Magnesium in PDB 8xw9: Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Udp

The structure of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Udp, PDB code: 8xw9 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)	40.73 / 1.75
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	81.464, 81.464, 398.91, 90, 90, 90
R / Rfree (%)	16 / 19.1

The structure of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Udp 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 Udp (pdb code 8xw9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 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 Udp, PDB code: 8xw9:
Jump to Magnesium binding site number: 1; 2; 3;

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


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 Udp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:42.4 occ:1.00 O2A A:UDP606 2.1 31.6 1.0 O A:HOH1103 2.1 44.6 1.0 O A:HOH1060 2.2 42.1 1.0 O A:HOH1014 2.2 47.8 1.0 O A:HOH760 2.3 38.3 1.0 O2B A:UDP606 2.4 33.4 1.0 PB A:UDP606 3.3 30.8 1.0 PA A:UDP606 3.3 28.0 1.0 O3A A:UDP606 3.6 27.7 1.0 O3B A:UDP606 3.8 30.6 1.0 OG A:SER340 4.1 31.9 1.0 O A:HOH779 4.1 45.2 1.0 O1A A:UDP606 4.2 27.1 1.0 O A:HOH898 4.3 36.8 1.0 CB A:SER340 4.3 26.9 1.0 C1 A:OXL604 4.3 43.1 1.0 O A:HOH1040 4.4 37.3 1.0 O3 A:OXL604 4.4 49.2 1.0 OG1 A:THR306 4.5 30.3 1.0 O5' A:UDP606 4.5 27.8 1.0 C2 A:OXL604 4.6 37.9 1.0 O A:HOH1013 4.6 40.6 1.0 O1B A:UDP606 4.7 33.3 1.0 O1 A:OXL604 4.7 36.3 1.0 NH2 A:ARG54 4.7 29.3 1.0 C5' A:UDP606 4.7 30.0 1.0 O4 A:OXL604 4.9 37.4 1.0 CG2 A:THR306 4.9 29.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Udp


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 Udp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:31.9 occ:1.00 OE1 A:GLU250 2.0 27.9 1.0 OD1 A:ASP274 2.0 30.2 1.0 O A:HOH768 2.1 29.9 1.0 O1 A:OXL604 2.1 36.3 1.0 O A:HOH898 2.2 36.8 1.0 O2 A:OXL604 2.2 30.9 1.0 C2 A:OXL604 2.9 37.9 1.0 C1 A:OXL604 2.9 43.1 1.0 CD A:GLU250 3.1 29.0 1.0 CG A:ASP274 3.1 34.2 1.0 OE2 A:GLU250 3.4 28.0 1.0 CB A:ASP274 3.6 28.5 1.0 O A:HOH967 3.9 47.4 1.0 O A:HOH1013 4.0 40.6 1.0 O4 A:OXL604 4.1 37.4 1.0 NZ A:LYS248 4.1 30.8 1.0 OD2 A:ASP274 4.2 35.0 1.0 O3 A:OXL604 4.2 49.2 1.0 O A:HOH1103 4.4 44.6 1.0 CG A:GLU250 4.4 29.7 1.0 CE A:LYS248 4.4 32.1 1.0 CE2 A:PHE221 4.4 34.1 1.0 O A:HOH1060 4.4 42.1 1.0 CB A:ALA271 4.5 28.1 1.0 CZ A:PHE221 4.5 32.1 1.0 N A:ASP274 4.5 27.4 1.0 O A:HOH914 4.7 34.5 1.0 CA A:ASP274 4.7 29.2 1.0 CB A:GLU250 4.7 30.1 1.0

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


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 Udp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:31.3 occ:1.00 OD1 B:ASP274 2.0 31.7 1.0 OE1 B:GLU250 2.1 31.4 1.0 O B:HOH811 2.1 33.3 1.0 O2 B:OXL603 2.1 39.8 1.0 O1 B:OXL603 2.1 33.0 1.0 O B:HOH820 2.1 32.1 1.0 C1 B:OXL603 2.9 37.9 1.0 C2 B:OXL603 2.9 40.1 1.0 CG B:ASP274 3.1 31.7 1.0 CD B:GLU250 3.1 33.9 1.0 OE2 B:GLU250 3.5 29.4 1.0 CB B:ASP274 3.6 30.1 1.0 O B:HOH987 3.8 59.7 1.0 O B:HOH988 4.1 41.6 1.0 O3 B:OXL603 4.1 35.5 1.0 NZ B:LYS248 4.2 31.4 1.0 OD2 B:ASP274 4.2 36.2 1.0 O4 B:OXL603 4.2 47.3 1.0 N B:ASP274 4.4 27.6 1.0 CE2 B:PHE221 4.4 39.6 1.0 CG B:GLU250 4.5 34.2 1.0 O B:HOH795 4.5 35.5 1.0 CE B:LYS248 4.5 31.0 1.0 CB B:ALA271 4.6 30.3 1.0 CA B:ASP274 4.6 28.1 1.0 CZ B:PHE221 4.6 38.6 1.0 CB B:GLU250 4.8 36.3 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