Atomistry » Sodium » PDB 7t3s-7u1r » 7tl7
Atomistry »
  Sodium »
    PDB 7t3s-7u1r »
      7tl7 »

Sodium in PDB 7tl7: 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2)

Enzymatic activity of 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2)

All present enzymatic activity of 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2):
5.4.2.12;

Protein crystallography data

The structure of 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2), PDB code: 7tl7 was solved by L.Liu, S.Lovell, K.P.Battaile, P.Dranchak, B.Queme, M.Aitha, R.H.P.Vanneer, H.Kimura, T.Katho, H.Suga, J.Inglese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.84 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.999, 87.624, 151.341, 90, 97.13, 90
R / Rfree (%) 17.1 / 21.6

Other elements in 7tl7:

The structure of 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2) also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2) (pdb code 7tl7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2), PDB code: 7tl7:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7tl7

Go back to Sodium Binding Sites List in 7tl7
Sodium binding site 1 out of 4 in the 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:28.5
occ:1.00
 O A:HOH801 2.2 29.0 1.0
O A:ALA53 2.3 31.7 1.0
O A:ILE50 2.5 26.3 1.0
OG1 A:THR55 2.6 23.9 1.0
O A:HOH723 2.6 34.6 1.0
O A:LEU51 2.8 30.0 1.0
C A:LEU51 3.4 33.4 1.0
C A:ALA53 3.5 33.1 1.0
C A:ILE50 3.6 26.2 1.0
CB A:THR55 3.7 27.9 1.0
CA A:LEU51 3.7 27.3 1.0
CG2 A:THR55 3.8 26.3 1.0
N A:THR55 3.8 30.2 1.0
N A:ALA53 4.1 27.0 1.0
OD1 A:ASP59 4.1 35.5 1.0
N A:LEU51 4.1 24.2 1.0
CA A:ALA53 4.2 29.5 1.0
CA A:THR55 4.3 30.4 1.0
N A:ASN52 4.3 32.8 1.0
O A:HOH954 4.3 35.6 1.0
OD2 A:ASP59 4.4 31.8 1.0
N A:GLN54 4.5 34.4 1.0
C A:ASN52 4.5 33.6 1.0
C A:GLN54 4.5 31.3 1.0
CB A:ALA53 4.6 25.5 1.0
CA A:GLN54 4.6 37.7 1.0
CG A:ASP59 4.7 28.4 1.0
CA A:ILE50 4.9 28.1 1.0
CA A:ASN52 4.9 30.6 1.0
O A:THR55 4.9 28.6 1.0
C A:THR55 5.0 25.8 1.0
O A:ASN52 5.0 35.5 1.0

Sodium binding site 2 out of 4 in 7tl7

Go back to Sodium Binding Sites List in 7tl7
Sodium binding site 2 out of 4 in the 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na603

b:45.0
occ:1.00
 O B:HOH812 2.3 37.5 1.0
OG1 B:THR55 2.4 43.1 1.0
O B:ILE50 2.5 45.8 1.0
O B:ALA53 2.6 48.4 1.0
O B:HOH707 2.8 44.5 1.0
O B:LEU51 3.2 44.6 1.0
C B:LEU51 3.5 46.2 1.0
CB B:THR55 3.5 43.6 1.0
CG2 B:THR55 3.5 35.4 1.0
C B:ILE50 3.6 43.1 1.0
CA B:LEU51 3.7 47.3 1.0
C B:ALA53 3.7 46.7 1.0
N B:THR55 3.9 36.8 1.0
OD1 B:ASP59 4.0 55.2 1.0
N B:LEU51 4.2 43.0 1.0
N B:ALA53 4.2 61.5 1.0
CA B:THR55 4.3 43.5 1.0
N B:ASN52 4.3 53.5 1.0
C B:ASN52 4.4 57.8 1.0
CA B:ALA53 4.5 53.0 1.0
OD2 B:ASP59 4.5 52.0 1.0
CG B:ASP59 4.7 51.1 1.0
C B:GLN54 4.7 37.9 1.0
N B:GLN54 4.7 46.3 1.0
O B:ASN52 4.8 56.0 1.0
O B:THR55 4.8 38.1 1.0
CB B:ALA53 4.9 50.6 1.0
CA B:ILE50 4.9 42.2 1.0
CA B:ASN52 4.9 57.4 1.0
C B:THR55 4.9 38.5 1.0
CA B:GLN54 4.9 57.6 1.0

Sodium binding site 3 out of 4 in 7tl7

Go back to Sodium Binding Sites List in 7tl7
Sodium binding site 3 out of 4 in the 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na604

b:27.9
occ:1.00
 O C:HOH805 2.3 34.3 1.0
OG1 C:THR55 2.4 21.4 1.0
O C:ILE50 2.4 23.3 1.0
O C:ALA53 2.5 22.1 1.0
O C:LEU51 2.9 32.1 1.0
O C:HOH751 3.0 28.7 1.0
C C:LEU51 3.4 29.6 1.0
CB C:THR55 3.5 20.4 1.0
C C:ILE50 3.6 24.2 1.0
C C:ALA53 3.6 23.2 1.0
CG2 C:THR55 3.6 22.8 1.0
CA C:LEU51 3.6 27.6 1.0
N C:THR55 3.8 25.1 1.0
O C:HOH824 3.8 35.0 1.0
N C:ALA53 4.0 27.6 1.0
N C:LEU51 4.1 23.6 1.0
OD1 C:ASP59 4.1 27.9 1.0
CA C:THR55 4.2 22.6 1.0
CA C:ALA53 4.3 26.8 1.0
N C:ASN52 4.3 27.2 1.0
OD2 C:ASP59 4.5 34.5 1.0
CB C:ALA53 4.6 19.9 1.0
C C:GLN54 4.6 20.7 1.0
N C:GLN54 4.6 23.9 1.0
C C:ASN52 4.6 29.1 1.0
CG C:ASP59 4.7 28.5 1.0
CA C:GLN54 4.8 29.1 1.0
CA C:ILE50 4.8 24.9 1.0
C C:THR55 4.9 22.0 1.0
O C:THR55 4.9 26.1 1.0
CA C:ASN52 4.9 22.7 1.0
CG2 C:ILE50 5.0 26.6 1.0

Sodium binding site 4 out of 4 in 7tl7

Go back to Sodium Binding Sites List in 7tl7
Sodium binding site 4 out of 4 in the 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na604

b:48.5
occ:1.00
 O D:HOH810 2.2 34.6 1.0
O D:ALA53 2.3 36.3 1.0
OG1 D:THR55 2.5 39.4 1.0
O D:ILE50 2.6 39.0 1.0
O D:LEU51 2.8 48.2 1.0
C D:LEU51 3.2 49.9 1.0
C D:ALA53 3.4 40.5 1.0
CA D:LEU51 3.6 48.6 1.0
CB D:THR55 3.7 37.6 1.0
C D:ILE50 3.7 47.2 1.0
N D:THR55 3.8 39.9 1.0
CG2 D:THR55 3.9 38.5 1.0
N D:ALA53 3.9 44.5 1.0
N D:ASN52 4.1 49.2 1.0
N D:LEU51 4.1 45.1 1.0
C D:ASN52 4.2 57.2 1.0
CA D:ALA53 4.2 42.3 1.0
OD1 D:ASP59 4.2 48.7 1.0
CA D:THR55 4.3 48.5 1.0
OD2 D:ASP59 4.4 51.9 1.0
N D:GLN54 4.5 46.6 1.0
C D:GLN54 4.5 44.4 1.0
CA D:ASN52 4.6 53.8 1.0
CA D:GLN54 4.6 45.4 1.0
O D:ASN52 4.7 65.5 1.0
CB D:ALA53 4.7 42.8 1.0
CG D:ASP59 4.8 50.3 1.0
CB D:LEU51 4.9 49.8 1.0

Reference:

R.H.P.Van Neer, P.K.Dranchak, L.Liu, M.Aitha, B.Queme, H.Kimura, T.Katoh, K.P.Battaile, S.Lovell, J.Inglese, H.Suga. Serum-Stable and Selective Backbone-N-Methylated Cyclic Peptides That Inhibit Prokaryotic Glycolytic Mutases. Acs Chem.Biol. V. 17 2284 2022.
ISSN: ESSN 1554-8937
PubMed: 35904259
DOI: 10.1021/ACSCHEMBIO.2C00403
Page generated: Wed Oct 9 09:07:31 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy