Calcium in PDB 3qmn: Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor

All present enzymatic activity of Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor:
2.7.8.7;

The structure of Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor, PDB code: 3qmn was solved by Y.Kim, A.S.Halavaty, M.Zhou, K.Kwon, W.F.Anderson, A.Joachimiak, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.89 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	94.553, 139.039, 138.319, 90.00, 93.72, 90.00
R / Rfree (%)	15.6 / 19.1

The structure of Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor also contains other interesting chemical elements:

Chlorine

(Cl)

9 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 46;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor (pdb code 3qmn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 46 binding sites of Calcium where determined in the Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor, PDB code: 3qmn:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 46 in the Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2514 b:36.1 occ:0.70 OE1 A:GLU57 2.2 23.0 0.5 OD1 A:ASP8 2.4 21.8 1.0 O B:HOH155 2.4 29.9 1.0 O A:HOH166 2.4 36.2 1.0 O4A A:COA129 2.5 42.2 1.0 O2A A:COA129 2.6 32.2 1.0 O A:HOH142 2.7 37.9 1.0 CG A:ASP8 3.3 19.2 1.0 CD A:GLU57 3.4 22.9 0.5 OD2 A:ASP8 3.5 23.8 1.0 P1A A:COA129 3.5 33.8 1.0 P2A A:COA129 3.7 44.5 1.0 O A:HOH223 3.7 32.0 1.0 O3A A:COA129 3.8 42.3 1.0 OE2 A:GLU57 4.1 26.7 0.5 CCP A:COA129 4.2 48.5 1.0 O1A A:COA129 4.3 38.6 1.0 OG B:SER111 4.3 23.0 1.0 CG A:GLU57 4.3 22.6 0.5 O A:ILE9 4.4 19.2 1.0 O6A A:COA129 4.4 46.0 1.0 CD A:GLU57 4.5 28.0 0.5 CB A:GLU57 4.5 19.1 0.5 CB A:GLU57 4.6 18.4 0.5 CG A:GLU57 4.6 21.2 0.5 OE2 A:GLU57 4.6 32.8 0.5 NZ A:LYS61 4.6 22.0 1.0 CB A:ASP8 4.7 16.6 1.0 O B:ASP112 4.7 22.9 1.0 CE2 A:PHE53 4.7 32.4 1.0 O5B A:COA129 4.9 36.2 1.0 O5A A:COA129 4.9 45.1 1.0 CE A:LYS61 5.0 24.8 1.0 CA B:CA2551 5.0 38.7 0.8

Calcium binding site 2 out of 46 in the Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2552 b:35.6 occ:0.70 O A:HOH2366 2.3 49.5 1.0 O A:ACT2597 2.4 35.8 0.9 OD1 A:ASP112 2.4 30.1 1.0 O A:ASP112 2.5 19.6 1.0 O1A A:COA127 2.7 27.4 1.0 O A:HOH2183 2.8 17.4 0.5 C A:ASP112 3.4 19.3 1.0 C A:ACT2597 3.6 37.6 0.9 CG A:ASP112 3.6 25.0 1.0 P1A A:COA127 3.8 23.5 1.0 O C:HOH196 4.0 20.6 1.0 O3A A:COA127 4.0 32.4 1.0 O4A A:COA127 4.0 34.1 1.0 OXT A:ACT2597 4.2 38.6 0.9 CA A:ASP112 4.2 19.1 1.0 O5A A:COA127 4.2 32.8 1.0 P2A A:COA127 4.2 29.6 1.0 N A:ASP112 4.2 17.3 1.0 N A:GLU113 4.2 19.7 1.0 O C:HOH127 4.3 40.4 1.0 CA A:GLU113 4.3 20.5 1.0 OD2 A:ASP112 4.4 29.6 1.0 O2A A:COA127 4.5 21.9 1.0 O A:HOH2387 4.5 26.2 0.5 CB A:ASP112 4.5 19.6 1.0 O A:HOH2182 4.5 30.8 1.0 O A:HOH2183 4.6 18.9 0.5 CH3 A:ACT2597 4.7 36.7 0.9 CA C:CA2513 4.8 24.0 0.7 NH2 A:ARG47 4.8 31.1 1.0

Calcium binding site 3 out of 46 in the Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2515 b:29.1 occ:0.70 OE1 B:GLU57 2.3 31.6 1.0 O C:HOH194 2.4 23.2 1.0 OD1 B:ASP8 2.4 25.2 1.0 O2A C:COA169 2.5 20.9 1.0 O B:HOH174 2.7 29.1 1.0 O4A C:COA169 2.7 38.7 1.0 O C:HOH164 2.8 52.5 1.0 CG B:ASP8 3.3 21.2 1.0 P1A C:COA169 3.4 24.9 1.0 OD2 B:ASP8 3.5 24.9 1.0 CD B:GLU57 3.5 30.6 1.0 O3A C:COA169 3.6 36.5 1.0 P2A C:COA169 3.8 36.3 1.0 O C:HOH281 3.8 55.5 1.0 O B:HOH243 4.0 33.0 1.0 OG C:SER111 4.1 18.5 1.0 OE2 B:GLU57 4.2 34.2 1.0 O B:ILE9 4.2 18.3 1.0 CCP C:COA169 4.2 42.6 1.0 O1A C:COA169 4.3 28.0 1.0 NZ B:LYS61 4.6 17.6 1.0 CB B:GLU57 4.6 20.3 1.0 O6A C:COA169 4.6 40.8 1.0 CG B:GLU57 4.6 23.8 1.0 O5B C:COA169 4.6 29.8 1.0 CB B:ASP8 4.7 16.7 1.0 CE2 B:PHE53 4.7 31.0 1.0 O C:ASP112 4.7 19.2 1.0 CA C:CA2553 5.0 32.2 0.7 CE B:LYS61 5.0 19.6 1.0

Calcium binding site 4 out of 46 in the Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2551 b:38.7 occ:0.80 OD1 B:ASP112 2.3 33.9 1.0 O1A A:COA129 2.4 38.6 1.0 O B:ASP112 2.5 22.9 1.0 O B:HOH166 2.8 22.5 0.5 O A:HOH142 2.8 37.9 1.0 O B:HOH2181 2.9 25.6 1.0 C B:ASP112 3.4 22.5 1.0 CG B:ASP112 3.5 28.7 1.0 P1A A:COA129 3.7 33.8 1.0 O B:HOH166 3.8 10.5 0.5 O5A A:COA129 3.9 45.1 1.0 O B:HOH155 4.0 29.9 1.0 O4A A:COA129 4.2 42.2 1.0 CA B:ASP112 4.2 22.5 1.0 P2A A:COA129 4.2 44.5 1.0 N B:GLU113 4.3 22.0 1.0 N B:ASP112 4.3 21.0 1.0 O3A A:COA129 4.3 42.3 1.0 OD2 B:ASP112 4.3 31.4 1.0 CA B:GLU113 4.3 22.9 1.0 O2A A:COA129 4.4 32.2 1.0 CB B:ASP112 4.5 23.0 1.0 O B:HOH2185 4.5 31.3 1.0 O B:HOH178 4.6 22.9 1.0 NH2 B:ARG47 4.8 33.3 1.0 O5B A:COA129 4.9 36.2 1.0 C B:GLU113 5.0 23.5 1.0 CA A:CA2514 5.0 36.1 0.7

Calcium binding site 5 out of 46 in the Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2513 b:24.0 occ:0.70 OD1 C:ASP8 2.3 20.4 1.0 O C:HOH196 2.3 20.6 1.0 OE1 C:GLU57 2.4 24.0 1.0 O2A A:COA127 2.4 21.9 1.0 O C:HOH197 2.7 21.2 1.0 O3A A:COA127 2.9 32.4 1.0 CG C:ASP8 3.2 19.3 1.0 P1A A:COA127 3.3 23.5 1.0 OD2 C:ASP8 3.4 21.0 1.0 CD C:GLU57 3.6 23.8 1.0 O C:HOH127 3.8 40.4 1.0 O5A A:COA127 3.8 32.8 1.0 OG A:SER111 4.1 17.9 1.0 O C:HOH193 4.1 22.2 1.0 P2A A:COA127 4.1 29.6 1.0 O1A A:COA127 4.2 27.4 1.0 O C:ILE9 4.2 17.8 1.0 OE2 C:GLU57 4.4 23.9 1.0 NZ C:LYS61 4.4 15.1 1.0 CCP A:COA127 4.4 26.7 1.0 O5B A:COA127 4.6 29.6 1.0 CB C:GLU57 4.6 14.6 1.0 O A:ASP112 4.6 19.6 1.0 CB C:ASP8 4.6 15.8 1.0 CG C:GLU57 4.7 16.9 1.0 O A:HOH2366 4.8 49.5 1.0 O6A A:COA127 4.8 26.9 1.0 CA A:CA2552 4.8 35.6 0.7 CE2 C:PHE53 4.9 27.7 1.0 CE C:LYS61 4.9 16.5 1.0

Calcium binding site 6 out of 46 in the Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2553 b:32.2 occ:0.70 O C:HOH281 2.2 55.5 1.0 O C:HOH280 2.3 11.2 0.5 OD1 C:ASP112 2.4 26.6 1.0 O C:ASP112 2.5 19.2 1.0 O C:HOH279 2.6 40.6 1.0 O1A C:COA169 2.6 28.0 1.0 O C:HOH266 2.8 22.1 0.5 C C:ASP112 3.4 19.2 1.0 CG C:ASP112 3.6 24.3 1.0 P1A C:COA169 3.7 24.9 1.0 O C:HOH280 3.7 16.1 0.5 O5A C:COA169 3.8 39.3 1.0 O C:HOH194 4.0 23.2 1.0 O4A C:COA169 4.1 38.7 1.0 P2A C:COA169 4.1 36.3 1.0 CA C:ASP112 4.1 18.5 1.0 O3A C:COA169 4.1 36.5 1.0 N C:ASP112 4.2 17.8 1.0 N C:GLU113 4.3 19.1 1.0 OD2 C:ASP112 4.4 24.8 1.0 CA C:GLU113 4.4 20.1 1.0 O2A C:COA169 4.4 20.9 1.0 O C:HOH266 4.4 17.1 0.5 CB C:ASP112 4.4 18.7 1.0 O C:HOH219 4.5 32.9 1.0 O C:HOH278 4.7 40.0 1.0 NH1 C:ARG47 4.9 25.0 1.0 O5B C:COA169 5.0 29.8 1.0 CA B:CA2515 5.0 29.1 0.7

Calcium binding site 7 out of 46 in the Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca2517 b:27.9 occ:0.70 O D:HOH443 2.2 21.3 1.0 OD1 D:ASP8 2.4 23.9 1.0 OE1 D:GLU57 2.4 31.5 1.0 O2A E:COA387 2.4 23.1 1.0 O4A E:COA387 2.5 37.3 1.0 O D:HOH317 2.8 29.6 1.0 CG D:ASP8 3.3 21.4 1.0 O E:HOH469 3.3 39.9 1.0 P1A E:COA387 3.4 27.2 1.0 OD2 D:ASP8 3.5 22.7 1.0 CD D:GLU57 3.6 29.1 1.0 P2A E:COA387 3.7 35.5 1.0 O3A E:COA387 3.7 37.1 1.0 O E:HOH433 3.9 40.1 1.0 O D:HOH346 4.0 27.6 1.0 OG E:SER111 4.0 21.9 1.0 O D:ILE9 4.2 18.9 1.0 O1A E:COA387 4.2 30.1 1.0 CCP E:COA387 4.3 40.8 1.0 OE2 D:GLU57 4.3 33.3 1.0 O6A E:COA387 4.5 39.4 1.0 O E:ASP112 4.5 22.3 1.0 NZ D:LYS61 4.5 20.8 1.0 CB D:GLU57 4.6 18.7 1.0 CB D:ASP8 4.7 18.1 1.0 O5B E:COA387 4.7 31.9 1.0 CG D:GLU57 4.7 24.0 1.0 CE2 D:PHE53 4.8 31.2 1.0 O5A E:COA387 5.0 40.0 1.0 CA E:CA2554 5.0 44.4 0.8

Calcium binding site 8 out of 46 in the Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca2540 b:30.9 occ:0.70 O D:HOH2197 2.2 38.3 1.0 O D:HOH383 2.3 37.1 1.0 OD1 D:ASP112 2.3 29.8 1.0 O1A D:COA283 2.4 28.7 1.0 O D:ASP112 2.5 21.6 1.0 C D:ASP112 3.3 21.0 1.0 CG D:ASP112 3.5 25.2 1.0 P1A D:COA283 3.6 27.1 1.0 O D:HOH349 3.9 26.0 1.0 O D:HOH358 4.0 31.8 1.0 O5A D:COA283 4.0 40.9 1.0 CA D:ASP112 4.1 19.5 1.0 N D:ASP112 4.1 19.5 1.0 O3A D:COA283 4.1 35.9 1.0 N D:GLU113 4.2 21.6 1.0 O4A D:COA283 4.2 37.0 1.0 P2A D:COA283 4.2 37.5 1.0 CA D:GLU113 4.3 22.9 1.0 CB D:ASP112 4.4 20.6 1.0 OD2 D:ASP112 4.4 28.9 1.0 O D:HOH2188 4.5 31.7 1.0 O2A D:COA283 4.5 24.2 1.0 O D:HOH2368 4.7 44.8 1.0 NH2 D:ARG47 4.8 29.1 1.0 O5B D:COA283 4.8 30.2 1.0 CA F:CA2516 5.0 34.4 0.7

Calcium binding site 9 out of 46 in the Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca2519 b:27.0 occ:0.70 OD1 E:ASP8 2.3 23.3 1.0 O2A F:COA477 2.3 27.8 1.0 OE1 E:GLU57 2.3 30.9 1.0 O E:HOH450 2.4 25.3 1.0 O4A F:COA477 2.8 39.2 1.0 O E:HOH414 2.8 34.0 1.0 CG E:ASP8 3.2 20.9 1.0 O F:HOH481 3.2 56.4 1.0 P1A F:COA477 3.4 27.8 1.0 OD2 E:ASP8 3.4 24.1 1.0 CD E:GLU57 3.5 28.5 1.0 O3A F:COA477 3.8 38.9 1.0 O E:HOH417 3.8 25.5 1.0 P2A F:COA477 3.9 36.9 1.0 O E:HOH2199 4.0 45.8 1.0 OG F:SER111 4.0 20.4 1.0 OE2 E:GLU57 4.2 30.4 1.0 O E:ILE9 4.3 19.0 1.0 CCP F:COA477 4.3 37.8 1.0 O1A F:COA477 4.4 30.5 1.0 NZ E:LYS61 4.5 20.1 1.0 O5B F:COA477 4.5 31.3 1.0 O6A F:COA477 4.5 38.0 1.0 CB E:GLU57 4.6 19.3 1.0 CB E:ASP8 4.6 17.6 1.0 CG E:GLU57 4.6 23.0 1.0 O F:ASP112 4.6 20.8 1.0 CE2 E:PHE53 4.9 29.2 1.0 CA F:CA2518 4.9 54.1 1.0 CE E:LYS61 4.9 20.5 1.0

Calcium binding site 10 out of 46 in the Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of 4'-Phosphopantetheinyl Transferase Acps From Vibrio Cholerae O1 Biovar Eltor within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca2554 b:44.4 occ:0.80 O E:HOH469 2.4 39.9 1.0 O E:HOH2388 2.4 34.6 1.0 OXT E:ACT2594 2.4 50.4 1.0 OD1 E:ASP112 2.4 31.1 1.0 O E:ASP112 2.6 22.3 1.0 O1A E:COA387 2.6 30.1 1.0 C E:ASP112 3.4 22.8 1.0 C E:ACT2594 3.5 50.6 1.0 CG E:ASP112 3.5 27.6 1.0 P1A E:COA387 3.8 27.2 1.0 O E:ACT2594 3.8 50.4 1.0 O E:HOH2389 3.9 50.4 1.0 O5A E:COA387 3.9 40.0 1.0 O D:HOH443 4.1 21.3 1.0 O4A E:COA387 4.1 37.3 1.0 CA E:ASP112 4.2 21.9 1.0 N E:GLU113 4.2 22.5 1.0 O3A E:COA387 4.2 37.1 1.0 P2A E:COA387 4.2 35.5 1.0 CA E:GLU113 4.3 23.5 1.0 N E:ASP112 4.3 20.5 1.0 O E:HOH433 4.3 40.1 1.0 OD2 E:ASP112 4.3 29.9 1.0 CB E:ASP112 4.4 22.6 1.0 O2A E:COA387 4.5 23.1 1.0 CH3 E:ACT2594 4.8 50.3 1.0 NH2 E:ARG47 4.8 34.0 1.0 C E:GLU113 5.0 24.8 1.0 CA D:CA2517 5.0 27.9 0.7

A.S.Halavaty, Y.Kim, G.Minasov, L.Shuvalova, I.Dubrovska, J.Winsor, M.Zhou, O.Onopriyenko, T.Skarina, L.Papazisi, K.Kwon, S.N.Peterson, A.Joachimiak, A.Savchenko, W.F.Anderson. Structural Characterization and Comparison of Three Acyl-Carrier-Protein Synthases From Pathogenic Bacteria. Acta Crystallogr.,Sect.D V. 68 1359 2012.
ISSN: ISSN 0907-4449
PubMed: 22993090
DOI: 10.1107/S0907444912029101