Calcium in PDB 6plm: Legionella Pneumophila Sidj/ Calmodulin 2 Complex

The structure of Legionella Pneumophila Sidj/ Calmodulin 2 Complex, PDB code: 6plm was solved by Y.Mao, A.Sulpizio, M.E.Minelli, X.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.33 / 2.59
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	105.351, 103.792, 110.194, 90.00, 104.69, 90.00
R / Rfree (%)	17.6 / 24.1

The binding sites of Calcium atom in the Legionella Pneumophila Sidj/ Calmodulin 2 Complex (pdb code 6plm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Legionella Pneumophila Sidj/ Calmodulin 2 Complex, PDB code: 6plm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Legionella Pneumophila Sidj/ Calmodulin 2 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Legionella Pneumophila Sidj/ Calmodulin 2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:57.7 occ:1.00 O5 A:POP1003 2.3 52.3 1.0 OD2 A:ASP545 2.3 54.8 1.0 OD2 A:ASP542 2.6 54.4 1.0 OD1 A:ASP542 2.8 53.3 1.0 CG A:ASP542 3.0 51.3 1.0 CG A:ASP545 3.3 51.2 1.0 OD1 A:ASP545 3.5 48.6 1.0 P2 A:POP1003 3.6 55.3 1.0 O6 A:POP1003 4.0 50.6 1.0 NH1 A:ARG352 4.1 30.0 1.0 NZ A:LYS367 4.2 43.8 1.0 O4 A:POP1003 4.4 58.9 1.0 CA A:CA1002 4.5 53.9 1.0 CB A:ASP542 4.5 48.3 1.0 CB A:ASP545 4.6 45.9 1.0 O A:POP1003 4.9 49.1 1.0 O2 A:POP1003 4.9 45.5 1.0

Calcium binding site 2 out of 6 in the Legionella Pneumophila Sidj/ Calmodulin 2 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Legionella Pneumophila Sidj/ Calmodulin 2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:53.9 occ:1.00 O2 A:POP1003 2.3 45.5 1.0 O6 A:POP1003 2.3 50.6 1.0 OD1 A:ASN534 2.4 45.2 1.0 OD2 A:ASP542 2.5 54.4 1.0 CG A:ASP542 3.5 51.3 1.0 CG A:ASN534 3.5 40.4 1.0 P1 A:POP1003 3.5 49.3 1.0 P2 A:POP1003 3.5 55.3 1.0 O A:POP1003 3.8 49.1 1.0 O5 A:POP1003 3.9 52.3 1.0 CB A:ASP542 3.9 48.3 1.0 ND2 A:ASN534 4.0 39.9 1.0 O A:TYR532 4.0 46.8 1.0 NH2 A:ARG536 4.1 52.5 1.0 O A:HOH1173 4.2 52.4 1.0 O3 A:POP1003 4.3 49.2 1.0 OD1 A:ASP542 4.5 53.3 1.0 CA A:CA1001 4.5 57.7 1.0 O1 A:POP1003 4.6 46.6 1.0 CB A:ASN534 4.7 41.7 1.0 O4 A:POP1003 4.8 58.9 1.0 O A:HOH1144 5.0 68.1 1.0 CA A:ASN534 5.0 41.3 1.0

Calcium binding site 3 out of 6 in the Legionella Pneumophila Sidj/ Calmodulin 2 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Legionella Pneumophila Sidj/ Calmodulin 2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:57.4 occ:1.00 OD2 B:ASP545 2.3 64.3 1.0 O3 B:POP1003 2.4 55.7 1.0 OD1 B:ASP542 2.6 48.4 1.0 OD2 B:ASP542 2.6 50.6 1.0 CG B:ASP542 2.9 47.1 1.0 CG B:ASP545 3.2 59.8 1.0 OD1 B:ASP545 3.6 63.7 1.0 P1 B:POP1003 3.7 52.1 1.0 O2 B:POP1003 4.0 50.4 1.0 NH2 B:ARG352 4.0 53.4 1.0 NZ B:LYS367 4.2 47.0 1.0 CA B:CA1002 4.3 55.6 1.0 CB B:ASP542 4.5 45.3 1.0 CB B:ASP545 4.5 54.1 1.0 O4 B:POP1003 4.6 52.7 1.0 O1 B:POP1003 4.7 57.0 1.0 O B:POP1003 4.7 51.0 1.0 CE B:LYS367 4.9 47.5 1.0

Calcium binding site 4 out of 6 in the Legionella Pneumophila Sidj/ Calmodulin 2 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Legionella Pneumophila Sidj/ Calmodulin 2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:55.6 occ:1.00 O4 B:POP1003 2.0 52.7 1.0 O2 B:POP1003 2.4 50.4 1.0 OD1 B:ASN534 2.5 40.3 1.0 OD2 B:ASP542 2.5 50.6 1.0 P2 B:POP1003 3.5 50.1 1.0 P1 B:POP1003 3.5 52.1 1.0 CG B:ASP542 3.6 47.1 1.0 CG B:ASN534 3.6 41.9 1.0 O B:POP1003 3.9 51.0 1.0 O3 B:POP1003 3.9 55.7 1.0 O B:TYR532 3.9 45.1 1.0 CB B:ASP542 4.0 45.3 1.0 ND2 B:ASN534 4.0 42.5 1.0 NH2 B:ARG536 4.2 45.5 1.0 O5 B:POP1003 4.3 51.2 1.0 CA B:CA1001 4.3 57.4 1.0 O6 B:POP1003 4.5 53.7 1.0 OD1 B:ASP542 4.5 48.4 1.0 CB B:ASN534 4.9 40.9 1.0 O1 B:POP1003 4.9 57.0 1.0

Calcium binding site 5 out of 6 in the Legionella Pneumophila Sidj/ Calmodulin 2 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Legionella Pneumophila Sidj/ Calmodulin 2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:0.1 occ:1.00 O C:THR26 2.2 77.3 1.0 OD1 C:ASP22 2.6 71.6 1.0 OD1 C:ASP20 2.8 73.5 1.0 OD1 C:ASP24 2.9 67.6 1.0 C C:THR26 3.4 77.8 1.0 CG C:ASP22 3.5 70.7 1.0 OG1 C:THR26 3.7 78.6 1.0 CG C:ASP24 3.8 66.7 1.0 OD2 C:ASP22 3.9 74.0 1.0 CG C:ASP20 4.1 71.1 1.0 OD2 C:ASP24 4.2 66.8 1.0 N C:ILE27 4.3 78.6 1.0 CA C:ILE27 4.3 78.9 1.0 N C:ASP22 4.4 66.6 1.0 CA C:THR26 4.4 77.1 1.0 N C:THR26 4.5 74.5 1.0 CB C:ASP22 4.6 68.1 1.0 N C:LYS21 4.6 68.7 1.0 CB C:THR26 4.7 79.0 1.0 CA C:ASP20 4.7 68.4 1.0 C C:ASP20 4.8 67.0 1.0 C C:ILE27 4.8 81.0 1.0 CA C:ASP22 4.9 66.3 1.0 N C:ASP24 4.9 64.2 1.0 CB C:ASP24 4.9 65.5 1.0 CB C:ASP20 4.9 69.6 1.0 CG2 C:THR28 4.9 86.1 1.0 OD2 C:ASP20 4.9 71.1 1.0 N C:THR28 4.9 82.5 1.0

Calcium binding site 6 out of 6 in the Legionella Pneumophila Sidj/ Calmodulin 2 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Legionella Pneumophila Sidj/ Calmodulin 2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:79.9 occ:1.00 O D:THR26 2.4 49.9 1.0 O D:HOH306 2.6 55.1 1.0 OD1 D:ASP22 2.6 55.8 1.0 OD1 D:ASP20 2.7 56.9 1.0 OD1 D:ASP24 2.8 55.1 1.0 C D:THR26 3.4 52.6 1.0 CG D:ASP20 3.4 54.5 1.0 CG D:ASP22 3.5 55.6 1.0 OG1 D:THR26 3.6 57.1 1.0 CG D:ASP24 3.6 53.7 1.0 N D:ASP24 4.0 50.6 1.0 OD2 D:ASP22 4.0 57.8 1.0 CA D:ASP20 4.0 51.7 1.0 N D:THR26 4.0 49.4 1.0 N D:ASP22 4.0 52.2 1.0 CB D:ASP20 4.1 52.8 1.0 CA D:THR26 4.2 51.6 1.0 OD2 D:ASP20 4.2 54.6 1.0 OD2 D:ASP24 4.2 55.4 1.0 C D:ASP20 4.3 52.3 1.0 N D:LYS21 4.3 54.4 1.0 O D:HOH302 4.3 55.1 1.0 N D:ILE27 4.4 57.3 1.0 CB D:ASP24 4.4 53.3 1.0 N D:GLY23 4.4 50.2 1.0 CB D:THR26 4.5 54.9 1.0 CB D:ASP22 4.5 53.7 1.0 CA D:ILE27 4.5 59.0 1.0 CA D:ASP24 4.5 51.3 1.0 CA D:ASP22 4.6 52.5 1.0 N D:GLY25 4.6 47.7 1.0 C D:ASP22 4.7 51.8 1.0 C D:ASP24 4.8 49.6 1.0 O D:ASP20 4.9 52.4 1.0

A.Sulpizio, M.E.Minelli, M.Wan, P.D.Burrowes, X.Wu, E.J.Sanford, J.H.Shin, B.C.Williams, M.L.Goldberg, M.B.Smolka, Y.Mao. Protein Polyglutamylation Catalyzed By the Bacterial Calmodulin-Dependent Pseudokinase Sidj. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 31682223
DOI: 10.7554/ELIFE.51162