Magnesium in PDB 8xw8: Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Gdp

Protein crystallography data

The structure of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Gdp, PDB code: 8xw8 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) 47.30 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 123.335, 256.08, 88.575, 90, 90.04, 90
R / Rfree (%) 19.8 / 23.4

Other elements in 8xw8:

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

Potassium (K) 4 atoms

Magnesium Binding Sites:

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 Gdp (pdb code 8xw8). 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 Oxalate and Fructose 1,6-Bisphosphate and Gdp, PDB code: 8xw8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8xw8

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


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 Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:24.5
occ:1.00
 OD1 A:ASP274 1.9 22.4 1.0
OE1 A:GLU250 2.0 20.0 1.0
O1 A:OXL606 2.1 23.6 1.0
O A:HOH778 2.1 19.1 1.0
O A:HOH747 2.1 22.7 1.0
O2 A:OXL606 2.2 23.9 1.0
C1 A:OXL606 2.8 25.3 1.0
C2 A:OXL606 2.9 23.4 1.0
CG A:ASP274 3.0 22.2 1.0
CD A:GLU250 3.0 22.2 1.0
OE2 A:GLU250 3.4 21.7 1.0
CB A:ASP274 3.5 22.5 1.0
O A:HOH1066 4.0 37.0 1.0
O3 A:OXL606 4.1 30.1 1.0
OD2 A:ASP274 4.1 26.2 1.0
O4 A:OXL606 4.1 28.7 1.0
NZ A:LYS248 4.2 21.8 1.0
O A:HOH755 4.2 43.1 1.0
CB A:ALA271 4.3 19.1 1.0
N A:ASP274 4.3 22.2 1.0
CG A:GLU250 4.4 21.6 1.0
CE A:LYS248 4.4 20.5 1.0
O A:HOH992 4.5 25.4 1.0
CA A:ASP274 4.6 20.1 1.0
CZ A:PHE221 4.6 23.9 1.0
CB A:GLU250 4.6 20.6 1.0
CE2 A:PHE221 4.6 26.0 1.0
O A:HOH989 4.6 26.5 1.0
O A:HOH1034 4.7 41.0 1.0
O A:HOH947 4.8 32.4 1.0

Magnesium binding site 2 out of 8 in 8xw8

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


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 Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:21.5
occ:1.00
 O A:HOH992 2.0 25.4 1.0
O2A A:GDP605 2.0 19.5 1.0
O A:HOH769 2.0 24.9 1.0
O3B A:GDP605 2.0 23.2 1.0
O A:HOH767 2.1 23.1 1.0
O A:HOH989 2.2 26.5 1.0
PB A:GDP605 3.2 20.9 1.0
PA A:GDP605 3.2 20.5 1.0
O3A A:GDP605 3.5 18.9 1.0
O1B A:GDP605 3.7 22.0 1.0
O A:HOH736 3.9 33.2 1.0
OD1 A:ASP153 4.0 33.4 1.0
O3 A:OXL606 4.2 30.1 1.0
O A:HOH887 4.2 22.3 1.0
O1A A:GDP605 4.2 23.8 1.0
OG A:SER340 4.2 24.1 1.0
O A:HOH747 4.3 22.7 1.0
CB A:SER340 4.3 20.5 1.0
C1 A:OXL606 4.4 25.3 1.0
OG1 A:THR306 4.4 22.4 1.0
O5' A:GDP605 4.5 19.7 1.0
O2B A:GDP605 4.5 23.8 1.0
C5' A:GDP605 4.5 19.7 1.0
OD2 A:ASP153 4.5 28.2 1.0
CG A:ASP153 4.7 32.2 1.0
O A:HOH1034 4.7 41.0 1.0
C2 A:OXL606 4.7 23.4 1.0
CG2 A:THR306 4.8 23.2 1.0
O1 A:OXL606 4.9 23.6 1.0
O4 A:OXL606 5.0 28.7 1.0
NH2 A:ARG54 5.0 19.1 1.0

Magnesium binding site 3 out of 8 in 8xw8

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


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 Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:23.4
occ:1.00
 O B:HOH968 2.0 24.6 1.0
O1A B:GDP605 2.0 18.9 1.0
O1B B:GDP605 2.0 22.5 1.0
O B:HOH789 2.1 28.4 1.0
O B:HOH739 2.1 23.1 1.0
O B:HOH993 2.2 25.3 1.0
PB B:GDP605 3.2 20.8 1.0
PA B:GDP605 3.3 20.3 1.0
O3A B:GDP605 3.5 19.5 1.0
O2B B:GDP605 3.7 21.4 1.0
O2 B:OXL606 4.0 30.2 1.0
OD1 B:ASP153 4.1 35.3 1.0
O B:HOH750 4.1 30.4 1.0
O B:HOH897 4.2 27.1 1.0
O2A B:GDP605 4.2 23.2 1.0
OG B:SER340 4.3 25.8 1.0
C2 B:OXL606 4.3 26.1 1.0
CB B:SER340 4.3 21.8 1.0
O B:HOH736 4.3 23.9 1.0
OG1 B:THR306 4.4 23.2 1.0
O5' B:GDP605 4.4 20.4 1.0
O3B B:GDP605 4.5 22.1 1.0
C5' B:GDP605 4.6 20.6 1.0
O B:HOH1041 4.6 42.4 1.0
OD2 B:ASP153 4.6 28.1 1.0
C1 B:OXL606 4.7 24.6 1.0
CG B:ASP153 4.7 31.8 1.0
O4 B:OXL606 4.8 24.3 1.0
NH2 B:ARG54 4.8 19.6 1.0
CG2 B:THR306 4.9 22.3 1.0
O1 B:OXL606 4.9 28.3 1.0

Magnesium binding site 4 out of 8 in 8xw8

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


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 Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:23.7
occ:1.00
 OD1 B:ASP274 1.9 25.5 1.0
O4 B:OXL606 2.0 24.3 1.0
OE1 B:GLU250 2.0 22.5 1.0
O B:HOH736 2.1 23.9 1.0
O B:HOH775 2.1 17.9 1.0
O3 B:OXL606 2.2 23.8 1.0
C2 B:OXL606 2.8 26.1 1.0
C1 B:OXL606 2.8 24.6 1.0
CG B:ASP274 3.0 25.1 1.0
CD B:GLU250 3.1 23.6 1.0
OE2 B:GLU250 3.5 23.1 1.0
CB B:ASP274 3.5 23.7 1.0
O2 B:OXL606 4.0 30.2 1.0
O B:HOH1045 4.1 33.2 1.0
O1 B:OXL606 4.1 28.3 1.0
OD2 B:ASP274 4.1 29.1 1.0
NZ B:LYS248 4.2 20.2 1.0
N B:ASP274 4.3 22.6 1.0
CB B:ALA271 4.3 19.2 1.0
CG B:GLU250 4.4 22.4 1.0
O B:HOH968 4.4 24.6 1.0
CE B:LYS248 4.4 19.6 1.0
O B:HOH1041 4.5 42.4 1.0
O B:HOH993 4.5 25.3 1.0
CA B:ASP274 4.5 21.4 1.0
CB B:GLU250 4.6 21.7 1.0
CE2 B:PHE221 4.6 25.6 1.0
CZ B:PHE221 4.7 22.5 1.0
O B:HOH948 4.7 30.5 1.0

Magnesium binding site 5 out of 8 in 8xw8

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


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 Oxalate and Fructose 1,6-Bisphosphate and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:47.0
occ:1.00
 O2A C:GDP605 2.2 34.6 1.0
O3B C:GDP605 2.2 34.9 1.0
O C:HOH916 2.3 40.1 1.0
PB C:GDP605 3.5 40.5 1.0
PA C:GDP605 3.5 41.4 1.0
O3A C:GDP605 3.8 34.0 1.0
O C:HOH880 3.9 56.2 1.0
O C:HOH1001 4.1 39.1 1.0
C1 C:OXL606 4.1 37.4 1.0
O3 C:OXL606 4.2 37.9 1.0
C2 C:OXL606 4.2 34.1 1.0
O C:HOH716 4.2 26.2 1.0
OD1 C:ASP153 4.2 73.0 1.0
O1B C:GDP605 4.2 45.8 1.0
OG1 C:THR306 4.4 29.5 1.0
O4 C:OXL606 4.4 32.5 1.0
O1 C:OXL606 4.5 35.7 1.0
O1A C:GDP605 4.6 33.4 1.0
OG C:SER340 4.6 29.7 1.0
CG2 C:THR306 4.6 29.5 1.0
CB C:SER340 4.7 27.4 1.0
O2B C:GDP605 4.7 51.1 1.0
O2 C:OXL606 4.7 30.6 1.0
O5' C:GDP605 4.8 30.7 1.0
C5' C:GDP605 4.9 36.7 1.0
O C:HOH964 5.0 40.9 1.0

Magnesium binding site 6 out of 8 in 8xw8

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


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 Oxalate and Fructose 1,6-Bisphosphate and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:30.8
occ:1.00
 OE1 C:GLU250 1.8 28.0 1.0
OD1 C:ASP274 1.8 28.8 1.0
O C:HOH716 2.2 26.2 1.0
O C:HOH754 2.2 28.3 1.0
O1 C:OXL606 2.3 35.7 1.0
O2 C:OXL606 2.4 30.6 1.0
CD C:GLU250 2.7 32.5 1.0
CG C:ASP274 2.9 30.3 1.0
OE2 C:GLU250 3.1 36.2 1.0
C1 C:OXL606 3.1 37.4 1.0
C2 C:OXL606 3.1 34.1 1.0
CB C:ASP274 3.4 27.7 1.0
OD2 C:ASP274 4.0 35.6 1.0
O C:HOH964 4.1 40.9 1.0
CG C:GLU250 4.1 30.8 1.0
CE2 C:PHE221 4.2 35.3 1.0
CB C:ALA271 4.3 24.1 1.0
O C:HOH916 4.3 40.1 1.0
N C:ASP274 4.3 26.9 1.0
O4 C:OXL606 4.3 32.5 1.0
O3 C:OXL606 4.3 37.9 1.0
CB C:GLU250 4.4 29.0 1.0
CE C:LYS248 4.4 30.2 1.0
NZ C:LYS248 4.4 30.4 1.0
CA C:ASP274 4.5 25.9 1.0
O C:HOH920 4.5 53.3 1.0
CZ C:PHE221 4.7 33.3 1.0
CD2 C:PHE221 4.8 32.5 1.0
O C:HOH959 5.0 46.0 1.0

Magnesium binding site 7 out of 8 in 8xw8

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


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 Oxalate and Fructose 1,6-Bisphosphate and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:31.9
occ:1.00
 OE1 D:GLU250 1.8 27.2 1.0
OD1 D:ASP274 1.8 26.5 1.0
O4 D:OXL606 2.2 35.3 1.0
O D:HOH911 2.3 23.5 1.0
O D:HOH704 2.3 23.4 1.0
O3 D:OXL606 2.4 31.9 1.0
CD D:GLU250 2.7 33.2 1.0
CG D:ASP274 2.9 28.5 1.0
C2 D:OXL606 3.1 39.9 1.0
C1 D:OXL606 3.1 35.7 1.0
OE2 D:GLU250 3.1 37.3 1.0
CB D:ASP274 3.4 27.3 1.0
OD2 D:ASP274 3.9 36.1 1.0
CG D:GLU250 4.1 31.1 1.0
CB D:ALA271 4.2 28.6 1.0
O D:HOH766 4.2 42.5 1.0
CE2 D:PHE221 4.2 35.2 1.0
NZ D:LYS248 4.3 29.5 1.0
O2 D:OXL606 4.3 41.0 1.0
O1 D:OXL606 4.3 34.7 1.0
CE D:LYS248 4.3 32.4 1.0
N D:ASP274 4.3 26.4 1.0
CB D:GLU250 4.4 29.0 1.0
O D:HOH913 4.4 38.0 1.0
CA D:ASP274 4.5 25.9 1.0
CZ D:PHE221 4.7 34.6 1.0
CD2 D:PHE221 4.8 34.5 1.0
O D:HOH959 5.0 43.5 1.0
O D:ALA271 5.0 24.2 1.0

Magnesium binding site 8 out of 8 in 8xw8

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


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 Oxalate and Fructose 1,6-Bisphosphate and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg602

b:49.8
occ:1.00
 O1A D:GDP605 2.2 39.0 1.0
O2B D:GDP605 2.3 35.8 1.0
O D:HOH913 2.3 38.0 1.0
O D:HOH766 2.6 42.5 1.0
O D:HOH725 2.8 42.1 1.0
PB D:GDP605 3.5 41.5 1.0
PA D:GDP605 3.5 39.2 1.0
O D:HOH704 3.8 23.4 1.0
O3A D:GDP605 3.8 33.8 1.0
O2 D:OXL606 4.0 41.0 1.0
O D:HOH803 4.0 57.1 1.0
C2 D:OXL606 4.0 39.9 1.0
C1 D:OXL606 4.2 35.7 1.0
O D:HOH967 4.2 36.3 1.0
O3B D:GDP605 4.2 51.0 1.0
OD1 D:ASP153 4.4 69.9 1.0
O1 D:OXL606 4.5 34.7 1.0
O2A D:GDP605 4.5 38.1 1.0
OG1 D:THR306 4.5 29.2 1.0
O3 D:OXL606 4.5 31.9 1.0
O4 D:OXL606 4.6 35.3 1.0
OG D:SER340 4.6 28.9 1.0
CG2 D:THR306 4.6 27.9 1.0
CB D:SER340 4.7 30.2 1.0
O1B D:GDP605 4.7 52.1 1.0
O5' D:GDP605 4.8 30.6 1.0
C5' D:GDP605 5.0 37.2 1.0

Reference:

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
Page generated: Sat Oct 5 07:49:37 2024

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