Atomistry » Sodium » PDB 7kkb-7ktg » 7knf
Atomistry »
  Sodium »
    PDB 7kkb-7ktg »
      7knf »

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: Tue Oct 8 17:24:17 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy