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Magnesium in PDB 5kgn: 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (2D)

Enzymatic activity of 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (2D)

All present enzymatic activity of 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (2D):
5.4.2.12;

Protein crystallography data

The structure of 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (2D), PDB code: 5kgn was solved by S.Lovell, N.Mehzabeen, K.P.Battaile, H.Yu, P.Dranchak, R.Macarthur, Z.Li, T.Carlow, H.Suga, J.Inglese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.49 / 1.95
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 73.782, 75.832, 101.420, 90.00, 95.66, 90.00
R / Rfree (%) 15.4 / 20.4

Other elements in 5kgn:

The structure of 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (2D) also contains other interesting chemical elements:

Manganese (Mn) 2 atoms
Zinc (Zn) 2 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (2D) (pdb code 5kgn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (2D), PDB code: 5kgn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5kgn

Go back to Magnesium Binding Sites List in 5kgn
Magnesium binding site 1 out of 2 in the 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (2D)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (2D) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:18.0
occ:1.00
 O A:HOH944 2.3 15.1 1.0
O A:ILE50 2.3 13.2 1.0
O A:ALA53 2.3 13.8 1.0
OG1 A:THR55 2.4 16.2 1.0
O A:HOH808 2.6 14.7 1.0
O A:LEU51 2.7 22.7 1.0
C A:LEU51 3.2 15.6 1.0
C A:ILE50 3.4 14.0 1.0
CB A:THR55 3.4 17.9 1.0
C A:ALA53 3.5 12.0 1.0
CG2 A:THR55 3.5 15.0 1.0
CA A:LEU51 3.6 18.6 1.0
N A:THR55 3.7 13.2 1.0
N A:ALA53 4.0 15.8 1.0
N A:LEU51 4.0 14.4 1.0
CA A:THR55 4.1 18.4 1.0
N A:ASN52 4.1 17.6 1.0
CA A:ALA53 4.2 15.1 1.0
OD1 A:ASP59 4.2 18.5 1.0
C A:ASN52 4.3 20.9 1.0
OD2 A:ASP59 4.4 20.0 1.0
C A:GLN54 4.4 14.0 1.0
N A:GLN54 4.5 15.6 1.0
CB A:ALA53 4.6 15.0 1.0
CA A:GLN54 4.7 13.2 1.0
O A:HOH1050 4.7 36.7 1.0
CA A:ILE50 4.7 13.9 1.0
CA A:ASN52 4.7 14.1 1.0
CG A:ASP59 4.8 22.2 1.0
C A:THR55 4.8 14.3 1.0
O A:ASN52 4.9 14.5 1.0
O A:THR55 4.9 13.3 1.0
CD1 A:LEU51 5.0 30.5 1.0
CG2 A:ILE50 5.0 16.6 1.0

Magnesium binding site 2 out of 2 in 5kgn

Go back to Magnesium Binding Sites List in 5kgn
Magnesium binding site 2 out of 2 in the 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (2D)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (2D) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:16.9
occ:1.00
 OG1 B:THR55 2.3 13.4 1.0
O B:ALA53 2.3 13.4 1.0
O B:HOH807 2.4 19.0 1.0
O B:ILE50 2.4 16.8 1.0
O B:HOH735 2.5 17.9 1.0
O B:LEU51 2.8 18.0 1.0
C B:LEU51 3.3 13.7 1.0
CB B:THR55 3.4 15.2 1.0
C B:ALA53 3.4 12.6 1.0
CG2 B:THR55 3.5 17.4 1.0
C B:ILE50 3.5 19.4 1.0
N B:THR55 3.6 13.2 1.0
CA B:LEU51 3.6 17.6 1.0
N B:ALA53 4.0 15.6 1.0
CA B:THR55 4.0 19.5 1.0
N B:LEU51 4.1 16.6 1.0
OD1 B:ASP59 4.2 18.5 1.0
CA B:ALA53 4.2 10.7 1.0
N B:ASN52 4.2 18.8 1.0
OD2 B:ASP59 4.3 18.8 1.0
O B:HOH1029 4.4 34.7 1.0
C B:GLN54 4.4 12.5 1.0
C B:ASN52 4.4 13.4 1.0
N B:GLN54 4.4 11.6 1.0
CB B:ALA53 4.5 12.3 1.0
CA B:GLN54 4.6 14.6 1.0
CG B:ASP59 4.7 19.5 1.0
C B:THR55 4.8 11.0 1.0
CA B:ASN52 4.8 16.7 1.0
CA B:ILE50 4.8 13.7 1.0
O B:THR55 4.8 13.0 1.0
CG2 B:ILE50 5.0 21.3 1.0

Reference:

H.Yu, P.Dranchak, Z.Li, R.Macarthur, M.S.Munson, N.Mehzabeen, N.J.Baird, K.P.Battalie, D.Ross, S.Lovell, C.K.Carlow, H.Suga, J.Inglese. Macrocycle Peptides Delineate Locked-Open Inhibition Mechanism For Microorganism Phosphoglycerate Mutases. Nat Commun V. 8 14932 2017.
ISSN: ESSN 2041-1723
PubMed: 28368002
DOI: 10.1038/NCOMMS14932
Page generated: Sun Sep 29 19:07:25 2024

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