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Zinc 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:

Magnesium (Mg) 2 atoms
Manganese (Mn) 2 atoms
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc 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 Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5kgn

Go back to Zinc Binding Sites List in 5kgn
Zinc 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 Zinc with other atoms in the Zn 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:Zn605

b:11.8
occ:1.00
 OD2 A:ASP467 1.9 11.5 1.0
OD1 A:ASP37 2.0 9.8 1.0
OG A:SER86 2.0 12.7 1.0
NE2 A:HIS468 2.0 10.2 1.0
CG A:ASP37 2.6 10.1 1.0
OD2 A:ASP37 2.7 10.3 1.0
CG A:ASP467 2.8 11.9 1.0
CB A:SER86 2.8 13.3 1.0
CD2 A:HIS468 2.8 9.7 1.0
CE1 A:HIS468 3.0 10.4 1.0
OD1 A:ASP467 3.1 9.3 1.0
CA A:SER86 3.1 11.1 1.0
N A:SER86 3.6 11.1 1.0
NZ A:LYS359 3.7 10.3 1.0
OD2 A:ASP426 3.8 9.3 1.0
CB A:ASP37 4.0 12.2 1.0
CG A:HIS468 4.0 12.6 1.0
CG A:ASP426 4.0 13.0 1.0
ND1 A:HIS468 4.0 11.2 1.0
O A:HOH770 4.1 11.3 1.0
CB A:ASP467 4.2 8.6 1.0
C A:ASN85 4.3 8.4 1.0
CA A:ASP37 4.3 11.5 1.0
N A:GLY38 4.3 13.2 1.0
OD1 A:ASP426 4.4 11.6 1.0
CB A:ASP426 4.5 9.9 1.0
C A:SER86 4.6 10.2 1.0
CE A:LYS359 4.6 12.2 1.0
CE1 A:HIS90 4.7 13.7 1.0
C A:ASP37 4.7 7.0 1.0
MN A:MN604 4.7 16.2 1.0
O A:ASN85 4.7 10.9 1.0
ND1 A:HIS90 4.9 13.6 1.0
NE2 A:HIS485 5.0 13.3 1.0
O A:SER86 5.0 11.5 1.0

Zinc binding site 2 out of 2 in 5kgn

Go back to Zinc Binding Sites List in 5kgn
Zinc 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 Zinc with other atoms in the Zn 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:Zn605

b:13.3
occ:1.00
 OD2 B:ASP467 2.0 10.4 1.0
NE2 B:HIS468 2.0 10.7 1.0
OD1 B:ASP37 2.0 11.0 1.0
OG B:SER86 2.0 13.3 1.0
CG B:ASP37 2.6 13.2 1.0
OD2 B:ASP37 2.8 11.6 1.0
CG B:ASP467 2.8 11.8 1.0
CD2 B:HIS468 2.9 10.4 1.0
CB B:SER86 2.9 11.8 1.0
CE1 B:HIS468 2.9 12.1 1.0
OD1 B:ASP467 3.1 7.6 1.0
CA B:SER86 3.2 12.0 1.0
N B:SER86 3.6 12.9 1.0
NZ B:LYS359 3.7 10.6 1.0
O B:HOH711 4.0 12.3 1.0
OD2 B:ASP426 4.0 11.4 1.0
CG B:HIS468 4.0 10.0 1.0
ND1 B:HIS468 4.0 11.1 1.0
CB B:ASP37 4.0 9.1 1.0
CG B:ASP426 4.1 12.6 1.0
CB B:ASP467 4.2 10.0 1.0
C B:ASN85 4.3 9.8 1.0
N B:GLY38 4.3 13.9 1.0
CA B:ASP37 4.4 15.2 1.0
OD1 B:ASP426 4.4 13.9 1.0
CB B:ASP426 4.5 9.8 1.0
C B:SER86 4.6 16.0 1.0
CE B:LYS359 4.6 14.8 1.0
CE1 B:HIS90 4.6 13.6 1.0
C B:ASP37 4.7 10.7 1.0
MN B:MN604 4.7 18.8 1.0
O B:ASN85 4.7 9.7 1.0
ND1 B:HIS90 4.9 16.0 1.0
NE2 B:HIS485 5.0 13.2 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 Oct 27 20:23:54 2024

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