Calcium in PDB 5yps: The Structural Basis of Histone CHAPERONEVPS75

The structure of The Structural Basis of Histone CHAPERONEVPS75, PDB code: 5yps was solved by Y.Chen, Y.Zhang, Y.Dou, D.Lu, W.Meilin, X.Sidan, J.Hua, A.H.Limper, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.26 / 2.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	141.672, 76.404, 130.448, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 23.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the The Structural Basis of Histone CHAPERONEVPS75 (pdb code 5yps). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the The Structural Basis of Histone CHAPERONEVPS75, PDB code: 5yps:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the The Structural Basis of Histone CHAPERONEVPS75


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structural Basis of Histone CHAPERONEVPS75 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:31.1 occ:1.00 OE2 D:GLU194 2.4 30.0 1.0 OD2 A:ASP189 2.4 35.1 1.0 O A:PHE191 2.5 28.7 1.0 O D:HOH401 2.5 28.8 1.0 OE2 A:GLU192 2.6 30.9 1.0 OD1 A:ASP189 2.7 34.5 1.0 CG A:ASP189 2.9 38.2 1.0 OE1 D:GLU194 3.0 28.7 1.0 OE2 D:GLU192 3.0 52.8 1.0 CD D:GLU194 3.0 30.6 1.0 CD A:GLU192 3.4 34.0 1.0 C A:PHE191 3.5 31.8 1.0 CG D:GLU192 3.5 35.8 1.0 CD D:GLU192 3.7 42.6 1.0 CA D:CA302 3.9 32.3 1.0 CG A:GLU192 3.9 25.8 1.0 CB A:PHE191 4.1 26.1 1.0 OE1 A:GLU192 4.2 38.9 1.0 O A:HOH409 4.2 30.9 1.0 CB D:GLU192 4.3 37.1 1.0 CA A:PHE191 4.3 25.1 1.0 N A:GLU192 4.3 28.1 1.0 CA A:GLU192 4.4 33.2 1.0 CB A:ASP189 4.4 34.1 1.0 CG D:GLU194 4.5 25.1 1.0 CA D:GLU192 4.5 30.3 1.0 N A:PHE191 4.7 32.1 1.0 CB A:GLU192 4.8 26.0 1.0 O D:PHE191 4.8 27.4 1.0 OD2 D:ASP189 4.9 33.8 1.0 OE1 D:GLU192 4.9 62.9 1.0 N D:ASP193 4.9 26.3 1.0

Calcium binding site 2 out of 12 in the The Structural Basis of Histone CHAPERONEVPS75


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structural Basis of Histone CHAPERONEVPS75 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:30.2 occ:1.00 OE1 A:GLU196 2.4 28.1 1.0 OD1 A:ASP193 2.4 23.6 1.0 O A:GLU192 2.4 31.6 1.0 OE1 A:GLU147 2.5 33.4 1.0 OD2 D:ASP193 2.5 35.2 1.0 OD1 D:ASP193 2.6 25.3 1.0 OE2 A:GLU147 2.8 43.6 1.0 CG D:ASP193 2.9 32.1 1.0 CD A:GLU147 3.0 35.4 1.0 CD A:GLU196 3.3 37.9 1.0 C A:GLU192 3.4 33.8 1.0 CG A:ASP193 3.6 31.9 1.0 OE2 A:GLU196 3.6 39.5 1.0 CA D:CA301 3.9 30.6 1.0 CA A:ASP193 3.9 31.1 1.0 N A:ASP193 4.1 28.0 1.0 CB A:ASP193 4.3 25.3 1.0 O A:HOH423 4.4 30.7 1.0 CB D:ASP193 4.5 25.1 1.0 CG A:GLU147 4.5 42.0 1.0 N A:GLU192 4.5 28.1 1.0 OD2 A:ASP193 4.5 31.7 1.0 CA A:GLU192 4.6 33.2 1.0 OH D:TYR80 4.6 26.8 1.0 CG A:GLU196 4.7 34.4 1.0

Calcium binding site 3 out of 12 in the The Structural Basis of Histone CHAPERONEVPS75


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Structural Basis of Histone CHAPERONEVPS75 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:29.5 occ:1.00 OE2 C:GLU194 2.3 30.7 1.0 O B:PHE191 2.4 27.7 1.0 OD2 B:ASP189 2.5 32.7 1.0 O C:HOH401 2.6 35.6 1.0 OD1 B:ASP189 2.8 35.6 1.0 OE1 C:GLU194 2.8 26.8 1.0 CG B:GLU192 2.8 26.5 1.0 CG C:GLU192 2.9 26.1 1.0 CD C:GLU194 2.9 33.3 1.0 CG B:ASP189 3.0 36.5 1.0 OE2 C:GLU192 3.1 53.8 1.0 C B:PHE191 3.4 28.6 1.0 CD C:GLU192 3.4 41.3 1.0 CD B:GLU192 3.8 48.3 1.0 CB C:GLU192 3.9 47.6 1.0 CA B:CA302 4.0 30.2 1.0 CB B:PHE191 4.0 29.2 1.0 CB B:GLU192 4.0 55.2 1.0 N B:GLU192 4.2 27.9 1.0 CA B:PHE191 4.2 31.1 1.0 CA B:GLU192 4.2 40.1 1.0 OE2 B:GLU192 4.3 58.8 1.0 O B:HOH401 4.3 27.6 1.0 CA C:GLU192 4.4 30.6 1.0 CG C:GLU194 4.4 22.1 1.0 OE1 B:GLU192 4.5 63.5 1.0 C1 C:GOL305 4.5 66.5 1.0 CB B:ASP189 4.5 31.3 1.0 OE1 C:GLU192 4.5 58.8 1.0 N B:PHE191 4.7 28.6 1.0 O1 C:GOL305 4.8 50.6 1.0 N C:ASP193 4.8 30.0 1.0 O C:PHE191 4.8 29.0 1.0 C2 C:GOL305 4.8 67.3 1.0 OD2 C:ASP189 5.0 39.5 1.0 CD1 C:TRP183 5.0 25.7 1.0

Calcium binding site 4 out of 12 in the The Structural Basis of Histone CHAPERONEVPS75


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Structural Basis of Histone CHAPERONEVPS75 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:30.2 occ:1.00 OE2 B:GLU194 2.4 29.9 1.0 O C:PHE191 2.4 29.0 1.0 O B:HOH401 2.4 27.6 1.0 OD2 C:ASP189 2.5 39.5 1.0 OD1 C:ASP189 2.8 31.9 1.0 CG B:GLU192 2.8 26.5 1.0 OE1 B:GLU194 2.8 29.1 1.0 CG C:GLU192 3.0 26.1 1.0 CD B:GLU194 3.0 28.2 1.0 OE2 B:GLU192 3.0 58.8 1.0 CG C:ASP189 3.0 38.8 1.0 CD B:GLU192 3.4 48.3 1.0 C C:PHE191 3.4 27.7 1.0 CB B:GLU192 3.8 55.2 1.0 CD C:GLU192 3.9 41.3 1.0 CA B:CA301 4.0 29.5 1.0 CB C:PHE191 4.0 30.7 1.0 CB C:GLU192 4.1 47.6 1.0 OE2 C:GLU192 4.2 53.8 1.0 CA C:GLU192 4.2 30.6 1.0 N C:GLU192 4.2 26.9 1.0 CA C:PHE191 4.2 29.1 1.0 CA B:GLU192 4.4 40.1 1.0 CG B:GLU194 4.5 24.6 1.0 O C:HOH401 4.5 35.6 1.0 O B:HOH419 4.6 37.9 1.0 CB C:ASP189 4.6 34.6 1.0 OE1 B:GLU192 4.6 63.5 1.0 N C:PHE191 4.7 38.7 1.0 OE1 C:GLU192 4.8 58.8 1.0 N B:ASP193 4.8 27.9 1.0 O B:PHE191 4.9 27.7 1.0 OD2 B:ASP189 4.9 32.7 1.0 CD1 B:TRP183 4.9 27.8 1.0

Calcium binding site 5 out of 12 in the The Structural Basis of Histone CHAPERONEVPS75


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Structural Basis of Histone CHAPERONEVPS75 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:32.6 occ:1.00 OE1 B:GLU147 2.3 35.6 1.0 OD1 B:ASP193 2.3 24.3 1.0 OE1 B:GLU196 2.4 32.8 1.0 O B:GLU192 2.4 32.6 1.0 OD2 C:ASP193 2.5 30.4 1.0 OD1 C:ASP193 2.6 23.8 1.0 CG C:ASP193 2.9 26.0 1.0 CD B:GLU147 2.9 29.9 1.0 OE2 B:GLU147 2.9 38.1 1.0 CD B:GLU196 3.2 44.1 1.0 OE2 B:GLU196 3.4 46.0 1.0 C B:GLU192 3.4 36.2 1.0 CG B:ASP193 3.6 28.3 1.0 CA C:CA301 3.9 31.1 1.0 CA B:ASP193 4.0 31.0 1.0 N B:ASP193 4.1 27.9 1.0 CB B:ASP193 4.3 24.6 1.0 CG B:GLU147 4.4 41.1 1.0 CB C:ASP193 4.4 22.4 1.0 O C:HOH403 4.4 34.4 1.0 N B:GLU192 4.5 27.9 1.0 OH C:TYR80 4.5 29.5 1.0 OD2 B:ASP193 4.5 32.4 1.0 CA B:GLU192 4.5 40.1 1.0 O B:HOH430 4.6 30.2 1.0 CG B:GLU196 4.6 36.9 1.0

Calcium binding site 6 out of 12 in the The Structural Basis of Histone CHAPERONEVPS75


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Structural Basis of Histone CHAPERONEVPS75 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:31.1 occ:1.00 OE1 C:GLU147 2.4 37.7 1.0 OD1 C:ASP193 2.4 23.8 1.0 OD2 B:ASP193 2.4 32.4 1.0 OE1 C:GLU196 2.5 36.9 1.0 O C:GLU192 2.5 30.6 1.0 OD1 B:ASP193 2.6 24.3 1.0 CG B:ASP193 2.9 28.3 1.0 OE2 C:GLU147 2.9 36.4 1.0 CD C:GLU147 2.9 38.5 1.0 CD C:GLU196 3.3 40.0 1.0 C C:GLU192 3.5 29.8 1.0 OE2 C:GLU196 3.6 49.3 1.0 CG C:ASP193 3.6 26.0 1.0 CA B:CA303 3.9 32.6 1.0 CA C:ASP193 4.0 33.0 1.0 N C:ASP193 4.1 30.0 1.0 O C:HOH403 4.1 34.4 1.0 CB C:ASP193 4.3 22.4 1.0 CB B:ASP193 4.4 24.6 1.0 O C:HOH423 4.4 27.2 1.0 O C:HOH402 4.4 44.0 1.0 OH B:TYR80 4.4 33.6 1.0 CG C:GLU147 4.4 54.4 1.0 N C:GLU192 4.5 26.9 1.0 OD2 C:ASP193 4.5 30.4 1.0 CA C:GLU192 4.6 30.6 1.0 CG C:GLU196 4.7 29.5 1.0

Calcium binding site 7 out of 12 in the The Structural Basis of Histone CHAPERONEVPS75


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The Structural Basis of Histone CHAPERONEVPS75 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:30.6 occ:1.00 OD1 D:ASP193 2.3 25.3 1.0 OE1 D:GLU147 2.3 40.3 1.0 OE1 D:GLU196 2.4 37.2 1.0 O D:GLU192 2.4 31.8 1.0 OD2 A:ASP193 2.5 31.7 1.0 OD1 A:ASP193 2.6 23.6 1.0 CG A:ASP193 2.9 31.9 1.0 CD D:GLU147 3.1 38.4 1.0 OE2 D:GLU147 3.2 41.6 1.0 CD D:GLU196 3.3 40.8 1.0 C D:GLU192 3.4 34.3 1.0 OE2 D:GLU196 3.5 48.2 1.0 CG D:ASP193 3.5 32.1 1.0 CA A:CA302 3.9 30.2 1.0 CA D:ASP193 3.9 29.3 1.0 N D:ASP193 4.0 26.3 1.0 CB D:ASP193 4.3 25.1 1.0 O D:HOH424 4.4 30.8 1.0 N D:GLU192 4.4 26.1 1.0 CB A:ASP193 4.4 25.3 1.0 OD2 D:ASP193 4.5 35.2 1.0 CG D:GLU147 4.5 45.1 1.0 CA D:GLU192 4.5 30.3 1.0 OH A:TYR80 4.6 33.4 1.0 CG D:GLU196 4.6 34.3 1.0

Calcium binding site 8 out of 12 in the The Structural Basis of Histone CHAPERONEVPS75


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The Structural Basis of Histone CHAPERONEVPS75 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca302 b:32.3 occ:1.00 OE2 A:GLU194 2.3 26.9 1.0 OE2 A:GLU192 2.4 30.9 1.0 O D:PHE191 2.5 27.4 1.0 OD2 D:ASP189 2.5 33.8 1.0 O A:HOH409 2.6 30.9 1.0 OD1 D:ASP189 2.7 36.6 1.0 OE1 A:GLU194 2.9 28.4 1.0 CD A:GLU194 2.9 32.5 1.0 CG D:ASP189 3.0 35.7 1.0 CG D:GLU192 3.2 35.8 1.0 CD A:GLU192 3.3 34.0 1.0 C D:PHE191 3.4 30.1 1.0 OE1 A:GLU192 3.7 38.9 1.0 CA A:CA301 3.9 31.1 1.0 CB D:PHE191 4.0 28.9 1.0 CD D:GLU192 4.1 42.6 1.0 CA D:PHE191 4.2 27.7 1.0 OE2 D:GLU192 4.2 52.8 1.0 N D:GLU192 4.3 26.1 1.0 CA D:GLU192 4.3 30.3 1.0 CB D:GLU192 4.4 37.1 1.0 CG A:GLU194 4.4 28.4 1.0 CB D:ASP189 4.5 33.4 1.0 O D:HOH401 4.5 28.8 1.0 CG A:GLU192 4.6 25.8 1.0 CA A:GLU192 4.6 33.2 1.0 O A:HOH421 4.7 36.5 1.0 N D:PHE191 4.7 28.0 1.0 CB A:GLU192 4.7 26.0 1.0 O A:HOH433 4.8 47.6 1.0 N A:ASP193 4.8 28.0 1.0 O A:PHE191 4.9 28.7 1.0 OD2 A:ASP189 4.9 35.1 1.0 CD1 A:TRP183 4.9 30.0 1.0

Calcium binding site 9 out of 12 in the The Structural Basis of Histone CHAPERONEVPS75


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of The Structural Basis of Histone CHAPERONEVPS75 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca301 b:25.6 occ:1.00 OD2 E:ASP189 2.4 30.6 1.0 O E:PHE191 2.5 21.9 1.0 OE2 E:GLU192 2.5 29.2 1.0 OD1 E:ASP189 2.9 25.2 1.0 CG E:ASP189 3.0 31.7 1.0 C E:PHE191 3.4 23.8 1.0 CD E:GLU192 3.4 30.2 1.0 CB E:PHE191 4.0 21.1 1.0 CG E:GLU192 4.1 23.4 1.0 O E:HOH438 4.2 60.5 1.0 CA E:PHE191 4.2 24.0 1.0 OE1 E:GLU192 4.2 33.1 1.0 N E:GLU192 4.2 24.1 1.0 CA E:GLU192 4.4 22.0 1.0 O E:HOH420 4.5 28.5 1.0 CB E:ASP189 4.5 27.6 1.0 N E:PHE191 4.6 24.2 1.0 CB E:GLU192 4.8 21.9 1.0

Calcium binding site 10 out of 12 in the The Structural Basis of Histone CHAPERONEVPS75


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of The Structural Basis of Histone CHAPERONEVPS75 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca302 b:28.9 occ:1.00 OE1 E:GLU196 2.3 36.9 1.0 O E:GLU192 2.4 27.9 1.0 OD1 E:ASP193 2.4 30.1 1.0 OE1 E:GLU147 2.4 27.7 1.0 OE2 E:GLU147 2.7 33.8 1.0 CD E:GLU147 2.9 23.6 1.0 CD E:GLU196 3.3 37.7 1.0 C E:GLU192 3.4 26.9 1.0 CG E:ASP193 3.6 24.1 1.0 OE2 E:GLU196 3.6 40.7 1.0 CA E:ASP193 4.0 28.7 1.0 O E:HOH415 4.0 36.0 1.0 N E:ASP193 4.1 21.1 1.0 CB E:ASP193 4.3 16.4 1.0 CG E:GLU147 4.4 30.1 1.0 N E:GLU192 4.5 24.1 1.0 O E:HOH449 4.6 26.2 1.0 OD2 E:ASP193 4.6 27.6 1.0 CA E:GLU192 4.6 22.0 1.0 CG E:GLU196 4.7 28.8 1.0 O E:LYS146 4.9 44.8 1.0

Y.Chen, Y.Zhang, H.Ye, Y.Dou, D.Lu, X.Li, A.H.Limper, J.Han, D.Su. Structural Basis For the Acetylation of Histone H3K9 and H3K27 Mediated By the Histone Chaperone VPS75 Inpneumocystis Carinii. Signal Transduct Target Ther V. 4 14 2019.
ISSN: ESSN 2059-3635
PubMed: 31098304
DOI: 10.1038/S41392-019-0047-8