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Potassium in PDB 3hqp: Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate

Enzymatic activity of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate

All present enzymatic activity of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate:
2.7.1.40;

Protein crystallography data

The structure of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate, PDB code: 3hqp was solved by H.P.Morgan, M.D.Walkinshaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.46 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 127.486, 151.140, 160.319, 89.73, 80.17, 71.64
R / Rfree (%) 19.8 / 25.2

Other elements in 3hqp:

The structure of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate also contains other interesting chemical elements:

Magnesium (Mg) 30 atoms

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Potassium atom in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate (pdb code 3hqp). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 32 binding sites of Potassium where determined in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate, PDB code: 3hqp:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 32 in 3hqp

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Potassium binding site 1 out of 32 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K504

b:0.5
occ:1.00
 O3G A:ATP1001 2.4 73.5 1.0
O A:THR84 3.0 55.6 1.0
OD1 A:ASP83 3.3 55.6 1.0
OG A:SER53 3.3 56.9 1.0
OG A:SER211 3.5 41.1 1.0
OD1 A:ASN51 3.5 57.0 1.0
NZ A:LYS238 3.6 42.6 1.0
PG A:ATP1001 3.7 74.7 1.0
O2G A:ATP1001 4.0 70.1 1.0
OE2 A:GLU88 4.0 59.0 1.0
O A:LYS85 4.1 56.6 1.0
C A:THR84 4.2 55.8 1.0
CG A:ASN51 4.3 56.2 1.0
CB A:SER53 4.3 57.2 1.0
O3B A:ATP1001 4.3 76.5 1.0
CG A:ASP83 4.4 55.0 1.0
ND2 A:ASN51 4.4 55.9 1.0
CB A:SER211 4.4 41.0 1.0
NH2 A:ARG90 4.4 58.0 1.0
MG A:MG502 4.4 58.3 1.0
CA A:LYS85 4.5 56.4 1.0
OE1 A:GLU88 4.5 59.2 1.0
CD A:GLU88 4.6 58.8 1.0
CE A:LYS238 4.7 42.3 1.0
C A:LYS85 4.7 56.6 1.0
NH2 A:ARG49 4.8 54.5 1.0
N A:LYS85 4.8 56.1 1.0
O1G A:ATP1001 4.9 74.7 1.0
O A:ASP83 5.0 55.2 1.0

Potassium binding site 2 out of 32 in 3hqp

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Potassium binding site 2 out of 32 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K499

b:60.6
occ:1.00
 O A:LEU357 2.8 41.8 1.0
OE2 A:GLU359 2.9 46.2 1.0
O A:HOH1499 3.0 50.2 1.0
O A:GLN354 3.0 40.2 1.0
O A:HOH1009 3.3 52.7 1.0
OE1 A:GLU359 3.3 44.8 1.0
O A:SER355 3.4 41.1 1.0
CD A:GLU359 3.4 45.1 1.0
O A:HOH1273 3.7 41.3 1.0
C A:SER355 3.9 40.8 1.0
C A:LEU357 4.0 41.9 1.0
C A:GLN354 4.1 40.3 1.0
CA A:SER355 4.2 40.8 1.0
N A:LEU357 4.5 41.3 1.0
N A:SER355 4.6 40.4 1.0
CA A:LEU357 4.7 41.7 1.0
CG A:GLU359 4.8 43.9 1.0
N A:ALA356 4.8 41.0 1.0
CB A:LEU357 4.9 41.7 1.0

Potassium binding site 3 out of 32 in 3hqp

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Potassium binding site 3 out of 32 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K504

b:39.0
occ:1.00
 O B:HOH505 2.4 30.5 1.0
OD1 B:ASP83 2.5 25.0 1.0
OG B:SER53 2.7 24.9 1.0
O B:THR84 2.8 23.1 1.0
O3G B:ATP1001 2.8 34.1 1.0
OD1 B:ASN51 2.8 23.8 1.0
OG B:SER211 3.4 20.6 1.0
CG B:ASN51 3.6 23.8 1.0
CG B:ASP83 3.7 23.7 1.0
C B:THR84 3.8 23.1 1.0
CB B:SER53 3.8 24.7 1.0
ND2 B:ASN51 3.9 22.8 1.0
O B:HOH1726 4.0 26.2 1.0
NZ B:LYS238 4.0 18.5 1.0
O B:ASP83 4.2 22.8 1.0
PG B:ATP1001 4.2 35.0 1.0
CA B:LYS85 4.3 23.5 1.0
O B:HOH1882 4.3 38.5 1.0
N B:SER53 4.4 24.6 1.0
N B:LYS85 4.4 23.2 1.0
C B:ASP83 4.4 22.8 1.0
NH2 B:ARG90 4.5 22.8 1.0
CB B:SER211 4.5 20.7 1.0
O B:LYS85 4.5 24.5 1.0
OD2 B:ASP83 4.5 25.4 1.0
CB B:ASP83 4.6 22.6 1.0
OE2 B:GLU88 4.6 27.1 1.0
N B:THR84 4.6 22.8 1.0
O3B B:ATP1001 4.7 35.3 1.0
CA B:SER53 4.7 25.0 1.0
C B:LYS85 4.8 24.1 1.0
CA B:THR84 4.8 22.9 1.0
O2G B:ATP1001 4.9 33.2 1.0
N B:PHE52 4.9 24.5 1.0
CB B:ASN51 4.9 24.0 1.0
OE1 B:GLU88 5.0 27.7 1.0

Potassium binding site 4 out of 32 in 3hqp

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Potassium binding site 4 out of 32 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K499

b:61.0
occ:1.00
 OE2 B:GLU359 2.9 31.7 1.0
O B:GLN354 2.9 25.6 1.0
O B:LEU357 3.0 27.7 1.0
O B:SER355 3.5 26.0 1.0
CD B:GLU359 3.6 31.2 1.0
OE1 B:GLU359 3.7 33.2 1.0
O B:HOH629 3.7 46.9 1.0
C B:SER355 3.9 26.0 1.0
C B:GLN354 4.1 25.4 1.0
C B:LEU357 4.1 27.4 1.0
CA B:SER355 4.1 26.1 1.0
O B:HOH665 4.3 43.3 1.0
N B:LEU357 4.3 26.9 1.0
N B:SER355 4.6 25.6 1.0
CA B:LEU357 4.6 27.2 1.0
O B:HOH648 4.6 39.9 1.0
CB B:LEU357 4.7 27.5 1.0
N B:ALA356 4.7 26.1 1.0

Potassium binding site 5 out of 32 in 3hqp

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Potassium binding site 5 out of 32 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K504

b:56.5
occ:1.00
 O3G C:ATP1001 2.5 44.0 1.0
O C:HOH1131 2.7 45.1 1.0
OG C:SER53 2.8 43.3 1.0
O C:THR84 3.0 41.7 1.0
OD1 C:ASN51 3.0 40.4 1.0
OD1 C:ASP83 3.1 42.5 1.0
OG C:SER211 3.5 32.7 1.0
O C:HOH1778 3.6 44.8 1.0
NZ C:LYS238 3.7 33.9 1.0
CG C:ASN51 3.7 40.9 1.0
ND2 C:ASN51 3.9 40.2 1.0
CB C:SER53 3.9 43.1 1.0
PG C:ATP1001 3.9 46.7 1.0
NH2 C:ARG90 4.0 42.8 1.0
CG C:ASP83 4.0 41.6 1.0
O3B C:ATP1001 4.1 46.7 1.0
C C:THR84 4.2 41.9 1.0
NH2 C:ARG49 4.3 45.5 1.0
CB C:SER211 4.5 33.2 1.0
N C:SER53 4.6 43.0 1.0
O C:ASP83 4.6 41.3 1.0
OD2 C:ASP83 4.6 41.0 1.0
OE2 C:GLU88 4.6 44.8 1.0
CA C:LYS85 4.7 41.5 1.0
O C:LYS85 4.8 40.8 1.0
O1G C:ATP1001 4.8 44.7 1.0
O2G C:ATP1001 4.8 46.4 1.0
CA C:SER53 4.9 43.3 1.0
C C:ASP83 4.9 41.5 1.0
O4 C:OXL510 4.9 41.9 1.0
N C:LYS85 4.9 41.8 1.0
CB C:ASP83 4.9 41.2 1.0

Potassium binding site 6 out of 32 in 3hqp

Go back to Potassium Binding Sites List in 3hqp
Potassium binding site 6 out of 32 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K499

b:68.8
occ:1.00
 O C:GLN354 2.9 42.0 1.0
O C:LEU357 2.9 43.0 1.0
OE2 C:GLU359 3.0 47.4 1.0
OE1 C:GLU359 3.2 46.4 1.0
CD C:GLU359 3.5 46.2 1.0
O C:SER355 3.5 42.2 1.0
C C:SER355 4.0 42.1 1.0
C C:GLN354 4.0 42.0 1.0
C C:LEU357 4.1 43.0 1.0
CA C:SER355 4.2 42.2 1.0
O C:HOH781 4.3 56.0 1.0
N C:LEU357 4.5 42.2 1.0
N C:SER355 4.6 42.1 1.0
CA C:LEU357 4.7 42.6 1.0
CG C:GLU359 4.8 44.5 1.0
CB C:LEU357 4.9 42.7 1.0
N C:ALA356 4.9 42.0 1.0

Potassium binding site 7 out of 32 in 3hqp

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Potassium binding site 7 out of 32 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K504

b:33.3
occ:1.00
 O D:HOH501 2.6 35.2 1.0
OD1 D:ASP83 2.6 24.1 1.0
O D:THR84 2.7 25.6 1.0
OD1 D:ASN51 2.7 23.6 1.0
O3G D:ATP1001 2.9 37.9 1.0
OG D:SER53 2.9 26.1 1.0
OG D:SER211 3.4 20.6 1.0
CG D:ASP83 3.7 24.5 1.0
CG D:ASN51 3.7 24.8 1.0
C D:THR84 3.8 24.9 1.0
CB D:SER53 3.9 25.9 1.0
NZ D:LYS238 3.9 15.7 1.0
ND2 D:ASN51 4.2 27.4 1.0
O D:ASP83 4.2 23.9 1.0
PG D:ATP1001 4.2 38.4 1.0
O D:HOH736 4.3 50.6 1.0
N D:SER53 4.4 25.8 1.0
NH2 D:ARG90 4.4 26.4 1.0
C D:ASP83 4.4 23.9 1.0
CA D:LYS85 4.4 25.9 1.0
N D:LYS85 4.5 25.4 1.0
CB D:ASP83 4.5 23.7 1.0
CB D:SER211 4.5 20.7 1.0
OD2 D:ASP83 4.5 25.2 1.0
NH2 D:ARG49 4.6 29.3 1.0
N D:THR84 4.6 24.1 1.0
O2G D:ATP1001 4.6 35.5 1.0
O D:LYS85 4.7 25.7 1.0
CA D:SER53 4.7 26.1 1.0
O3B D:ATP1001 4.7 38.7 1.0
CA D:THR84 4.8 24.4 1.0
N D:PHE52 4.9 24.5 1.0
OE2 D:GLU88 4.9 27.5 1.0
C D:LYS85 4.9 25.8 1.0

Potassium binding site 8 out of 32 in 3hqp

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Potassium binding site 8 out of 32 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K499

b:53.1
occ:1.00
 O D:GLN354 2.9 28.3 1.0
O D:LEU357 2.9 31.7 1.0
OE2 D:GLU359 2.9 33.9 1.0
O D:HOH654 3.1 59.0 1.0
O D:HOH577 3.4 59.3 1.0
O D:SER355 3.6 29.8 1.0
CD D:GLU359 3.6 33.1 1.0
OE1 D:GLU359 3.6 33.4 1.0
O D:HOH691 3.8 54.1 1.0
C D:SER355 3.8 29.5 1.0
O D:HOH686 3.8 52.1 1.0
C D:GLN354 3.9 28.0 1.0
CA D:SER355 4.0 29.4 1.0
C D:LEU357 4.1 31.4 1.0
O D:HOH630 4.3 45.9 1.0
N D:LEU357 4.3 30.4 1.0
N D:SER355 4.4 28.6 1.0
O D:HOH1286 4.4 59.3 1.0
O D:HOH652 4.5 61.8 1.0
N D:ALA356 4.6 29.7 1.0
CA D:LEU357 4.6 31.1 1.0
CB D:LEU357 4.8 31.1 1.0
C D:ALA356 4.9 30.2 1.0
CG D:GLU359 5.0 31.7 1.0
O D:HOH1608 5.0 51.1 1.0

Potassium binding site 9 out of 32 in 3hqp

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Potassium binding site 9 out of 32 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K504

b:48.2
occ:1.00
 O E:HOH737 2.6 52.5 1.0
OG E:SER53 2.7 43.8 1.0
O3G E:ATP1001 2.7 54.4 1.0
OD1 E:ASP83 2.8 42.2 1.0
O E:THR84 2.9 41.8 1.0
OD1 E:ASN51 2.9 43.7 1.0
OG E:SER211 3.4 38.2 1.0
CG E:ASN51 3.6 43.4 1.0
CG E:ASP83 3.7 41.4 1.0
ND2 E:ASN51 3.8 43.4 1.0
NZ E:LYS238 3.9 38.4 1.0
CB E:SER53 3.9 43.7 1.0
C E:THR84 3.9 41.7 1.0
O E:HOH556 3.9 52.6 1.0
PG E:ATP1001 4.1 53.3 1.0
NH2 E:ARG90 4.2 46.4 1.0
O E:ASP83 4.3 40.5 1.0
OD2 E:ASP83 4.4 41.7 1.0
CA E:LYS85 4.5 42.3 1.0
N E:SER53 4.5 43.6 1.0
CB E:SER211 4.5 38.7 1.0
O3B E:ATP1001 4.5 54.7 1.0
C E:ASP83 4.5 40.8 1.0
O E:LYS85 4.6 42.5 1.0
N E:LYS85 4.6 42.0 1.0
NH2 E:ARG49 4.6 46.1 1.0
CB E:ASP83 4.6 40.9 1.0
OE2 E:GLU88 4.7 48.1 1.0
O2G E:ATP1001 4.8 52.3 1.0
CA E:SER53 4.8 43.8 1.0
N E:THR84 4.8 41.1 1.0
OE1 E:GLU88 4.8 47.8 1.0
C E:LYS85 4.9 42.5 1.0
CB E:ASN51 4.9 43.4 1.0
CA E:THR84 5.0 41.4 1.0

Potassium binding site 10 out of 32 in 3hqp

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Potassium binding site 10 out of 32 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K501

b:75.1
occ:1.00
 OE2 E:GLU359 2.7 44.5 1.0
O E:LEU357 2.9 46.2 1.0
O E:GLN354 3.1 47.6 1.0
CD E:GLU359 3.5 45.5 1.0
OE1 E:GLU359 3.6 44.9 1.0
O E:SER355 3.7 47.4 1.0
C E:LEU357 4.1 46.1 1.0
C E:SER355 4.1 47.3 1.0
C E:GLN354 4.2 47.4 1.0
CA E:SER355 4.3 47.7 1.0
N E:LEU357 4.6 46.1 1.0
N E:SER355 4.7 47.4 1.0
CA E:LEU357 4.8 46.1 1.0
CG E:GLU359 5.0 45.1 1.0

Reference:

H.P.Morgan, I.W.Mcnae, M.W.Nowicki, V.Hannaert, P.A.M.Michels, L.A.Fothergill-Gilmore, M.D.Walkinshaw. The Allosteric Mechanism of Pryuvate Kinase From Leishmania Mexicana: A Rock and Lock Model J.Biol.Chem. V. 285 12892 2010.
ISSN: ISSN 0021-9258
PubMed: 20123988
DOI: 10.1074/JBC.M109.079905
Page generated: Mon Aug 12 08:27:32 2024

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