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Sodium in PDB 8f5t: Rabbit Muscle Pyruvate Kinase in Complex with Sodium and Magnesium

Enzymatic activity of Rabbit Muscle Pyruvate Kinase in Complex with Sodium and Magnesium

All present enzymatic activity of Rabbit Muscle Pyruvate Kinase in Complex with Sodium and Magnesium:
2.7.1.40; 2.7.10.2; 2.7.11.1;

Protein crystallography data

The structure of Rabbit Muscle Pyruvate Kinase in Complex with Sodium and Magnesium, PDB code: 8f5t was solved by T.Holyoak, A.W.Fenton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.16 / 2.41
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 142.453, 113.759, 169.144, 90, 94.05, 90
R / Rfree (%) 18.5 / 23.2

Other elements in 8f5t:

The structure of Rabbit Muscle Pyruvate Kinase in Complex with Sodium and Magnesium also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Rabbit Muscle Pyruvate Kinase in Complex with Sodium and Magnesium (pdb code 8f5t). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Rabbit Muscle Pyruvate Kinase in Complex with Sodium and Magnesium, PDB code: 8f5t:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 8f5t

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Sodium binding site 1 out of 8 in the Rabbit Muscle Pyruvate Kinase in Complex with Sodium and Magnesium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Rabbit Muscle Pyruvate Kinase in Complex with Sodium and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:25.4
occ:1.00
 O A:HOH848 2.9 35.5 1.0
OG1 A:THR431 2.9 31.2 1.0
O A:HOH764 3.0 38.1 1.0
OG A:SER436 3.1 30.2 1.0
N A:SER436 3.5 29.2 1.0
OG A:SER433 3.6 36.4 1.0
CB A:THR431 3.7 29.4 1.0
CB A:SER436 3.8 27.1 1.0
N A:ARG435 4.0 28.2 1.0
CA A:THR431 4.2 31.2 1.0
CB A:ARG435 4.3 31.7 1.0
CA A:SER436 4.3 28.9 1.0
O A:GLY519 4.3 40.1 1.0
CA A:ARG435 4.5 29.9 1.0
N A:GLU432 4.5 31.1 1.0
C A:ARG435 4.5 30.9 1.0
N A:GLY434 4.5 31.1 1.0
CA A:PHE520 4.5 30.9 1.0
N A:SER433 4.6 30.7 1.0
C A:GLY434 4.7 29.3 1.0
NH1 A:ARG435 4.7 53.0 1.0
C A:THR431 4.8 30.0 1.0
CB A:SER433 4.9 35.0 1.0
O A:LEU430 4.9 28.9 1.0
CG A:ARG435 5.0 43.6 1.0

Sodium binding site 2 out of 8 in 8f5t

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Sodium binding site 2 out of 8 in the Rabbit Muscle Pyruvate Kinase in Complex with Sodium and Magnesium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Rabbit Muscle Pyruvate Kinase in Complex with Sodium and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na602

b:27.4
occ:1.00
 OG1 B:THR431 2.8 31.9 1.0
O B:HOH823 3.0 43.0 1.0
OG B:SER436 3.0 27.2 1.0
N B:SER436 3.4 30.7 1.0
O B:HOH711 3.4 39.2 1.0
CB B:SER436 3.5 29.4 1.0
CB B:THR431 3.6 33.5 1.0
O B:HOH747 3.6 54.1 1.0
OG B:SER433 3.9 35.2 1.0
N B:ARG435 4.0 32.0 1.0
CA B:SER436 4.1 33.0 1.0
CA B:THR431 4.1 32.5 1.0
CB B:ARG435 4.3 34.6 1.0
C B:ARG435 4.4 29.1 1.0
CA B:ARG435 4.5 33.5 1.0
N B:GLY434 4.5 32.8 1.0
CA B:PHE520 4.5 33.3 1.0
O B:GLY519 4.6 38.6 1.0
N B:GLU432 4.6 30.9 1.0
C B:GLY434 4.6 29.3 1.0
NH1 B:ARG435 4.7 51.8 1.0
O B:LEU430 4.8 32.1 1.0
N B:SER433 4.8 30.9 1.0
C B:THR431 4.9 31.2 1.0
CA B:GLY434 5.0 30.7 1.0
CG2 B:THR431 5.0 23.9 1.0
N B:THR521 5.0 28.5 1.0

Sodium binding site 3 out of 8 in 8f5t

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Sodium binding site 3 out of 8 in the Rabbit Muscle Pyruvate Kinase in Complex with Sodium and Magnesium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Rabbit Muscle Pyruvate Kinase in Complex with Sodium and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na602

b:31.9
occ:1.00
 O C:HOH769 2.7 46.6 1.0
OG1 C:THR431 2.9 36.6 1.0
OG C:SER436 3.0 42.4 1.0
N C:SER436 3.4 38.5 1.0
CB C:SER436 3.6 37.3 1.0
CB C:THR431 3.8 41.4 1.0
OG C:SER433 3.8 47.2 1.0
N C:ARG435 4.1 39.1 1.0
CA C:SER436 4.1 38.2 1.0
CA C:THR431 4.2 41.5 1.0
CB C:ARG435 4.2 38.2 1.0
O C:GLY519 4.3 50.5 1.0
C C:ARG435 4.4 37.0 1.0
CA C:PHE520 4.4 42.2 1.0
CA C:ARG435 4.4 36.8 1.0
N C:GLY434 4.6 44.0 1.0
N C:GLU432 4.6 43.2 1.0
C C:GLY434 4.7 39.3 1.0
N C:SER433 4.9 43.0 1.0
O C:LEU430 4.9 40.1 1.0
C C:THR431 4.9 43.4 1.0

Sodium binding site 4 out of 8 in 8f5t

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Sodium binding site 4 out of 8 in the Rabbit Muscle Pyruvate Kinase in Complex with Sodium and Magnesium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Rabbit Muscle Pyruvate Kinase in Complex with Sodium and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na602

b:34.8
occ:1.00
 OG1 D:THR431 2.8 38.0 1.0
O D:HOH731 3.0 45.5 1.0
OG D:SER436 3.0 36.5 1.0
N D:SER436 3.3 37.3 1.0
O D:HOH748 3.3 41.4 1.0
CB D:SER436 3.5 35.5 1.0
CB D:THR431 3.6 38.7 1.0
OG D:SER433 3.9 41.0 1.0
N D:ARG435 4.0 37.8 1.0
CA D:SER436 4.0 36.9 1.0
O D:HOH897 4.1 45.4 1.0
CA D:THR431 4.1 41.9 1.0
CB D:ARG435 4.3 40.8 1.0
C D:ARG435 4.3 38.9 1.0
CA D:ARG435 4.4 39.7 1.0
CA D:PHE520 4.5 40.9 1.0
N D:GLY434 4.6 40.6 1.0
C D:GLY434 4.6 38.3 1.0
N D:GLU432 4.6 37.5 1.0
O D:GLY519 4.7 44.7 1.0
O D:LEU430 4.8 42.4 1.0
NH1 D:ARG435 4.8 58.9 1.0
C D:THR431 4.9 40.5 1.0
N D:SER433 4.9 38.5 1.0
N D:THR521 5.0 37.4 1.0
CG2 D:THR431 5.0 35.0 1.0

Sodium binding site 5 out of 8 in 8f5t

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Sodium binding site 5 out of 8 in the Rabbit Muscle Pyruvate Kinase in Complex with Sodium and Magnesium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Rabbit Muscle Pyruvate Kinase in Complex with Sodium and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na602

b:29.7
occ:1.00
 OG E:SER436 2.8 34.1 1.0
OG1 E:THR431 3.0 37.8 1.0
O E:HOH765 3.1 42.0 1.0
N E:SER436 3.3 38.3 1.0
O E:HOH742 3.4 47.5 1.0
CB E:SER436 3.5 34.8 1.0
OG E:SER433 3.5 45.5 1.0
CB E:THR431 3.8 38.3 1.0
N E:ARG435 4.0 40.6 1.0
CA E:SER436 4.0 34.6 1.0
CB E:ARG435 4.1 43.0 1.0
CA E:THR431 4.3 37.4 1.0
C E:ARG435 4.3 36.5 1.0
CA E:ARG435 4.3 38.8 1.0
O E:GLY519 4.4 38.2 1.0
CA E:PHE520 4.4 38.5 1.0
N E:GLY434 4.6 39.0 1.0
N E:GLU432 4.6 37.1 1.0
C E:GLY434 4.7 38.5 1.0
N E:SER433 4.7 38.3 1.0
CB E:SER433 4.8 44.5 1.0
C E:THR431 4.9 37.0 1.0
O E:LEU430 5.0 37.6 1.0

Sodium binding site 6 out of 8 in 8f5t

Go back to Sodium Binding Sites List in 8f5t
Sodium binding site 6 out of 8 in the Rabbit Muscle Pyruvate Kinase in Complex with Sodium and Magnesium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Rabbit Muscle Pyruvate Kinase in Complex with Sodium and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na602

b:43.3
occ:1.00
 OG1 F:THR431 2.6 48.7 1.0
O F:HOH795 2.8 47.3 1.0
N F:SER436 3.4 46.5 1.0
OG F:SER436 3.5 46.8 1.0
CB F:THR431 3.6 50.6 1.0
CB F:SER436 3.7 45.1 1.0
OG F:SER433 3.7 49.4 1.0
N F:ARG435 4.0 45.9 1.0
CA F:THR431 4.1 55.0 1.0
CA F:SER436 4.2 47.7 1.0
CB F:ARG435 4.2 49.7 1.0
N F:GLU432 4.4 51.8 1.0
C F:ARG435 4.4 48.0 1.0
CA F:ARG435 4.4 47.6 1.0
N F:GLY434 4.5 49.1 1.0
CA F:PHE520 4.5 54.8 1.0
O F:GLY519 4.6 60.8 1.0
C F:GLY434 4.6 45.4 1.0
N F:SER433 4.6 50.9 1.0
C F:THR431 4.8 52.8 1.0
CG2 F:THR431 4.9 42.6 1.0
O F:LEU430 4.9 48.9 1.0
CB F:SER433 5.0 49.8 1.0
CA F:GLY434 5.0 44.8 1.0

Sodium binding site 7 out of 8 in 8f5t

Go back to Sodium Binding Sites List in 8f5t
Sodium binding site 7 out of 8 in the Rabbit Muscle Pyruvate Kinase in Complex with Sodium and Magnesium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Rabbit Muscle Pyruvate Kinase in Complex with Sodium and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na602

b:31.4
occ:1.00
 OG1 G:THR431 2.9 42.0 1.0
O G:HOH742 2.9 55.5 1.0
OG G:SER436 3.0 42.3 1.0
O G:HOH723 3.0 43.8 1.0
N G:SER436 3.3 35.9 1.0
CB G:SER436 3.4 36.4 1.0
CB G:THR431 3.7 38.1 1.0
OG G:SER433 3.8 44.6 1.0
CA G:SER436 4.0 36.9 1.0
N G:ARG435 4.1 41.5 1.0
CA G:THR431 4.2 35.9 1.0
CB G:ARG435 4.3 40.7 1.0
C G:ARG435 4.4 37.5 1.0
CA G:ARG435 4.5 39.7 1.0
N G:GLY434 4.5 37.5 1.0
CA G:PHE520 4.5 35.1 1.0
N G:GLU432 4.6 39.2 1.0
O G:GLY519 4.6 43.9 1.0
C G:GLY434 4.7 39.4 1.0
N G:SER433 4.8 38.3 1.0
C G:THR431 4.9 39.8 1.0
O G:LEU430 5.0 34.8 1.0
CA G:GLY434 5.0 39.6 1.0

Sodium binding site 8 out of 8 in 8f5t

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Sodium binding site 8 out of 8 in the Rabbit Muscle Pyruvate Kinase in Complex with Sodium and Magnesium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Rabbit Muscle Pyruvate Kinase in Complex with Sodium and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na602

b:39.8
occ:1.00
 OG1 H:THR431 2.3 50.6 1.0
OG H:SER436 3.2 47.3 1.0
N H:SER436 3.3 50.7 1.0
CB H:SER436 3.4 41.5 1.0
CB H:THR431 3.4 53.1 1.0
OG H:SER433 3.6 65.4 1.0
CA H:SER436 4.0 48.0 1.0
N H:ARG435 4.1 47.2 1.0
CA H:THR431 4.1 55.4 1.0
CB H:ARG435 4.2 50.2 1.0
N H:GLY434 4.4 55.4 1.0
C H:ARG435 4.4 51.1 1.0
CA H:ARG435 4.4 49.1 1.0
N H:GLU432 4.5 50.5 1.0
C H:GLY434 4.6 47.7 1.0
O H:GLY519 4.6 60.6 1.0
CG2 H:THR431 4.7 47.5 1.0
CA H:PHE520 4.7 54.1 1.0
N H:SER433 4.7 58.3 1.0
CB H:SER433 4.8 58.2 1.0
C H:THR431 4.8 54.0 1.0
CA H:GLY434 4.9 50.2 1.0
O H:LEU430 5.0 53.3 1.0
N H:THR521 5.0 50.1 1.0

Reference:

L.Swint-Kruse, L.L.Dougherty, B.Page, T.Wu, P.T.O'neil, C.B.Prasannan, C.Timmons, Q.Tang, D.J.Parente, S.Sreenivasan, T.Holyoak, A.W.Fenton. Pyk-Substitutionome: An Integrated Database Containing Allosteric Coupling, Ligand Affinity and Mutational, Structural, Pathological, Bioinformatic and Computational Information About Pyruvate Kinase Isozymes. Database (Oxford) V.2023 2023.
ISSN: ISSN 1758-0463
PubMed: 37171062
DOI: 10.1093/DATABASE/BAAD030
Page generated: Wed Oct 9 11:49:20 2024

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