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Magnesium in PDB 3hqo: Crystal Structures of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp and Oxalate

Enzymatic activity of Crystal Structures of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp and Oxalate

All present enzymatic activity of Crystal Structures of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp and Oxalate:
2.7.1.40;

Protein crystallography data

The structure of Crystal Structures of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp and Oxalate, PDB code: 3hqo 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) 41.18 / 3.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 107.516, 128.133, 204.361, 90.00, 90.03, 90.00
R / Rfree (%) 25.1 / 29

Other elements in 3hqo:

The structure of Crystal Structures of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp and Oxalate also contains other interesting chemical elements:

Potassium (K) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structures of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp and Oxalate (pdb code 3hqo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structures of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp and Oxalate, PDB code: 3hqo:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3hqo

Go back to Magnesium Binding Sites List in 3hqo
Magnesium binding site 1 out of 6 in the Crystal Structures of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp and Oxalate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structures of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp and Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg500

b:13.8
occ:1.00
 O1B K:ATP1001 2.4 46.6 1.0
O1G K:ATP1001 2.6 46.5 1.0
O1A K:ATP1001 3.0 48.3 1.0
O3 K:OXL510 3.1 57.0 1.0
OD2 K:ASP145 3.4 54.9 1.0
C1 K:OXL510 3.5 57.7 1.0
OG1 K:THR296 3.5 38.6 1.0
PG K:ATP1001 3.6 46.6 1.0
O2G K:ATP1001 3.7 47.2 1.0
PB K:ATP1001 3.7 46.9 1.0
CG2 K:THR296 3.9 38.2 1.0
O2 K:OXL510 4.0 59.4 1.0
C2 K:OXL510 4.0 58.7 1.0
O3B K:ATP1001 4.1 46.6 1.0
OG K:SER330 4.1 41.7 1.0
O1 K:OXL510 4.2 56.5 1.0
PA K:ATP1001 4.2 47.8 1.0
O3A K:ATP1001 4.3 47.5 1.0
CB K:THR296 4.3 37.9 1.0
CG K:ASP145 4.3 54.5 1.0
CB K:SER330 4.4 40.0 1.0
OD1 K:ASP145 4.6 55.4 1.0
O4 K:OXL510 4.9 58.6 1.0
O3G K:ATP1001 4.9 46.8 1.0
O2B K:ATP1001 5.0 47.0 1.0
CA K:GLY263 5.0 31.6 1.0

Magnesium binding site 2 out of 6 in 3hqo

Go back to Magnesium Binding Sites List in 3hqo
Magnesium binding site 2 out of 6 in the Crystal Structures of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp and Oxalate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structures of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp and Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg502

b:8.1
occ:1.00
 O4 K:OXL510 2.0 58.6 1.0
OD2 K:ASP264 2.4 34.3 1.0
OE1 K:GLU240 2.5 36.0 1.0
O2G K:ATP1001 2.7 47.2 1.0
C2 K:OXL510 3.1 58.7 1.0
OE2 K:GLU240 3.2 38.2 1.0
CD K:GLU240 3.2 38.5 1.0
O3G K:ATP1001 3.3 46.8 1.0
O1 K:OXL510 3.4 56.5 1.0
PG K:ATP1001 3.5 46.6 1.0
NZ K:LYS238 3.5 27.0 1.0
CG K:ASP264 3.6 33.8 1.0
CE2 K:PHE212 3.7 42.1 1.0
C1 K:OXL510 3.7 57.7 1.0
K K:K504 4.1 36.9 1.0
CE K:LYS238 4.2 29.5 1.0
O2 K:OXL510 4.2 59.4 1.0
OG K:SER211 4.2 33.7 1.0
CD2 K:PHE212 4.3 41.2 1.0
OD1 K:ASP264 4.5 37.1 1.0
OE2 K:GLU88 4.5 47.4 1.0
CB K:ASP264 4.5 32.2 1.0
O1G K:ATP1001 4.5 46.5 1.0
CZ K:PHE212 4.6 42.4 1.0
O3B K:ATP1001 4.6 46.6 1.0
CG K:GLU240 4.7 41.5 1.0
CB K:SER211 4.8 34.1 1.0
O3 K:OXL510 5.0 57.0 1.0

Magnesium binding site 3 out of 6 in 3hqo

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Magnesium binding site 3 out of 6 in the Crystal Structures of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp and Oxalate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structures of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp and Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg500

b:22.1
occ:1.00
 O1G A:ATP1001 2.2 44.0 1.0
O1B A:ATP1001 2.6 43.4 1.0
O1A A:ATP1001 3.0 47.2 1.0
OD2 A:ASP145 3.2 46.7 1.0
O3 A:OXL510 3.4 50.0 1.0
OG1 A:THR296 3.6 38.7 1.0
PG A:ATP1001 3.6 43.9 1.0
PB A:ATP1001 3.7 43.5 1.0
CG2 A:THR296 3.8 38.2 1.0
C1 A:OXL510 3.8 50.8 1.0
O3A A:ATP1001 3.9 45.0 1.0
OG A:SER330 4.0 41.7 1.0
O3B A:ATP1001 4.0 43.5 1.0
PA A:ATP1001 4.1 46.5 1.0
CG A:ASP145 4.2 47.0 1.0
O2 A:OXL510 4.2 52.4 1.0
CB A:SER330 4.2 40.0 1.0
CB A:THR296 4.2 38.0 1.0
C2 A:OXL510 4.3 51.3 1.0
O2G A:ATP1001 4.3 44.6 1.0
OD1 A:ASP145 4.4 46.6 1.0
O1 A:OXL510 4.5 50.3 1.0
O3G A:ATP1001 4.7 43.9 1.0
CA A:THR296 4.9 37.9 1.0

Magnesium binding site 4 out of 6 in 3hqo

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Magnesium binding site 4 out of 6 in the Crystal Structures of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp and Oxalate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structures of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp and Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:46.7
occ:1.00
 O4 A:OXL510 2.2 49.4 1.0
O2G A:ATP1001 2.3 44.6 1.0
OD2 A:ASP264 2.7 34.3 1.0
OE1 A:GLU240 2.7 35.9 1.0
OE2 A:GLU240 3.1 38.3 1.0
CD A:GLU240 3.3 38.5 1.0
C2 A:OXL510 3.3 51.3 1.0
PG A:ATP1001 3.4 43.9 1.0
NZ A:LYS238 3.4 27.0 1.0
O3G A:ATP1001 3.5 43.9 1.0
O1 A:OXL510 3.6 50.3 1.0
CE2 A:PHE212 3.7 42.1 1.0
K A:K504 3.8 41.5 1.0
CG A:ASP264 3.9 33.7 1.0
OG A:SER211 3.9 33.6 1.0
C1 A:OXL510 3.9 50.8 1.0
CE A:LYS238 4.1 29.5 1.0
CD2 A:PHE212 4.2 41.1 1.0
O2 A:OXL510 4.3 52.4 1.0
O1G A:ATP1001 4.4 44.0 1.0
O3B A:ATP1001 4.4 43.5 1.0
CB A:SER211 4.6 34.1 1.0
OE2 A:GLU88 4.6 47.3 1.0
CZ A:PHE212 4.6 42.4 1.0
OD1 A:ASP264 4.7 37.1 1.0
CG A:GLU240 4.7 41.5 1.0
CB A:ASP264 4.7 32.2 1.0
NH2 A:ARG90 4.9 43.8 1.0

Magnesium binding site 5 out of 6 in 3hqo

Go back to Magnesium Binding Sites List in 3hqo
Magnesium binding site 5 out of 6 in the Crystal Structures of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp and Oxalate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structures of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp and Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:37.1
occ:1.00
 O4 B:OXL510 2.2 42.7 1.0
OD2 B:ASP264 2.2 34.3 1.0
OE1 B:GLU240 2.6 35.9 1.0
CD B:GLU240 3.3 38.5 1.0
OE2 B:GLU240 3.3 38.4 1.0
C2 B:OXL510 3.3 45.9 1.0
CG B:ASP264 3.4 33.7 1.0
CE2 B:PHE212 3.5 42.1 1.0
O1 B:OXL510 3.6 45.1 1.0
K B:K504 3.8 83.2 1.0
NZ B:LYS238 3.9 27.1 1.0
C1 B:OXL510 4.0 45.7 1.0
CD2 B:PHE212 4.1 41.2 1.0
OD1 B:ASP264 4.2 37.1 1.0
CZ B:PHE212 4.3 42.4 1.0
OG B:SER211 4.3 33.6 1.0
O2 B:OXL510 4.3 46.5 1.0
CB B:ASP264 4.4 32.2 1.0
OE2 B:GLU88 4.4 52.0 1.0
CE B:LYS238 4.5 29.5 1.0
CG B:GLU240 4.7 41.4 1.0
O3G B:ATP1001 4.9 0.3 1.0
CB B:SER211 4.9 34.1 1.0

Magnesium binding site 6 out of 6 in 3hqo

Go back to Magnesium Binding Sites List in 3hqo
Magnesium binding site 6 out of 6 in the Crystal Structures of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp and Oxalate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structures of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp and Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:36.4
occ:1.00
 O4 C:OXL510 2.2 43.1 1.0
OD2 C:ASP264 2.2 34.4 1.0
OE1 C:GLU240 2.8 35.9 1.0
CE2 C:PHE212 3.3 42.1 1.0
C2 C:OXL510 3.3 47.6 1.0
CG C:ASP264 3.3 33.8 1.0
CD C:GLU240 3.4 38.5 1.0
OE2 C:GLU240 3.4 38.4 1.0
O1 C:OXL510 3.6 47.8 1.0
CD2 C:PHE212 3.9 41.2 1.0
C1 C:OXL510 4.0 48.1 1.0
OD1 C:ASP264 4.1 37.1 1.0
CZ C:PHE212 4.1 42.4 1.0
NZ C:LYS238 4.1 27.1 1.0
K C:K504 4.3 59.5 1.0
O2 C:OXL510 4.3 48.0 1.0
CB C:ASP264 4.4 32.3 1.0
OE2 C:GLU88 4.4 55.4 1.0
OG C:SER211 4.4 33.6 1.0
CG C:GLU240 4.8 41.5 1.0
CE C:LYS238 4.8 29.5 1.0
CB C:SER211 4.9 34.1 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 Dec 14 08:14:22 2020

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