Zinc 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:

Manganese	(Mn)	2 atoms
Chlorine	(Cl)	4 atoms

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

Zinc 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 Zinc with other atoms in the Zn 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:Zn604 b:54.8 occ:1.00 OD2 A:ASP467 1.9 29.9 1.0 OD1 A:ASP37 2.0 46.1 1.0 NE2 A:HIS468 2.0 50.7 1.0 OG A:SER86 2.1 33.8 1.0 CG A:ASP37 2.7 37.1 1.0 CG A:ASP467 2.8 38.6 1.0 CD2 A:HIS468 2.9 47.7 1.0 OD2 A:ASP37 2.9 26.4 1.0 CE1 A:HIS468 2.9 49.4 1.0 CB A:SER86 3.0 39.3 1.0 OD1 A:ASP467 3.1 33.9 1.0 CA A:SER86 3.3 44.3 1.0 NZ A:LYS359 3.6 45.8 1.0 N A:SER86 3.7 36.5 1.0 OD2 A:ASP426 3.9 44.7 1.0 ND1 A:HIS468 3.9 49.4 1.0 CG A:HIS468 3.9 49.2 1.0 CB A:ASP37 4.1 36.6 1.0 CG A:ASP426 4.1 45.7 1.0 CB A:ASP467 4.2 43.8 1.0 C A:ASN85 4.4 37.9 1.0 CA A:ASP37 4.4 31.4 1.0 CE A:LYS359 4.5 39.2 1.0 N A:GLY38 4.5 53.6 1.0 OD1 A:ASP426 4.5 47.3 1.0 CB A:ASP426 4.5 44.6 1.0 MN A:MN603 4.7 52.5 1.0 C A:SER86 4.8 40.0 1.0 CE1 A:HIS90 4.8 40.3 1.0 C A:ASP37 4.8 41.0 1.0 O A:ASN85 4.9 38.4 1.0 NE2 A:HIS485 5.0 60.5 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn604 b:41.8 occ:1.00 OD2 B:ASP467 2.0 31.5 1.0 OD2 B:ASP37 2.0 51.4 1.0 OG B:SER86 2.1 45.5 1.0 NE2 B:HIS468 2.1 56.5 1.0 CG B:ASP37 2.7 43.4 1.0 OD1 B:ASP37 2.8 41.5 1.0 CG B:ASP467 2.9 43.0 1.0 CB B:SER86 2.9 44.0 1.0 CE1 B:HIS468 3.0 54.2 1.0 CD2 B:HIS468 3.0 50.0 1.0 CA B:SER86 3.2 46.5 1.0 OD1 B:ASP467 3.2 38.3 1.0 N B:SER86 3.6 40.8 1.0 NZ B:LYS359 3.7 43.4 1.0 ND1 B:HIS468 4.0 52.2 1.0 OD2 B:ASP426 4.0 53.5 1.0 CG B:HIS468 4.0 47.8 1.0 CB B:ASP37 4.1 43.7 1.0 CG B:ASP426 4.2 49.3 1.0 CB B:ASP467 4.3 47.8 1.0 C B:ASN85 4.3 43.9 1.0 CA B:ASP37 4.5 36.2 1.0 CE B:LYS359 4.5 38.1 1.0 N B:GLY38 4.5 46.5 1.0 OD1 B:ASP426 4.5 43.4 1.0 CB B:ASP426 4.6 50.6 1.0 C B:SER86 4.6 42.3 1.0 O B:ASN85 4.7 48.4 1.0 MN B:MN603 4.8 46.0 1.0 C B:ASP37 4.8 41.9 1.0 CE1 B:HIS90 4.8 43.4 1.0 CD B:LYS359 4.9 51.1 1.0 O B:SER86 5.0 40.7 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