Magnesium in PDB 8xw7: Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Adp

The structure of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Adp, PDB code: 8xw7 was solved by R.Nakashima, A.Taguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.21 / 2.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	123.184, 255.539, 88.133, 90, 90, 90
R / Rfree (%)	18.6 / 22.7

The structure of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Adp also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Adp (pdb code 8xw7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Adp, PDB code: 8xw7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:59.9 occ:1.00 O A:HOH838 2.0 57.2 1.0 O A:HOH786 2.3 47.2 1.0 O1A A:ADP606 2.3 52.2 1.0 O1B A:ADP606 2.4 49.8 1.0 O A:HOH879 2.6 53.0 1.0 PB A:ADP606 3.6 46.2 1.0 PA A:ADP606 3.6 52.5 1.0 OD1 A:ASP153 3.8 68.6 1.0 O3A A:ADP606 3.9 49.9 1.0 O A:HOH764 4.0 52.8 1.0 CB A:SER340 4.0 39.0 1.0 OG A:SER340 4.1 51.3 1.0 O3B A:ADP606 4.2 47.0 1.0 CG2 A:THR306 4.3 45.1 1.0 O A:HOH721 4.4 44.2 1.0 OG1 A:THR306 4.4 40.5 1.0 O1 A:OXL605 4.4 54.5 1.0 C5' A:ADP606 4.5 54.0 1.0 C1 A:OXL605 4.5 47.0 1.0 O5' A:ADP606 4.6 51.0 1.0 O2A A:ADP606 4.7 53.1 1.0 CG A:ASP153 4.7 64.8 1.0 C2 A:OXL605 4.8 44.2 1.0 O2B A:ADP606 4.8 45.6 1.0 OD2 A:ASP153 4.8 59.2 1.0 O2 A:OXL605 4.9 46.9 1.0 NH2 A:ARG54 4.9 42.6 1.0 O3 A:OXL605 5.0 44.8 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:44.9 occ:1.00 OD1 A:ASP274 1.9 46.3 1.0 O3 A:OXL605 2.0 44.8 1.0 OE1 A:GLU250 2.1 42.7 1.0 O A:HOH727 2.1 40.2 1.0 O A:HOH721 2.2 44.2 1.0 O4 A:OXL605 2.2 40.4 1.0 C1 A:OXL605 2.8 47.0 1.0 C2 A:OXL605 2.9 44.2 1.0 CG A:ASP274 3.0 43.0 1.0 CD A:GLU250 3.1 44.9 1.0 OE2 A:GLU250 3.5 45.7 1.0 CB A:ASP274 3.6 41.2 1.0 O A:HOH821 4.0 56.4 1.0 O1 A:OXL605 4.1 54.5 1.0 O2 A:OXL605 4.1 46.9 1.0 OD2 A:ASP274 4.1 51.1 1.0 NZ A:LYS248 4.1 42.6 1.0 O A:HOH879 4.3 53.0 1.0 N A:ASP274 4.3 41.3 1.0 CB A:ALA271 4.4 42.9 1.0 O A:HOH838 4.4 57.2 1.0 CE A:LYS248 4.4 41.9 1.0 CG A:GLU250 4.5 43.4 1.0 O A:HOH839 4.6 44.9 1.0 CE2 A:PHE221 4.6 52.7 1.0 CA A:ASP274 4.6 39.6 1.0 CZ A:PHE221 4.6 45.9 1.0 CB A:GLU250 4.7 44.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:55.8 occ:1.00 OD1 B:ASP274 1.9 53.4 1.0 O2 B:OXL605 2.0 68.6 1.0 OE1 B:GLU250 2.3 53.1 1.0 O B:HOH713 2.3 52.3 1.0 O1 B:OXL605 2.5 58.1 1.0 C2 B:OXL605 2.9 72.3 1.0 CG B:ASP274 3.1 56.9 1.0 C1 B:OXL605 3.1 69.2 1.0 CD B:GLU250 3.4 57.4 1.0 CB B:ASP274 3.7 53.8 1.0 OE2 B:GLU250 3.8 60.7 1.0 O B:HOH822 4.0 76.1 1.0 O4 B:OXL605 4.0 66.3 1.0 O B:HOH830 4.2 57.9 1.0 OD2 B:ASP274 4.2 63.3 1.0 CE2 B:PHE221 4.2 58.3 1.0 O3 B:OXL605 4.3 69.2 1.0 NZ B:LYS248 4.4 56.1 1.0 N B:ASP274 4.4 44.4 1.0 CG B:GLU250 4.6 53.6 1.0 CE B:LYS248 4.7 53.1 1.0 CA B:ASP274 4.7 44.7 1.0 CZ B:PHE221 4.7 55.7 1.0 CB B:ALA271 5.0 52.5 1.0 CD2 B:PHE221 5.0 58.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:90.1 occ:1.00 O1A B:ADP606 2.4 124.6 1.0 O B:HOH822 2.6 76.1 1.0 O2B B:ADP606 2.7 104.3 1.0 PA B:ADP606 3.8 133.2 1.0 PB B:ADP606 4.0 112.0 1.0 O3A B:ADP606 4.1 132.9 1.0 CG2 B:THR306 4.2 49.9 1.0 CB B:SER340 4.3 51.5 1.0 OG B:SER340 4.3 55.2 1.0 O4 B:OXL605 4.4 66.3 1.0 O5' B:ADP606 4.4 129.3 1.0 C1 B:OXL605 4.5 69.2 1.0 O3 B:OXL605 4.5 69.2 1.0 C5' B:ADP606 4.5 119.4 1.0 C2 B:OXL605 4.5 72.3 1.0 OG1 B:THR306 4.5 46.7 1.0 O1B B:ADP606 5.0 90.6 1.0 CB B:THR306 5.0 49.5 1.0 O3B B:ADP606 5.0 111.8 1.0 O1 B:OXL605 5.0 58.1 1.0 O2A B:ADP606 5.0 109.2 1.0

A.Taguchi, R.Nakashima, K.Nishino. Structural Basis of Nucleotide Selectivity in Pyruvate Kinase. J.Mol.Biol. 68708 2024.
ISSN: ESSN 1089-8638
PubMed: 39009072
DOI: 10.1016/J.JMB.2024.168708