Magnesium in PDB 3gcm: Crystal Structure of E. Coli Polynucleotide Phosphorylase Bound to Rna and Rnase E

All present enzymatic activity of Crystal Structure of E. Coli Polynucleotide Phosphorylase Bound to Rna and Rnase E:
2.7.7.8;

The structure of Crystal Structure of E. Coli Polynucleotide Phosphorylase Bound to Rna and Rnase E, PDB code: 3gcm was solved by S.Nurmohamed, B.L.Luisi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.50
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	176.335, 176.335, 189.628, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 22.1

The binding sites of Magnesium atom in the Crystal Structure of E. Coli Polynucleotide Phosphorylase Bound to Rna and Rnase E (pdb code 3gcm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of E. Coli Polynucleotide Phosphorylase Bound to Rna and Rnase E, PDB code: 3gcm:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of E. Coli Polynucleotide Phosphorylase Bound to Rna and Rnase E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of E. Coli Polynucleotide Phosphorylase Bound to Rna and Rnase E within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg552 b:33.7 occ:1.00 OB2 A:FLC551 2.8 40.5 1.0 O A:HOH749 3.2 14.1 1.0 OD2 A:ASP492 3.2 32.5 1.0 OD1 A:ASP492 3.3 30.0 1.0 CB A:ALA465 3.5 12.9 1.0 CG A:ASP492 3.6 27.6 1.0 CB A:SER437 3.8 20.0 1.0 CA A:SER437 3.8 20.0 1.0 CD1 A:ILE481 3.8 14.0 1.0 CG1 A:ILE481 3.8 14.7 1.0 N A:SER437 3.8 20.0 1.0 CBC A:FLC551 4.0 43.2 1.0 CA A:GLY436 4.1 14.0 1.0 CG A:FLC551 4.3 41.8 1.0 OD2 A:ASP486 4.3 33.1 1.0 O A:ILE481 4.4 15.9 1.0 CG A:ASP486 4.4 26.4 1.0 C A:GLY436 4.5 15.4 1.0 OG A:SER437 4.5 20.0 1.0 CB A:ASP486 4.5 23.3 1.0 CB A:FLC551 4.7 44.6 1.0 OB1 A:FLC551 4.9 42.0 1.0 CA A:ALA465 4.9 14.9 1.0 OD1 A:ASP486 5.0 32.2 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of E. Coli Polynucleotide Phosphorylase Bound to Rna and Rnase E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of E. Coli Polynucleotide Phosphorylase Bound to Rna and Rnase E within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg556 b:36.8 occ:1.00 OB2 B:FLC555 2.5 47.8 1.0 OD2 B:ASP492 3.1 30.3 1.0 OD1 B:ASP492 3.2 30.0 1.0 CG B:ASP492 3.6 28.7 1.0 CB B:ALA465 3.7 18.6 1.0 CA B:SER437 3.7 17.6 1.0 N B:SER437 3.7 17.1 1.0 CBC B:FLC555 3.7 48.2 1.0 CB B:SER437 3.7 18.4 1.0 CD1 B:ILE481 3.8 15.3 1.0 CG1 B:ILE481 3.9 14.9 1.0 CA B:GLY436 4.0 14.8 1.0 CG B:FLC555 4.2 46.0 1.0 OD2 B:ASP486 4.4 38.4 1.0 C B:GLY436 4.4 16.1 1.0 CG B:ASP486 4.4 30.4 1.0 CB B:FLC555 4.4 47.9 1.0 CB B:ASP486 4.5 27.1 1.0 OG B:SER437 4.5 19.0 1.0 O B:ILE481 4.5 18.2 1.0 OB1 B:FLC555 4.6 43.7 1.0 CA B:FLC555 4.8 50.0 1.0 OG2 B:FLC555 4.8 40.3 1.0 CGC B:FLC555 4.9 43.7 1.0 OD1 B:ASP486 4.9 34.8 1.0 CE B:LYS494 4.9 23.4 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of E. Coli Polynucleotide Phosphorylase Bound to Rna and Rnase E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of E. Coli Polynucleotide Phosphorylase Bound to Rna and Rnase E within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg553 b:40.5 occ:1.00 OB2 C:FLC552 2.5 43.4 1.0 OD2 C:ASP492 3.0 35.2 1.0 OD1 C:ASP492 3.4 32.6 1.0 O C:HOH573 3.5 21.6 1.0 CG C:ASP492 3.5 30.6 1.0 CBC C:FLC552 3.6 46.5 1.0 CB C:ALA465 3.7 18.0 1.0 CB C:SER437 3.7 20.0 1.0 CA C:SER437 3.8 20.0 1.0 N C:SER437 3.8 20.0 1.0 CD1 C:ILE481 4.0 19.6 1.0 CG C:FLC552 4.0 42.0 1.0 CG1 C:ILE481 4.1 18.3 1.0 CA C:GLY436 4.2 17.7 1.0 CB C:FLC552 4.3 46.2 1.0 OG C:SER437 4.3 20.0 1.0 OD2 C:ASP486 4.5 36.5 1.0 CG C:ASP486 4.5 32.4 1.0 C C:GLY436 4.5 19.2 1.0 OB1 C:FLC552 4.5 43.5 1.0 O C:ILE481 4.6 20.7 1.0 CB C:ASP486 4.6 26.4 1.0 CA C:FLC552 4.6 48.5 1.0 OG2 C:FLC552 4.8 30.0 1.0 CGC C:FLC552 4.8 36.3 1.0 CE C:LYS494 4.9 24.3 1.0 OD1 C:ASP486 4.9 39.4 1.0

S.Nurmohamed, B.Vaidialingam, A.J.Callaghan, B.F.Luisi. Crystal Structure of Escherichia Coli Polynucleotide Phosphorylase Core Bound to Rnase E, Rna and Manganese: Implications For Catalytic Mechanism and Rna Degradosome Assembly. J.Mol.Biol. V. 389 17 2009.
ISSN: ISSN 0022-2836
PubMed: 19327365
DOI: 10.1016/J.JMB.2009.03.051