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

Protein crystallography data

The structure of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate, PDB code: 8iax 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) 48.37 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 221.061, 86.644, 258.148, 90, 100.86, 90
R / Rfree (%) 18.3 / 22.1

Other elements in 8iax:

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

Potassium (K) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate (pdb code 8iax). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate, PDB code: 8iax:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8iax

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Magnesium binding site 1 out of 8 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate


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 Phosphoenolpyruvate and Fructose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:35.4
occ:1.00
 OD1 A:ASP274 2.0 32.4 1.0
O3P A:PEP602 2.1 35.3 1.0
O1 A:PEP602 2.1 30.8 1.0
O A:HOH836 2.2 31.9 1.0
OE1 A:GLU250 2.2 33.5 1.0
O2 A:PEP602 2.4 39.9 1.0
P A:PEP602 2.9 42.7 1.0
C1 A:PEP602 3.0 34.8 1.0
C2 A:PEP602 3.1 34.8 1.0
CG A:ASP274 3.1 33.5 1.0
CD A:GLU250 3.2 36.2 1.0
OE2 A:GLU250 3.6 34.0 1.0
CB A:ASP274 3.6 30.7 1.0
O1P A:PEP602 3.8 38.7 1.0
O2P A:PEP602 4.1 39.7 1.0
O2' A:PEP602 4.2 31.8 1.0
N A:ASP274 4.2 29.1 1.0
OD2 A:ASP274 4.2 31.6 1.0
NZ A:LYS248 4.3 32.1 1.0
CE2 A:PHE221 4.4 41.2 1.0
C3 A:PEP602 4.4 37.0 1.0
O A:HOH786 4.5 37.1 1.0
CA A:ASP274 4.5 31.3 1.0
CG A:GLU250 4.6 33.2 1.0
CB A:ALA271 4.6 28.1 1.0
CE A:LYS248 4.6 33.2 1.0
CB A:GLU250 4.8 36.4 1.0
CZ A:PHE221 4.8 43.7 1.0

Magnesium binding site 2 out of 8 in 8iax

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Magnesium binding site 2 out of 8 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate


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 Phosphoenolpyruvate and Fructose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:35.3
occ:1.00
 O B:HOH773 2.1 31.2 1.0
O2P B:PEP602 2.1 38.2 1.0
OD1 B:ASP274 2.1 32.3 1.0
OE1 B:GLU250 2.2 31.9 1.0
O2' B:PEP602 2.2 30.2 1.0
O2 B:PEP602 2.4 36.0 1.0
P B:PEP602 2.9 40.8 1.0
C1 B:PEP602 3.0 32.7 1.0
C2 B:PEP602 3.1 33.0 1.0
CG B:ASP274 3.2 32.1 1.0
CD B:GLU250 3.2 32.5 1.0
OE2 B:GLU250 3.6 30.6 1.0
CB B:ASP274 3.6 32.1 1.0
O3P B:PEP602 3.8 36.4 1.0
O B:HOH960 3.9 64.5 1.0
O1P B:PEP602 4.1 41.1 1.0
O1 B:PEP602 4.2 31.1 1.0
NZ B:LYS248 4.2 33.3 1.0
CE2 B:PHE221 4.2 34.5 1.0
OD2 B:ASP274 4.3 35.5 1.0
N B:ASP274 4.3 30.7 1.0
C3 B:PEP602 4.4 28.7 1.0
CE B:LYS248 4.4 30.3 1.0
O B:HOH783 4.5 36.9 1.0
CG B:GLU250 4.5 34.0 1.0
CA B:ASP274 4.6 28.6 1.0
CB B:ALA271 4.6 31.4 1.0
CB B:GLU250 4.8 34.6 1.0
CZ B:PHE221 4.8 38.7 1.0
CD2 B:PHE221 4.9 41.3 1.0

Magnesium binding site 3 out of 8 in 8iax

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Magnesium binding site 3 out of 8 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate


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 Phosphoenolpyruvate and Fructose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:33.6
occ:1.00
 OE1 C:GLU250 2.1 30.0 1.0
O2P C:PEP602 2.1 35.6 1.0
OD1 C:ASP274 2.1 30.4 1.0
O C:HOH746 2.1 29.7 1.0
O2' C:PEP602 2.2 28.3 1.0
O2 C:PEP602 2.5 34.7 1.0
P C:PEP602 3.0 39.3 1.0
C1 C:PEP602 3.1 32.5 1.0
CD C:GLU250 3.1 33.3 1.0
CG C:ASP274 3.2 34.5 1.0
C2 C:PEP602 3.3 31.0 1.0
OE2 C:GLU250 3.5 31.4 1.0
CB C:ASP274 3.6 27.8 1.0
O3P C:PEP602 3.9 38.4 1.0
O1P C:PEP602 4.1 39.5 1.0
O1 C:PEP602 4.2 27.7 1.0
N C:ASP274 4.3 28.4 1.0
NZ C:LYS248 4.3 29.1 1.0
OD2 C:ASP274 4.3 32.3 1.0
CE2 C:PHE221 4.4 44.9 1.0
CG C:GLU250 4.4 31.0 1.0
CZ C:PHE221 4.4 38.0 1.0
CE C:LYS248 4.4 30.6 1.0
CB C:ALA271 4.5 28.3 1.0
O C:HOH789 4.5 36.4 1.0
C3 C:PEP602 4.5 29.4 1.0
CA C:ASP274 4.6 26.1 1.0
CB C:GLU250 4.6 33.9 1.0
O C:HOH715 4.8 49.2 1.0

Magnesium binding site 4 out of 8 in 8iax

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Magnesium binding site 4 out of 8 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate


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 Phosphoenolpyruvate and Fructose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg603

b:41.6
occ:1.00
 O D:HOH833 2.0 39.5 1.0
O1P D:PEP602 2.1 45.5 1.0
OD1 D:ASP274 2.2 36.9 1.0
OE1 D:GLU250 2.4 36.0 1.0
O1 D:PEP602 2.5 33.9 1.0
O2 D:PEP602 2.6 49.7 1.0
P D:PEP602 3.2 43.7 1.0
CG D:ASP274 3.2 35.9 1.0
C1 D:PEP602 3.3 40.0 1.0
C2 D:PEP602 3.3 42.5 1.0
CD D:GLU250 3.3 37.2 1.0
OE2 D:GLU250 3.6 32.5 1.0
CB D:ASP274 3.7 32.0 1.0
O3P D:PEP602 3.9 43.8 1.0
O D:HOH1007 4.2 49.0 1.0
NZ D:LYS248 4.3 30.6 1.0
CE2 D:PHE221 4.3 42.1 1.0
O D:HOH1029 4.3 59.2 1.0
OD2 D:ASP274 4.3 36.5 1.0
O2P D:PEP602 4.4 50.0 1.0
O2' D:PEP602 4.4 32.1 1.0
CE D:LYS248 4.4 28.9 1.0
N D:ASP274 4.4 31.5 1.0
C3 D:PEP602 4.6 36.2 1.0
CB D:ALA271 4.6 31.8 1.0
CG D:GLU250 4.7 33.1 1.0
CA D:ASP274 4.7 29.4 1.0
CB D:GLU250 4.9 35.8 1.0
CD2 D:PHE221 4.9 42.5 1.0

Magnesium binding site 5 out of 8 in 8iax

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Magnesium binding site 5 out of 8 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg603

b:40.8
occ:1.00
 OD1 E:ASP274 1.9 41.2 1.0
O E:HOH775 2.1 40.1 1.0
OE1 E:GLU250 2.2 39.0 1.0
O2P E:PEP602 2.2 42.2 1.0
O2' E:PEP602 2.3 39.4 1.0
O2 E:PEP602 2.5 46.7 1.0
CG E:ASP274 3.0 37.1 1.0
P E:PEP602 3.1 46.8 1.0
C1 E:PEP602 3.1 40.6 1.0
CD E:GLU250 3.2 40.9 1.0
C2 E:PEP602 3.2 37.3 1.0
OE2 E:GLU250 3.5 38.3 1.0
CB E:ASP274 3.5 35.2 1.0
O3P E:PEP602 3.9 45.6 1.0
OD2 E:ASP274 4.1 39.2 1.0
CE2 E:PHE221 4.2 53.2 1.0
N E:ASP274 4.3 32.7 1.0
O1P E:PEP602 4.3 48.8 1.0
O1 E:PEP602 4.3 39.4 1.0
NZ E:LYS248 4.3 42.3 1.0
CZ E:PHE221 4.4 45.1 1.0
O E:HOH818 4.4 47.7 1.0
C3 E:PEP602 4.5 41.7 1.0
CA E:ASP274 4.5 34.8 1.0
CG E:GLU250 4.6 37.0 1.0
CB E:ALA271 4.6 45.8 1.0
CE E:LYS248 4.6 43.1 1.0
CB E:GLU250 4.8 41.6 1.0

Magnesium binding site 6 out of 8 in 8iax

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Magnesium binding site 6 out of 8 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg603

b:40.2
occ:1.00
 OD1 F:ASP274 2.0 38.1 1.0
O F:HOH782 2.1 36.1 1.0
O3P F:PEP602 2.1 43.4 1.0
OE1 F:GLU250 2.2 40.7 1.0
O1 F:PEP602 2.3 36.5 1.0
O2 F:PEP602 2.4 42.0 1.0
P F:PEP602 2.9 44.3 1.0
C1 F:PEP602 3.1 36.8 1.0
CG F:ASP274 3.1 36.9 1.0
C2 F:PEP602 3.2 37.5 1.0
CD F:GLU250 3.2 41.3 1.0
OE2 F:GLU250 3.5 38.1 1.0
CB F:ASP274 3.6 33.3 1.0
O F:HOH722 3.7 62.0 1.0
O1P F:PEP602 3.8 39.1 1.0
O2P F:PEP602 4.0 45.5 1.0
NZ F:LYS248 4.2 36.1 1.0
OD2 F:ASP274 4.2 38.4 1.0
O F:HOH862 4.2 42.3 1.0
O2' F:PEP602 4.2 33.8 1.0
CE2 F:PHE221 4.3 46.1 1.0
N F:ASP274 4.3 33.3 1.0
O F:HOH882 4.5 55.1 1.0
CE F:LYS248 4.5 32.3 1.0
C3 F:PEP602 4.5 33.6 1.0
CG F:GLU250 4.5 38.9 1.0
CA F:ASP274 4.6 31.9 1.0
CZ F:PHE221 4.6 45.1 1.0
CB F:ALA271 4.6 36.5 1.0
CB F:GLU250 4.8 42.0 1.0

Magnesium binding site 7 out of 8 in 8iax

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Magnesium binding site 7 out of 8 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg603

b:36.0
occ:1.00
 O1P G:PEP602 2.0 36.7 1.0
OE1 G:GLU250 2.0 31.2 1.0
OD1 G:ASP274 2.1 35.5 1.0
O G:HOH778 2.1 33.5 1.0
O1 G:PEP602 2.3 32.0 1.0
O2 G:PEP602 2.5 39.7 1.0
P G:PEP602 3.0 40.3 1.0
CD G:GLU250 3.1 34.6 1.0
C1 G:PEP602 3.1 34.5 1.0
CG G:ASP274 3.1 37.1 1.0
C2 G:PEP602 3.2 32.3 1.0
OE2 G:GLU250 3.5 32.5 1.0
CB G:ASP274 3.6 29.9 1.0
O3P G:PEP602 3.8 43.8 1.0
O2P G:PEP602 4.2 42.4 1.0
OD2 G:ASP274 4.2 36.1 1.0
NZ G:LYS248 4.3 32.4 1.0
O2' G:PEP602 4.3 35.1 1.0
N G:ASP274 4.3 29.8 1.0
CE2 G:PHE221 4.3 43.6 1.0
CZ G:PHE221 4.3 39.4 1.0
CG G:GLU250 4.4 33.9 1.0
O G:HOH793 4.4 41.8 1.0
CB G:ALA271 4.5 31.1 1.0
CE G:LYS248 4.5 32.7 1.0
C3 G:PEP602 4.5 33.1 1.0
CA G:ASP274 4.6 28.2 1.0
CB G:GLU250 4.7 35.6 1.0
O G:HOH807 4.8 47.3 1.0

Magnesium binding site 8 out of 8 in 8iax

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Magnesium binding site 8 out of 8 in the Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Phosphoenolpyruvate and Fructose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg603

b:43.4
occ:1.00
 O2P H:PEP602 2.1 46.3 1.0
O H:HOH783 2.1 40.7 1.0
OD1 H:ASP274 2.1 39.1 1.0
OE1 H:GLU250 2.2 35.9 1.0
O2' H:PEP602 2.3 34.3 1.0
O2 H:PEP602 2.5 44.1 1.0
P H:PEP602 3.1 45.0 1.0
C1 H:PEP602 3.1 37.6 1.0
CG H:ASP274 3.2 37.6 1.0
C2 H:PEP602 3.2 42.9 1.0
CD H:GLU250 3.2 38.2 1.0
OE2 H:GLU250 3.5 33.1 1.0
CB H:ASP274 3.6 31.6 1.0
O3P H:PEP602 3.9 40.4 1.0
O1P H:PEP602 4.2 47.9 1.0
OD2 H:ASP274 4.3 36.5 1.0
O1 H:PEP602 4.3 33.5 1.0
CE2 H:PHE221 4.3 38.6 1.0
N H:ASP274 4.3 31.9 1.0
NZ H:LYS248 4.4 34.7 1.0
C3 H:PEP602 4.5 41.3 1.0
CG H:GLU250 4.5 35.4 1.0
CE H:LYS248 4.5 31.5 1.0
CB H:ALA271 4.6 31.2 1.0
CA H:ASP274 4.6 28.6 1.0
CB H:GLU250 4.8 35.0 1.0
CD2 H:PHE221 4.9 41.2 1.0

Reference:

A.Taguchi, R.Nakashima, K.Nishino. Functional and Structural Characterization of Streptococcus Pneumoniae Pyruvate Kinase Involved in Fosfomycin Resistance. J.Biol.Chem. 2023.
ISSN: ESSN 1083-351X
DOI: 10.1016/J.JBC.2023.104892
Page generated: Fri Oct 4 09:20:19 2024

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