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Sodium in PDB 7qdn: Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted

Enzymatic activity of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted

All present enzymatic activity of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted:
2.7.1.40;

Protein crystallography data

The structure of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted, PDB code: 7qdn was solved by A.Lulla, M.Hyvonen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 103.69 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 207.448, 112.687, 188.333, 90, 91.36, 90
R / Rfree (%) 20.5 / 21.7

Other elements in 7qdn:

The structure of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted also contains other interesting chemical elements:

Potassium (K) 8 atoms
Magnesium (Mg) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted (pdb code 7qdn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted, PDB code: 7qdn:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 7qdn

Go back to Sodium Binding Sites List in 7qdn
Sodium binding site 1 out of 6 in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na605

b:40.2
occ:1.00
 O B:CYS478 2.6 35.3 1.0
O B:VAL481 2.8 38.5 1.0
O B:HOH774 3.0 33.4 1.0
O B:HOH829 3.3 43.7 1.0
OG B:SER58 3.3 37.0 1.0
N B:VAL481 3.3 36.7 1.0
O B:HOH885 3.5 44.2 1.0
O B:HIS476 3.5 40.6 1.0
C B:CYS478 3.6 35.9 1.0
O B:SER56 3.7 36.2 1.0
C B:VAL481 3.7 38.4 1.0
N B:GLY480 3.7 34.5 1.0
O B:VAL475 3.8 41.8 1.0
CA B:VAL481 3.9 37.7 1.0
CA B:HIS476 3.9 40.0 1.0
C B:HIS476 4.0 39.5 1.0
C B:ARG479 4.1 35.0 1.0
CB B:VAL481 4.1 39.0 1.0
CA B:ARG479 4.2 35.5 1.0
C B:GLY480 4.3 36.7 1.0
N B:ARG479 4.3 35.6 1.0
CA B:GLY480 4.5 35.9 1.0
N B:CYS478 4.5 37.1 1.0
ND1 B:HIS476 4.5 39.4 1.0
CB B:SER58 4.6 34.7 1.0
CA B:CYS478 4.6 36.8 1.0
C B:VAL475 4.7 41.5 1.0
N B:HIS476 4.7 40.6 1.0
C B:SER56 4.8 36.6 1.0
N B:SER58 4.9 33.0 1.0
CB B:HIS476 4.9 39.3 1.0
N B:PHE482 4.9 38.8 1.0
O B:ARG479 5.0 35.5 1.0
CG2 B:VAL481 5.0 39.2 1.0

Sodium binding site 2 out of 6 in 7qdn

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Sodium binding site 2 out of 6 in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na605

b:37.9
occ:1.00
 O C:HOH998 2.2 42.4 1.0
O C:HOH764 2.2 29.4 1.0
O C:SER56 2.4 29.1 1.0
OG C:SER58 2.4 29.8 1.0
O C:HOH734 2.5 29.8 1.0
N C:SER58 3.0 26.5 1.0
CB C:SER58 3.3 27.5 1.0
C C:SER56 3.3 28.9 1.0
O C:HOH845 3.4 38.2 1.0
CA C:SER58 3.5 27.1 1.0
C C:THR57 3.6 26.6 1.0
O C:HIS476 3.8 29.4 1.0
O C:CYS478 3.9 27.6 1.0
N C:GLY480 4.0 26.4 1.0
CA C:THR57 4.0 27.0 1.0
N C:THR57 4.0 27.7 1.0
CA C:SER56 4.3 29.9 1.0
CA C:ARG479 4.4 26.8 1.0
O C:VAL481 4.4 26.1 1.0
O C:THR57 4.4 26.5 1.0
C C:CYS478 4.6 27.7 1.0
C C:ARG479 4.6 25.9 1.0
O C:ASP369 4.7 26.6 1.0
C C:HIS476 4.7 27.7 1.0
N C:VAL481 4.7 26.9 1.0
CA C:HIS476 4.8 26.5 1.0
N C:ARG479 4.9 27.3 1.0
CA C:GLY480 4.9 27.4 1.0
ND1 C:HIS476 5.0 31.1 1.0
C C:SER58 5.0 26.6 1.0

Sodium binding site 3 out of 6 in 7qdn

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Sodium binding site 3 out of 6 in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na605

b:38.1
occ:1.00
 O D:HOH751 2.1 29.5 1.0
OG D:SER58 2.3 28.0 1.0
O D:SER56 2.4 27.6 1.0
O D:HOH995 2.5 39.7 1.0
O D:HOH723 2.6 28.3 1.0
N D:SER58 2.9 24.6 1.0
CB D:SER58 3.2 25.8 1.0
O D:HOH935 3.3 34.6 1.0
CA D:SER58 3.3 24.4 1.0
C D:SER56 3.4 28.0 1.0
C D:THR57 3.5 25.9 1.0
O D:HIS476 3.8 26.7 1.0
CA D:THR57 4.0 25.8 1.0
O D:CYS478 4.0 26.9 1.0
N D:GLY480 4.1 25.9 1.0
N D:THR57 4.1 26.7 1.0
O D:THR57 4.3 26.2 1.0
O D:VAL481 4.3 26.8 1.0
CA D:SER56 4.4 29.4 1.0
CA D:ARG479 4.4 27.1 1.0
O D:ASP369 4.5 24.3 1.0
N D:VAL481 4.7 25.6 1.0
C D:ARG479 4.7 26.1 1.0
C D:CYS478 4.7 26.9 1.0
C D:HIS476 4.7 25.8 1.0
C D:SER58 4.8 23.9 1.0
CA D:HIS476 4.9 25.3 1.0
N D:ARG479 4.9 26.8 1.0
CA D:GLY480 4.9 26.4 1.0
ND1 D:HIS476 5.0 26.9 1.0

Sodium binding site 4 out of 6 in 7qdn

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Sodium binding site 4 out of 6 in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na605

b:40.0
occ:1.00
 O F:HOH747 2.2 39.5 1.0
O F:HOH887 2.2 42.1 1.0
O F:SER56 2.5 34.0 1.0
OG F:SER58 2.5 37.1 1.0
O F:HOH768 3.0 35.5 1.0
O F:HOH850 3.1 46.2 1.0
N F:SER58 3.2 32.5 1.0
C F:SER56 3.3 34.5 1.0
CB F:SER58 3.5 35.0 1.0
CA F:SER58 3.6 33.3 1.0
C F:THR57 3.7 33.0 1.0
N F:THR57 4.1 33.9 1.0
N F:GLY480 4.1 33.2 1.0
CA F:SER56 4.1 34.8 1.0
CA F:THR57 4.2 33.7 1.0
O F:HIS476 4.2 38.1 1.0
O F:VAL481 4.2 36.8 1.0
O F:CYS478 4.3 35.1 1.0
O F:THR57 4.3 32.4 1.0
O F:ARG55 4.6 37.5 1.0
N F:VAL481 4.7 35.4 1.0
CA F:ARG479 4.7 34.0 1.0
ND1 F:HIS476 4.8 43.2 1.0
OD1 F:ASN82 4.8 37.3 1.0
C F:ARG479 4.9 33.2 1.0
CA F:GLY480 4.9 34.1 1.0

Sodium binding site 5 out of 6 in 7qdn

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Sodium binding site 5 out of 6 in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na605

b:36.8
occ:1.00
 O G:HOH995 2.2 40.5 1.0
O G:HOH723 2.2 32.5 1.0
O G:SER56 2.3 30.1 1.0
OG G:SER58 2.4 28.6 1.0
O G:HOH801 2.5 32.4 1.0
N G:SER58 2.9 26.8 1.0
CB G:SER58 3.3 27.2 1.0
C G:SER56 3.3 30.9 1.0
CA G:SER58 3.3 26.9 1.0
O G:HOH949 3.4 38.5 1.0
C G:THR57 3.5 27.6 1.0
O G:HIS476 3.9 27.8 1.0
CA G:THR57 3.9 28.6 1.0
N G:THR57 3.9 29.8 1.0
O G:CYS478 4.0 28.6 1.0
N G:GLY480 4.0 27.0 1.0
CA G:SER56 4.3 31.9 1.0
O G:THR57 4.3 27.9 1.0
CA G:ARG479 4.3 28.4 1.0
O G:VAL481 4.4 27.1 1.0
O G:ASP369 4.5 26.6 1.0
C G:ARG479 4.7 27.2 1.0
C G:CYS478 4.7 28.6 1.0
N G:VAL481 4.7 27.3 1.0
C G:HIS476 4.8 25.8 1.0
C G:SER58 4.8 26.5 1.0
N G:ARG479 4.9 27.9 1.0
CA G:GLY480 4.9 27.8 1.0
CA G:HIS476 4.9 25.5 1.0

Sodium binding site 6 out of 6 in 7qdn

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Sodium binding site 6 out of 6 in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na605

b:40.0
occ:1.00
 O H:HOH720 2.1 31.3 1.0
O H:HOH1009 2.2 38.6 1.0
O H:SER56 2.2 28.1 1.0
OG H:SER58 2.5 28.1 1.0
O H:HOH709 2.7 35.8 1.0
N H:SER58 3.0 24.2 1.0
C H:SER56 3.2 27.9 1.0
O H:HOH901 3.3 32.2 1.0
CB H:SER58 3.4 25.2 1.0
CA H:SER58 3.4 24.7 1.0
C H:THR57 3.6 24.8 1.0
N H:GLY480 3.9 25.3 1.0
N H:THR57 3.9 26.1 1.0
CA H:THR57 4.0 25.0 1.0
O H:CYS478 4.0 25.8 1.0
O H:HIS476 4.0 27.5 1.0
CA H:SER56 4.2 29.1 1.0
O H:THR57 4.3 24.2 1.0
CA H:ARG479 4.3 26.4 1.0
O H:VAL481 4.3 26.1 1.0
C H:ARG479 4.5 25.9 1.0
N H:VAL481 4.6 25.7 1.0
O H:ASP369 4.6 24.2 1.0
C H:CYS478 4.7 26.3 1.0
CA H:GLY480 4.7 26.2 1.0
N H:ARG479 4.9 26.0 1.0
O H:ARG55 4.9 30.5 1.0
C H:HIS476 4.9 25.6 1.0
C H:SER58 5.0 24.5 1.0
OD1 H:ASN82 5.0 23.6 1.0

Reference:

A.Nain-Perez, A.Foller Fuchtbauer, L.Haversen, A.Lulla, C.Gao, J.Matic, L.Monjas, A.Rodriguez, P.Brear, W.Kim, M.Hyvonen, J.Boren, A.Mardinoglu, M.Uhlen, M.Grotli. Anthraquinone Derivatives As Adp-Competitive Inhibitors of Liver Pyruvate Kinase. Eur.J.Med.Chem. V. 234 14270 2022.
ISSN: ISSN 0223-5234
PubMed: 35290845
DOI: 10.1016/J.EJMECH.2022.114270
Page generated: Fri Apr 7 15:44:22 2023

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