Manganese in PDB 5kgm: 2.95A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Monoclinic Form)

All present enzymatic activity of 2.95A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Monoclinic Form):
5.4.2.12;

The structure of 2.95A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Monoclinic Form), PDB code: 5kgm 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)	42.98 / 2.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.850, 94.375, 102.201, 90.00, 96.57, 90.00
R / Rfree (%)	18.4 / 23.7

The structure of 2.95A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Monoclinic Form) also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Zinc	(Zn)	2 atoms

The binding sites of Manganese atom in the 2.95A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Monoclinic Form) (pdb code 5kgm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the 2.95A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Monoclinic Form), PDB code: 5kgm:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the 2.95A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Monoclinic Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 2.95A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Monoclinic Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn603 b:52.5 occ:1.00 OD2 A:ASP426 2.2 44.7 1.0 NE2 A:HIS485 2.3 60.5 1.0 NE2 A:HIS430 2.3 40.8 1.0 CG A:ASP426 2.9 45.7 1.0 OD1 A:ASP426 3.0 47.3 1.0 CE1 A:HIS485 3.0 52.1 1.0 CD2 A:HIS430 3.3 58.0 1.0 CE1 A:HIS430 3.3 48.6 1.0 CD2 A:HIS485 3.5 48.9 1.0 NZ A:LYS359 4.1 45.8 1.0 OG A:SER86 4.1 33.8 1.0 ND1 A:HIS485 4.2 64.5 1.0 CE1 A:HIS468 4.3 49.4 1.0 CB A:ASP426 4.4 44.6 1.0 ND1 A:HIS430 4.4 47.6 1.0 CG A:HIS430 4.4 48.8 1.0 NE2 A:HIS468 4.5 50.7 1.0 CG A:HIS485 4.5 62.2 1.0 ZN A:ZN604 4.7 54.8 1.0 OD1 A:ASP37 4.9 46.1 1.0

Manganese binding site 2 out of 2 in the 2.95A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Monoclinic Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 2.95A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Monoclinic Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn603 b:46.0 occ:1.00 OD2 B:ASP426 2.2 53.5 1.0 NE2 B:HIS485 2.3 63.2 1.0 NE2 B:HIS430 2.3 53.1 1.0 OD1 B:ASP426 2.4 43.4 1.0 CG B:ASP426 2.7 49.3 1.0 CE1 B:HIS485 2.9 49.9 1.0 CE1 B:HIS430 3.2 55.9 1.0 CD2 B:HIS430 3.3 62.9 1.0 CD2 B:HIS485 3.5 56.4 1.0 OG B:SER86 4.0 45.5 1.0 NZ B:LYS359 4.0 43.4 1.0 ND1 B:HIS485 4.2 54.4 1.0 CB B:ASP426 4.2 50.6 1.0 ND1 B:HIS430 4.4 54.6 1.0 CE1 B:HIS468 4.4 54.2 1.0 CG B:HIS430 4.5 52.2 1.0 CG B:HIS485 4.5 61.2 1.0 NE2 B:HIS468 4.7 56.5 1.0 ZN B:ZN604 4.8 41.8 1.0 ND2 B:ASN470 4.9 58.8 1.0

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