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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

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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

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