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Sodium in PDB 7kng: 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F)

Enzymatic activity of 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F)

All present enzymatic activity of 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F):
5.4.2.12;

Protein crystallography data

The structure of 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F), PDB code: 7kng 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) 44.69 / 2.10
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 73.862, 75.471, 101.36, 90, 99.11, 90
R / Rfree (%) 16.7 / 22

Other elements in 7kng:

The structure of 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F) also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F) (pdb code 7kng). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F), PDB code: 7kng:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7kng

Go back to Sodium Binding Sites List in 7kng
Sodium binding site 1 out of 4 in the 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:26.6
occ:1.00
 O A:ALA53 2.2 28.5 1.0
O A:HOH784 2.3 25.1 1.0
O A:ILE50 2.4 27.7 1.0
OG1 A:THR55 2.4 22.4 1.0
O A:LEU51 2.4 30.7 1.0
O A:HOH728 2.6 29.1 1.0
C A:LEU51 3.1 30.7 1.0
C A:ALA53 3.4 26.9 1.0
CA A:LEU51 3.5 30.4 1.0
C A:ILE50 3.5 32.4 1.0
CB A:THR55 3.6 29.5 1.0
N A:THR55 3.7 27.6 1.0
CG2 A:THR55 3.9 25.6 1.0
N A:LEU51 3.9 26.4 1.0
N A:ALA53 3.9 27.8 1.0
N A:ASN52 4.0 28.1 1.0
CA A:ALA53 4.2 31.1 1.0
CA A:THR55 4.2 20.9 1.0
OD1 A:ASP59 4.3 33.7 1.0
C A:ASN52 4.3 33.6 1.0
C A:GLN54 4.4 22.5 1.0
N A:GLN54 4.4 26.0 1.0
OD2 A:ASP59 4.5 29.9 1.0
CA A:GLN54 4.6 24.9 1.0
CA A:ASN52 4.6 26.0 1.0
CB A:ALA53 4.6 25.1 1.0
CA A:ILE50 4.8 28.8 1.0
CG A:ASP59 4.8 30.0 1.0
CB A:LEU51 4.9 33.7 1.0
O A:ASN52 4.9 36.8 1.0
C A:THR55 4.9 25.3 1.0

Sodium binding site 2 out of 4 in 7kng

Go back to Sodium Binding Sites List in 7kng
Sodium binding site 2 out of 4 in the 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:19.8
occ:1.00
 O A:HIS482 2.6 31.9 1.0
O A:LYS473 2.6 29.6 1.0
O A:ALA484 2.7 26.2 1.0
OD1 A:ASN470 2.7 26.4 1.0
O A:ASN470 2.8 26.4 1.0
ND1 A:HIS482 3.0 34.9 1.0
C A:HIS482 3.6 31.2 1.0
N A:ALA484 3.6 30.3 1.0
C A:ASN470 3.6 28.6 1.0
C A:LYS473 3.7 28.9 1.0
CE1 A:HIS482 3.7 36.8 1.0
CG A:ASN470 3.8 28.3 1.0
C A:ALA484 3.8 28.5 1.0
CG A:HIS482 3.9 32.4 1.0
SD A:MET474 3.9 26.6 1.0
CA A:ASN470 4.1 25.8 1.0
CB A:HIS482 4.2 34.7 1.0
C A:THR483 4.2 29.2 1.0
N A:THR483 4.2 33.1 1.0
CA A:ALA484 4.3 30.1 1.0
CA A:THR483 4.3 24.8 1.0
CA A:MET474 4.4 25.1 1.0
N A:MET474 4.4 24.3 1.0
CA A:HIS482 4.5 27.1 1.0
CB A:ASN470 4.5 25.5 1.0
N A:ALA471 4.6 23.8 1.0
CA A:LYS473 4.7 25.0 1.0
NE2 A:HIS482 4.7 33.4 1.0
ND2 A:ASN470 4.7 27.2 1.0
O A:GLY429 4.7 25.2 1.0
CD2 A:HIS482 4.8 40.2 1.0
N A:LYS473 4.8 28.1 1.0
CE A:MET474 4.8 21.3 1.0
CB A:LYS473 4.9 25.3 1.0
CA A:ALA471 4.9 26.3 1.0
N A:HIS485 4.9 24.1 1.0

Sodium binding site 3 out of 4 in 7kng

Go back to Sodium Binding Sites List in 7kng
Sodium binding site 3 out of 4 in the 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na603

b:27.8
occ:1.00
 O B:HOH819 2.1 31.7 1.0
O B:ALA53 2.2 27.0 1.0
O B:ILE50 2.3 28.3 1.0
OG1 B:THR55 2.4 23.3 1.0
O B:HOH739 2.5 32.2 1.0
O B:LEU51 2.5 30.7 1.0
C B:LEU51 3.1 24.3 1.0
C B:ALA53 3.4 28.1 1.0
C B:ILE50 3.5 25.6 1.0
CB B:THR55 3.5 30.9 1.0
CA B:LEU51 3.5 25.1 1.0
CG2 B:THR55 3.6 25.0 1.0
N B:THR55 3.7 26.5 1.0
N B:ALA53 3.9 32.6 1.0
N B:LEU51 4.0 29.8 1.0
N B:ASN52 4.1 23.4 1.0
CA B:THR55 4.1 27.4 1.0
OD1 B:ASP59 4.2 31.6 1.0
CA B:ALA53 4.2 30.0 1.0
C B:ASN52 4.3 32.0 1.0
OD2 B:ASP59 4.3 32.7 1.0
C B:GLN54 4.4 29.4 1.0
N B:GLN54 4.4 30.4 1.0
CA B:GLN54 4.6 30.4 1.0
CA B:ASN52 4.6 24.3 1.0
CB B:ALA53 4.7 31.1 1.0
CG B:ASP59 4.7 27.0 1.0
O B:HOH871 4.7 39.9 1.0
CA B:ILE50 4.7 25.8 1.0
O B:ASN52 4.8 33.1 1.0
C B:THR55 4.8 28.2 1.0
O B:THR55 4.9 29.0 1.0
CB B:LEU51 5.0 30.8 1.0
CG2 B:ILE50 5.0 33.4 1.0

Sodium binding site 4 out of 4 in 7kng

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Sodium binding site 4 out of 4 in the 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na604

b:18.2
occ:1.00
 O B:ASN470 2.6 22.9 1.0
O B:LYS473 2.6 34.5 1.0
OD1 B:ASN470 2.6 20.0 1.0
O B:ALA484 2.8 25.5 1.0
O B:HIS482 2.8 29.8 1.0
ND1 B:HIS482 2.9 37.8 1.0
C B:ASN470 3.5 28.9 1.0
C B:LYS473 3.6 28.7 1.0
CE1 B:HIS482 3.6 32.9 1.0
C B:HIS482 3.7 30.0 1.0
CG B:ASN470 3.7 22.6 1.0
N B:ALA484 3.7 27.9 1.0
CG B:HIS482 3.9 36.1 1.0
SD B:MET474 3.9 28.2 1.0
C B:ALA484 3.9 26.4 1.0
CA B:ASN470 4.0 23.1 1.0
C B:THR483 4.2 30.0 1.0
CB B:HIS482 4.2 31.1 1.0
CA B:MET474 4.3 28.4 1.0
N B:THR483 4.3 34.7 1.0
CA B:THR483 4.3 29.6 1.0
N B:MET474 4.3 29.5 1.0
CB B:ASN470 4.5 24.3 1.0
CA B:ALA484 4.5 26.8 1.0
N B:ALA471 4.5 27.0 1.0
ND2 B:ASN470 4.6 27.7 1.0
CA B:LYS473 4.6 27.5 1.0
CA B:HIS482 4.6 34.6 1.0
NE2 B:HIS482 4.7 32.4 1.0
N B:LYS473 4.8 30.4 1.0
O B:GLY429 4.8 20.5 1.0
CE B:MET474 4.8 22.5 1.0
CB B:LYS473 4.8 32.2 1.0
CA B:ALA471 4.9 25.4 1.0
CD2 B:HIS482 4.9 34.0 1.0
CG2 B:THR486 4.9 30.8 1.0
CG B:MET474 5.0 33.4 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 17:24:59 2024

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