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Sodium in PDB 7knf: 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh)

Enzymatic activity of 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh)

All present enzymatic activity of 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh):
5.4.2.12;

Protein crystallography data

The structure of 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh), PDB code: 7knf was solved by S.Lovell, M.M.Kashipathy, K.P.Battaile, M.Weidmann, P.Dranchak, M.Aitha, B.Queme, C.D.Collmus, L.Kanter, L.Lamy, D.Tao, G.Rai, H.Suga, J.Inglese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.13 / 1.80
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 73.669, 75.846, 100.424, 90, 98.31, 90
R / Rfree (%) 15.2 / 19.4

Other elements in 7knf:

The structure of 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh) also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh) (pdb code 7knf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh), PDB code: 7knf:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7knf

Go back to Sodium Binding Sites List in 7knf
Sodium binding site 1 out of 4 in the 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:19.4
occ:1.00
 O A:ALA53 2.4 16.7 1.0
OG1 A:THR55 2.4 16.7 1.0
O A:HOH779 2.4 18.6 1.0
O A:ILE50 2.4 15.9 1.0
O A:HOH741 2.7 20.7 1.0
O A:LEU51 2.7 19.8 1.0
C A:LEU51 3.3 19.6 1.0
CB A:THR55 3.5 15.8 1.0
C A:ALA53 3.5 17.5 1.0
C A:ILE50 3.5 15.8 1.0
CA A:LEU51 3.6 16.5 1.0
N A:THR55 3.7 15.2 1.0
CG2 A:THR55 3.7 15.3 1.0
N A:LEU51 4.0 15.9 1.0
N A:ALA53 4.0 19.5 1.0
OD1 A:ASP59 4.1 18.9 1.0
CA A:THR55 4.1 15.9 1.0
CA A:ALA53 4.2 18.4 1.0
N A:ASN52 4.2 19.0 1.0
OD2 A:ASP59 4.4 21.2 1.0
O A:HOH1064 4.4 40.0 1.0
C A:GLN54 4.4 15.8 1.0
C A:ASN52 4.5 20.4 1.0
N A:GLN54 4.5 17.2 1.0
CB A:ALA53 4.6 17.9 1.0
CA A:GLN54 4.6 22.5 1.0
CG A:ASP59 4.7 20.4 1.0
CA A:ILE50 4.8 15.4 1.0
CA A:ASN52 4.8 19.6 1.0
C A:THR55 4.8 13.5 1.0
O A:THR55 4.9 18.3 1.0
O A:HOH901 4.9 32.6 1.0
CB A:LEU51 5.0 20.9 1.0

Sodium binding site 2 out of 4 in 7knf

Go back to Sodium Binding Sites List in 7knf
Sodium binding site 2 out of 4 in the 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:15.4
occ:1.00
 OD1 A:ASN470 2.7 14.5 1.0
O A:LYS473 2.8 17.1 1.0
O A:ALA484 2.8 17.1 1.0
O A:HIS482 2.8 19.8 1.0
O A:ASN470 2.8 13.8 1.0
ND1 A:HIS482 3.1 22.5 1.0
C A:HIS482 3.6 20.6 1.0
C A:ASN470 3.6 17.9 1.0
N A:ALA484 3.7 20.8 1.0
CG A:ASN470 3.7 16.8 1.0
C A:LYS473 3.8 16.6 1.0
CE1 A:HIS482 3.9 25.7 1.0
C A:ALA484 3.9 17.4 1.0
SD A:MET474 3.9 17.8 1.0
CG A:HIS482 4.0 21.3 1.0
C A:THR483 4.0 22.7 1.0
CA A:ASN470 4.1 12.2 1.0
N A:THR483 4.2 19.9 1.0
CA A:THR483 4.2 17.3 1.0
CB A:HIS482 4.3 22.1 1.0
CA A:MET474 4.4 14.8 1.0
CA A:ALA484 4.4 19.0 1.0
O A:GLY429 4.5 15.4 1.0
N A:MET474 4.5 15.8 1.0
CB A:ASN470 4.5 12.0 1.0
ND2 A:ASN470 4.6 16.9 1.0
CA A:HIS482 4.6 20.4 1.0
N A:ALA471 4.6 15.1 1.0
CA A:LYS473 4.8 15.2 1.0
O A:THR483 4.8 24.8 1.0
CE A:MET474 4.8 20.3 1.0
CA A:ALA471 4.9 14.3 1.0
N A:LYS473 4.9 15.3 1.0
CB A:LYS473 4.9 17.8 1.0
C A:GLY429 4.9 18.3 1.0
NE2 A:HIS482 5.0 27.1 1.0

Sodium binding site 3 out of 4 in 7knf

Go back to Sodium Binding Sites List in 7knf
Sodium binding site 3 out of 4 in the 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na603

b:22.2
occ:1.00
 O B:ALA53 2.3 19.3 1.0
O B:HOH770 2.4 23.8 1.0
O B:ILE50 2.4 18.8 1.0
OG1 B:THR55 2.4 19.3 1.0
O B:HOH748 2.5 23.8 1.0
O B:LEU51 2.6 24.1 1.0
C B:LEU51 3.2 24.4 1.0
C B:ALA53 3.4 19.2 1.0
CB B:THR55 3.6 23.0 1.0
C B:ILE50 3.6 26.9 1.0
CA B:LEU51 3.6 23.2 1.0
N B:THR55 3.6 20.7 1.0
CG2 B:THR55 3.7 17.5 1.0
N B:ALA53 3.9 26.8 1.0
N B:LEU51 4.1 22.9 1.0
OD1 B:ASP59 4.1 26.0 1.0
CA B:ALA53 4.2 23.1 1.0
CA B:THR55 4.2 20.9 1.0
N B:ASN52 4.2 24.6 1.0
C B:ASN52 4.4 26.3 1.0
OD2 B:ASP59 4.4 26.6 1.0
C B:GLN54 4.4 25.8 1.0
N B:GLN54 4.5 21.9 1.0
CB B:ALA53 4.6 20.1 1.0
CA B:GLN54 4.6 24.2 1.0
CG B:ASP59 4.7 26.5 1.0
CA B:ASN52 4.7 25.1 1.0
CA B:ILE50 4.8 21.3 1.0
C B:THR55 4.9 18.8 1.0
O B:THR55 4.9 21.9 1.0
O B:ASN52 5.0 25.0 1.0

Sodium binding site 4 out of 4 in 7knf

Go back to Sodium Binding Sites List in 7knf
Sodium binding site 4 out of 4 in the 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na604

b:18.8
occ:1.00
 O B:LYS473 2.7 19.9 1.0
OD1 B:ASN470 2.7 20.9 1.0
O B:ALA484 2.8 24.1 1.0
O B:HIS482 2.9 22.6 1.0
O B:ASN470 2.9 18.4 1.0
ND1 B:HIS482 3.1 30.4 1.0
C B:HIS482 3.6 24.1 1.0
C B:ASN470 3.6 22.4 1.0
N B:ALA484 3.7 22.9 1.0
C B:LYS473 3.7 19.7 1.0
CG B:ASN470 3.7 22.1 1.0
CE1 B:HIS482 3.8 30.6 1.0
SD B:MET474 3.9 20.6 1.0
C B:ALA484 3.9 20.4 1.0
C B:THR483 4.1 25.7 1.0
CG B:HIS482 4.1 30.3 1.0
CA B:ASN470 4.1 14.7 1.0
CA B:THR483 4.2 21.4 1.0
N B:THR483 4.2 22.9 1.0
CA B:MET474 4.3 17.9 1.0
CB B:HIS482 4.4 20.8 1.0
N B:MET474 4.4 16.4 1.0
CA B:ALA484 4.5 21.4 1.0
CB B:ASN470 4.5 18.4 1.0
O B:GLY429 4.6 19.1 1.0
N B:ALA471 4.6 18.0 1.0
CA B:HIS482 4.6 19.2 1.0
ND2 B:ASN470 4.6 19.5 1.0
CA B:LYS473 4.7 19.9 1.0
CE B:MET474 4.8 17.9 1.0
N B:LYS473 4.8 18.9 1.0
CB B:LYS473 4.9 18.7 1.0
O B:THR483 4.9 26.2 1.0
CA B:ALA471 4.9 17.5 1.0
C B:GLY429 5.0 21.2 1.0

Reference:

M.Weidmann, P.Dranchak, M.Aitha, B.Queme, C.D.Collmus, L.Kanter, L.Lamy, D.Tao, M.M.Kashipathy, K.P.Battaile, G.Rai, S.Lovell, H.Suga, J.Inglese. Structure-Activity Relationship of Ipglycermide Binding to Phosphoglycerate Mutases J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X
Page generated: Mon Aug 18 10:25:12 2025

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