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Sodium in PDB 3n25: The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+

Enzymatic activity of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+

All present enzymatic activity of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+:
2.7.1.40;

Protein crystallography data

The structure of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+, PDB code: 3n25 was solved by A.W.Fenton, T.A.Johnson, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.59 / 2.41
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 82.373, 108.747, 144.256, 95.18, 93.38, 112.23
R / Rfree (%) 20.4 / 26.8

Other elements in 3n25:

The structure of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ 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 Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ (pdb code 3n25). 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 Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+, PDB code: 3n25:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 3n25

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Sodium binding site 1 out of 12 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1300

b:40.4
occ:1.00
 O A:LYS124 2.5 6.3 1.0
O A:HOH1392 2.7 2.0 1.0
O A:GLY127 2.8 11.5 1.0
O A:SER126 3.3 10.7 1.0
O A:THR128 3.3 12.1 1.0
C A:GLY125 3.6 8.9 1.0
C A:LYS124 3.7 6.3 1.0
O A:GLY125 3.7 8.9 1.0
C A:SER126 3.8 10.6 1.0
C A:THR128 3.9 11.8 1.0
C A:GLY127 3.9 11.5 1.0
CG2 A:ILE123 3.9 4.1 1.0
CA A:ALA129 4.0 11.1 1.0
N A:SER126 4.0 9.6 1.0
CA A:GLY125 4.0 8.1 1.0
N A:ALA129 4.2 11.5 1.0
N A:GLY125 4.3 7.1 1.0
O A:ALA129 4.3 10.7 1.0
CA A:SER126 4.4 10.2 1.0
C A:ALA129 4.4 10.9 1.0
N A:GLY127 4.5 11.0 1.0
CB A:ILE123 4.7 4.1 1.0
CA A:GLY127 4.7 11.3 1.0
N A:THR128 4.7 11.7 1.0
O A:HOH967 4.8 2.0 1.0
CA A:THR128 4.9 11.8 1.0
C A:ILE123 4.9 4.9 1.0
O A:ILE123 4.9 5.1 1.0
CA A:LYS124 4.9 5.8 1.0
N A:LYS124 4.9 5.5 1.0

Sodium binding site 2 out of 12 in 3n25

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Sodium binding site 2 out of 12 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2100

b:29.4
occ:1.00
 OG1 A:THR431 2.8 3.8 1.0
OG A:SER436 2.9 7.3 1.0
OG A:SER433 3.3 5.7 1.0
N A:SER436 3.6 7.0 1.0
CB A:SER436 3.6 6.8 1.0
CB A:THR431 3.7 4.2 1.0
CA A:SER436 4.2 6.9 1.0
CA A:THR431 4.2 4.2 1.0
O A:HOH1393 4.3 7.0 1.0
N A:ARG435 4.3 7.0 1.0
N A:GLU432 4.3 5.3 1.0
CB A:ARG435 4.4 7.5 1.0
N A:GLY434 4.5 6.6 1.0
N A:SER433 4.5 6.1 1.0
C A:ARG435 4.6 7.0 1.0
CB A:SER433 4.6 6.2 1.0
CA A:ARG435 4.6 7.4 1.0
C A:GLY434 4.7 7.0 1.0
C A:THR431 4.8 4.6 1.0
CA A:PHE520 4.9 6.2 1.0
O A:LEU430 4.9 2.9 1.0
O A:GLY519 5.0 7.2 1.0
CA A:SER433 5.0 6.2 1.0

Sodium binding site 3 out of 12 in 3n25

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Sodium binding site 3 out of 12 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2000

b:48.4
occ:1.00
 O B:HOH1602 2.0 8.8 1.0
OG B:SER436 2.9 7.5 1.0
O B:HOH1176 3.3 2.0 1.0
OG1 B:THR431 3.7 3.9 1.0
OG B:SER433 3.8 3.9 1.0
CB B:SER436 3.8 7.3 1.0
N B:SER436 4.0 7.1 1.0
CA B:PHE520 4.2 8.0 1.0
O B:HOH1230 4.3 7.9 1.0
CB B:THR431 4.4 3.6 1.0
CA B:THR431 4.5 3.6 1.0
N B:GLU432 4.5 3.6 1.0
CA B:SER436 4.6 7.0 1.0
O B:GLY519 4.6 8.2 1.0
N B:PHE520 4.6 8.1 1.0
N B:SER433 4.7 4.0 1.0
N B:ARG435 4.7 6.8 1.0
C B:GLY519 4.7 8.2 1.0
CB B:SER433 4.9 4.3 1.0
O B:LEU430 4.9 3.8 1.0
CB B:ARG435 4.9 8.0 1.0
CB B:PHE520 5.0 8.0 1.0
N B:GLY434 5.0 5.1 1.0
C B:ARG435 5.0 7.3 1.0

Sodium binding site 4 out of 12 in 3n25

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Sodium binding site 4 out of 12 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na2000

b:22.6
occ:1.00
 O C:HOH1263 1.8 2.0 1.0
OG C:SER436 2.9 5.3 1.0
OG1 C:THR431 3.0 2.0 1.0
N C:SER436 3.4 4.5 1.0
OG C:SER433 3.5 4.5 1.0
CB C:SER436 3.6 4.6 1.0
N C:ARG435 3.9 4.6 1.0
O C:HOH1630 3.9 27.6 1.0
CB C:THR431 4.0 2.0 1.0
CA C:THR431 4.1 2.1 1.0
CA C:SER436 4.1 4.8 1.0
N C:GLU432 4.2 2.4 1.0
CB C:ARG435 4.3 5.3 1.0
C C:ARG435 4.4 4.4 1.0
CA C:ARG435 4.4 4.9 1.0
N C:GLY434 4.4 4.0 1.0
N C:SER433 4.5 3.2 1.0
C C:GLY434 4.6 4.2 1.0
C C:THR431 4.6 2.1 1.0
CB C:SER433 4.7 3.9 1.0
O C:LEU430 4.7 3.6 1.0
O C:HOH1189 4.7 12.0 1.0
CA C:PHE520 4.8 5.4 1.0
O C:GLY519 4.9 8.0 1.0
CA C:GLY434 5.0 3.8 1.0

Sodium binding site 5 out of 12 in 3n25

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Sodium binding site 5 out of 12 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na2000

b:35.9
occ:1.00
 O D:LYS124 2.4 11.4 1.0
O D:THR128 2.9 15.2 1.0
O D:HOH1394 2.9 2.0 1.0
O D:GLY125 3.3 14.2 1.0
C D:LYS124 3.6 11.6 1.0
C D:GLY125 3.6 13.9 1.0
C D:THR128 3.7 15.4 1.0
CA D:GLY125 3.8 13.2 1.0
CG2 D:ILE123 3.9 9.9 1.0
CA D:ALA129 4.0 14.8 1.0
O D:ALA129 4.0 14.7 1.0
O D:SER126 4.1 15.7 1.0
O D:GLY127 4.1 16.3 1.0
N D:GLY125 4.1 12.3 1.0
N D:ALA129 4.2 15.2 1.0
O D:HOH1270 4.2 2.0 1.0
C D:ALA129 4.3 14.8 1.0
C D:GLY127 4.4 16.1 1.0
C D:SER126 4.4 15.4 1.0
N D:SER126 4.4 14.5 1.0
N D:THR128 4.7 15.9 1.0
O D:HOH1269 4.7 5.0 1.0
CB D:ILE123 4.8 10.1 1.0
O D:ILE123 4.8 10.2 1.0
CA D:LYS124 4.8 11.4 1.0
CA D:THR128 4.8 15.7 1.0
C D:ILE123 4.8 10.3 1.0
N D:GLY127 4.8 15.9 1.0
N D:LYS124 4.8 10.8 1.0

Sodium binding site 6 out of 12 in 3n25

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Sodium binding site 6 out of 12 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na2100

b:21.3
occ:1.00
 O D:HOH1395 2.7 2.0 1.0
OG1 D:THR431 2.9 4.8 1.0
OG D:SER436 3.1 5.5 1.0
OG D:SER433 3.7 4.0 1.0
CB D:THR431 3.7 4.5 1.0
N D:SER436 3.7 5.5 1.0
CB D:SER436 3.8 5.0 1.0
N D:GLU432 3.9 5.3 1.0
CA D:THR431 3.9 4.5 1.0
N D:ARG435 4.2 6.4 1.0
O D:HOH873 4.2 22.2 1.0
N D:GLY434 4.2 5.9 1.0
N D:SER433 4.2 5.3 1.0
CA D:SER436 4.4 5.2 1.0
C D:THR431 4.4 4.7 1.0
CB D:ARG435 4.6 7.0 1.0
C D:GLY434 4.7 6.2 1.0
C D:ARG435 4.7 6.1 1.0
CA D:ARG435 4.7 6.7 1.0
O D:GLY519 4.8 5.7 1.0
CB D:SER433 4.8 5.2 1.0
O D:LEU430 4.9 4.5 1.0
CA D:GLY434 4.9 6.1 1.0
CA D:GLU432 4.9 5.4 1.0
CA D:SER433 5.0 5.4 1.0
CA D:PHE520 5.0 3.8 1.0

Sodium binding site 7 out of 12 in 3n25

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Sodium binding site 7 out of 12 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na2000

b:31.5
occ:1.00
 O E:LYS124 2.7 9.7 1.0
O E:SER126 3.0 16.7 1.0
O E:GLY125 3.2 13.7 1.0
O E:THR128 3.2 17.8 1.0
O E:GLY127 3.4 17.5 1.0
C E:GLY125 3.4 13.7 1.0
C E:SER126 3.6 16.3 1.0
C E:THR128 3.6 17.9 1.0
C E:GLY127 3.7 17.8 1.0
C E:LYS124 3.8 10.0 1.0
CA E:ALA129 3.9 17.2 1.0
N E:SER126 3.9 14.6 1.0
N E:ALA129 4.0 17.6 1.0
CA E:GLY125 4.0 12.6 1.0
N E:THR128 4.2 18.1 1.0
N E:GLY127 4.2 16.9 1.0
N E:GLY125 4.3 11.2 1.0
CA E:SER126 4.3 15.6 1.0
CG2 E:ILE123 4.3 7.7 1.0
CA E:GLY127 4.3 17.4 1.0
C E:ALA129 4.4 17.2 1.0
O E:ALA129 4.4 17.0 1.0
CA E:THR128 4.5 18.1 1.0
CG E:LYS124 4.8 8.5 1.0
CA E:LYS124 5.0 9.3 1.0

Sodium binding site 8 out of 12 in 3n25

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Sodium binding site 8 out of 12 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na2100

b:13.1
occ:1.00
 O E:HOH1396 2.0 2.0 1.0
OG1 E:THR431 2.8 4.2 1.0
OG E:SER436 2.9 4.5 1.0
O E:HOH1310 3.1 15.5 1.0
OG E:SER433 3.5 4.8 1.0
N E:SER436 3.6 6.4 1.0
CB E:THR431 3.8 3.9 1.0
CB E:SER436 3.8 6.1 1.0
N E:ARG435 4.0 6.9 1.0
CA E:THR431 4.1 3.8 1.0
N E:GLU432 4.1 4.9 1.0
CB E:ARG435 4.3 7.8 1.0
CA E:SER436 4.3 6.0 1.0
CA E:ARG435 4.4 7.5 1.0
C E:ARG435 4.4 7.1 1.0
N E:SER433 4.5 5.5 1.0
N E:GLY434 4.5 6.0 1.0
C E:THR431 4.6 4.3 1.0
C E:GLY434 4.6 6.6 1.0
O E:HOH1313 4.7 9.7 1.0
CB E:SER433 4.7 5.2 1.0
O E:GLY519 4.8 3.8 1.0
CA E:PHE520 4.8 2.8 1.0
O E:LEU430 5.0 3.1 1.0

Sodium binding site 9 out of 12 in 3n25

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Sodium binding site 9 out of 12 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na2000

b:27.8
occ:1.00
 O F:HOH1339 2.1 5.2 1.0
OG F:SER436 2.9 2.0 1.0
OG1 F:THR431 3.0 2.0 1.0
N F:SER436 3.5 2.0 1.0
CB F:SER436 3.6 2.0 1.0
OG F:SER433 3.7 4.5 1.0
O F:HOH1632 3.9 5.7 1.0
CB F:THR431 4.0 2.6 1.0
O F:HOH1338 4.0 4.4 1.0
CA F:THR431 4.1 2.8 1.0
N F:ARG435 4.2 2.7 1.0
CA F:SER436 4.2 2.0 1.0
N F:GLU432 4.3 3.5 1.0
CB F:ARG435 4.4 2.5 1.0
C F:ARG435 4.5 2.1 1.0
CA F:ARG435 4.5 2.5 1.0
CA F:PHE520 4.6 5.2 1.0
N F:GLY434 4.6 3.5 1.0
N F:SER433 4.6 3.8 1.0
C F:THR431 4.7 3.0 1.0
O F:LEU430 4.7 3.2 1.0
O F:GLY519 4.8 7.0 1.0
CB F:SER433 4.8 3.6 1.0
C F:GLY434 4.8 2.7 1.0

Sodium binding site 10 out of 12 in 3n25

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Sodium binding site 10 out of 12 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na2000

b:41.7
occ:1.00
 OG1 G:THR431 3.2 2.0 1.0
OG G:SER436 3.3 2.1 1.0
CB G:SER436 3.8 2.0 1.0
OG G:SER433 3.9 2.8 1.0
CB G:THR431 4.0 2.0 1.0
CA G:THR431 4.1 2.0 1.0
N G:GLU432 4.1 2.0 1.0
N G:SER436 4.2 2.0 1.0
CA G:PHE520 4.4 2.0 1.0
N G:SER433 4.5 2.1 1.0
O G:HOH1608 4.6 2.0 1.0
CA G:SER436 4.6 2.0 1.0
O G:LEU430 4.6 2.4 1.0
C G:THR431 4.7 2.0 1.0
O G:GLY519 4.7 2.7 1.0
NH2 G:ARG435 4.8 5.4 1.0
N G:ARG435 4.8 2.7 1.0
CB G:SER433 4.9 2.4 1.0
N G:GLY434 4.9 2.9 1.0
N G:THR521 4.9 2.0 1.0

Reference:

A.W.Fenton, T.A.Johnson, T.Holyoak. The Pyruvate Kinase Model System, A Cautionary Tale For the Use of Osmolyte Perturbations to Support Conformational Equilibria in Allostery. Protein Sci. V. 19 1796 2010.
ISSN: ISSN 0961-8368
PubMed: 20629175
DOI: 10.1002/PRO.450
Page generated: Mon Oct 7 11:44:43 2024

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