Calcium in PDB 5vf4: Thermus Aquaticus Variable Protein (Taqvp) From Diversity-Generating Retroelements (Dgr)

The structure of Thermus Aquaticus Variable Protein (Taqvp) From Diversity-Generating Retroelements (Dgr), PDB code: 5vf4 was solved by S.Handa, P.Ghosh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.81 / 2.81
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	155.039, 155.039, 202.394, 90.00, 90.00, 120.00
R / Rfree (%)	17.8 / 22.9

The binding sites of Calcium atom in the Thermus Aquaticus Variable Protein (Taqvp) From Diversity-Generating Retroelements (Dgr) (pdb code 5vf4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Thermus Aquaticus Variable Protein (Taqvp) From Diversity-Generating Retroelements (Dgr), PDB code: 5vf4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Thermus Aquaticus Variable Protein (Taqvp) From Diversity-Generating Retroelements (Dgr)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermus Aquaticus Variable Protein (Taqvp) From Diversity-Generating Retroelements (Dgr) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:77.5 occ:1.00 O A:SER264 2.3 1.0 1.0 O A:THR268 2.4 97.9 1.0 OD1 A:ASP295 2.5 99.3 1.0 OD2 A:ASP295 2.6 90.1 1.0 OE1 A:GLN270 2.6 80.1 1.0 OD1 A:ASP266 2.6 93.7 1.0 CG A:ASP295 2.8 93.4 1.0 OG A:SER264 2.9 76.3 1.0 C A:SER264 3.4 95.8 1.0 CG A:ASP266 3.5 88.1 1.0 C A:THR268 3.6 90.5 1.0 CD A:GLN270 3.6 81.5 1.0 N A:ASP266 3.9 92.5 1.0 CB A:SER264 4.0 78.3 1.0 N A:THR268 4.0 91.9 1.0 OD2 A:ASP266 4.0 90.8 1.0 NE2 A:GLN270 4.0 81.3 1.0 CA A:SER264 4.1 85.6 1.0 CA A:THR268 4.3 86.3 1.0 CB A:ASP295 4.3 87.2 1.0 N A:SER264 4.3 86.6 1.0 OE1 A:GLN294 4.4 76.1 1.0 N A:ASN265 4.5 90.9 1.0 N A:ILE269 4.6 82.5 1.0 N A:ASN267 4.6 86.1 1.0 N A:GLN270 4.6 65.6 1.0 CA A:ASP266 4.7 88.0 1.0 CB A:ASP266 4.7 83.5 1.0 CA A:ASN265 4.7 89.3 1.0 N A:ASP295 4.7 78.2 1.0 CB A:THR268 4.7 71.0 1.0 CA A:ILE269 4.7 70.3 1.0 C A:ASP266 4.8 86.9 1.0 C A:ASN265 4.8 87.7 1.0 CH2 A:TRP288 4.8 90.1 1.0 CG A:GLN270 4.9 76.3 1.0 CA A:ASP295 5.0 81.2 1.0 CB A:GLN270 5.0 76.1 1.0

Calcium binding site 2 out of 8 in the Thermus Aquaticus Variable Protein (Taqvp) From Diversity-Generating Retroelements (Dgr)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermus Aquaticus Variable Protein (Taqvp) From Diversity-Generating Retroelements (Dgr) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:63.8 occ:1.00 O A:VAL198 2.5 49.3 1.0 O A:LEU194 2.7 41.8 1.0 O A:GLY196 2.7 55.7 1.0 O A:ASP193 2.8 56.7 1.0 OE2 A:GLU200 3.1 63.4 1.0 C A:LEU194 3.4 48.2 1.0 O A:GLY347 3.7 50.7 1.0 C A:VAL198 3.7 45.5 1.0 N A:GLY196 3.8 37.6 1.0 C A:GLY196 3.8 46.6 1.0 CD A:GLU200 3.9 59.5 1.0 C A:ASP193 3.9 53.3 1.0 CA A:LEU194 4.0 45.9 1.0 N A:VAL195 4.1 52.9 1.0 C A:VAL195 4.1 42.3 1.0 N A:VAL198 4.2 32.1 1.0 CG A:GLU200 4.3 49.1 1.0 CA A:GLY196 4.3 37.0 1.0 CA A:VAL195 4.4 40.0 1.0 CA A:GLY346 4.4 49.0 1.0 O A:ARG345 4.4 51.1 1.0 N A:LEU194 4.4 48.0 1.0 C A:GLY346 4.5 48.3 1.0 NH2 A:ARG376 4.6 50.8 1.0 CA A:VAL198 4.6 34.8 1.0 N A:TRP199 4.6 44.0 1.0 O A:GLY346 4.7 47.5 1.0 CA A:TRP199 4.7 48.9 1.0 O A:VAL195 4.7 50.1 1.0 OE1 A:GLU200 4.8 63.4 1.0 C A:TRP199 4.8 56.4 1.0 C A:GLY347 4.9 51.8 1.0 N A:GLY347 4.9 47.4 1.0 CH2 A:TRP117 4.9 66.2 1.0 N A:ASN197 4.9 49.7 1.0 CG2 A:VAL198 4.9 43.1 1.0 N A:GLU200 5.0 59.3 1.0

Calcium binding site 3 out of 8 in the Thermus Aquaticus Variable Protein (Taqvp) From Diversity-Generating Retroelements (Dgr)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermus Aquaticus Variable Protein (Taqvp) From Diversity-Generating Retroelements (Dgr) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:46.9 occ:1.00 O B:VAL198 2.6 41.3 1.0 O B:GLY196 2.7 24.9 1.0 O B:LEU194 2.9 26.6 1.0 O B:ASP193 2.9 36.9 1.0 OE2 B:GLU200 3.1 42.1 1.0 C B:LEU194 3.4 26.0 1.0 O B:GLY347 3.6 29.5 1.0 C B:VAL198 3.7 27.2 1.0 N B:GLY196 3.7 29.3 1.0 C B:GLY196 3.8 30.9 1.0 CD B:GLU200 3.8 37.0 1.0 C B:ASP193 4.0 31.1 1.0 CA B:LEU194 4.1 22.8 1.0 C B:VAL195 4.1 27.2 1.0 N B:VAL195 4.1 28.0 1.0 CG B:GLU200 4.2 29.6 1.0 N B:VAL198 4.3 24.4 1.0 O B:ARG345 4.3 27.6 1.0 C B:GLY346 4.3 30.1 1.0 CA B:GLY346 4.3 27.9 1.0 CA B:GLY196 4.3 15.5 1.0 CA B:VAL195 4.4 23.2 1.0 O B:GLY346 4.4 31.2 1.0 N B:LEU194 4.5 26.2 1.0 N B:TRP199 4.5 31.5 1.0 CA B:TRP199 4.6 31.3 1.0 CA B:VAL198 4.6 24.1 1.0 C B:GLY347 4.7 28.2 1.0 C B:TRP199 4.7 34.3 1.0 O B:VAL195 4.7 28.4 1.0 N B:GLY347 4.7 28.7 1.0 OE1 B:GLU200 4.7 33.4 1.0 N B:GLU200 4.9 25.3 1.0 CB B:GLU200 5.0 22.8 1.0 N B:ASN197 5.0 26.5 1.0 CG2 B:VAL198 5.0 29.5 1.0

Calcium binding site 4 out of 8 in the Thermus Aquaticus Variable Protein (Taqvp) From Diversity-Generating Retroelements (Dgr)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermus Aquaticus Variable Protein (Taqvp) From Diversity-Generating Retroelements (Dgr) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:50.2 occ:1.00 O B:SER264 2.3 59.3 1.0 O B:THR268 2.3 57.0 1.0 OD1 B:ASP295 2.5 54.2 1.0 OE1 B:GLN270 2.5 53.7 1.0 OG B:SER264 2.6 53.2 1.0 OD2 B:ASP295 2.7 55.9 1.0 OD1 B:ASP266 2.7 55.9 1.0 CG B:ASP295 2.9 53.6 1.0 C B:SER264 3.4 39.2 1.0 C B:THR268 3.5 48.0 1.0 CD B:GLN270 3.6 47.5 1.0 CG B:ASP266 3.6 49.9 1.0 CB B:SER264 3.7 44.6 1.0 N B:THR268 3.8 36.5 1.0 OD2 B:ASP266 3.9 57.7 1.0 CA B:SER264 4.0 33.0 1.0 NE2 B:GLN270 4.0 47.5 1.0 N B:ASP266 4.1 53.1 1.0 CA B:THR268 4.2 32.5 1.0 OE1 B:GLN294 4.2 42.2 1.0 N B:SER264 4.3 44.1 1.0 CB B:ASP295 4.3 50.3 1.0 N B:ILE269 4.5 40.2 1.0 N B:ASN265 4.6 39.3 1.0 N B:GLN270 4.6 35.6 1.0 N B:ASN267 4.6 53.2 1.0 CA B:ILE269 4.6 38.3 1.0 N B:ASP295 4.7 41.6 1.0 CB B:THR268 4.7 37.6 1.0 CB B:ASP266 4.8 48.6 1.0 CA B:ASP266 4.8 50.8 1.0 CA B:ASN265 4.8 40.7 1.0 CH2 B:TRP288 4.9 38.2 1.0 CG B:GLN270 4.9 24.3 1.0 C B:ASP266 4.9 47.3 1.0 CA B:ASP295 4.9 43.5 1.0 CB B:GLN270 5.0 28.8 1.0 C B:ILE269 5.0 39.2 1.0 C B:ASN265 5.0 47.2 1.0 C B:ASN267 5.0 48.0 1.0 O B:HOH541 5.0 51.5 1.0

Calcium binding site 5 out of 8 in the Thermus Aquaticus Variable Protein (Taqvp) From Diversity-Generating Retroelements (Dgr)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Thermus Aquaticus Variable Protein (Taqvp) From Diversity-Generating Retroelements (Dgr) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:48.4 occ:1.00 O C:THR268 2.3 45.4 1.0 O C:SER264 2.4 39.0 1.0 OD1 C:ASP295 2.5 41.3 1.0 OD2 C:ASP295 2.6 46.3 1.0 OD1 C:ASP266 2.7 53.4 1.0 OE1 C:GLN270 2.8 42.5 1.0 OG C:SER264 2.8 58.7 1.0 CG C:ASP295 2.9 46.6 1.0 O C:HOH524 3.4 47.5 1.0 C C:THR268 3.4 45.3 1.0 C C:SER264 3.5 38.5 1.0 CG C:ASP266 3.5 52.3 1.0 N C:THR268 3.7 47.0 1.0 CD C:GLN270 3.8 40.2 1.0 N C:ASP266 3.9 30.2 1.0 OD2 C:ASP266 3.9 61.6 1.0 CB C:SER264 4.0 59.0 1.0 CA C:THR268 4.1 44.0 1.0 CA C:SER264 4.1 42.3 1.0 NE2 C:GLN270 4.2 43.0 1.0 OE1 C:GLN294 4.3 47.0 1.0 CB C:ASP295 4.3 46.6 1.0 N C:SER264 4.4 38.0 1.0 N C:ILE269 4.4 41.5 1.0 N C:ASN267 4.5 36.9 1.0 N C:ASN265 4.6 44.9 1.0 CA C:ILE269 4.6 35.2 1.0 N C:GLN270 4.6 32.9 1.0 CA C:ASP266 4.6 34.0 1.0 CB C:ASP266 4.7 40.5 1.0 C C:ASP266 4.7 37.5 1.0 CB C:THR268 4.7 42.1 1.0 N C:ASP295 4.8 35.3 1.0 CA C:ASN265 4.8 40.9 1.0 C C:ASN265 4.8 39.9 1.0 C C:ASN267 4.9 50.9 1.0 C C:ILE269 4.9 36.0 1.0 CH2 C:TRP288 4.9 39.8 1.0 CA C:ASP295 4.9 41.5 1.0

Calcium binding site 6 out of 8 in the Thermus Aquaticus Variable Protein (Taqvp) From Diversity-Generating Retroelements (Dgr)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Thermus Aquaticus Variable Protein (Taqvp) From Diversity-Generating Retroelements (Dgr) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca402 b:42.8 occ:1.00 O C:GLY196 2.6 25.4 1.0 O C:VAL198 2.6 34.2 1.0 O C:LEU194 2.9 30.6 1.0 O C:ASP193 3.0 35.7 1.0 OE2 C:GLU200 3.3 29.9 1.0 C C:LEU194 3.4 25.9 1.0 O C:GLY347 3.5 33.3 1.0 N C:GLY196 3.6 29.5 1.0 C C:GLY196 3.7 26.0 1.0 C C:VAL198 3.7 26.2 1.0 C C:VAL195 3.9 27.6 1.0 CD C:GLU200 4.0 31.6 1.0 C C:ASP193 4.1 24.4 1.0 N C:VAL195 4.1 18.1 1.0 CA C:GLY196 4.2 27.7 1.0 CA C:LEU194 4.2 20.5 1.0 N C:VAL198 4.2 20.6 1.0 CA C:VAL195 4.3 16.9 1.0 CA C:GLY346 4.3 23.5 1.0 C C:GLY346 4.3 31.1 1.0 CG C:GLU200 4.3 21.2 1.0 O C:GLY346 4.3 29.7 1.0 O C:ARG345 4.4 33.9 1.0 O C:VAL195 4.6 28.3 1.0 N C:TRP199 4.6 36.8 1.0 CA C:TRP199 4.6 37.2 1.0 N C:LEU194 4.6 25.8 1.0 CA C:VAL198 4.6 22.4 1.0 C C:GLY347 4.6 26.4 1.0 C C:TRP199 4.8 35.1 1.0 N C:GLY347 4.8 30.5 1.0 N C:ASN197 4.8 27.2 1.0 OE1 C:GLU200 4.9 32.1 1.0 N C:GLU200 4.9 26.8 1.0

Calcium binding site 7 out of 8 in the Thermus Aquaticus Variable Protein (Taqvp) From Diversity-Generating Retroelements (Dgr)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Thermus Aquaticus Variable Protein (Taqvp) From Diversity-Generating Retroelements (Dgr) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca403 b:58.1 occ:1.00 H1 C:ACT406 2.4 37.6 1.0 O C:HOH501 3.3 19.6 1.0 CB C:ARG370 3.4 36.1 1.0 O C:ACT404 3.4 53.5 1.0 CH3 C:ACT406 3.5 31.3 1.0 N C:GLY372 3.5 26.4 1.0 CD1 C:TRP371 3.7 29.2 1.0 CA C:GLY372 3.8 18.1 1.0 H3 C:ACT406 3.8 37.6 1.0 H2 C:ACT406 3.8 37.6 1.0 CG C:ARG370 4.1 39.9 1.0 NE1 C:TRP371 4.1 24.2 1.0 N C:TRP371 4.2 25.3 1.0 OD2 C:ASP348 4.2 31.5 1.0 C C:GLY372 4.2 26.6 1.0 CG2 C:VAL373 4.4 38.2 1.0 CA C:ARG370 4.4 23.6 1.0 CD C:ARG370 4.4 33.3 1.0 C C:ARG370 4.5 24.2 1.0 C C:ACT406 4.5 50.2 1.0 OXT C:ACT406 4.5 51.7 1.0 C C:TRP371 4.6 33.7 1.0 C C:ACT404 4.6 52.5 1.0 N C:VAL373 4.6 29.3 1.0 O C:GLY372 4.7 26.1 1.0 CG C:TRP371 4.9 25.4 1.0 CA C:TRP371 4.9 25.1 1.0

Calcium binding site 8 out of 8 in the Thermus Aquaticus Variable Protein (Taqvp) From Diversity-Generating Retroelements (Dgr)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Thermus Aquaticus Variable Protein (Taqvp) From Diversity-Generating Retroelements (Dgr) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:95.0 occ:1.00 O D:VAL198 2.5 99.8 1.0 O D:ASP193 2.8 91.5 1.0 O D:GLY196 2.8 0.5 1.0 OE2 D:GLU200 3.0 76.2 1.0 O D:LEU194 3.1 91.7 1.0 C D:LEU194 3.6 97.4 1.0 CD D:GLU200 3.7 76.2 1.0 C D:VAL198 3.7 97.2 1.0 O D:GLY347 3.8 0.6 1.0 C D:ASP193 3.9 88.5 1.0 C D:GLY196 4.0 97.1 1.0 CG D:GLU200 4.1 74.2 1.0 N D:GLY196 4.1 0.6 1.0 CA D:LEU194 4.2 88.7 1.0 N D:VAL198 4.2 99.8 1.0 N D:VAL195 4.3 0.5 1.0 C D:VAL195 4.4 0.9 1.0 N D:LEU194 4.5 91.5 1.0 CA D:VAL198 4.5 95.6 1.0 OE1 D:GLU200 4.6 73.6 1.0 O D:ARG345 4.6 88.4 1.0 CA D:GLY196 4.6 97.9 1.0 CG2 D:VAL198 4.6 90.0 1.0 CA D:VAL195 4.7 98.1 1.0 N D:TRP199 4.7 100.0 1.0 C D:TRP199 4.8 92.4 1.0 CA D:TRP199 4.8 0.7 1.0 CA D:GLY346 4.9 89.1 1.0 CB D:GLU200 4.9 77.8 1.0 C D:GLY346 4.9 95.4 1.0 O D:VAL195 5.0 0.1 1.0 CH2 D:TRP117 5.0 71.4 1.0

S.Handa, K.L.Shaw, P.Ghosh. Crystal Structure of A Thermus Aquaticus Diversity-Generating Retroelement Variable Protein. Plos One V. 14 05618 2019.
ISSN: ESSN 1932-6203
PubMed: 30629599
DOI: 10.1371/JOURNAL.PONE.0205618