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Sodium in PDB 2g50: The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase.

Enzymatic activity of The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase.

All present enzymatic activity of The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase.:
2.7.1.40;

Protein crystallography data

The structure of The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase., PDB code: 2g50 was solved by T.Holyoak, R.Williams, A.W.Fenton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 76.47 / 1.65
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 82.626, 109.014, 144.463, 95.15, 93.45, 112.26
R / Rfree (%) 14.8 / 17.4

Other elements in 2g50:

The structure of The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase. also contains other interesting chemical elements:

Potassium (K) 8 atoms
Manganese (Mn) 8 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase. (pdb code 2g50). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase., PDB code: 2g50:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 2g50

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Sodium binding site 1 out of 12 in the The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na6019

b:21.7
occ:1.00
 O A:HOH7006 2.5 34.4 1.0
O A:LYS124 2.6 11.4 1.0
O A:THR128 2.8 16.7 1.0
O A:HOH7007 2.9 38.0 1.0
O A:SER126 2.9 17.3 1.0
O A:GLY125 3.0 15.2 1.0
O A:GLY127 3.2 17.7 1.0
C A:GLY125 3.4 14.8 1.0
C A:THR128 3.6 17.0 1.0
C A:SER126 3.6 16.8 1.0
O A:HOH7010 3.8 31.4 1.0
C A:LYS124 3.8 11.6 1.0
C A:GLY127 3.8 17.5 1.0
CA A:GLY125 4.0 13.8 1.0
CA A:ALA129 4.1 16.1 1.0
CG2 A:ILE123 4.1 9.1 1.0
N A:SER126 4.1 15.4 1.0
N A:ALA129 4.1 16.4 1.0
O A:HOH7008 4.2 32.4 1.0
N A:GLY127 4.3 17.2 1.0
N A:THR128 4.3 17.6 1.0
N A:GLY125 4.4 12.8 1.0
CA A:SER126 4.4 16.3 1.0
CA A:THR128 4.5 17.4 1.0
CA A:GLY127 4.5 17.3 1.0
O A:ALA129 4.5 15.9 1.0
C A:ALA129 4.6 15.8 1.0
O A:HOH7005 4.8 21.2 1.0
CA A:LYS124 5.0 10.8 1.0

Sodium binding site 2 out of 12 in 2g50

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Sodium binding site 2 out of 12 in the The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na6023

b:14.5
occ:1.00
 O A:HOH6812 2.8 26.0 1.0
OG A:SER436 2.8 10.7 1.0
OG1 A:THR431 3.0 11.7 1.0
N A:SER436 3.3 9.7 1.0
O A:HOH6811 3.5 29.0 1.0
CB A:SER436 3.6 9.6 1.0
O A:HOH7127 3.7 44.5 1.0
OG A:SER433 3.7 12.3 1.0
CB A:THR431 3.9 10.9 1.0
O A:HOH6813 3.9 39.2 1.0
N A:ARG435 4.0 10.1 1.0
CA A:SER436 4.0 9.0 1.0
O A:HOH6810 4.1 29.2 1.0
CA A:THR431 4.2 10.7 1.0
CB A:ARG435 4.2 10.8 1.0
C A:ARG435 4.3 10.0 1.0
CA A:ARG435 4.4 10.6 1.0
N A:GLU432 4.5 10.7 1.0
CA A:PHE520 4.6 12.8 1.0
N A:GLY434 4.6 9.7 1.0
C A:GLY434 4.6 9.8 1.0
O A:GLY519 4.7 17.6 1.0
N A:SER433 4.7 10.6 1.0
O A:HOH6953 4.8 38.5 1.0
O A:LEU430 4.9 9.7 1.0
C A:THR431 4.9 10.9 1.0
CB A:SER433 5.0 10.9 1.0

Sodium binding site 3 out of 12 in 2g50

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Sodium binding site 3 out of 12 in the The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na6024

b:21.1
occ:1.00
 O B:HOH6556 2.3 31.5 1.0
OG B:SER436 2.9 9.9 1.0
OG1 B:THR431 2.9 9.9 1.0
N B:SER436 3.3 9.2 1.0
CB B:SER436 3.5 9.4 1.0
O B:HOH6557 3.6 30.6 1.0
CB B:THR431 3.8 10.4 1.0
OG B:SER433 3.8 11.7 1.0
N B:ARG435 4.0 9.8 1.0
CA B:SER436 4.0 9.2 1.0
CA B:THR431 4.1 10.2 1.0
O B:HOH6558 4.2 24.3 1.0
N B:GLU432 4.2 11.0 1.0
CB B:ARG435 4.3 11.2 1.0
C B:ARG435 4.3 9.9 1.0
CA B:ARG435 4.4 10.5 1.0
N B:GLY434 4.5 10.0 1.0
N B:SER433 4.6 10.8 1.0
C B:GLY434 4.6 9.9 1.0
C B:THR431 4.7 11.3 1.0
CA B:PHE520 4.8 11.1 1.0
O B:LEU430 4.8 11.4 1.0
O B:GLY519 4.9 15.6 1.0
CB B:SER433 4.9 11.5 1.0

Sodium binding site 4 out of 12 in 2g50

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Sodium binding site 4 out of 12 in the The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na6025

b:18.6
occ:1.00
 O C:HOH6628 2.5 28.6 1.0
OG C:SER436 2.9 10.7 1.0
OG1 C:THR431 2.9 11.2 1.0
N C:SER436 3.3 10.1 1.0
CB C:SER436 3.5 10.8 1.0
CB C:THR431 3.8 10.8 1.0
OG C:SER433 3.8 11.2 1.0
O C:HOH6627 3.8 30.4 1.0
N C:ARG435 4.0 10.8 1.0
CA C:SER436 4.0 10.3 1.0
CA C:THR431 4.1 10.3 1.0
O C:HOH6626 4.1 24.9 1.0
C C:ARG435 4.3 11.0 1.0
N C:GLU432 4.3 10.6 1.0
CB C:ARG435 4.4 12.2 1.0
CA C:ARG435 4.4 11.3 1.0
N C:GLY434 4.6 9.9 1.0
N C:SER433 4.6 10.6 1.0
C C:GLY434 4.6 9.8 1.0
CA C:PHE520 4.7 12.8 1.0
C C:THR431 4.7 10.7 1.0
O C:LEU430 4.8 10.2 1.0
CB C:SER433 4.9 10.9 1.0
O C:GLY519 4.9 18.0 1.0

Sodium binding site 5 out of 12 in 2g50

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Sodium binding site 5 out of 12 in the The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na6020

b:23.1
occ:1.00
 O D:LYS124 2.6 11.9 1.0
O D:HOH6753 2.6 42.4 1.0
O D:THR128 2.9 20.9 1.0
O D:GLY127 2.9 20.6 1.0
O D:GLY125 2.9 17.3 1.0
O D:SER126 3.0 19.5 1.0
C D:GLY125 3.4 16.8 1.0
C D:THR128 3.6 20.8 1.0
C D:SER126 3.7 19.3 1.0
C D:GLY127 3.7 20.5 1.0
O D:HOH6771 3.7 32.8 1.0
C D:LYS124 3.7 12.0 1.0
CA D:GLY125 4.0 15.5 1.0
CA D:ALA129 4.0 20.0 1.0
N D:SER126 4.1 17.8 1.0
CG2 D:ILE123 4.1 9.0 1.0
N D:ALA129 4.1 20.4 1.0
O D:HOH7129 4.2 34.4 1.0
N D:GLY127 4.3 19.9 1.0
N D:GLY125 4.3 13.9 1.0
N D:THR128 4.4 20.7 1.0
CA D:SER126 4.4 18.9 1.0
CA D:GLY127 4.5 20.2 1.0
O D:ALA129 4.5 19.6 1.0
CA D:THR128 4.5 20.8 1.0
C D:ALA129 4.6 19.8 1.0
O D:HOH6752 4.7 35.4 1.0
O D:HOH6751 4.8 24.2 1.0
O D:ILE123 4.9 8.8 1.0
CA D:LYS124 5.0 11.4 1.0

Sodium binding site 6 out of 12 in 2g50

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Sodium binding site 6 out of 12 in the The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na6026

b:19.1
occ:1.00
 O D:HOH6516 2.6 34.1 1.0
OG D:SER436 2.9 11.7 1.0
OG1 D:THR431 3.0 11.4 1.0
N D:SER436 3.4 9.9 1.0
O D:HOH6515 3.4 35.8 1.0
CB D:SER436 3.5 10.0 1.0
OG D:SER433 3.8 12.0 1.0
CB D:THR431 3.9 11.0 1.0
O D:HOH6514 4.0 24.0 1.0
N D:ARG435 4.1 11.0 1.0
CA D:SER436 4.1 9.8 1.0
O D:HOH6517 4.1 39.5 1.0
CB D:ARG435 4.2 11.7 0.4
CA D:THR431 4.2 11.3 1.0
C D:ARG435 4.3 10.9 1.0
CB D:ARG435 4.4 11.9 0.6
CA D:ARG435 4.4 11.2 0.4
CA D:ARG435 4.4 11.2 0.6
N D:GLU432 4.4 12.3 1.0
N D:GLY434 4.6 11.2 1.0
N D:SER433 4.6 12.0 1.0
CA D:PHE520 4.7 12.6 1.0
C D:GLY434 4.7 11.1 1.0
C D:THR431 4.8 11.8 1.0
O D:LEU430 4.8 11.4 1.0
O D:GLY519 4.9 16.6 1.0
CB D:SER433 5.0 11.8 1.0
CG D:ARG435 5.0 13.4 0.4

Sodium binding site 7 out of 12 in 2g50

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Sodium binding site 7 out of 12 in the The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na6021

b:21.9
occ:1.00
 O E:LYS124 2.6 11.1 1.0
O E:THR128 2.8 21.2 1.0
O E:HOH4539 2.8 29.0 1.0
O E:SER126 2.9 20.2 1.0
O E:GLY125 3.1 18.0 1.0
O E:GLY127 3.2 21.6 1.0
C E:GLY125 3.4 17.2 1.0
O E:HOH3565 3.6 28.5 1.0
C E:THR128 3.6 21.6 1.0
C E:SER126 3.6 19.9 1.0
C E:LYS124 3.7 11.5 1.0
C E:GLY127 3.8 21.5 1.0
N E:SER126 4.0 18.5 1.0
CA E:ALA129 4.0 21.1 1.0
CA E:GLY125 4.1 15.6 1.0
CG2 E:ILE123 4.1 9.2 1.0
O E:HOH5109 4.1 66.8 1.0
N E:ALA129 4.1 21.3 1.0
O E:HOH3576 4.2 30.9 1.0
N E:GLY125 4.3 13.4 1.0
N E:GLY127 4.4 20.4 1.0
N E:THR128 4.4 21.7 1.0
CA E:SER126 4.4 19.5 1.0
O E:ALA129 4.5 20.9 1.0
C E:ALA129 4.5 21.1 1.0
CA E:THR128 4.5 21.8 1.0
CA E:GLY127 4.5 20.9 1.0
CG E:LYS124 4.8 10.7 1.0
CA E:LYS124 4.9 10.7 1.0
O E:HOH3416 5.0 22.7 1.0

Sodium binding site 8 out of 12 in 2g50

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Sodium binding site 8 out of 12 in the The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na6030

b:16.9
occ:1.00
 O E:HOH4160 2.6 26.4 1.0
OG E:SER436 2.8 11.3 1.0
OG1 E:THR431 3.0 11.1 1.0
N E:SER436 3.3 10.0 1.0
O E:HOH5115 3.3 52.1 1.0
CB E:SER436 3.5 9.6 1.0
O E:HOH4068 3.7 31.5 1.0
CB E:THR431 3.8 11.5 1.0
OG E:SER433 3.8 11.9 1.0
CA E:SER436 4.0 9.9 1.0
N E:ARG435 4.0 10.3 1.0
O E:HOH4069 4.1 20.9 1.0
CA E:THR431 4.2 10.9 1.0
C E:ARG435 4.3 10.7 1.0
CB E:ARG435 4.3 12.3 1.0
CA E:ARG435 4.4 11.4 1.0
N E:GLU432 4.4 11.7 1.0
CA E:PHE520 4.6 11.7 1.0
N E:GLY434 4.6 10.6 1.0
C E:GLY434 4.6 10.6 1.0
N E:SER433 4.7 11.4 1.0
O E:HOH4106 4.8 39.8 1.0
C E:THR431 4.8 11.6 1.0
O E:GLY519 4.8 16.6 1.0
O E:LEU430 4.9 10.5 1.0
CB E:SER433 5.0 11.2 1.0

Sodium binding site 9 out of 12 in 2g50

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Sodium binding site 9 out of 12 in the The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na6027

b:17.0
occ:1.00
 O F:HOH6754 2.4 28.8 1.0
OG F:SER436 2.9 10.4 1.0
OG1 F:THR431 3.0 10.8 1.0
N F:SER436 3.4 9.1 1.0
CB F:SER436 3.5 10.6 1.0
O F:HOH6753 3.8 28.5 1.0
OG F:SER433 3.8 12.2 1.0
CB F:THR431 3.8 11.3 1.0
O F:HOH7057 3.9 55.2 1.0
N F:ARG435 4.0 9.2 1.0
CA F:SER436 4.0 9.5 1.0
CA F:THR431 4.1 10.6 1.0
O F:HOH6752 4.1 22.2 1.0
N F:GLU432 4.3 11.2 1.0
C F:ARG435 4.3 9.6 1.0
CB F:ARG435 4.4 10.1 1.0
CA F:ARG435 4.4 9.9 1.0
N F:GLY434 4.6 9.7 1.0
N F:SER433 4.6 11.2 1.0
CA F:PHE520 4.6 12.4 1.0
C F:GLY434 4.6 9.3 1.0
C F:THR431 4.7 11.1 1.0
O F:GLY519 4.7 16.2 1.0
O F:LEU430 4.8 10.9 1.0
CB F:SER433 4.9 11.4 1.0

Sodium binding site 10 out of 12 in 2g50

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Sodium binding site 10 out of 12 in the The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of The Location of the Allosteric Amino Acid Binding Site of Muscle Pyruvate Kinase. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na6028

b:21.0
occ:1.00
 O G:HOH3003 2.3 36.1 1.0
OG G:SER436 2.9 10.8 1.0
OG1 G:THR431 3.0 10.9 1.0
N G:SER436 3.3 10.0 1.0
CB G:SER436 3.5 10.6 1.0
O G:HOH1536 3.6 34.4 1.0
OG G:SER433 3.7 10.9 1.0
CB G:THR431 3.9 10.9 1.0
N G:ARG435 4.0 9.9 1.0
CA G:SER436 4.0 9.6 1.0
O G:HOH4699 4.1 48.1 1.0
O G:HOH1535 4.2 25.6 1.0
CA G:THR431 4.2 10.6 1.0
CB G:ARG435 4.3 11.4 1.0
C G:ARG435 4.3 10.3 1.0
N G:GLU432 4.4 11.2 1.0
CA G:ARG435 4.4 10.9 1.0
N G:GLY434 4.5 10.1 1.0
N G:SER433 4.6 11.4 1.0
C G:GLY434 4.6 10.1 1.0
CA G:PHE520 4.6 12.8 1.0
C G:THR431 4.8 11.0 1.0
O G:GLY519 4.8 16.3 1.0
O G:LEU430 4.9 10.5 1.0
CB G:SER433 4.9 10.9 1.0

Reference:

R.Williams, T.Holyoak, G.Mcdonald, C.Gui, A.W.Fenton. Differentiating A Ligand'S Chemical Requirements For Allosteric Interactions From Those For Protein Binding. Phenylalanine Inhibition of Pyruvate Kinase. Biochemistry V. 45 5421 2006.
ISSN: ISSN 0006-2960
PubMed: 16634623
DOI: 10.1021/BI0524262
Page generated: Mon Oct 7 02:32:19 2024

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