Magnesium in PDB 6oqq: Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex

The structure of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex, PDB code: 6oqq was solved by D.R.Tomchick, V.S.Tagliabracci, M.Black, A.Osinski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.83 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	105.490, 104.749, 107.770, 90.00, 103.97, 90.00
R / Rfree (%)	20.2 / 23.4

The structure of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Sodium	(Na)	2 atoms

The binding sites of Magnesium atom in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex (pdb code 6oqq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex, PDB code: 6oqq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:46.5 occ:1.00 O6 A:POP902 2.3 59.3 1.0 OD2 A:ASP542 2.3 56.6 1.0 OD2 A:ASP545 2.5 72.5 1.0 OD1 A:ASP542 2.6 71.4 1.0 CG A:ASP542 2.8 80.5 1.0 CG A:ASP545 3.4 65.1 1.0 HZ3 A:LYS367 3.6 67.7 1.0 OD1 A:ASP545 3.7 67.0 1.0 P2 A:POP902 3.7 63.6 1.0 HH21 A:ARG352 3.9 83.5 1.0 HZ1 A:LYS367 3.9 67.7 1.0 O5 A:POP902 4.0 48.4 1.0 O A:HOH1006 4.1 45.0 1.0 NZ A:LYS367 4.1 56.4 1.0 CB A:ASP542 4.3 21.8 1.0 O3 A:POP902 4.4 70.7 1.0 HZ2 A:LYS367 4.4 67.7 1.0 HD21 A:ASN534 4.6 41.2 1.0 O4 A:POP902 4.6 60.9 1.0 O A:POP902 4.6 77.3 1.0 HB2 A:ASP542 4.7 26.2 1.0 HB3 A:ASP542 4.7 26.2 1.0 NH2 A:ARG352 4.7 69.6 1.0 CB A:ASP545 4.7 36.0 1.0 HB2 A:ASP545 4.7 43.3 1.0 HE A:ARG352 4.8 75.6 1.0 HA A:ASP542 4.9 30.6 1.0 HE2 A:LYS370 5.0 63.5 1.0

Magnesium binding site 2 out of 7 in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg904 b:35.1 occ:1.00 O1 A:POP902 2.1 49.9 1.0 HH12 A:ARG536 2.2 22.0 1.0 HH22 A:ARG536 2.7 29.8 1.0 HE2 A:TYR449 2.9 26.7 1.0 NH1 A:ARG536 3.0 18.4 1.0 P1 A:POP902 3.2 65.7 1.0 O2 A:POP902 3.3 57.1 1.0 NH2 A:ARG536 3.4 24.8 1.0 HD1 A:PHE450 3.6 37.7 1.0 CE2 A:TYR449 3.6 22.3 1.0 HH11 A:ARG536 3.6 22.0 1.0 CZ A:ARG536 3.7 21.1 1.0 OH A:TYR443 3.7 27.9 1.0 HH A:TYR443 3.7 33.5 1.0 O A:HOH1033 3.8 26.4 1.0 HE1 A:PHE450 3.9 42.6 1.0 O3 A:POP902 3.9 70.7 1.0 HD2 A:TYR449 4.0 26.8 1.0 HH A:TYR449 4.1 35.1 1.0 HB1 A:ALA541 4.1 30.6 1.0 CD1 A:PHE450 4.1 31.4 1.0 CD2 A:TYR449 4.2 22.5 1.0 HH21 A:ARG536 4.2 29.8 1.0 CE1 A:PHE450 4.3 35.5 1.0 HA A:PHE450 4.5 42.1 1.0 CZ A:TYR449 4.5 21.4 1.0 O A:POP902 4.5 77.3 1.0 OH A:TYR449 4.7 29.3 1.0 O A:HOH1283 4.7 27.2 1.0 HG1 A:THR353 4.7 42.7 1.0 MG A:MG905 4.7 50.5 1.0 HG21 A:THR353 4.8 48.9 1.0 O A:TYR449 4.8 21.0 1.0 CB A:ALA541 5.0 25.5 1.0 CZ A:TYR443 5.0 27.6 1.0

Magnesium binding site 3 out of 7 in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg905 b:50.5 occ:1.00 O2 A:POP902 2.2 57.1 1.0 OH A:TYR452 2.3 36.3 1.0 HH A:TYR452 2.8 43.6 1.0 HB3 A:TYR532 2.9 30.8 1.0 HE1 A:TYR452 3.0 31.7 1.0 HE21 A:GLN350 3.1 89.5 1.0 CZ A:TYR452 3.3 32.5 1.0 HH22 A:ARG536 3.5 29.8 1.0 NE2 A:GLN350 3.5 74.6 1.0 CE1 A:TYR452 3.5 26.4 1.0 P1 A:POP902 3.6 65.7 1.0 HH21 A:ARG536 3.6 29.8 1.0 NH2 A:ARG536 3.6 24.8 1.0 HG3 A:GLN350 3.8 64.2 1.0 HE22 A:GLN350 3.8 89.5 1.0 HG2 A:GLN350 3.9 64.2 1.0 CB A:TYR532 3.9 25.7 1.0 O5 A:POP902 3.9 48.4 1.0 HD1 A:TYR532 3.9 51.2 1.0 O3 A:POP902 4.0 70.7 1.0 CD A:GLN350 4.0 62.7 1.0 CG A:GLN350 4.1 53.5 1.0 O A:HOH1160 4.1 42.0 1.0 O A:TYR532 4.3 22.3 1.0 HA A:TYR532 4.3 22.4 1.0 CD1 A:TYR532 4.4 42.7 1.0 HB2 A:TYR532 4.4 30.8 1.0 O A:POP902 4.5 77.3 1.0 CG A:TYR532 4.5 24.4 1.0 CZ A:ARG536 4.5 21.1 1.0 O1 A:POP902 4.5 49.9 1.0 CA A:TYR532 4.6 18.6 1.0 CE2 A:TYR452 4.6 25.8 1.0 MG A:MG904 4.7 35.1 1.0 C A:TYR532 4.8 15.4 1.0 O A:HOH1283 4.8 27.2 1.0 CD1 A:TYR452 4.8 21.0 1.0 P2 A:POP902 4.8 63.6 1.0 OE1 A:GLN350 4.9 59.5 1.0 HE2 A:TYR452 4.9 30.9 1.0 HH12 A:ARG536 4.9 22.0 1.0 O A:HOH1004 5.0 42.0 1.0

Magnesium binding site 4 out of 7 in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg906 b:76.9 occ:1.00 HD2 A:PHE495 3.0 0.7 1.0 HE1 A:TYR732 3.2 38.7 1.0 HB2 A:PHE495 3.2 85.2 1.0 OG1 A:THR493 3.3 54.5 1.0 HG21 A:THR493 3.5 61.7 1.0 O A:HOH1286 3.5 58.0 1.0 HG1 A:THR493 3.6 65.5 1.0 CD2 A:PHE495 3.7 90.6 1.0 O A:HOH1257 3.8 45.5 1.0 CE1 A:TYR732 3.9 32.2 1.0 HB A:THR493 3.9 27.9 1.0 O2P A:AMP901 3.9 75.3 1.0 HH11 A:ARG500 3.9 32.6 1.0 CB A:THR493 4.0 23.2 1.0 HH12 A:ARG500 4.0 32.6 1.0 OH A:TYR732 4.0 84.2 1.0 CG2 A:THR493 4.0 51.4 1.0 CB A:PHE495 4.1 71.0 1.0 OD1 A:ASN733 4.1 0.4 1.0 HG23 A:THR493 4.2 61.7 1.0 NH1 A:ARG500 4.2 27.1 1.0 NA A:NA907 4.2 40.0 1.0 CG A:PHE495 4.3 84.8 1.0 CZ A:TYR732 4.4 63.9 1.0 HD21 A:ASN733 4.4 66.5 1.0 HB3 A:PHE495 4.4 85.2 1.0 H A:PHE495 4.5 99.5 1.0 CE2 A:PHE495 4.6 76.0 1.0 CG A:ASN733 4.7 33.0 1.0 HE2 A:PHE495 4.7 91.2 1.0 HH A:TYR732 4.7 0.1 1.0 H A:GLY496 4.7 49.8 1.0 ND2 A:ASN733 4.8 55.4 1.0 CD1 A:TYR732 4.8 40.1 1.0 HE1 A:HIS492 4.8 20.9 1.0 HD2 A:ARG500 4.9 44.1 1.0 HD1 A:TYR732 4.9 48.1 1.0 HG22 A:THR493 4.9 61.7 1.0 HH21 A:ARG522 5.0 54.0 1.0

Magnesium binding site 5 out of 7 in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg904 b:41.5 occ:1.00 OD2 C:ASP542 2.1 69.7 1.0 O3 C:POP902 2.2 58.0 1.0 O C:HOH1186 2.3 40.3 1.0 OD2 C:ASP545 2.3 73.9 1.0 OD1 C:ASP542 2.4 63.6 1.0 CG C:ASP542 2.6 63.3 1.0 HZ1 C:LYS367 3.1 59.9 1.0 O C:HOH1224 3.2 44.9 1.0 CG C:ASP545 3.3 67.0 1.0 P1 C:POP902 3.5 63.1 1.0 O C:HOH1064 3.6 35.7 1.0 OD1 C:ASP545 3.6 51.9 1.0 O2 C:POP902 3.7 81.5 1.0 HH21 C:ARG352 3.9 43.4 1.0 HZ2 C:LYS367 3.9 59.9 1.0 NZ C:LYS367 3.9 49.9 1.0 O C:HOH1001 3.9 37.3 1.0 CB C:ASP542 4.1 46.5 1.0 O1 C:POP902 4.2 59.4 1.0 O5 C:POP902 4.3 71.0 1.0 HB2 C:ASP542 4.4 55.9 1.0 HZ3 C:LYS367 4.4 59.9 1.0 HD21 C:ASN534 4.4 38.3 1.0 HB3 C:ASP542 4.4 55.9 1.0 CB C:ASP545 4.6 30.5 1.0 HE3 C:LYS367 4.6 75.7 1.0 HB2 C:ASP545 4.6 36.6 1.0 NH2 C:ARG352 4.7 36.2 1.0 O C:POP902 4.7 81.5 1.0 HA C:ASP542 4.8 34.7 1.0 HH22 C:ARG352 4.8 43.4 1.0 CE C:LYS367 4.8 63.1 1.0

Magnesium binding site 6 out of 7 in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg905 b:46.0 occ:1.00 O4 C:POP902 2.3 54.1 1.0 O6 C:POP902 2.4 80.1 1.0 HH12 C:ARG536 2.5 35.3 1.0 P2 C:POP902 2.8 71.8 1.0 HH22 C:ARG536 2.9 45.6 1.0 HE2 C:TYR449 3.2 44.3 1.0 NH1 C:ARG536 3.3 29.4 1.0 O C:HOH1003 3.4 39.0 1.0 O C:HOH1062 3.6 35.7 1.0 NH2 C:ARG536 3.6 38.0 1.0 O5 C:POP902 3.6 71.0 1.0 HH C:TYR443 3.7 44.6 1.0 OH C:TYR443 3.7 37.3 1.0 HD1 C:PHE450 3.7 47.6 1.0 HE21 C:GLN350 3.9 56.9 1.0 CZ C:ARG536 3.9 28.7 1.0 HH11 C:ARG536 4.0 35.3 1.0 HE1 C:PHE450 4.0 47.9 1.0 CE2 C:TYR449 4.0 37.0 1.0 O C:POP902 4.2 81.5 1.0 HB1 C:ALA541 4.3 52.1 1.0 CD1 C:PHE450 4.3 39.8 1.0 HH21 C:ARG536 4.3 45.6 1.0 NE2 C:GLN350 4.4 47.4 1.0 HD2 C:TYR449 4.4 45.7 1.0 CE1 C:PHE450 4.4 40.0 1.0 O C:HOH1039 4.5 27.6 1.0 HE22 C:GLN350 4.5 56.9 1.0 HG1 C:THR353 4.6 47.8 1.0 CD2 C:TYR449 4.6 38.2 1.0 HG21 C:THR353 4.6 50.8 1.0 HG2 C:GLN350 4.8 75.5 1.0 HA C:PHE450 4.8 47.4 1.0 CZ C:TYR449 4.9 36.4 1.0 OH C:TYR449 4.9 35.3 1.0 HH C:TYR452 5.0 42.5 1.0

Magnesium binding site 7 out of 7 in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg906 b:50.3 occ:1.00 O3P C:AMP901 2.0 77.6 1.0 OD1 C:ASN733 2.2 47.4 1.0 O2 C:POP903 2.2 56.3 1.0 O5 C:POP903 2.3 62.8 1.0 O C:POP903 2.6 82.7 1.0 P2 C:POP903 2.7 91.2 1.0 HA C:ASN733 2.9 20.1 1.0 P1 C:POP903 2.9 70.1 1.0 CG C:ASN733 3.1 39.5 1.0 O4 C:POP903 3.2 70.5 1.0 P C:AMP901 3.4 89.6 1.0 HE1 C:HIS492 3.4 28.0 1.0 H5'1 C:AMP901 3.6 31.2 1.0 CA C:ASN733 3.7 16.7 1.0 O C:HOH1112 3.8 19.2 1.0 CB C:ASN733 3.8 37.1 1.0 O3 C:POP903 3.9 64.5 1.0 HB3 C:ASN733 3.9 44.5 1.0 ND2 C:ASN733 4.0 72.3 1.0 H C:ASN733 4.0 21.4 1.0 O1P C:AMP901 4.1 47.5 1.0 O1 C:POP903 4.1 66.6 1.0 HD21 C:ASN733 4.1 86.8 1.0 O6 C:POP903 4.2 79.8 1.0 O2P C:AMP901 4.2 42.0 1.0 HH12 C:ARG500 4.2 51.5 1.0 CE1 C:HIS492 4.2 23.5 1.0 N C:ASN733 4.3 17.8 1.0 O5' C:AMP901 4.4 49.8 1.0 C5' C:AMP901 4.4 26.0 1.0 HG21 C:THR493 4.7 59.9 1.0 HB2 C:ASN733 4.7 44.5 1.0 O C:HOH1015 4.7 26.9 1.0 HD22 C:ASN733 4.7 86.8 1.0 H5'2 C:AMP901 4.8 31.2 1.0 NH1 C:ARG500 4.8 42.9 1.0 NE2 C:HIS492 4.8 23.5 1.0 C C:ASN733 4.9 21.4 1.0 HE1 C:TYR732 4.9 50.6 1.0 CE1 C:TYR732 4.9 42.2 1.0 HH C:TYR732 5.0 64.0 1.0 CZ C:TYR732 5.0 51.5 1.0

M.H.Black, A.Osinski, M.Gradowski, K.A.Servage, K.Pawlowski, D.R.Tomchick, V.S.Tagliabracci. Bacterial Pseudokinase Catalyzes Protein Polyglutamylation to Inhibit the Side-Family Ubiquitin Ligases. Science V. 364 787 2019.
ISSN: ESSN 1095-9203
PubMed: 31123136
DOI: 10.1126/SCIENCE.AAW7446