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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: Sun Oct 6 01:44:45 2024

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