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Magnesium in PDB 6ksh: Crystal Structure of Pyruvate Kinase (Pyk) From Plasmodium Falciparum in Complex with Oxalate and Atp

Enzymatic activity of Crystal Structure of Pyruvate Kinase (Pyk) From Plasmodium Falciparum in Complex with Oxalate and Atp

All present enzymatic activity of Crystal Structure of Pyruvate Kinase (Pyk) From Plasmodium Falciparum in Complex with Oxalate and Atp:
2.7.1.40;

Protein crystallography data

The structure of Crystal Structure of Pyruvate Kinase (Pyk) From Plasmodium Falciparum in Complex with Oxalate and Atp, PDB code: 6ksh was solved by W.Zhong, Q.Cai, K.Li, J.Lescar, P.C.Dedon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.99 / 2.60
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 139.410, 139.410, 453.156, 90.00, 90.00, 120.00
R / Rfree (%) 15.1 / 20.7

Other elements in 6ksh:

The structure of Crystal Structure of Pyruvate Kinase (Pyk) From Plasmodium Falciparum in Complex with Oxalate and Atp also contains other interesting chemical elements:

Potassium (K) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Pyruvate Kinase (Pyk) From Plasmodium Falciparum in Complex with Oxalate and Atp (pdb code 6ksh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Pyruvate Kinase (Pyk) From Plasmodium Falciparum in Complex with Oxalate and Atp, PDB code: 6ksh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6ksh

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Magnesium binding site 1 out of 8 in the Crystal Structure of Pyruvate Kinase (Pyk) From Plasmodium Falciparum in Complex with Oxalate and Atp


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 (Pyk) From Plasmodium Falciparum in Complex with Oxalate and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:26.4
occ:1.00
 OD2 A:ASP281 2.1 44.5 1.0
O3 A:OXL605 2.1 43.8 1.0
O A:HOH773 2.2 32.6 1.0
OE2 A:GLU257 2.3 41.9 1.0
O2G A:ATP603 2.3 32.5 1.0
O4 A:OXL605 2.3 48.2 1.0
C1 A:OXL605 2.9 43.7 1.0
C2 A:OXL605 3.1 47.3 1.0
CG A:ASP281 3.1 44.2 1.0
CD A:GLU257 3.3 53.5 1.0
PG A:ATP603 3.4 32.4 1.0
CB A:ASP281 3.6 35.2 1.0
O3G A:ATP603 3.6 25.3 1.0
OE1 A:GLU257 3.7 43.5 1.0
NZ A:LYS255 4.0 47.2 1.0
O1G A:ATP603 4.0 32.3 1.0
O1 A:OXL605 4.1 42.4 1.0
O A:HOH714 4.2 29.4 1.0
OD1 A:ASP281 4.2 47.1 1.0
O2 A:OXL605 4.3 47.7 1.0
CE A:LYS255 4.4 49.3 1.0
O A:HOH704 4.4 45.0 1.0
CZ A:PHE229 4.6 32.9 1.0
N A:ASP281 4.6 32.5 1.0
CG A:GLU257 4.6 41.7 1.0
CB A:ALA278 4.6 31.6 1.0
ND2 A:ASN192 4.7 32.2 1.0
O3B A:ATP603 4.7 33.0 1.0
CA A:ASP281 4.7 32.4 1.0
CE1 A:PHE229 4.8 32.0 1.0
CB A:GLU257 4.9 34.8 1.0

Magnesium binding site 2 out of 8 in 6ksh

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Magnesium binding site 2 out of 8 in the Crystal Structure of Pyruvate Kinase (Pyk) From Plasmodium Falciparum in Complex with Oxalate and Atp


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 (Pyk) From Plasmodium Falciparum in Complex with Oxalate and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:33.7
occ:1.00
 O1G A:ATP603 1.9 32.3 1.0
O A:HOH714 2.0 29.4 1.0
O A:HOH745 2.0 31.9 1.0
O A:HOH794 2.0 33.3 1.0
O2A A:ATP603 2.2 42.2 1.0
O2B A:ATP603 2.3 32.4 1.0
PG A:ATP603 3.1 32.4 1.0
PB A:ATP603 3.3 34.6 1.0
PA A:ATP603 3.4 34.8 1.0
O3B A:ATP603 3.5 33.0 1.0
O3A A:ATP603 3.6 37.5 1.0
O2G A:ATP603 3.6 32.5 1.0
C2 A:OXL605 3.9 47.3 1.0
C1 A:OXL605 4.0 43.7 1.0
OG A:SER347 4.0 35.2 1.0
O2 A:OXL605 4.1 47.7 1.0
O1 A:OXL605 4.2 42.4 1.0
O1A A:ATP603 4.2 30.5 1.0
OG1 A:THR313 4.2 34.4 1.0
OD2 A:ASP162 4.3 45.5 1.0
OD1 A:ASP162 4.4 46.7 1.0
O4 A:OXL605 4.4 48.2 1.0
NH1 A:ARG67 4.4 28.7 1.0
CB A:SER347 4.4 33.1 1.0
CG2 A:THR313 4.4 27.1 1.0
O3G A:ATP603 4.4 25.3 1.0
O A:HOH839 4.5 31.9 1.0
O3 A:OXL605 4.5 43.8 1.0
O5' A:ATP603 4.5 36.7 1.0
O A:HOH910 4.5 34.7 1.0
O1B A:ATP603 4.6 32.8 1.0
C5' A:ATP603 4.7 40.0 1.0
NH2 A:ARG67 4.8 27.0 1.0
CG A:ASP162 4.8 43.8 1.0
ND2 A:ASN192 4.8 32.2 1.0
CB A:THR313 5.0 35.3 1.0

Magnesium binding site 3 out of 8 in 6ksh

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Magnesium binding site 3 out of 8 in the Crystal Structure of Pyruvate Kinase (Pyk) From Plasmodium Falciparum in Complex with Oxalate and Atp


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 (Pyk) From Plasmodium Falciparum in Complex with Oxalate and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:42.9
occ:1.00
 O B:HOH754 2.0 52.2 1.0
O4 B:OXL605 2.0 61.6 1.0
OD2 B:ASP281 2.0 64.2 1.0
OE2 B:GLU257 2.3 50.2 1.0
O1G B:ATP603 2.4 53.1 1.0
O3 B:OXL605 2.5 58.6 1.0
C2 B:OXL605 2.9 60.8 1.0
C1 B:OXL605 3.1 57.4 1.0
CG B:ASP281 3.2 57.4 1.0
CD B:GLU257 3.2 56.1 1.0
PG B:ATP603 3.3 58.4 1.0
O3G B:ATP603 3.4 56.6 1.0
OE1 B:GLU257 3.5 50.5 1.0
CB B:ASP281 3.8 44.8 1.0
NZ B:LYS255 3.9 46.1 1.0
O2 B:OXL605 4.1 61.2 1.0
OD1 B:ASP281 4.2 57.7 1.0
O2G B:ATP603 4.2 61.5 1.0
O B:HOH705 4.3 40.7 1.0
O1 B:OXL605 4.4 53.4 1.0
CZ B:PHE229 4.4 53.6 1.0
CE B:LYS255 4.5 43.4 1.0
O B:HOH712 4.5 57.7 1.0
ND2 B:ASN192 4.6 47.9 1.0
CG B:GLU257 4.6 48.3 1.0
O3B B:ATP603 4.6 57.3 1.0
N B:ASP281 4.7 43.2 1.0
CE1 B:PHE229 4.7 55.2 1.0
CB B:ALA278 4.8 39.8 1.0
CA B:ASP281 4.9 43.2 1.0
CE2 B:PHE229 4.9 55.7 1.0
CB B:GLU257 4.9 47.3 1.0
NH1 B:ARG109 5.0 41.0 1.0

Magnesium binding site 4 out of 8 in 6ksh

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Magnesium binding site 4 out of 8 in the Crystal Structure of Pyruvate Kinase (Pyk) From Plasmodium Falciparum in Complex with Oxalate and Atp


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 (Pyk) From Plasmodium Falciparum in Complex with Oxalate and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:42.9
occ:1.00
 O2A B:ATP603 1.9 54.1 1.0
O B:HOH743 2.0 47.2 1.0
O B:HOH708 2.2 44.1 1.0
O2G B:ATP603 2.3 61.5 1.0
O B:HOH705 2.3 40.7 1.0
O2B B:ATP603 2.4 56.5 1.0
PA B:ATP603 3.2 54.3 1.0
PG B:ATP603 3.3 58.4 1.0
PB B:ATP603 3.3 56.1 1.0
O3A B:ATP603 3.5 58.2 1.0
O1G B:ATP603 3.6 53.1 1.0
O3B B:ATP603 3.7 57.3 1.0
OG B:SER347 3.7 50.6 1.0
CB B:SER347 4.0 41.8 1.0
O2 B:OXL605 4.0 61.2 1.0
O1A B:ATP603 4.0 53.5 1.0
C2 B:OXL605 4.0 60.8 1.0
OG1 B:THR313 4.2 38.6 1.0
OD2 B:ASP162 4.2 51.9 1.0
O B:HOH828 4.3 46.2 1.0
C1 B:OXL605 4.3 57.4 1.0
O5' B:ATP603 4.4 56.2 1.0
O B:HOH735 4.4 51.1 1.0
O4 B:OXL605 4.5 61.6 1.0
O1 B:OXL605 4.5 53.4 1.0
NH1 B:ARG67 4.5 46.8 1.0
CG2 B:THR313 4.6 41.7 1.0
OD1 B:ASP162 4.6 51.2 1.0
O3G B:ATP603 4.6 56.6 1.0
C5' B:ATP603 4.7 59.4 1.0
O1B B:ATP603 4.7 56.3 1.0
NH2 B:ARG67 4.8 39.2 1.0
CG B:ASP162 4.9 52.6 1.0
O3 B:OXL605 4.9 58.6 1.0

Magnesium binding site 5 out of 8 in 6ksh

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Magnesium binding site 5 out of 8 in the Crystal Structure of Pyruvate Kinase (Pyk) From Plasmodium Falciparum in Complex with Oxalate and Atp


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 (Pyk) From Plasmodium Falciparum in Complex with Oxalate and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:60.2
occ:1.00
 OD2 C:ASP281 1.9 63.9 1.0
O2 C:OXL605 1.9 58.7 1.0
O3G C:ATP603 2.0 63.6 1.0
O1 C:OXL605 2.0 61.4 1.0
O C:HOH715 2.3 56.8 1.0
OE2 C:GLU257 2.6 48.8 1.0
C2 C:OXL605 2.7 59.4 1.0
C1 C:OXL605 2.7 59.2 1.0
CG C:ASP281 3.0 64.5 1.0
PG C:ATP603 3.3 67.2 1.0
CB C:ASP281 3.6 51.3 1.0
O C:HOH731 3.7 56.1 1.0
O2G C:ATP603 3.7 68.5 1.0
CD C:GLU257 3.7 58.7 1.0
O1G C:ATP603 3.8 68.5 1.0
O4 C:OXL605 3.9 59.3 1.0
O3 C:OXL605 3.9 57.3 1.0
ND2 C:ASN192 4.0 69.2 1.0
OD1 C:ASP281 4.0 67.7 1.0
NZ C:LYS255 4.2 48.2 1.0
OE1 C:GLU257 4.2 59.0 1.0
N C:ASP281 4.2 48.8 1.0
O3B C:ATP603 4.5 69.2 1.0
CA C:ASP281 4.5 48.8 1.0
O C:HOH707 4.6 52.2 1.0
CE C:LYS255 4.7 46.0 1.0
CB C:ALA278 4.7 42.4 1.0
CZ C:PHE229 4.7 60.6 1.0
NH1 C:ARG109 4.9 76.2 1.0
CG C:GLU257 5.0 52.5 1.0

Magnesium binding site 6 out of 8 in 6ksh

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Magnesium binding site 6 out of 8 in the Crystal Structure of Pyruvate Kinase (Pyk) From Plasmodium Falciparum in Complex with Oxalate and Atp


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 (Pyk) From Plasmodium Falciparum in Complex with Oxalate and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:56.8
occ:1.00
 O2A C:ATP603 1.9 59.3 1.0
O C:HOH732 2.0 67.9 1.0
O C:HOH731 2.1 56.1 1.0
O C:HOH729 2.1 60.7 1.0
O2B C:ATP603 2.2 68.7 1.0
O1G C:ATP603 2.6 68.5 1.0
PA C:ATP603 3.3 62.3 1.0
PB C:ATP603 3.3 68.6 1.0
PG C:ATP603 3.5 67.2 1.0
O3A C:ATP603 3.6 64.8 1.0
O3B C:ATP603 3.8 69.2 1.0
OG C:SER347 3.8 49.3 1.0
O3G C:ATP603 3.9 63.6 1.0
CB C:SER347 4.1 42.6 1.0
O4 C:OXL605 4.1 59.3 1.0
C2 C:OXL605 4.2 59.4 1.0
OD2 C:ASP162 4.2 63.8 1.0
O1A C:ATP603 4.2 63.0 1.0
OG1 C:THR313 4.2 46.3 1.0
O5' C:ATP603 4.3 66.7 1.0
CG2 C:THR313 4.3 47.0 1.0
OD1 C:ASP162 4.3 64.8 1.0
C1 C:OXL605 4.4 59.2 1.0
C5' C:ATP603 4.5 68.7 1.0
O3 C:OXL605 4.5 57.3 1.0
O C:HOH810 4.5 51.3 1.0
O1B C:ATP603 4.6 70.7 1.0
O2 C:OXL605 4.6 58.7 1.0
CG C:ASP162 4.7 65.3 1.0
NH1 C:ARG67 4.8 56.5 1.0
O2G C:ATP603 4.9 68.5 1.0
O1 C:OXL605 4.9 61.4 1.0
CB C:THR313 4.9 46.6 1.0
NH2 C:ARG67 5.0 56.0 1.0
ND2 C:ASN192 5.0 69.2 1.0

Magnesium binding site 7 out of 8 in 6ksh

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Magnesium binding site 7 out of 8 in the Crystal Structure of Pyruvate Kinase (Pyk) From Plasmodium Falciparum in Complex with Oxalate and Atp


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 (Pyk) From Plasmodium Falciparum in Complex with Oxalate and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:30.8
occ:1.00
 O D:HOH712 1.9 44.5 1.0
OD2 D:ASP281 2.0 41.8 1.0
O1 D:OXL605 2.0 45.3 1.0
O1G D:ATP603 2.1 34.8 1.0
OE2 D:GLU257 2.3 47.6 1.0
O2 D:OXL605 2.4 49.0 1.0
C1 D:OXL605 2.9 48.5 1.0
C2 D:OXL605 3.1 49.5 1.0
CG D:ASP281 3.2 42.4 1.0
PG D:ATP603 3.3 37.5 1.0
CD D:GLU257 3.3 51.4 1.0
OE1 D:GLU257 3.6 37.3 1.0
O2G D:ATP603 3.6 35.7 1.0
CB D:ASP281 3.8 34.5 1.0
NZ D:LYS255 4.0 40.2 1.0
O3G D:ATP603 4.0 35.9 1.0
O3 D:OXL605 4.1 49.8 1.0
O D:HOH809 4.2 18.2 1.0
OD1 D:ASP281 4.2 43.1 1.0
O4 D:OXL605 4.3 47.5 1.0
N D:ASP281 4.5 31.4 1.0
O D:HOH738 4.5 45.7 1.0
CE D:LYS255 4.5 31.8 1.0
ND2 D:ASN192 4.6 33.7 1.0
O3B D:ATP603 4.6 36.1 1.0
CB D:ALA278 4.6 29.4 1.0
CZ D:PHE229 4.7 40.0 1.0
CG D:GLU257 4.7 40.3 1.0
CA D:ASP281 4.8 32.1 1.0
CB D:GLU257 4.9 33.7 1.0
CE1 D:PHE229 5.0 41.7 1.0

Magnesium binding site 8 out of 8 in 6ksh

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Magnesium binding site 8 out of 8 in the Crystal Structure of Pyruvate Kinase (Pyk) From Plasmodium Falciparum in Complex with Oxalate and Atp


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 (Pyk) From Plasmodium Falciparum in Complex with Oxalate and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg602

b:29.6
occ:1.00
 O D:HOH742 1.9 38.2 1.0
O D:HOH706 1.9 36.2 1.0
O D:HOH809 2.0 18.2 1.0
O1A D:ATP603 2.0 34.9 1.0
O3G D:ATP603 2.3 35.9 1.0
O1B D:ATP603 2.4 39.6 1.0
PA D:ATP603 3.3 32.8 1.0
PB D:ATP603 3.4 35.7 1.0
PG D:ATP603 3.4 37.5 1.0
O3A D:ATP603 3.6 33.7 1.0
O3B D:ATP603 3.8 36.1 1.0
O1G D:ATP603 3.9 34.8 1.0
OG D:SER347 3.9 44.2 1.0
OG1 D:THR313 4.0 33.9 1.0
CB D:SER347 4.1 37.6 1.0
OD2 D:ASP162 4.1 51.9 1.0
C2 D:OXL605 4.1 49.5 1.0
O4 D:OXL605 4.1 47.5 1.0
O D:HOH882 4.2 39.9 1.0
O2A D:ATP603 4.2 32.1 1.0
C1 D:OXL605 4.2 48.5 1.0
O5' D:ATP603 4.3 31.6 1.0
O D:HOH818 4.4 28.9 1.0
OD1 D:ASP162 4.4 50.3 1.0
O3 D:OXL605 4.4 49.8 1.0
C5' D:ATP603 4.5 33.6 1.0
CG2 D:THR313 4.5 34.1 1.0
O2 D:OXL605 4.6 49.0 1.0
CG D:ASP162 4.7 49.1 1.0
NH1 D:ARG67 4.7 27.7 1.0
O2G D:ATP603 4.7 35.7 1.0
O1 D:OXL605 4.7 45.3 1.0
O2B D:ATP603 4.7 34.3 1.0
NH2 D:ARG67 4.8 34.4 1.0
CB D:THR313 4.9 37.4 1.0

Reference:

W.Zhong, K.Li, Q.Cai, J.Guo, M.Yuan, Y.H.Wong, M.D.Walkinshaw, L.A.Fothergill-Gilmore, P.A.M.Michels, P.C.Dedon, J.Lescar. Pyruvate Kinase From Plasmodium Falciparum: Structural and Kinetic Insights Into the Allosteric Mechanism. Biochem.Biophys.Res.Commun. V. 532 370 2020.
ISSN: ESSN 1090-2104
PubMed: 32878705
DOI: 10.1016/J.BBRC.2020.08.048
Page generated: Tue Oct 1 09:51:37 2024

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