Magnesium in PDB 6ixw: Pcbh Parm Non-Polymerisable Quadruple Mutant

The structure of Pcbh Parm Non-Polymerisable Quadruple Mutant, PDB code: 6ixw was solved by F.Koh, D.Popp, A.Narita, R.C.Robinson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 3.25
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	164.153, 93.922, 114.699, 90.00, 131.55, 90.00
R / Rfree (%)	15.8 / 21.4

The binding sites of Magnesium atom in the Pcbh Parm Non-Polymerisable Quadruple Mutant (pdb code 6ixw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Pcbh Parm Non-Polymerisable Quadruple Mutant, PDB code: 6ixw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Pcbh Parm Non-Polymerisable Quadruple Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pcbh Parm Non-Polymerisable Quadruple Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:26.9 occ:1.00 O1B C:ADP401 2.1 0.7 1.0 PB C:ADP401 3.2 47.6 1.0 OD2 C:ASP195 3.3 73.0 1.0 O3A C:ADP401 3.5 0.7 1.0 O3B C:ADP401 3.5 85.1 1.0 OE1 C:GLN168 3.7 74.7 1.0 OD2 C:ASP9 3.9 60.7 1.0 NE2 C:GLN168 4.2 65.2 1.0 CG C:ASP195 4.2 56.6 1.0 OD1 C:ASP195 4.3 89.0 1.0 OD1 C:ASP9 4.3 65.7 1.0 ND2 C:ASN338 4.3 68.7 1.0 CD C:GLN168 4.3 70.4 1.0 O1A C:ADP401 4.5 59.4 1.0 PA C:ADP401 4.5 57.2 1.0 CG C:ASP9 4.5 43.2 1.0 O2B C:ADP401 4.6 47.0 1.0 CA C:GLY197 4.6 25.6 1.0 CE C:LYS16 4.9 46.4 1.0

Magnesium binding site 2 out of 5 in the Pcbh Parm Non-Polymerisable Quadruple Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pcbh Parm Non-Polymerisable Quadruple Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg403 b:52.7 occ:1.00 OE1 C:GLU125 2.5 71.6 1.0 O C:THR223 3.1 39.7 1.0 CD C:GLU125 3.7 75.1 1.0 OD2 C:ASP225 3.9 80.2 1.0 C C:THR223 4.2 41.0 1.0 OE2 C:GLU125 4.3 73.1 1.0 N C:THR223 4.5 59.3 1.0 CA C:THR223 4.9 40.8 1.0 CB C:ALA222 4.9 19.2 1.0 CG C:GLU125 4.9 38.6 1.0 CB C:GLU125 4.9 45.9 1.0

Magnesium binding site 3 out of 5 in the Pcbh Parm Non-Polymerisable Quadruple Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pcbh Parm Non-Polymerisable Quadruple Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:33.8 occ:1.00 O1B B:ADP401 1.9 70.0 1.0 OD2 B:ASP195 3.1 83.5 1.0 PB B:ADP401 3.4 67.1 1.0 OD2 B:ASP9 3.6 67.2 1.0 O3A B:ADP401 3.8 76.3 1.0 OE1 B:GLN168 4.0 84.9 1.0 NE2 B:GLN168 4.0 57.1 1.0 CG B:ASP195 4.0 67.2 1.0 OD1 B:ASP195 4.2 99.5 1.0 O3B B:ADP401 4.2 41.6 1.0 ND2 B:ASN338 4.2 75.0 1.0 OD1 B:ASP9 4.2 72.3 1.0 O1A B:ADP401 4.4 67.7 1.0 CG B:ASP9 4.4 49.8 1.0 CD B:GLN168 4.4 87.5 1.0 O2B B:ADP401 4.4 33.6 1.0 CA B:GLY197 4.7 23.2 1.0 PA B:ADP401 4.8 62.7 1.0

Magnesium binding site 4 out of 5 in the Pcbh Parm Non-Polymerisable Quadruple Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pcbh Parm Non-Polymerisable Quadruple Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:16.2 occ:1.00 O1B A:ADP401 2.3 56.1 1.0 OD2 A:ASP195 3.2 80.0 1.0 PB A:ADP401 3.3 52.3 1.0 O3A A:ADP401 3.5 0.3 1.0 O3B A:ADP401 3.7 82.2 1.0 ND2 A:ASN338 4.0 64.2 1.0 OD1 A:ASP9 4.0 71.0 1.0 OE1 A:GLN168 4.0 81.8 1.0 CG A:ASP195 4.1 63.7 1.0 NE2 A:GLN168 4.2 56.0 1.0 OD1 A:ASP195 4.3 96.0 1.0 OD2 A:ASP9 4.4 65.9 1.0 CD A:GLN168 4.4 76.6 1.0 CA A:GLY197 4.5 28.5 1.0 O1A A:ADP401 4.6 59.3 1.0 PA A:ADP401 4.7 61.0 1.0 CG A:ASP9 4.7 48.5 1.0 O2B A:ADP401 4.8 40.0 1.0

Magnesium binding site 5 out of 5 in the Pcbh Parm Non-Polymerisable Quadruple Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pcbh Parm Non-Polymerisable Quadruple Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:59.3 occ:1.00 OD1 A:ASP225 2.6 68.8 1.0 OD2 A:ASP225 2.8 56.2 1.0 CG A:ASP225 3.1 76.1 1.0 O A:THR223 3.4 50.1 1.0 OE2 A:GLU125 3.5 77.2 1.0 CD2 A:HIS126 3.7 60.0 1.0 NE2 A:HIS126 3.7 58.1 1.0 CB A:GLU125 3.8 50.1 1.0 CG2 A:THR223 3.8 5.4 1.0 CB A:THR223 4.1 52.8 1.0 C A:THR223 4.3 38.3 1.0 CB A:ASP225 4.5 67.9 1.0 CD A:GLU125 4.6 79.3 1.0 C A:GLU125 4.7 52.1 1.0 O A:GLU125 4.7 90.1 1.0 CA A:THR223 4.7 33.3 1.0 CG A:GLU125 4.8 42.8 1.0 CA A:GLU125 4.8 41.4 1.0 N A:THR223 5.0 29.4 1.0 CE1 A:HIS126 5.0 81.9 1.0 N A:ASP225 5.0 52.5 1.0

F.Koh, A.Narita, L.J.Lee, K.Tanaka, Y.Z.Tan, V.P.Dandey, D.Popp, R.C.Robinson. The Structure of A 15-Stranded Actin-Like Filament From Clostridium Botulinum. Nat Commun V. 10 2856 2019.
ISSN: ESSN 2041-1723
PubMed: 31253774
DOI: 10.1038/S41467-019-10779-9