Magnesium in PDB 6qxl: Crystal Structure of Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate

Enzymatic activity of Crystal Structure of Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate

All present enzymatic activity of Crystal Structure of Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate:
2.7.1.40;

Protein crystallography data

The structure of Crystal Structure of Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate, PDB code: 6qxl was solved by Y.Abdelhamid, P.Brear, M.Welch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 158.03 / 2.43
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 182.477, 182.477, 405.044, 90.00, 90.00, 120.00
R / Rfree (%) 22.7 / 25.1

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate (pdb code 6qxl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate, PDB code: 6qxl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 6qxl

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Magnesium binding site 1 out of 12 in the Crystal Structure of Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate


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 Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:49.2
occ:1.00
 OE2 A:GLU223 1.6 43.0 1.0
O6 A:MLI503 1.8 48.2 1.0
O8 A:MLI503 2.0 49.5 1.0
OD2 A:ASP250 2.3 55.0 1.0
O A:HOH662 2.6 61.8 1.0
O A:HOH609 2.7 37.8 1.0
C2 A:MLI503 2.8 50.4 1.0
CD A:GLU223 2.9 44.1 1.0
C3 A:MLI503 2.9 54.2 1.0
C1 A:MLI503 3.3 53.5 1.0
CG A:ASP250 3.3 51.5 1.0
OE1 A:GLU223 3.6 47.7 1.0
CB A:ASP250 3.8 42.8 1.0
O7 A:MLI503 3.9 45.6 1.0
O9 A:MLI503 3.9 62.4 1.0
CG A:GLU223 3.9 41.6 1.0
NZ A:LYS221 4.2 41.3 1.0
CE A:LYS221 4.3 43.9 1.0
N A:ASP250 4.4 34.0 1.0
OD1 A:ASP250 4.4 58.3 1.0
O A:HOH735 4.4 48.4 1.0
NZ A:LYS73 4.5 73.6 1.0
CB A:ALA247 4.6 37.0 1.0
CA A:ASP250 4.7 35.7 1.0
O A:HOH617 4.8 44.4 1.0
CZ A:PHE195 5.0 57.9 1.0

Magnesium binding site 2 out of 12 in 6qxl

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Magnesium binding site 2 out of 12 in the Crystal Structure of Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate


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 Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:44.3
occ:1.00
 O8 B:MLI504 2.2 40.7 1.0
O6 B:MLI504 2.2 37.6 1.0
OE1 B:GLU223 2.3 39.6 1.0
O B:HOH642 2.3 48.5 1.0
OD2 B:ASP250 2.4 40.8 1.0
C2 B:MLI504 3.0 45.7 1.0
C3 B:MLI504 3.0 42.9 1.0
C1 B:MLI504 3.2 44.5 1.0
CD B:GLU223 3.5 37.2 1.0
CG B:ASP250 3.5 42.0 1.0
O B:HOH775 3.7 53.1 1.0
NZ B:LYS221 3.9 34.4 1.0
CB B:ASP250 3.9 39.2 1.0
OE2 B:GLU223 4.0 32.8 1.0
CE B:LYS221 4.0 32.9 1.0
O7 B:MLI504 4.1 46.4 1.0
O9 B:MLI504 4.2 42.1 1.0
CB B:ALA247 4.6 25.0 1.0
NZ B:LYS73 4.6 68.0 1.0
OD1 B:ASP250 4.6 48.2 1.0
O B:HOH826 4.7 37.4 1.0
CG B:GLU223 4.7 37.3 1.0
N B:ASP250 4.7 29.1 1.0
CB B:GLU223 4.8 37.5 1.0
CZ B:PHE195 4.9 52.0 1.0
CE2 B:PHE195 4.9 46.2 1.0
CA B:ASP250 5.0 33.5 1.0

Magnesium binding site 3 out of 12 in 6qxl

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Magnesium binding site 3 out of 12 in the Crystal Structure of Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate


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 Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:30.0
occ:1.00
 OE1 C:GLU223 1.9 41.1 1.0
OD2 C:ASP250 1.9 46.5 1.0
O8 C:MLI503 2.4 42.9 1.0
O6 C:MLI503 2.5 64.2 1.0
CD C:GLU223 3.1 46.4 1.0
CG C:ASP250 3.2 47.3 1.0
C2 C:MLI503 3.4 56.5 1.0
O C:HOH647 3.5 62.2 1.0
C3 C:MLI503 3.5 50.0 1.0
OE2 C:GLU223 3.5 48.1 1.0
NZ C:LYS73 3.6 0.7 1.0
C1 C:MLI503 3.8 51.7 1.0
CE C:LYS73 3.9 0.8 1.0
CB C:ASP250 4.0 44.5 1.0
NZ C:LYS221 4.0 36.4 1.0
OD1 C:ASP250 4.1 58.5 1.0
CE2 C:PHE195 4.3 72.2 1.0
CG C:GLU223 4.3 47.0 1.0
CE C:LYS221 4.4 37.7 1.0
O7 C:MLI503 4.5 68.3 1.0
CZ C:PHE195 4.5 69.2 1.0
O9 C:MLI503 4.7 38.4 1.0

Magnesium binding site 4 out of 12 in 6qxl

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Magnesium binding site 4 out of 12 in the Crystal Structure of Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate


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 Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:39.8
occ:1.00
 OD2 D:ASP250 2.1 37.1 1.0
O9 D:MLI504 2.2 50.0 1.0
O7 D:MLI504 2.2 40.8 1.0
OE1 D:GLU223 2.8 42.6 1.0
C3 D:MLI504 3.1 48.8 1.0
CG D:ASP250 3.2 38.1 1.0
C2 D:MLI504 3.2 41.1 1.0
C1 D:MLI504 3.5 48.1 1.0
CD D:GLU223 3.6 41.9 1.0
O D:HOH681 3.7 40.7 1.0
CB D:ASP250 3.7 36.5 1.0
O D:HOH652 3.8 65.7 1.0
OE2 D:GLU223 4.0 44.8 1.0
NZ D:LYS221 4.0 43.8 1.0
O8 D:MLI504 4.2 50.5 1.0
OD1 D:ASP250 4.2 38.4 1.0
CE1 D:PHE195 4.3 47.5 1.0
CE D:LYS221 4.3 41.3 1.0
O6 D:MLI504 4.4 33.2 1.0
CG D:GLU223 4.7 38.3 1.0
N D:ASP250 4.8 35.9 1.0
CB D:GLU223 4.8 39.6 1.0
O D:HOH668 4.8 43.5 1.0
CD1 D:PHE195 4.8 48.6 1.0
CA D:ASP250 4.9 36.3 1.0
CB D:ALA247 5.0 28.5 1.0

Magnesium binding site 5 out of 12 in 6qxl

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Magnesium binding site 5 out of 12 in the Crystal Structure of Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate


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 Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg502

b:40.0
occ:1.00
 OD2 E:ASP250 1.8 35.5 1.0
O9 E:MLI504 2.1 42.2 1.0
O7 E:MLI504 2.4 29.9 1.0
OE1 E:GLU223 2.6 35.7 1.0
CG E:ASP250 3.0 32.3 1.0
C3 E:MLI504 3.2 42.6 1.0
C2 E:MLI504 3.4 34.1 1.0
CD E:GLU223 3.6 36.2 1.0
CB E:ASP250 3.6 33.2 1.0
C1 E:MLI504 3.7 36.9 1.0
OD1 E:ASP250 4.0 32.2 1.0
OE2 E:GLU223 4.0 35.8 1.0
O8 E:MLI504 4.2 46.4 1.0
CE1 E:PHE195 4.2 37.0 1.0
NZ E:LYS221 4.3 40.1 1.0
O E:HOH741 4.5 60.2 1.0
O6 E:MLI504 4.6 32.8 1.0
CE E:LYS221 4.6 37.6 1.0
N E:ASP250 4.7 29.4 1.0
CA E:ASP250 4.8 32.1 1.0
CD1 E:PHE195 4.8 37.0 1.0
O E:HOH835 4.8 51.5 1.0
CG E:GLU223 4.9 33.0 1.0
CB E:GLU223 5.0 35.2 1.0

Magnesium binding site 6 out of 12 in 6qxl

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Magnesium binding site 6 out of 12 in the Crystal Structure of Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate


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 Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg502

b:49.8
occ:1.00
 O7 F:MLI503 1.9 61.1 1.0
O9 F:MLI503 1.9 58.6 1.0
OD2 F:ASP250 2.1 70.8 1.0
OE1 F:GLU223 2.1 63.9 1.0
C2 F:MLI503 3.0 60.4 1.0
C3 F:MLI503 3.0 55.0 1.0
CG F:ASP250 3.3 68.0 1.0
CD F:GLU223 3.4 56.6 1.0
C1 F:MLI503 3.4 59.5 1.0
NZ F:LYS73 3.8 90.5 1.0
CB F:ASP250 3.9 62.1 1.0
OE2 F:GLU223 4.1 56.9 1.0
O8 F:MLI503 4.1 46.0 1.0
O6 F:MLI503 4.1 64.5 1.0
OD1 F:ASP250 4.2 71.2 1.0
NZ F:LYS221 4.3 52.2 1.0
CG F:GLU223 4.5 55.3 1.0
CE F:LYS73 4.5 85.9 1.0
CD F:LYS73 4.6 84.6 1.0
OD1 F:ASP129 4.6 72.0 1.0
N F:ASP250 4.6 49.6 1.0
CE F:LYS221 4.6 48.4 1.0
O F:HOH603 4.8 67.2 1.0
CA F:ASP250 4.9 53.9 1.0

Magnesium binding site 7 out of 12 in 6qxl

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Magnesium binding site 7 out of 12 in the Crystal Structure of Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate


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 Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg502

b:45.5
occ:1.00
 OD2 G:ASP250 1.9 75.9 1.0
O7 G:MLI503 1.9 60.3 1.0
OE1 G:GLU223 2.5 69.7 1.0
O9 G:MLI503 2.7 52.4 1.0
C2 G:MLI503 3.0 55.3 1.0
CG G:ASP250 3.2 70.7 1.0
C3 G:MLI503 3.5 54.8 1.0
CD G:GLU223 3.5 65.2 1.0
C1 G:MLI503 3.7 56.6 1.0
OE2 G:GLU223 3.8 57.5 1.0
CB G:ASP250 3.8 61.4 1.0
NZ G:LYS221 4.1 61.5 1.0
O6 G:MLI503 4.1 60.4 1.0
NZ G:LYS73 4.2 88.1 1.0
OD1 G:ASP250 4.2 69.5 1.0
CD G:LYS73 4.3 73.6 1.0
CE G:LYS221 4.4 60.6 1.0
CE1 G:PHE195 4.4 84.7 1.0
CE G:LYS73 4.6 78.7 1.0
O8 G:MLI503 4.7 53.5 1.0
CG G:GLU223 4.8 62.0 1.0
N G:ASP250 4.8 52.8 1.0
CD1 G:PHE195 4.9 81.5 1.0
CB G:GLU223 4.9 58.9 1.0
CA G:ASP250 4.9 56.9 1.0

Magnesium binding site 8 out of 12 in 6qxl

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Magnesium binding site 8 out of 12 in the Crystal Structure of Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate


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 Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg502

b:50.0
occ:1.00
 OE1 H:GLU223 1.7 57.6 1.0
O6 H:MLI503 2.2 49.5 1.0
OD2 H:ASP250 2.2 49.3 1.0
CD H:GLU223 2.8 50.6 1.0
O8 H:MLI503 2.8 52.4 1.0
C2 H:MLI503 3.2 53.0 1.0
OE2 H:GLU223 3.3 50.4 1.0
CG H:ASP250 3.4 49.5 1.0
C3 H:MLI503 3.6 54.5 1.0
C1 H:MLI503 3.7 53.6 1.0
NZ H:LYS221 3.8 44.3 1.0
CB H:ASP250 4.0 45.1 1.0
CG H:GLU223 4.1 48.6 1.0
CE H:LYS221 4.2 44.8 1.0
CE1 H:PHE195 4.2 92.6 1.0
O7 H:MLI503 4.3 57.3 1.0
OD1 H:ASP250 4.4 46.4 1.0
NZ H:LYS73 4.6 79.0 1.0
CD1 H:PHE195 4.7 91.0 1.0
O H:HOH711 4.7 54.3 1.0
O9 H:MLI503 4.9 47.8 1.0
OG H:SER194 4.9 49.9 1.0

Magnesium binding site 9 out of 12 in 6qxl

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Magnesium binding site 9 out of 12 in the Crystal Structure of Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate


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 Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg502

b:30.0
occ:1.00
 OD2 I:ASP250 2.1 70.1 1.0
O7 I:MLI503 2.3 61.3 1.0
O9 I:MLI503 2.4 62.1 1.0
OE1 I:GLU223 2.6 64.0 1.0
C2 I:MLI503 3.0 65.5 1.0
CG I:ASP250 3.2 66.9 1.0
C3 I:MLI503 3.3 63.8 1.0
C1 I:MLI503 3.5 65.5 1.0
CD I:GLU223 3.6 62.1 1.0
CB I:ASP250 3.8 67.9 1.0
O6 I:MLI503 3.9 83.2 1.0
OE2 I:GLU223 4.1 52.9 1.0
NZ I:LYS221 4.2 74.3 1.0
OD1 I:ASP250 4.2 61.9 1.0
O I:HOH679 4.4 69.5 1.0
CE I:LYS221 4.4 69.1 1.0
O8 I:MLI503 4.5 55.2 1.0
CE1 I:PHE195 4.5 63.0 1.0
N I:ASP250 4.6 52.9 1.0
O I:HOH697 4.8 62.1 1.0
CA I:ASP250 4.8 59.2 1.0
CG I:GLU223 4.9 60.0 1.0
CB I:ALA247 5.0 49.3 1.0
CB I:GLU223 5.0 57.1 1.0

Magnesium binding site 10 out of 12 in 6qxl

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Magnesium binding site 10 out of 12 in the Crystal Structure of Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate


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 Pyruvate Kinase II (Pyka) From Pseudomonas Aeruginosa in Complex with Sodium Malonate, Magnesium and Glucose-6- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg502

b:55.6
occ:1.00
 OD2 J:ASP250 2.1 67.3 1.0
O8 J:MLI503 2.3 60.2 1.0
OE1 J:GLU223 2.3 63.3 1.0
O6 J:MLI503 2.6 75.0 1.0
C3 J:MLI503 3.0 64.9 1.0
C1 J:MLI503 3.1 62.0 1.0
C2 J:MLI503 3.1 65.0 1.0
CD J:GLU223 3.3 62.2 1.0
CG J:ASP250 3.3 57.7 1.0
OE2 J:GLU223 3.5 65.8 1.0
O J:HOH671 3.5 58.3 1.0
CB J:ASP250 4.0 55.2 1.0
NZ J:LYS221 4.0 44.6 1.0
O9 J:MLI503 4.2 69.8 1.0
O J:HOH683 4.3 47.4 1.0
O7 J:MLI503 4.3 59.0 1.0
CE J:LYS221 4.4 47.0 1.0
OD1 J:ASP250 4.4 49.6 1.0
CE2 J:PHE195 4.7 98.4 1.0
CG J:GLU223 4.7 58.9 1.0
N J:ASP250 5.0 46.6 1.0

Reference:

Y.Abdelhamid, P.Brear, J.Greenhalgh, X.Chee, T.Rahman, M.Welch. Evolutionary Plasticity in the Allosteric Regulator-Binding Site of Pyruvate Kinase Isoform Pyka Frompseudomonas Aeruginosa. J.Biol.Chem. V. 294 15505 2019.
ISSN: ESSN 1083-351X
PubMed: 31484721
DOI: 10.1074/JBC.RA119.009156
Page generated: Mon Dec 14 23:54:53 2020

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