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

Protein crystallography data

The structure of Crystal Structure of Streptococcus Pneumoniae Pyruvate Kinase in Complex with Oxalate and Fructose 1,6-Bisphosphate and Udp, PDB code: 8zly 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) 48.16 / 1.89
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 115.809, 403.204, 113.593, 90, 90, 90
R / Rfree (%) 16.5 / 20.5

Other elements in 8zly:

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) 8 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

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 Udp (pdb code 8zly). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 15 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: 8zly:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 15 in 8zly

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Magnesium binding site 1 out of 15 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:Mg602

b:38.3
occ:1.00
 O A:HOH973 2.0 42.0 1.0
O2A A:UDP604 2.0 31.4 1.0
O A:HOH831 2.2 36.0 1.0
O A:HOH958 2.3 42.5 1.0
O2B A:UDP604 2.3 34.8 1.0
O A:HOH817 2.4 37.9 1.0
PB A:UDP604 3.3 32.6 1.0
PA A:UDP604 3.3 34.7 1.0
O3A A:UDP604 3.6 32.2 1.0
O1B A:UDP604 3.7 34.4 1.0
O A:HOH818 3.9 48.7 1.0
O1 A:OXL606 4.1 43.1 1.0
OG A:SER340 4.1 32.2 1.0
OD2 A:ASP153 4.2 67.4 1.0
O A:HOH1032 4.2 36.9 1.0
CB A:SER340 4.2 29.6 1.0
O1A A:UDP604 4.2 31.5 1.0
C1 A:OXL606 4.3 40.6 1.0
O A:HOH759 4.3 45.7 1.0
O5' A:UDP604 4.5 31.4 1.0
OG1 A:THR306 4.5 31.1 1.0
OD1 A:ASP153 4.5 56.5 1.0
O3B A:UDP604 4.6 38.7 1.0
C5' A:UDP604 4.6 31.9 1.0
O A:HOH994 4.6 49.4 1.0
C2 A:OXL606 4.6 35.9 1.0
NH2 A:ARG54 4.7 29.4 1.0
CG2 A:THR306 4.7 33.2 1.0
CG A:ASP153 4.8 57.6 1.0
O2 A:OXL606 4.8 36.1 1.0
O A:HOH946 4.9 41.1 1.0
O3 A:OXL606 4.9 35.7 1.0
NH1 A:ARG54 5.0 26.3 1.0

Magnesium binding site 2 out of 15 in 8zly

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Magnesium binding site 2 out of 15 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:Mg603

b:36.5
occ:1.00
 OD2 A:ASP274 1.9 36.9 1.0
O A:HOH832 2.0 30.4 1.0
O3 A:OXL606 2.0 35.7 1.0
OE1 A:GLU250 2.0 34.3 1.0
O A:HOH759 2.1 45.7 1.0
O4 A:OXL606 2.2 37.0 1.0
C1 A:OXL606 2.8 40.6 1.0
C2 A:OXL606 2.9 35.9 1.0
CG A:ASP274 3.0 36.1 1.0
CD A:GLU250 3.1 34.0 1.0
OE2 A:GLU250 3.5 32.5 1.0
CB A:ASP274 3.6 33.9 1.0
O A:HOH946 4.0 41.1 1.0
O1 A:OXL606 4.1 43.1 1.0
NZ A:LYS248 4.1 35.3 1.0
OD1 A:ASP274 4.1 41.8 1.0
O2 A:OXL606 4.1 36.1 1.0
N A:ASP274 4.3 32.3 1.0
CE A:LYS248 4.3 37.5 1.0
O A:HOH831 4.3 36.0 1.0
CZ A:PHE221 4.4 38.3 1.0
CG A:GLU250 4.4 32.3 1.0
CB A:ALA271 4.4 36.4 1.0
O A:HOH958 4.5 42.5 1.0
CE2 A:PHE221 4.5 39.7 1.0
CA A:ASP274 4.6 31.0 1.0
CB A:GLU250 4.7 34.6 1.0
O A:HOH994 4.7 49.4 1.0
O A:HOH815 4.8 32.5 1.0

Magnesium binding site 3 out of 15 in 8zly

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Magnesium binding site 3 out of 15 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:Mg602

b:38.0
occ:1.00
 OD2 B:ASP274 2.0 34.2 1.0
O3 B:OXL606 2.1 38.5 1.0
OE1 B:GLU250 2.1 35.3 1.0
O B:HOH813 2.1 40.0 1.0
O4 B:OXL606 2.2 36.2 1.0
O B:HOH789 2.2 40.0 1.0
C1 B:OXL606 2.8 47.0 1.0
C2 B:OXL606 2.9 38.5 1.0
CG B:ASP274 3.1 33.7 1.0
CD B:GLU250 3.1 33.8 1.0
OE2 B:GLU250 3.5 33.8 1.0
CB B:ASP274 3.5 34.0 1.0
O B:HOH924 4.0 54.4 1.0
NZ B:LYS248 4.1 36.9 1.0
O1 B:OXL606 4.1 49.1 1.0
O2 B:OXL606 4.1 38.7 1.0
OD1 B:ASP274 4.2 39.3 1.0
CE B:LYS248 4.3 32.7 1.0
CE2 B:PHE221 4.4 39.5 1.0
N B:ASP274 4.4 33.2 1.0
CG B:GLU250 4.4 34.1 1.0
CB B:ALA271 4.5 35.9 1.0
CZ B:PHE221 4.5 41.3 1.0
CA B:ASP274 4.6 32.8 1.0
O B:HOH927 4.6 56.9 1.0
CB B:GLU250 4.7 38.0 1.0
O B:HOH988 4.7 67.7 1.0

Magnesium binding site 4 out of 15 in 8zly

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Magnesium binding site 4 out of 15 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 4 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:Mg603

b:60.8
occ:1.00
 O2B B:UDP604 2.3 53.3 1.0
O1A B:UDP604 2.3 45.3 1.0
O B:HOH927 2.5 56.9 1.0
O B:HOH723 2.7 46.7 1.0
OD2 B:ASP153 3.3 69.5 1.0
PB B:UDP604 3.5 51.3 1.0
PA B:UDP604 3.7 44.7 1.0
O3A B:UDP604 4.0 49.6 1.0
O B:HOH826 4.0 54.0 1.0
O B:HOH789 4.0 40.0 1.0
O1B B:UDP604 4.0 52.8 1.0
CG B:ASP153 4.1 80.2 1.0
OD1 B:ASP153 4.1 67.8 1.0
O1 B:OXL606 4.2 49.1 1.0
C1 B:OXL606 4.3 47.0 1.0
O B:HOH829 4.3 52.2 1.0
OG B:SER340 4.4 36.1 1.0
C2 B:OXL606 4.4 38.5 1.0
CB B:SER340 4.4 32.7 1.0
OG1 B:THR306 4.4 32.0 1.0
O2 B:OXL606 4.6 38.7 1.0
CG2 B:THR306 4.7 30.8 1.0
O2A B:UDP604 4.7 43.2 1.0
O3B B:UDP604 4.8 52.7 1.0
O3 B:OXL606 4.8 38.5 1.0
O B:HOH924 4.8 54.4 1.0
O4 B:OXL606 4.8 36.2 1.0
O5' B:UDP604 4.9 49.0 1.0
C5' B:UDP604 5.0 47.0 1.0

Magnesium binding site 5 out of 15 in 8zly

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Magnesium binding site 5 out of 15 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 5 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
C:Mg602

b:37.4
occ:1.00
 O1A C:UDP604 2.0 29.2 1.0
O C:HOH1034 2.0 36.5 1.0
O C:HOH879 2.1 31.5 1.0
O2B C:UDP604 2.3 25.2 1.0
O C:HOH833 2.3 30.6 1.0
O C:HOH973 2.4 38.0 1.0
PB C:UDP604 3.3 27.8 1.0
PA C:UDP604 3.3 27.1 1.0
O3A C:UDP604 3.5 26.8 1.0
O1B C:UDP604 3.7 30.9 1.0
O C:HOH734 4.0 39.4 1.0
OG C:SER340 4.1 26.6 1.0
OD2 C:ASP153 4.1 49.2 1.0
O1 C:OXL606 4.2 39.0 1.0
CB C:SER340 4.2 23.0 1.0
O2A C:UDP604 4.2 27.8 1.0
O C:HOH1022 4.3 30.6 1.0
C1 C:OXL606 4.3 32.8 1.0
O5' C:UDP604 4.3 25.1 1.0
O C:HOH774 4.4 33.9 1.0
OG1 C:THR306 4.4 27.3 1.0
OD1 C:ASP153 4.4 45.9 1.0
O C:HOH1042 4.5 51.1 1.0
O3B C:UDP604 4.5 27.7 1.0
C5' C:UDP604 4.5 26.6 1.0
C2 C:OXL606 4.6 31.7 1.0
CG C:ASP153 4.7 48.0 1.0
O C:HOH915 4.7 36.6 1.0
NH2 C:ARG54 4.7 26.1 1.0
O2 C:OXL606 4.8 31.1 1.0
O3 C:OXL606 4.8 29.9 1.0
CG2 C:THR306 4.8 28.4 1.0

Magnesium binding site 6 out of 15 in 8zly

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Magnesium binding site 6 out of 15 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 6 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
C:Mg603

b:28.5
occ:1.00
 OD2 C:ASP274 2.0 28.3 1.0
O3 C:OXL606 2.0 29.9 1.0
OE1 C:GLU250 2.0 25.8 1.0
O C:HOH758 2.0 24.8 1.0
O C:HOH774 2.1 33.9 1.0
O4 C:OXL606 2.1 28.1 1.0
C1 C:OXL606 2.8 32.8 1.0
C2 C:OXL606 2.9 31.7 1.0
CG C:ASP274 3.1 30.3 1.0
CD C:GLU250 3.1 27.5 1.0
OE2 C:GLU250 3.4 28.5 1.0
CB C:ASP274 3.6 27.0 1.0
O C:HOH915 3.9 36.6 1.0
O1 C:OXL606 4.1 39.0 1.0
O2 C:OXL606 4.1 31.1 1.0
NZ C:LYS248 4.1 30.8 1.0
OD1 C:ASP274 4.2 33.2 1.0
O C:HOH879 4.3 31.5 1.0
O C:HOH973 4.3 38.0 1.0
N C:ASP274 4.4 23.7 1.0
CB C:ALA271 4.4 24.7 1.0
CZ C:PHE221 4.4 32.3 1.0
CE C:LYS248 4.4 28.2 1.0
CG C:GLU250 4.4 28.2 1.0
CE2 C:PHE221 4.5 34.8 1.0
CA C:ASP274 4.6 24.2 1.0
O C:HOH762 4.7 33.1 1.0
CB C:GLU250 4.7 30.2 1.0
O C:HOH1042 4.8 51.1 1.0

Magnesium binding site 7 out of 15 in 8zly

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Magnesium binding site 7 out of 15 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 7 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
D:Mg602

b:30.6
occ:1.00
 OD2 D:ASP274 2.0 28.6 1.0
O3 D:OXL606 2.0 32.9 1.0
O D:HOH760 2.1 30.2 1.0
OE1 D:GLU250 2.1 28.9 1.0
O D:HOH829 2.2 33.7 1.0
O4 D:OXL606 2.2 33.0 1.0
C1 D:OXL606 2.8 37.3 1.0
C2 D:OXL606 2.9 32.9 1.0
CG D:ASP274 3.1 31.5 1.0
CD D:GLU250 3.1 30.9 1.0
OE2 D:GLU250 3.4 31.1 1.0
CB D:ASP274 3.6 30.0 1.0
O D:HOH816 4.0 49.5 1.0
NZ D:LYS248 4.0 31.3 1.0
O1 D:OXL606 4.0 46.3 1.0
O D:HOH954 4.1 46.5 1.0
O2 D:OXL606 4.1 33.6 1.0
OD1 D:ASP274 4.2 30.8 1.0
N D:ASP274 4.4 26.1 1.0
CE2 D:PHE221 4.4 37.1 1.0
CB D:ALA271 4.4 28.2 1.0
CE D:LYS248 4.4 30.0 1.0
CG D:GLU250 4.5 32.5 1.0
CZ D:PHE221 4.5 38.0 1.0
O D:HOH870 4.6 50.4 1.0
CA D:ASP274 4.6 26.4 1.0
CB D:GLU250 4.7 33.7 1.0
O D:HOH777 4.7 33.8 1.0

Magnesium binding site 8 out of 15 in 8zly

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Magnesium binding site 8 out of 15 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 8 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
D:Mg603

b:50.7
occ:1.00
 O2A D:UDP604 2.1 47.9 1.0
O D:HOH816 2.1 49.5 1.0
O D:HOH768 2.3 50.3 1.0
O3B D:UDP604 2.3 41.3 1.0
O D:HOH870 2.4 50.4 1.0
O D:HOH790 2.4 35.3 1.0
PB D:UDP604 3.3 42.2 1.0
PA D:UDP604 3.4 37.5 1.0
O3A D:UDP604 3.7 36.6 1.0
O2B D:UDP604 3.9 43.6 1.0
O D:HOH749 3.9 41.5 1.0
OD2 D:ASP153 4.0 61.3 1.0
O1 D:OXL606 4.1 46.3 1.0
OG D:SER340 4.1 27.9 1.0
O D:HOH829 4.2 33.7 1.0
CB D:SER340 4.2 26.5 1.0
C1 D:OXL606 4.2 37.3 1.0
O D:HOH984 4.3 40.1 1.0
OD1 D:ASP153 4.3 50.1 1.0
O1A D:UDP604 4.4 36.9 1.0
OG1 D:THR306 4.5 29.5 1.0
C2 D:OXL606 4.5 32.9 1.0
CG D:ASP153 4.6 66.6 1.0
O5' D:UDP604 4.6 38.8 1.0
O D:HOH954 4.6 46.5 1.0
O2 D:OXL606 4.7 33.6 1.0
O1B D:UDP604 4.7 38.1 1.0
NH2 D:ARG54 4.7 28.6 1.0
CG2 D:THR306 4.7 29.1 1.0
O3 D:OXL606 4.7 32.9 1.0
C5' D:UDP604 4.8 40.0 1.0
NH1 D:ARG54 5.0 27.8 1.0

Magnesium binding site 9 out of 15 in 8zly

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Magnesium binding site 9 out of 15 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 9 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
E:Mg602

b:37.7
occ:1.00
 O2A E:UDP604 2.0 31.0 1.0
O E:HOH884 2.0 37.7 1.0
O E:HOH916 2.1 39.5 1.0
O1B E:UDP604 2.1 31.7 1.0
O E:HOH1004 2.3 45.7 1.0
O E:HOH863 2.3 38.4 1.0
PB E:UDP604 3.1 30.8 1.0
PA E:UDP604 3.3 32.9 1.0
O3A E:UDP604 3.6 31.8 1.0
O3B E:UDP604 3.6 30.2 1.0
O E:HOH774 4.0 42.8 1.0
O E:HOH873 4.0 38.0 1.0
OD2 E:ASP153 4.1 49.8 1.0
O1 E:OXL606 4.1 47.9 1.0
OG E:SER340 4.2 30.9 1.0
O1A E:UDP604 4.2 32.4 1.0
O E:HOH1074 4.3 53.6 1.0
C1 E:OXL606 4.3 42.7 1.0
O E:HOH1059 4.3 37.5 1.0
O E:HOH728 4.3 47.1 1.0
CB E:SER340 4.3 27.9 1.0
O5' E:UDP604 4.4 29.8 1.0
O2B E:UDP604 4.5 32.8 1.0
OD1 E:ASP153 4.5 41.9 1.0
OG1 E:THR306 4.5 34.0 1.0
C5' E:UDP604 4.5 35.0 1.0
C2 E:OXL606 4.6 40.4 1.0
CG E:ASP153 4.7 47.6 1.0
O3 E:OXL606 4.7 39.1 1.0
NH2 E:ARG54 4.7 32.5 1.0
O2 E:OXL606 4.8 40.5 1.0
CG2 E:THR306 4.8 30.6 1.0

Magnesium binding site 10 out of 15 in 8zly

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Magnesium binding site 10 out of 15 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 10 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
E:Mg603

b:35.5
occ:1.00
 OE1 E:GLU250 2.0 32.1 1.0
OD2 E:ASP274 2.0 34.1 1.0
O E:HOH852 2.1 28.1 1.0
O3 E:OXL606 2.1 39.1 1.0
O4 E:OXL606 2.2 33.4 1.0
O E:HOH873 2.3 38.0 1.0
C1 E:OXL606 2.9 42.7 1.0
C2 E:OXL606 2.9 40.4 1.0
CD E:GLU250 3.1 30.4 1.0
CG E:ASP274 3.1 33.0 1.0
OE2 E:GLU250 3.4 32.3 1.0
CB E:ASP274 3.6 30.3 1.0
O E:HOH728 4.0 47.1 1.0
NZ E:LYS248 4.0 33.0 1.0
O2 E:OXL606 4.1 40.5 1.0
O1 E:OXL606 4.1 47.9 1.0
OD1 E:ASP274 4.2 39.0 1.0
O E:HOH916 4.3 39.5 1.0
N E:ASP274 4.4 28.2 1.0
CE E:LYS248 4.4 32.7 1.0
CZ E:PHE221 4.4 34.9 1.0
O E:HOH1074 4.4 53.6 1.0
CG E:GLU250 4.4 34.1 1.0
CB E:ALA271 4.4 30.0 1.0
CE2 E:PHE221 4.5 38.3 1.0
O E:HOH884 4.6 37.7 1.0
CA E:ASP274 4.6 28.4 1.0
CB E:GLU250 4.7 35.3 1.0
O E:HOH922 4.7 36.8 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 08:42:51 2024

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