Magnesium in PDB 5ohg: Enolase in Complex with Rnase E

All present enzymatic activity of Enolase in Complex with Rnase E:
3.1.26.12; 4.2.1.11;

The structure of Enolase in Complex with Rnase E, PDB code: 5ohg was solved by D.Du, B.F.Luisi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.24 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.683, 116.923, 107.776, 90.00, 105.43, 90.00
R / Rfree (%)	16.1 / 19.7

The structure of Enolase in Complex with Rnase E also contains other interesting chemical elements:

Sodium

(Na)

5 atoms

The binding sites of Magnesium atom in the Enolase in Complex with Rnase E (pdb code 5ohg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Enolase in Complex with Rnase E, PDB code: 5ohg:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Enolase in Complex with Rnase E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Enolase in Complex with Rnase E within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:22.1 occ:1.00 OE2 A:GLU290 2.0 21.9 1.0 O A:HOH611 2.2 16.7 1.0 OD2 A:ASP317 2.2 22.1 1.0 O A:HOH632 2.3 18.2 1.0 OD2 A:ASP246 2.3 21.6 1.0 CG A:ASP246 3.2 21.9 1.0 CG A:ASP317 3.2 22.9 1.0 CD A:GLU290 3.2 22.5 1.0 OD1 A:ASP246 3.4 20.0 1.0 NZ A:LYS342 3.6 22.9 1.0 NZ A:LYS393 3.7 24.7 1.0 NE2 A:GLN167 3.8 20.9 1.0 CB A:ASP317 3.8 18.4 1.0 OE1 A:GLU290 4.0 24.0 1.0 OD1 A:ASP317 4.2 22.5 1.0 CD2 A:LEU340 4.3 17.7 1.0 CG A:GLU290 4.3 21.5 1.0 OD2 A:ASP291 4.3 24.8 1.0 O4 A:PO4503 4.3 30.0 1.0 CB A:ASP246 4.5 20.9 1.0 OE2 A:GLU168 4.6 25.6 1.0 O1 A:PO4503 4.6 30.0 1.0 CE A:LYS342 4.7 22.3 1.0 O A:HOH630 4.8 25.5 1.0 CD A:GLN167 4.9 20.5 1.0 OG A:SER42 5.0 24.7 1.0

Magnesium binding site 2 out of 4 in the Enolase in Complex with Rnase E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Enolase in Complex with Rnase E within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:25.6 occ:1.00 O B:HOH616 2.1 19.6 1.0 OD2 B:ASP317 2.1 26.7 1.0 OE2 B:GLU290 2.2 28.3 1.0 OD2 B:ASP246 2.2 27.4 1.0 O B:HOH619 2.4 28.3 1.0 CG B:ASP246 3.1 27.7 1.0 CG B:ASP317 3.3 23.9 1.0 CD B:GLU290 3.3 28.6 1.0 OD1 B:ASP246 3.4 24.7 1.0 NZ B:LYS393 3.7 22.9 1.0 NZ B:LYS342 3.7 27.0 1.0 CB B:ASP317 3.8 23.5 1.0 NE2 B:GLN167 3.9 22.1 1.0 OE1 B:GLU290 4.1 27.2 1.0 CD2 B:LEU340 4.1 23.0 1.0 OD2 B:ASP291 4.2 26.1 1.0 OD1 B:ASP317 4.3 23.7 1.0 CG B:GLU290 4.3 22.1 1.0 CB B:ASP246 4.5 22.6 1.0 O1 B:PO4503 4.5 30.0 1.0 OE2 B:GLU168 4.6 28.8 1.0 O4 B:PO4503 4.8 30.0 1.0 CE B:LYS342 4.8 23.1 1.0 O B:HOH711 4.9 27.0 1.0 CD B:GLN167 5.0 25.9 1.0

Magnesium binding site 3 out of 4 in the Enolase in Complex with Rnase E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Enolase in Complex with Rnase E within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg501 b:18.5 occ:1.00 OE2 H:GLU290 2.1 21.6 1.0 OD2 H:ASP246 2.1 18.9 1.0 OD2 H:ASP317 2.1 23.4 1.0 O H:HOH603 2.2 18.0 1.0 O H:HOH673 2.3 17.7 1.0 CG H:ASP246 3.1 22.1 1.0 CD H:GLU290 3.2 22.6 1.0 CG H:ASP317 3.3 21.1 1.0 OD1 H:ASP246 3.4 18.9 1.0 NZ H:LYS342 3.7 20.5 1.0 NZ H:LYS393 3.7 18.9 1.0 CB H:ASP317 3.8 21.5 1.0 NE2 H:GLN167 3.8 19.3 1.0 OE1 H:GLU290 4.0 22.0 1.0 CD2 H:LEU340 4.2 16.3 1.0 CG H:GLU290 4.2 18.2 1.0 OD2 H:ASP291 4.3 22.9 1.0 OD1 H:ASP317 4.3 19.1 1.0 CB H:ASP246 4.4 21.6 1.0 O1 H:PO4503 4.5 30.0 1.0 OE2 H:GLU168 4.5 23.0 1.0 O4 H:PO4503 4.7 30.0 1.0 CE H:LYS342 4.8 20.3 1.0 CD H:GLN167 4.9 18.6 1.0 O H:HOH632 5.0 22.9 1.0 OG H:SER42 5.0 21.0 1.0

Magnesium binding site 4 out of 4 in the Enolase in Complex with Rnase E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Enolase in Complex with Rnase E within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg501 b:20.6 occ:1.00 O I:HOH616 1.9 20.1 1.0 OE2 I:GLU290 2.2 26.6 1.0 OD2 I:ASP317 2.2 22.4 1.0 OD2 I:ASP246 2.2 25.4 1.0 O I:HOH621 2.3 21.7 1.0 CG I:ASP246 3.1 24.9 1.0 CD I:GLU290 3.3 23.8 1.0 CG I:ASP317 3.3 21.3 1.0 OD1 I:ASP246 3.4 24.4 1.0 NZ I:LYS342 3.6 21.9 1.0 NZ I:LYS393 3.8 19.2 1.0 NE2 I:GLN167 3.8 19.4 1.0 CB I:ASP317 3.8 20.9 1.0 OE1 I:GLU290 4.0 24.1 1.0 CD2 I:LEU340 4.2 24.1 1.0 OD2 I:ASP291 4.2 27.5 1.0 OD1 I:ASP317 4.3 20.4 1.0 O4 I:PO4504 4.4 30.0 1.0 CG I:GLU290 4.4 23.9 1.0 OE2 I:GLU168 4.5 26.4 1.0 CB I:ASP246 4.5 23.3 1.0 O1 I:PO4504 4.6 30.0 1.0 CE I:LYS342 4.8 21.2 1.0 CD I:GLN167 4.9 21.6 1.0 OG I:SER42 4.9 20.5 1.0

H.A.Bruce, D.Du, D.Matak-Vinkovic, K.J.Bandyra, R.W.Broadhurst, E.Martin, F.Sobott, A.V.Shkumatov, B.F.Luisi. Analysis of the Natively Unstructured Rna/Protein-Recognition Core in the Escherichia Coli Rna Degradosome and Its Interactions with Regulatory Rna/Hfq Complexes. Nucleic Acids Res. V. 46 387 2018.
ISSN: ESSN 1362-4962
PubMed: 29136196
DOI: 10.1093/NAR/GKX1083