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Potassium in PDB 3qv7: Crystal Structure of Leishmania Mexicana Pyruvate Kinase(Lmpyk)in Complex with Ponceau S and Acid Blue 25.

Enzymatic activity of Crystal Structure of Leishmania Mexicana Pyruvate Kinase(Lmpyk)in Complex with Ponceau S and Acid Blue 25.

All present enzymatic activity of Crystal Structure of Leishmania Mexicana Pyruvate Kinase(Lmpyk)in Complex with Ponceau S and Acid Blue 25.:
2.7.1.40;

Protein crystallography data

The structure of Crystal Structure of Leishmania Mexicana Pyruvate Kinase(Lmpyk)in Complex with Ponceau S and Acid Blue 25., PDB code: 3qv7 was solved by H.P.Morgan, D.S.Auld, I.W.Mcnae, M.W.Nowicki, P.A.M.Michels, L.A.Fothergill-Gilmore, M.D.Walkinshaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.14 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 182.109, 164.798, 123.348, 90.00, 115.80, 90.00
R / Rfree (%) 21.5 / 24.4

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase(Lmpyk)in Complex with Ponceau S and Acid Blue 25. (pdb code 3qv7). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase(Lmpyk)in Complex with Ponceau S and Acid Blue 25., PDB code: 3qv7:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 3qv7

Go back to Potassium Binding Sites List in 3qv7
Potassium binding site 1 out of 8 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase(Lmpyk)in Complex with Ponceau S and Acid Blue 25.


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 Ponceau S and Acid Blue 25. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K501

b:95.0
occ:1.00
 OG D:SER53 3.2 45.1 1.0
NZ D:LYS238 3.3 41.1 1.0
OD1 D:ASN51 3.4 41.4 1.0
O D:THR84 3.4 42.3 1.0
OD1 D:ASP83 3.7 40.9 1.0
OG D:SER211 3.9 39.0 1.0
CG D:ASP83 4.2 40.5 1.0
NH2 D:ARG49 4.3 38.5 1.0
CG D:ASN51 4.3 42.1 1.0
C D:THR84 4.4 42.3 1.0
CB D:SER53 4.4 45.1 1.0
CA D:LYS85 4.6 43.5 1.0
O D:LYS85 4.6 44.0 1.0
OD2 D:ASP83 4.6 40.5 1.0
K D:K502 4.6 65.5 1.0
ND2 D:ASN51 4.7 41.8 1.0
O D:ASP83 4.7 40.8 1.0
CE D:LYS238 4.8 41.1 1.0
N D:LYS85 4.9 42.9 1.0
CB D:ASP83 5.0 40.4 1.0
C D:LYS85 5.0 43.9 1.0

Potassium binding site 2 out of 8 in 3qv7

Go back to Potassium Binding Sites List in 3qv7
Potassium binding site 2 out of 8 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase(Lmpyk)in Complex with Ponceau S and Acid Blue 25.


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 Ponceau S and Acid Blue 25. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K502

b:65.5
occ:1.00
 OD1 D:ASP264 3.3 38.4 1.0
OE1 D:GLU240 3.7 43.2 1.0
OE2 D:GLU240 4.0 43.2 1.0
CD D:GLU240 4.2 42.7 1.0
O D:HOH554 4.3 46.9 1.0
CG D:ASP264 4.4 38.2 1.0
K D:K501 4.6 95.0 1.0
O D:LYS85 4.7 44.0 1.0
O4 D:SO4499 4.7 0.4 1.0

Potassium binding site 3 out of 8 in 3qv7

Go back to Potassium Binding Sites List in 3qv7
Potassium binding site 3 out of 8 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase(Lmpyk)in Complex with Ponceau S and Acid Blue 25.


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 Ponceau S and Acid Blue 25. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K501

b:65.0
occ:1.00
 OE1 A:GLU240 3.4 36.0 1.0
O A:HOH595 3.5 34.8 1.0
OD1 A:ASP264 3.6 35.6 1.0
OE2 A:GLU240 4.0 36.1 1.0
CD A:GLU240 4.1 35.6 1.0
O A:LYS85 4.5 38.7 1.0
CG A:ASP264 4.8 34.6 1.0
OG A:SER211 5.0 33.5 1.0
CB A:SER211 5.0 33.8 1.0

Potassium binding site 4 out of 8 in 3qv7

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Potassium binding site 4 out of 8 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase(Lmpyk)in Complex with Ponceau S and Acid Blue 25.


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 Ponceau S and Acid Blue 25. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K502

b:59.8
occ:1.00
 O A:LEU357 2.9 36.1 1.0
O A:GLN354 3.2 37.0 1.0
OE2 A:GLU359 3.3 36.2 1.0
O A:HOH663 3.4 34.5 1.0
OE1 A:GLU359 3.4 36.6 1.0
CD A:GLU359 3.7 36.2 1.0
O A:SER355 3.8 36.7 1.0
C A:LEU357 4.1 36.1 1.0
C A:SER355 4.2 36.8 1.0
C A:GLN354 4.3 37.0 1.0
CA A:SER355 4.4 36.9 1.0
NE2 A:HIS5 4.5 38.2 1.0
N A:LEU357 4.6 36.3 1.0
CE1 A:HIS5 4.8 38.1 1.0
N A:SER355 4.8 36.9 1.0
CA A:LEU357 4.8 36.2 1.0

Potassium binding site 5 out of 8 in 3qv7

Go back to Potassium Binding Sites List in 3qv7
Potassium binding site 5 out of 8 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase(Lmpyk)in Complex with Ponceau S and Acid Blue 25.


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 Ponceau S and Acid Blue 25. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K502

b:91.2
occ:1.00
 OE1 B:GLU240 4.1 49.6 1.0
OD1 B:ASP264 4.1 49.7 1.0
OE2 B:GLU240 4.2 49.1 1.0
CD B:GLU240 4.4 49.0 1.0
O B:LYS85 4.5 49.3 1.0
NZ B:LYS238 4.5 45.7 1.0
OG B:SER211 4.5 46.3 1.0
O B:HOH574 4.6 48.7 1.0
O B:HOH584 4.8 23.2 1.0
CB B:SER211 4.9 46.2 1.0

Potassium binding site 6 out of 8 in 3qv7

Go back to Potassium Binding Sites List in 3qv7
Potassium binding site 6 out of 8 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase(Lmpyk)in Complex with Ponceau S and Acid Blue 25.


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 Ponceau S and Acid Blue 25. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K503

b:58.6
occ:1.00
 O B:HOH575 2.8 45.3 1.0
O B:GLN354 3.1 43.5 1.0
O B:LEU357 3.1 41.6 1.0
OE2 B:GLU359 3.3 41.3 1.0
OE1 B:GLU359 3.3 42.0 1.0
CD B:GLU359 3.7 41.2 1.0
O B:SER355 4.0 43.0 1.0
C B:GLN354 4.2 43.4 1.0
C B:LEU357 4.3 41.5 1.0
C B:SER355 4.4 42.9 1.0
CA B:SER355 4.4 43.1 1.0
NE2 B:HIS5 4.6 40.6 1.0
N B:SER355 4.8 43.2 1.0
N B:LEU357 5.0 42.0 1.0
CE1 B:HIS5 5.0 40.7 1.0

Potassium binding site 7 out of 8 in 3qv7

Go back to Potassium Binding Sites List in 3qv7
Potassium binding site 7 out of 8 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase(Lmpyk)in Complex with Ponceau S and Acid Blue 25.


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 Ponceau S and Acid Blue 25. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K500

b:88.1
occ:1.00
 O C:HOH656 2.9 51.4 1.0
O C:THR84 3.2 50.6 1.0
OD1 C:ASP83 3.2 49.9 1.0
OG C:SER53 3.2 54.4 1.0
OD1 C:ASN51 3.2 52.0 1.0
NZ C:LYS238 3.3 48.2 1.0
OG C:SER211 3.8 49.9 1.0
CG C:ASP83 4.1 50.0 1.0
CG C:ASN51 4.2 52.2 1.0
NH2 C:ARG49 4.2 46.7 1.0
C C:THR84 4.3 50.6 1.0
CB C:SER53 4.4 54.5 1.0
O C:LYS85 4.5 51.2 1.0
O C:HOH529 4.6 43.2 1.0
ND2 C:ASN51 4.6 52.1 1.0
CA C:LYS85 4.6 51.0 1.0
OD2 C:ASP83 4.7 50.0 1.0
CE C:LYS238 4.8 48.5 1.0
O C:ASP83 4.8 50.2 1.0
N C:LYS85 4.9 50.8 1.0
O C:HOH513 4.9 39.8 1.0
C C:LYS85 4.9 51.2 1.0
CB C:SER211 5.0 49.8 1.0
CB C:ASP83 5.0 50.0 1.0

Potassium binding site 8 out of 8 in 3qv7

Go back to Potassium Binding Sites List in 3qv7
Potassium binding site 8 out of 8 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase(Lmpyk)in Complex with Ponceau S and Acid Blue 25.


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 Ponceau S and Acid Blue 25. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K501

b:61.5
occ:1.00
 O C:LEU357 3.1 44.0 1.0
O C:GLN354 3.1 47.8 1.0
OE1 C:GLU359 3.1 43.9 1.0
OE2 C:GLU359 3.2 43.4 1.0
CD C:GLU359 3.6 43.4 1.0
O C:SER355 3.8 46.6 1.0
O C:HOH534 3.9 44.9 1.0
C C:GLN354 4.1 47.6 1.0
CA C:SER355 4.2 46.9 1.0
C C:SER355 4.2 46.5 1.0
C C:LEU357 4.3 44.0 1.0
N C:SER355 4.6 47.3 1.0
NE2 C:HIS5 4.6 42.2 1.0
N C:LEU357 4.8 44.7 1.0
CE1 C:HIS5 4.9 42.1 1.0

Reference:

H.P.Morgan, I.W.Mcnae, M.W.Nowicki, W.Zhong, P.A.Michels, D.S.Auld, L.A.Fothergill-Gilmore, M.D.Walkinshaw. The Trypanocidal Drug Suramin and Other Trypan Blue Mimetics Are Inhibitors of Pyruvate Kinases and Bind to the Adenosine Site. J.Biol.Chem. V. 286 31232 2011.
ISSN: ISSN 0021-9258
PubMed: 21733839
DOI: 10.1074/JBC.M110.212613
Page generated: Mon Aug 12 09:14:06 2024

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