Atomistry » Zinc » PDB 5kas-5kia » 5kgn
Atomistry »
  Zinc »
    PDB 5kas-5kia »
      5kgn »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy