Manganese in PDB 7tl8: 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From S. Aureus in Complex with A Macrocyclic Peptide Inhibitor (Sa-D3)

Enzymatic activity of 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From S. Aureus in Complex with A Macrocyclic Peptide Inhibitor (Sa-D3)

All present enzymatic activity of 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From S. Aureus in Complex with A Macrocyclic Peptide Inhibitor (Sa-D3):
5.4.2.12;

Protein crystallography data

The structure of 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From S. Aureus in Complex with A Macrocyclic Peptide Inhibitor (Sa-D3), PDB code: 7tl8 was solved by L.Liu, S.Lovell, K.P.Battaile, P.Dranchak, B.Queme, M.Aitha, R.H.P.Vanneer, H.Kimura, T.Katho, H.Suga, J.Inglese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.11 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.898, 74.172, 75.017, 90, 100.54, 90
R / Rfree (%) 19.4 / 25.5

Manganese Binding Sites:

The binding sites of Manganese atom in the 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From S. Aureus in Complex with A Macrocyclic Peptide Inhibitor (Sa-D3) (pdb code 7tl8). 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 S. Aureus in Complex with A Macrocyclic Peptide Inhibitor (Sa-D3), PDB code: 7tl8:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 7tl8

Go back to Manganese Binding Sites List in 7tl8
Manganese binding site 1 out of 2 in the 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From S. Aureus in Complex with A Macrocyclic Peptide Inhibitor (Sa-D3)


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 S. Aureus in Complex with A Macrocyclic Peptide Inhibitor (Sa-D3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:19.8
occ:1.00
 OG A:SER62 2.0 20.1 1.0
OD1 A:ASP12 2.0 18.1 1.0
OD2 A:ASP438 2.0 19.5 1.0
NE2 A:HIS439 2.2 18.2 1.0
OD2 A:ASP12 2.5 17.2 1.0
CG A:ASP12 2.5 21.6 1.0
CG A:ASP438 2.7 18.4 1.0
OD1 A:ASP438 2.8 14.1 1.0
CB A:SER62 3.0 17.3 1.0
CD2 A:HIS439 3.0 20.6 1.0
CE1 A:HIS439 3.2 23.0 1.0
CA A:SER62 3.3 15.2 1.0
N A:SER62 3.8 18.6 1.0
NZ A:LYS330 3.8 20.2 1.0
CB A:ASP12 3.9 16.5 1.0
O A:HOH713 4.0 18.3 1.0
CG A:HIS439 4.1 21.5 1.0
CB A:ASP438 4.2 19.4 1.0
ND1 A:HIS439 4.2 22.7 1.0
OD2 A:ASP397 4.2 18.4 1.0
N A:GLY13 4.3 16.6 1.0
CG A:ASP397 4.4 16.5 1.0
CE1 A:HIS66 4.4 19.2 1.0
CE A:LYS330 4.4 13.6 1.0
CA A:ASP12 4.4 15.1 1.0
C A:ASN61 4.5 19.6 1.0
C A:SER62 4.6 15.2 1.0
CD A:LYS330 4.6 16.0 1.0
C A:ASP12 4.7 17.6 1.0
OD1 A:ASP397 4.7 18.7 1.0
CB A:ASP397 4.7 17.4 1.0
ND1 A:HIS66 4.8 19.4 1.0
O A:ASN61 4.8 18.7 1.0

Manganese binding site 2 out of 2 in 7tl8

Go back to Manganese Binding Sites List in 7tl8
Manganese binding site 2 out of 2 in the 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From S. Aureus in Complex with A Macrocyclic Peptide Inhibitor (Sa-D3)


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 S. Aureus in Complex with A Macrocyclic Peptide Inhibitor (Sa-D3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:20.8
occ:1.00
 NE2 A:HIS401 2.2 20.6 1.0
OD2 A:ASP397 2.2 18.4 1.0
NE2 A:HIS456 2.3 18.4 1.0
O A:HOH846 2.3 24.1 1.0
O A:HOH713 2.3 18.3 1.0
O A:HOH879 2.4 15.2 1.0
CG A:ASP397 3.0 16.5 1.0
OD1 A:ASP397 3.1 18.7 1.0
CE1 A:HIS401 3.2 21.3 1.0
CE1 A:HIS456 3.2 19.7 1.0
CD2 A:HIS401 3.2 18.4 1.0
CD2 A:HIS456 3.3 21.2 1.0
NZ A:LYS330 4.0 20.2 1.0
O A:HOH738 4.2 19.9 1.0
O A:HOH831 4.3 23.9 1.0
ND1 A:HIS401 4.3 21.5 1.0
OG A:SER62 4.3 20.1 1.0
ND1 A:HIS456 4.3 18.6 1.0
CG A:HIS401 4.3 19.5 1.0
CG A:HIS456 4.4 23.5 1.0
CE1 A:HIS439 4.5 23.0 1.0
CB A:ASP397 4.5 17.4 1.0
ND2 A:ASN441 4.7 17.9 1.0
O B:HOH111 4.8 41.4 1.0
NE2 A:HIS439 4.8 18.2 1.0
O A:ASP397 4.9 20.3 1.0
SD A:MET398 5.0 19.8 1.0

Reference:

R.H.P.Van Neer, P.K.Dranchak, L.Liu, M.Aitha, B.Queme, H.Kimura, T.Katoh, K.P.Battaile, S.Lovell, J.Inglese, H.Suga. Serum-Stable and Selective Backbone-N-Methylated Cyclic Peptides That Inhibit Prokaryotic Glycolytic Mutases. Acs Chem.Biol. V. 17 2284 2022.
ISSN: ESSN 1554-8937
PubMed: 35904259
DOI: 10.1021/ACSCHEMBIO.2C00403
Page generated: Fri Apr 7 12:29:12 2023

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