Atomistry » Manganese » PDB 5kg5-5lyw » 5kgn
Atomistry »
  Manganese »
    PDB 5kg5-5lyw »
      5kgn »

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

Manganese Binding Sites:

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

Manganese binding site 1 out of 2 in 5kgn

Go back to Manganese Binding Sites List in 5kgn
Manganese 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 Manganese with other atoms in the Mn 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:Mn604

b:16.2
occ:1.00
O A:HOH770 2.1 11.3 1.0
NE2 A:HIS485 2.1 13.3 1.0
OD2 A:ASP426 2.1 9.3 1.0
NE2 A:HIS430 2.2 16.0 1.0
O A:HOH1000 2.4 21.0 1.0
O A:HOH998 2.4 24.5 1.0
CG A:ASP426 2.8 13.0 1.0
OD1 A:ASP426 2.9 11.6 1.0
CE1 A:HIS485 3.0 14.2 1.0
CD2 A:HIS430 3.1 15.4 1.0
CD2 A:HIS485 3.2 15.1 1.0
CE1 A:HIS430 3.2 15.4 1.0
OG A:SER86 4.0 12.7 1.0
NZ A:LYS359 4.0 10.3 1.0
ND1 A:HIS485 4.2 18.0 1.0
O A:HOH724 4.3 19.7 1.0
CG A:HIS485 4.3 15.5 1.0
CG A:HIS430 4.3 13.6 1.0
CB A:ASP426 4.3 9.9 1.0
ND1 A:HIS430 4.3 18.9 1.0
CE1 A:HIS468 4.3 10.4 1.0
O A:HOH744 4.4 17.4 1.0
NE2 A:HIS468 4.5 10.2 1.0
O A:HOH1045 4.6 38.7 1.0
ZN A:ZN605 4.7 11.8 1.0
ND2 A:ASN470 4.7 17.0 1.0
OD1 A:ASP37 4.8 9.8 1.0
O A:ASP426 4.9 10.9 1.0
O A:HOH723 5.0 23.8 1.0

Manganese binding site 2 out of 2 in 5kgn

Go back to Manganese Binding Sites List in 5kgn
Manganese 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 Manganese with other atoms in the Mn 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:Mn604

b:18.8
occ:1.00
NE2 B:HIS485 2.1 13.2 1.0
NE2 B:HIS430 2.1 13.4 1.0
OD2 B:ASP426 2.2 11.4 1.0
O B:HOH711 2.2 12.3 1.0
O B:HOH952 2.4 17.0 1.0
O B:HOH933 2.5 20.7 1.0
OD1 B:ASP426 2.7 13.9 1.0
CG B:ASP426 2.8 12.6 1.0
CE1 B:HIS485 3.0 13.8 1.0
CD2 B:HIS430 3.1 13.2 1.0
CE1 B:HIS430 3.1 17.7 1.0
CD2 B:HIS485 3.2 13.5 1.0
OG B:SER86 4.0 13.3 1.0
NZ B:LYS359 4.1 10.6 1.0
ND1 B:HIS485 4.2 18.6 1.0
ND1 B:HIS430 4.2 16.8 1.0
CG B:HIS430 4.3 12.9 1.0
CB B:ASP426 4.3 9.8 1.0
CG B:HIS485 4.3 15.6 1.0
CE1 B:HIS468 4.4 12.1 1.0
O B:HOH727 4.4 22.4 1.0
O B:HOH854 4.5 18.3 1.0
O B:HOH1031 4.5 30.0 1.0
NE2 B:HIS468 4.6 10.7 1.0
ND2 B:ASN470 4.7 14.2 1.0
ZN B:ZN605 4.7 13.3 1.0
O B:HOH716 4.8 26.9 1.0
OD1 B:ASP37 4.8 11.0 1.0
O B:ASP426 4.8 12.8 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: Tue Dec 15 04:43:11 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy