Calcium in PDB 6h2b: Structure of the Macrobrachium Rosenbergii Nodavirus

The binding sites of Calcium atom in the Structure of the Macrobrachium Rosenbergii Nodavirus (pdb code 6h2b). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of the Macrobrachium Rosenbergii Nodavirus, PDB code: 6h2b:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Structure of the Macrobrachium Rosenbergii Nodavirus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Macrobrachium Rosenbergii Nodavirus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:30.0 occ:1.00 OD2 A:ASP144 2.1 41.5 1.0 OD1 B:ASN246 2.3 45.2 1.0 OD1 A:ASP147 2.4 48.2 1.0 HB3 A:ASP144 2.5 41.5 1.0 OD2 A:ASP147 2.5 48.2 1.0 CG A:ASP147 2.8 48.2 1.0 HB2 A:ASP144 2.8 41.5 1.0 CG A:ASP144 2.8 41.5 1.0 CB A:ASP144 2.8 41.5 1.0 CG B:ASN246 3.3 45.2 1.0 HD22 B:ASN246 3.4 45.2 1.0 HG3 B:GLU114 3.6 43.6 1.0 ND2 B:ASN246 3.8 45.2 1.0 OD1 A:ASP144 4.0 41.5 1.0 CB A:ASP147 4.3 48.2 1.0 CA A:CA402 4.3 34.4 1.0 HH11 A:ARG200 4.4 44.8 1.0 CA A:ASP144 4.4 41.5 1.0 HE22 B:GLN244 4.4 40.8 1.0 CG B:GLU114 4.4 43.6 1.0 OE2 B:GLU114 4.5 43.6 1.0 HG2 B:GLU114 4.5 43.6 1.0 H A:ASP147 4.6 48.2 1.0 HA B:ASN246 4.6 45.2 1.0 HB2 A:ASP147 4.6 48.2 1.0 HD1 B:TYR191 4.6 48.3 1.0 HH12 A:ARG200 4.6 44.8 1.0 HD21 B:ASN246 4.6 45.2 1.0 HE3 B:LYS196 4.6 56.4 1.0 OE1 B:GLN244 4.6 40.8 1.0 CB B:ASN246 4.7 45.2 1.0 NH1 A:ARG200 4.7 44.8 1.0 NE2 B:GLN244 4.7 40.8 1.0 H A:ASP144 4.8 41.5 1.0 HB3 A:ASP147 4.8 48.2 1.0 O A:ASP144 4.8 41.5 1.0 HA A:ASP144 4.8 41.5 1.0 HB3 B:ASN246 4.8 45.2 1.0 CD B:GLN244 4.9 40.8 1.0 OG1 B:THR192 4.9 47.4 1.0 HB3 B:TYR191 4.9 48.3 1.0 O B:THR192 4.9 47.4 1.0 CD B:GLU114 4.9 43.6 1.0 N A:ASP147 4.9 48.2 1.0 HA A:ASP147 4.9 48.2 1.0 CA A:ASP147 5.0 48.2 1.0 HA3 B:GLY193 5.0 50.8 1.0

Calcium binding site 2 out of 6 in the Structure of the Macrobrachium Rosenbergii Nodavirus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Macrobrachium Rosenbergii Nodavirus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:34.4 occ:1.00 OE1 B:GLN244 2.3 40.8 1.0 OD2 A:ASP142 2.3 38.7 1.0 OD1 A:ASP142 2.4 38.7 1.0 OD2 A:ASP147 2.4 48.2 1.0 CG A:ASP142 2.6 38.7 1.0 CD B:GLN244 3.2 40.8 1.0 HB2 B:GLN244 3.3 40.8 1.0 HG2 B:GLN244 3.4 40.8 1.0 CG A:ASP147 3.6 48.2 1.0 CG B:GLN244 3.7 40.8 1.0 HB3 A:ASP144 3.8 41.5 1.0 HB2 A:ASP147 3.8 48.2 1.0 H A:ASP144 3.9 41.5 1.0 OE1 A:GLN165 3.9 35.6 1.0 CB B:GLN244 3.9 40.8 1.0 HB3 A:ASP147 4.0 48.2 1.0 CB A:ASP147 4.1 48.2 1.0 OE2 B:GLU114 4.1 43.6 1.0 CB A:ASP142 4.1 38.7 1.0 H A:THR143 4.1 37.2 1.0 HB3 B:GLN244 4.2 40.8 1.0 O B:ILE245 4.2 39.6 1.0 NE2 B:GLN244 4.2 40.8 1.0 HG3 B:GLU114 4.2 43.6 1.0 CA A:CA401 4.3 30.0 1.0 HB2 A:ASP142 4.4 38.7 1.0 HE22 B:GLN244 4.4 40.8 1.0 CD B:GLU114 4.4 43.6 1.0 H B:ILE245 4.4 39.6 1.0 OD1 B:ASN246 4.5 45.2 1.0 CB A:ASP144 4.6 41.5 1.0 HB2 A:ASP144 4.6 41.5 1.0 OD1 A:ASP147 4.6 48.2 1.0 HA A:ASP142 4.6 38.7 1.0 HG3 B:GLN244 4.6 40.8 1.0 HA B:ASN246 4.6 45.2 1.0 HB3 A:ASP142 4.7 38.7 1.0 N A:ASP144 4.7 41.5 1.0 C B:ILE245 4.8 39.6 1.0 OE1 B:GLU114 4.8 43.6 1.0 CG B:GLU114 4.8 43.6 1.0 HE21 B:GLN244 4.9 40.8 1.0 N A:THR143 4.9 37.2 1.0 CA A:ASP142 4.9 38.7 1.0 O A:ASP144 4.9 41.5 1.0 HE22 A:GLN165 4.9 35.6 1.0 N B:ILE245 5.0 39.6 1.0 CD A:GLN165 5.0 35.6 1.0

Calcium binding site 3 out of 6 in the Structure of the Macrobrachium Rosenbergii Nodavirus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Macrobrachium Rosenbergii Nodavirus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:30.0 occ:1.00 OD2 C:ASP142 1.9 37.3 1.0 OD1 C:ASP142 2.0 37.3 1.0 CG C:ASP142 2.2 37.3 1.0 OE1 A:GLN244 2.5 32.6 1.0 OE2 A:GLU114 2.8 45.4 1.0 CD A:GLN244 3.3 32.6 1.0 CB C:ASP142 3.6 37.3 1.0 HG2 A:GLN244 3.7 32.6 1.0 H C:ASP144 3.8 43.3 1.0 HB3 C:ASP144 3.8 43.3 1.0 HB2 C:ASP142 3.8 37.3 1.0 OD2 C:ASP147 3.9 52.5 1.0 CD A:GLU114 4.0 45.4 1.0 OE1 C:GLN165 4.0 36.2 1.0 CG A:GLN244 4.0 32.6 1.0 HB2 A:GLN244 4.0 32.6 1.0 HG2 A:GLU114 4.1 45.4 1.0 HA C:ASP142 4.1 37.3 1.0 NE2 A:GLN244 4.1 32.6 1.0 HB3 C:ASP142 4.2 37.3 1.0 H C:THR143 4.2 35.5 1.0 HE22 A:GLN244 4.2 32.6 1.0 OD1 C:ASP147 4.3 52.5 1.0 CG C:ASP147 4.4 52.5 1.0 O A:ILE245 4.4 40.8 1.0 CA C:ASP142 4.4 37.3 1.0 CB A:GLN244 4.5 32.6 1.0 CG A:GLU114 4.5 45.4 1.0 N C:ASP144 4.6 43.3 1.0 CB C:ASP144 4.6 43.3 1.0 HA A:ASN246 4.6 41.8 1.0 HB2 C:ASP144 4.7 43.3 1.0 HG3 A:GLU114 4.7 45.4 1.0 OD1 A:ASN246 4.7 41.8 1.0 N C:THR143 4.7 35.5 1.0 HB3 A:GLN244 4.7 32.6 1.0 O C:ASP144 4.7 43.3 1.0 CA C:CA402 4.8 30.0 1.0 HE21 A:GLN244 4.8 32.6 1.0 HG3 A:GLN244 4.8 32.6 1.0 HE2 C:TYR140 4.9 35.4 1.0 O C:ASP147 4.9 52.5 1.0 C C:ASP142 5.0 37.3 1.0 OE1 A:GLU114 5.0 45.4 1.0 H A:ILE245 5.0 40.8 1.0

Calcium binding site 4 out of 6 in the Structure of the Macrobrachium Rosenbergii Nodavirus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Macrobrachium Rosenbergii Nodavirus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:21.1 occ:1.00 OE2 C:GLU114 2.3 34.6 1.0 OD1 B:ASP142 2.4 35.4 1.0 OD2 B:ASP142 2.4 35.4 1.0 OE1 C:GLN244 2.5 31.6 1.0 CG B:ASP142 2.7 35.4 1.0 CD C:GLN244 3.2 31.6 1.0 OD2 B:ASP147 3.3 45.3 1.0 HG2 C:GLN244 3.4 31.6 1.0 HB2 B:ASP147 3.6 45.3 1.0 CD C:GLU114 3.6 34.6 1.0 OE1 B:GLN165 3.7 34.6 1.0 HB2 C:GLN244 3.7 31.6 1.0 HB3 B:ASP144 3.7 38.9 1.0 HB3 B:ASP147 3.7 45.3 1.0 CG C:GLN244 3.8 31.6 1.0 CB B:ASP147 4.0 45.3 1.0 CG B:ASP147 4.1 45.3 1.0 OD1 C:ASN246 4.1 41.2 1.0 NE2 C:GLN244 4.1 31.6 1.0 CB B:ASP142 4.2 35.4 1.0 HE22 C:GLN244 4.2 31.6 1.0 CB C:GLN244 4.2 31.6 1.0 HG2 C:GLU114 4.3 34.6 1.0 OE1 C:GLU114 4.4 34.6 1.0 HA C:ASN246 4.4 41.2 1.0 CG C:GLU114 4.4 34.6 1.0 HB2 B:ASP142 4.5 35.4 1.0 HB3 C:GLN244 4.5 31.6 1.0 H C:ILE245 4.5 35.0 1.0 HG3 C:GLU114 4.5 34.6 1.0 CB B:ASP144 4.6 38.9 1.0 HB2 B:ASP144 4.6 38.9 1.0 HA B:ASP142 4.6 35.4 1.0 HG3 C:GLN244 4.7 31.6 1.0 HB3 B:ASP142 4.7 35.4 1.0 HE21 C:GLN244 4.7 31.6 1.0 H B:ASP144 4.8 38.9 1.0 O C:ILE245 4.8 35.0 1.0 CG C:ASN246 4.8 41.2 1.0 CD B:GLN165 4.8 34.6 1.0 CA C:CA401 4.9 30.0 1.0 CA B:ASP142 5.0 35.4 1.0 H B:THR143 5.0 33.7 1.0

Calcium binding site 5 out of 6 in the Structure of the Macrobrachium Rosenbergii Nodavirus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Macrobrachium Rosenbergii Nodavirus within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:30.0 occ:1.00 HD22 C:ASN246 1.9 41.2 1.0 OD2 B:ASP147 2.0 45.3 1.0 OD2 B:ASP144 2.0 38.9 1.0 OD1 B:ASP147 2.3 45.3 1.0 OD1 C:ASN246 2.4 41.2 1.0 OE1 C:GLU114 2.4 34.6 1.0 CG B:ASP147 2.5 45.3 1.0 ND2 C:ASN246 2.5 41.2 1.0 CG C:ASN246 2.8 41.2 1.0 CG B:ASP144 3.2 38.9 1.0 CD C:GLU114 3.3 34.6 1.0 HD21 C:ASN246 3.3 41.2 1.0 OE2 C:GLU114 3.4 34.6 1.0 HB3 B:ASP144 3.7 38.9 1.0 CB B:ASP144 3.9 38.9 1.0 HB2 B:ASP144 3.9 38.9 1.0 CB B:ASP147 4.0 45.3 1.0 O C:THR192 4.0 38.9 1.0 HH11 B:ARG200 4.1 42.7 1.0 HE22 C:GLN244 4.1 31.6 1.0 HH12 B:ARG200 4.1 42.7 1.0 HA C:GLU114 4.2 34.6 1.0 OD1 B:ASP144 4.2 38.9 1.0 HB2 B:ASP147 4.3 45.3 1.0 CB C:ASN246 4.3 41.2 1.0 HB3 B:ASP147 4.3 45.3 1.0 NH1 B:ARG200 4.4 42.7 1.0 OG1 C:THR192 4.4 38.9 1.0 HB3 C:ASN246 4.5 41.2 1.0 NE2 C:GLN244 4.6 31.6 1.0 HB3 C:TYR191 4.7 41.7 1.0 HZ1 C:LYS196 4.7 59.2 1.0 H C:THR192 4.7 38.9 1.0 CG C:GLU114 4.7 34.6 1.0 HB2 C:ASN246 4.7 41.2 1.0 HB3 C:GLU114 4.8 34.6 1.0 C C:THR192 4.8 38.9 1.0 HA3 C:GLY193 4.8 42.6 1.0 HE21 C:GLN244 4.9 31.6 1.0 HA B:ASP147 4.9 45.3 1.0 CA B:CA401 4.9 21.1 1.0 HG1 C:THR192 4.9 38.9 1.0 HA C:ASN246 4.9 41.2 1.0 CA B:ASP147 4.9 45.3 1.0 H B:ASP147 5.0 45.3 1.0

Calcium binding site 6 out of 6 in the Structure of the Macrobrachium Rosenbergii Nodavirus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Macrobrachium Rosenbergii Nodavirus within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca402 b:30.0 occ:1.00 OD2 C:ASP147 2.1 52.5 1.0 OD1 A:ASN246 2.2 41.8 1.0 OD2 C:ASP144 2.2 43.3 1.0 O A:THR192 2.7 47.3 1.0 CG C:ASP147 2.7 52.5 1.0 HB3 C:ASP144 2.8 43.3 1.0 HB2 C:ASP144 2.9 43.3 1.0 CG C:ASP144 3.0 43.3 1.0 OD1 C:ASP147 3.0 52.5 1.0 CB C:ASP144 3.0 43.3 1.0 CG A:ASN246 3.2 41.8 1.0 HD22 A:ASN246 3.4 41.8 1.0 HG2 A:GLU114 3.6 45.4 1.0 ND2 A:ASN246 3.7 41.8 1.0 HB3 C:ASP147 3.8 52.5 1.0 CB C:ASP147 3.9 52.5 1.0 C A:THR192 3.9 47.3 1.0 H A:THR192 4.1 47.3 1.0 HE22 A:GLN244 4.1 32.6 1.0 OD1 C:ASP144 4.2 43.3 1.0 HA A:GLU114 4.2 45.4 1.0 HA3 A:GLY193 4.3 48.6 1.0 HB2 C:ASP147 4.3 52.5 1.0 HE2 A:LYS196 4.3 58.9 1.0 CG A:GLU114 4.4 45.4 1.0 H C:ASP147 4.4 52.5 1.0 HB3 A:GLU114 4.4 45.4 1.0 HH11 C:ARG200 4.5 43.3 1.0 CB A:ASN246 4.5 41.8 1.0 NE2 A:GLN244 4.6 32.6 1.0 CA C:ASP144 4.6 43.3 1.0 HA A:ASN246 4.6 41.8 1.0 HD21 A:ASN246 4.6 41.8 1.0 HB3 A:ASN246 4.6 41.8 1.0 HB3 A:TYR191 4.7 48.3 1.0 HD1 A:TYR191 4.7 48.3 1.0 CD A:GLU114 4.7 45.4 1.0 HB A:THR192 4.8 47.3 1.0 N A:THR192 4.8 47.3 1.0 OE2 A:GLU114 4.8 45.4 1.0 CA A:CA403 4.8 30.0 1.0 HH12 C:ARG200 4.8 43.3 1.0 CB A:GLU114 4.8 45.4 1.0 N A:GLY193 4.8 48.6 1.0 HE21 A:GLN244 4.9 32.6 1.0 NH1 C:ARG200 4.9 43.3 1.0 CA A:THR192 4.9 47.3 1.0 HA C:ASP144 5.0 43.3 1.0 CA A:GLY193 5.0 48.6 1.0 CA A:GLU114 5.0 45.4 1.0

K.L.Ho, M.Gabrielsen, P.L.Beh, C.L.Kueh, Q.X.Thong, J.Streetley, W.S.Tan, D.Bhella. Structure of the Macrobrachium Rosenbergii Nodavirus: A New Genus Within the Nodaviridae? Plos Biol. V. 16 00038 2018.
ISSN: ESSN 1545-7885
PubMed: 30346944
DOI: 10.1371/JOURNAL.PBIO.3000038