.0 HA2 A:GLY193 4.8 33.4 1.0 OG1 A:THR192 4.8 29.0 1.0 CA A:GLU114 4.8 29.6 1.0 HD21 A:ASN246 4.9 33.8 1.0 HA A:ASN246 4.9 33.8 1.0 HZ1 A:LYS196 5.0 38.1 1.0 OD1 C:ASP144 5.0 32.2 1.0 HZ3 A:LYS196 5.0 38.1 1.0 HB2 C:ASP147 5.0 36.8 1.0 HE3 A:LYS196 5.0 38.1 1.0

Calcium binding site 2 out of 7 in the Cryo-Em Structure of Giant Freshwater Prawn Macrobrachium Rosenbergii Nodavirus (Mrnv) Semi-Empty 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) Semi-Empty Vlp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:48.5 occ:1.00 OD1 A:ASP142 1.8 32.5 1.0 OE1 B:GLN244 2.0 30.4 1.0 OD2 A:ASP142 2.2 32.5 1.0 CG A:ASP142 2.2 32.5 1.0 OD2 A:ASP147 2.8 35.9 1.0 OE2 B:GLU114 2.9 28.6 1.0 CD B:GLN244 3.1 30.4 1.0 HE22 A:GLN165 3.1 33.5 1.0 HB2 A:ASP147 3.4 35.9 1.0 HB3 A:ASP147 3.5 35.9 1.0 HB2 B:GLN244 3.6 30.4 1.0 HE22 B:GLN244 3.6 30.4 1.0 CG A:ASP147 3.6 35.9 1.0 CB A:ASP147 3.7 35.9 1.0 CB A:ASP142 3.7 32.5 1.0 NE2 B:GLN244 3.7 30.4 1.0 NE2 A:GLN165 3.8 33.5 1.0 CD B:GLU114 3.8 28.6 1.0 HB3 A:ASP144 3.8 31.9 1.0 HE21 A:GLN165 3.9 33.5 1.0 HB3 A:ASP142 4.1 32.5 1.0 HA A:ASP142 4.1 32.5 1.0 CG B:GLN244 4.2 30.4 1.0 H A:ASP144 4.2 31.9 1.0 CB B:GLN244 4.2 30.4 1.0 HB2 A:ASP142 4.2 32.5 1.0 HB3 B:GLN244 4.3 30.4 1.0 HG2 B:GLU114 4.3 28.6 1.0 CA A:ASP142 4.5 32.5 1.0 HG3 B:GLN244 4.5 30.4 1.0 OE1 B:GLU114 4.5 28.6 1.0 HE21 B:GLN244 4.6 30.4 1.0 CG B:GLU114 4.6 28.6 1.0 O B:ILE245 4.7 32.8 1.0 O A:ASP144 4.7 31.9 1.0 H A:THR143 4.7 30.9 1.0 CB A:ASP144 4.8 31.9 1.0 CA A:CA403 4.8 46.5 1.0 OD1 A:ASP147 4.8 35.9 1.0 OD1 B:ASN246 4.8 32.8 1.0 HG3 B:GLU114 4.9 28.6 1.0 HG2 B:GLN244 4.9 30.4 1.0 HE2 A:TYR140 4.9 34.0 1.0 N A:ASP144 4.9 31.9 1.0 H B:ILE245 4.9 32.8 1.0 CD A:GLN165 5.0 33.5 1.0

Calcium binding site 3 out of 7 in the Cryo-Em Structure of Giant Freshwater Prawn Macrobrachium Rosenbergii Nodavirus (Mrnv) Semi-Empty 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) Semi-Empty Vlp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:46.5 occ:1.00 OD2 A:ASP147 2.3 35.9 1.0 HE22 B:GLN244 2.3 30.4 1.0 OD2 A:ASP144 2.6 31.9 1.0 OD1 A:ASP147 2.7 35.9 1.0 OD1 B:ASN246 2.8 32.8 1.0 CG A:ASP147 2.8 35.9 1.0 OE1 B:GLU114 2.9 28.6 1.0 NE2 B:GLN244 3.1 30.4 1.0 HB3 A:ASP144 3.4 31.9 1.0 HE21 B:GLN244 3.4 30.4 1.0 H B:GLY193 3.5 35.6 1.0 CG A:ASP144 3.5 31.9 1.0 HD2 B:TYR191 3.7 28.5 1.0 HB2 A:ASP144 3.7 31.9 1.0 CG B:ASN246 3.8 32.8 1.0 CB A:ASP144 3.8 31.9 1.0 CD B:GLU114 3.8 28.6 1.0 HZ3 B:LYS196 3.9 37.1 1.0 HA3 B:GLY193 3.9 35.6 1.0 HZ2 B:LYS196 3.9 37.1 1.0 HA B:GLU114 4.1 28.6 1.0 HH21 A:ARG200 4.1 31.6 1.0 OE2 B:GLU114 4.1 28.6 1.0 HG1 B:THR192 4.1 28.6 1.0 HB3 B:TYR191 4.2 28.5 1.0 HD22 B:ASN246 4.2 32.8 1.0 CD B:GLN244 4.2 30.4 1.0 NZ B:LYS196 4.2 37.1 1.0 N B:GLY193 4.3 35.6 1.0 H B:THR192 4.3 28.6 1.0 CB A:ASP147 4.3 35.9 1.0 ND2 B:ASN246 4.4 32.8 1.0 HZ1 B:LYS196 4.4 37.1 1.0 HH22 A:ARG200 4.4 31.6 1.0 OE1 B:GLN244 4.4 30.4 1.0 NH2 A:ARG200 4.5 31.6 1.0 CA B:GLY193 4.5 35.6 1.0 CD2 B:TYR191 4.5 28.5 1.0 HB2 A:ASP147 4.6 35.9 1.0 OG1 B:THR192 4.6 28.6 1.0 HB3 B:ASN246 4.6 32.8 1.0 OD1 A:ASP144 4.7 31.9 1.0 HA B:ASN246 4.8 32.8 1.0 CB B:ASN246 4.8 32.8 1.0 CA A:CA402 4.8 48.5 1.0 HB3 A:ASP147 4.8 35.9 1.0 O B:GLU114 4.8 28.6 1.0 H A:ASP147 4.8 35.9 1.0 HA2 B:GLY193 4.8 35.6 1.0 CA B:GLU114 4.9 28.6 1.0

Calcium binding site 4 out of 7 in the Cryo-Em Structure of Giant Freshwater Prawn Macrobrachium Rosenbergii Nodavirus (Mrnv) Semi-Empty 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) Semi-Empty Vlp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:85.8 occ:1.00 OE1 A:GLN188 2.7 30.7 1.0 OD1 B:ASP187 2.7 32.9 1.0 OE1 C:GLN188 3.0 32.1 1.0 OE1 B:GLN188 3.1 31.0 1.0 OD1 A:ASP187 3.1 32.8 1.0 O B:ASP186 3.4 32.7 1.0 O A:ASP186 3.6 32.5 1.0 O C:ASP186 3.6 33.7 1.0 HA A:GLN188 3.7 30.7 1.0 HA B:GLN188 3.7 31.0 1.0 CD A:GLN188 3.8 30.7 1.0 OD1 C:ASP187 3.8 34.6 1.0 CG B:ASP187 3.8 32.9 1.0 HB2 A:ASP186 3.8 32.5 1.0 HB2 A:GLN188 3.9 30.7 1.0 HB2 C:ASP186 3.9 33.7 1.0 HA C:GLN188 4.1 32.1 1.0 CD B:GLN188 4.1 31.0 1.0 OD2 C:ASP186 4.1 33.7 1.0 CD C:GLN188 4.2 32.1 1.0 OD2 B:ASP187 4.2 32.9 1.0 CG A:ASP187 4.3 32.8 1.0 CA A:GLN188 4.3 30.7 1.0 N A:GLN188 4.3 30.7 1.0 OD2 A:ASP186 4.4 32.5 1.0 HE22 A:GLN188 4.4 30.7 1.0 H A:GLN188 4.4 30.7 1.0 HB2 B:GLN188 4.4 31.0 1.0 HB2 B:ASP186 4.4 32.7 1.0 CB A:GLN188 4.5 30.7 1.0 C A:ASP186 4.5 32.5 1.0 CA B:GLN188 4.5 31.0 1.0 NE2 A:GLN188 4.5 30.7 1.0 C B:ASP186 4.5 32.7 1.0 HB2 C:GLN188 4.6 32.1 1.0 N B:GLN188 4.6 31.0 1.0 CB A:ASP186 4.6 32.5 1.0 HE22 B:GLN188 4.6 31.0 1.0 C B:ASP187 4.7 32.9 1.0 HE22 C:GLN188 4.7 32.1 1.0 CG A:ASP186 4.7 32.5 1.0 O B:ASP187 4.7 32.9 1.0 C A:ASP187 4.7 32.8 1.0 CG A:GLN188 4.7 30.7 1.0 C C:ASP186 4.7 33.7 1.0 CB C:ASP186 4.8 33.7 1.0 OD2 B:ASP186 4.8 32.7 1.0 OD2 A:ASP187 4.8 32.8 1.0 NE2 B:GLN188 4.8 31.0 1.0 CG C:ASP186 4.8 33.7 1.0 CB B:GLN188 4.9 31.0 1.0 CA C:GLN188 4.9 32.1 1.0 NE2 C:GLN188 4.9 32.1 1.0

Calcium binding site 5 out of 7 in the Cryo-Em Structure of Giant Freshwater Prawn Macrobrachium Rosenbergii Nodavirus (Mrnv) Semi-Empty 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) Semi-Empty Vlp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:51.1 occ:1.00 OE1 A:GLN244 1.9 31.2 1.0 OD1 C:ASP142 2.4 32.8 1.0 OD2 C:ASP142 2.5 32.8 1.0 OD2 C:ASP147 2.5 36.8 1.0 HE22 A:GLN244 2.6 31.2 1.0 OE1 A:GLU114 2.7 29.6 1.0 CD A:GLN244 2.7 31.2 1.0 CG C:ASP142 2.8 32.8 1.0 NE2 A:GLN244 2.9 31.2 1.0 CG C:ASP147 3.4 36.8 1.0 HB2 C:ASP147 3.5 36.8 1.0 HB3 C:ASP147 3.6 36.8 1.0 HE21 C:GLN161 3.7 38.7 1.0 CD A:GLU114 3.7 29.6 1.0 CB C:ASP147 3.7 36.8 1.0 HE21 A:GLN244 3.8 31.2 1.0 HB3 C:ASP144 3.9 32.2 1.0 HB2 A:GLN244 4.0 31.2 1.0 CG A:GLN244 4.0 31.2 1.0 OE2 A:GLU114 4.1 29.6 1.0 OD1 A:ASN246 4.1 33.8 1.0 HE22 C:GLN165 4.1 34.9 1.0 HE22 C:GLN161 4.2 38.7 1.0 CB C:ASP142 4.3 32.8 1.0 HG3 A:GLN244 4.3 31.2 1.0 NE2 C:GLN161 4.3 38.7 1.0 HE21 C:GLN165 4.4 34.9 1.0 CB A:GLN244 4.4 31.2 1.0 OD1 C:ASP147 4.4 36.8 1.0 HA A:ASN246 4.4 33.8 1.0 CA A:CA401 4.5 48.8 1.0 HB3 A:GLN244 4.5 31.2 1.0 HD3 A:PRO247 4.5 40.2 1.0 HB2 C:ASP142 4.5 32.8 1.0 NE2 C:GLN165 4.6 34.9 1.0 HB2 A:GLU114 4.6 29.6 1.0 HG2 A:GLN244 4.7 31.2 1.0 H C:ASP144 4.7 32.2 1.0 O A:ILE245 4.7 33.6 1.0 HB3 C:ASP142 4.7 32.8 1.0 HA C:ASP142 4.7 32.8 1.0 CB C:ASP144 4.8 32.2 1.0 HB2 C:ASP144 4.9 32.2 1.0 HE2 C:TYR140 4.9 34.5 1.0 CG A:GLU114 5.0 29.6 1.0

Calcium binding site 6 out of 7 in the Cryo-Em Structure of Giant Freshwater Prawn Macrobrachium Rosenbergii Nodavirus (Mrnv) Semi-Empty 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) Semi-Empty Vlp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:49.5 occ:1.00 OE1 C:GLN244 1.9 31.8 1.0 OD1 B:ASP142 2.0 33.2 1.0 OD2 B:ASP142 2.1 33.2 1.0 CG B:ASP142 2.3 33.2 1.0 OD2 B:ASP147 2.8 35.3 1.0 CD C:GLN244 2.8 31.8 1.0 HE22 C:GLN244 3.2 31.8 1.0 HB2 B:ASP147 3.4 35.3 1.0 NE2 C:GLN244 3.4 31.8 1.0 HE22 B:GLN165 3.4 34.1 1.0 HB2 C:GLN244 3.5 31.8 1.0 HB3 B:ASP147 3.5 35.3 1.0 HB3 B:ASP144 3.6 32.5 1.0 CG B:ASP147 3.6 35.3 1.0 HE21 B:GLN165 3.7 34.1 1.0 CB B:ASP147 3.7 35.3 1.0 CB B:ASP142 3.8 33.2 1.0 NE2 B:GLN165 3.9 34.1 1.0 CG C:GLN244 3.9 31.8 1.0 HB2 B:ASP144 4.0 32.5 1.0 CB C:GLN244 4.1 31.8 1.0 OE1 C:GLU114 4.1 30.6 1.0 HB3 C:GLN244 4.2 31.8 1.0 H B:ASP144 4.2 32.5 1.0 HE21 C:GLN244 4.2 31.8 1.0 HB2 B:ASP142 4.2 33.2 1.0 HB3 B:ASP142 4.3 33.2 1.0 HG3 C:GLN244 4.3 31.8 1.0 CB B:ASP144 4.3 32.5 1.0 OD1 C:ASN246 4.3 33.4 1.0 HA B:ASP142 4.3 33.2 1.0 CA B:CA402 4.4 48.1 1.0 HG2 C:GLU114 4.4 30.6 1.0 CD C:GLU114 4.6 30.6 1.0 HB2 C:GLU114 4.6 30.6 1.0 HA C:ASN246 4.6 33.4 1.0 CA B:ASP142 4.6 33.2 1.0 HG2 C:GLN244 4.7 31.8 1.0 O C:ILE245 4.8 32.7 1.0 OD1 B:ASP147 4.8 35.3 1.0 H C:ILE245 4.8 32.7 1.0 HD3 C:PRO247 4.8 38.7 1.0 N B:ASP144 4.9 32.5 1.0 CG C:GLU114 4.9 30.6 1.0

Calcium binding site 7 out of 7 in the Cryo-Em Structure of Giant Freshwater Prawn Macrobrachium Rosenbergii Nodavirus (Mrnv) Semi-Empty 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) Semi-Empty Vlp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:48.1 occ:1.00 OE1 C:GLU114 2.1 30.6 1.0 HE22 C:GLN244 2.2 31.8 1.0 OD2 B:ASP147 2.2 35.3 1.0 OD2 B:ASP144 2.4 32.5 1.0 OD1 C:ASN246 2.5 33.4 1.0 OE2 C:GLU114 2.6 30.6 1.0 CD C:GLU114 2.7 30.6 1.0 CG B:ASP147 2.9 35.3 1.0 OD1 B:ASP147 2.9 35.3 1.0 NE2 C:GLN244 3.0 31.8 1.0 HE21 C:GLN244 3.3 31.8 1.0 CG B:ASP144 3.3 32.5 1.0 HB2 B:ASP144 3.4 32.5 1.0 CG C:ASN246 3.5 33.4 1.0 HD22 C:ASN246 3.6 33.4 1.0 HB3 B:ASP144 3.7 32.5 1.0 CB B:ASP144 3.7 32.5 1.0 ND2 C:ASN246 3.9 33.4 1.0 HG1 C:THR192 3.9 31.3 1.0 H C:GLY193 4.0 34.4 1.0 HH21 B:ARG200 4.0 31.9 1.0 HA C:GLU114 4.0 30.6 1.0 CD C:GLN244 4.1 31.8 1.0 HD1 C:TYR191 4.1 29.9 1.0 CG C:GLU114 4.2 30.6 1.0 OE1 C:GLN244 4.3 31.8 1.0 CB B:ASP147 4.3 35.3 1.0 OD1 B:ASP144 4.4 32.5 1.0 CA B:CA401 4.4 49.5 1.0 HH22 B:ARG200 4.4 31.9 1.0 OG1 C:THR192 4.4 31.3 1.0 HG2 C:GLU114 4.5 30.6 1.0 NH2 B:ARG200 4.5 31.9 1.0 HB2 B:ASP147 4.5 35.3 1.0 H C:THR192 4.6 31.3 1.0 HA3 C:GLY193 4.6 34.4 1.0 O C:GLU114 4.7 30.6 1.0 HB3 C:TYR191 4.7 29.9 1.0 HG3 C:GLU114 4.7 30.6 1.0 HD21 C:ASN246 4.7 33.4 1.0 CB C:ASN246 4.7 33.4 1.0 HB3 C:ASN246 4.8 33.4 1.0 N C:GLY193 4.8 34.4 1.0 CA C:GLU114 4.8 30.6 1.0 HB3 B:ASP147 4.8 35.3 1.0 H B:ASP147 4.8 35.3 1.0 HA C:ASN246 4.8 33.4 1.0 CB C:GLU114 4.9 30.6 1.0 HB2 C:GLU114 4.9 30.6 1.0 CD1 C:TYR191 4.9 29.9 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) Semi-Empty Vlp To Be Published.