Manganese in PDB 3gme: Crystal Structure of Polynucleotide Phosphorylase in Complex with Rnase E and Manganese

All present enzymatic activity of Crystal Structure of Polynucleotide Phosphorylase in Complex with Rnase E and Manganese:
2.7.7.8;

The structure of Crystal Structure of Polynucleotide Phosphorylase in Complex with Rnase E and Manganese, PDB code: 3gme 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)	25.91 / 2.40
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	158.574, 158.574, 156.118, 90.00, 90.00, 120.00
R / Rfree (%)	28.6 / 29.8

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

Manganese binding site 1 out of 2 in the Crystal Structure of Polynucleotide Phosphorylase in Complex with Rnase E and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Polynucleotide Phosphorylase in Complex with Rnase E and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn550 b:0.3 occ:1.00 OD2 A:ASP492 2.6 75.7 1.0 OD2 A:ASP486 3.0 89.4 1.0 OD1 A:ASP486 3.1 87.3 1.0 CG A:ASP486 3.3 84.4 1.0 O A:HOH702 3.4 67.2 1.0 CG A:ASP492 3.8 67.3 1.0 O A:HOH688 3.9 69.9 1.0 O A:HOH617 4.3 63.7 1.0 CB A:ASP492 4.6 62.1 1.0 OD1 A:ASP492 4.7 71.3 1.0 CB A:ASP486 4.7 83.8 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Polynucleotide Phosphorylase in Complex with Rnase E and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Polynucleotide Phosphorylase in Complex with Rnase E and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn551 b:82.3 occ:1.00 O A:PHE41 2.3 27.0 1.0 O A:ILE114 2.5 32.8 1.0 OG1 A:THR43 3.1 32.4 1.0 C A:PHE41 3.2 29.1 1.0 N A:THR43 3.4 35.2 1.0 C A:ILE114 3.5 32.5 1.0 CG2 A:THR116 3.5 29.9 1.0 CD2 A:PHE41 3.5 31.2 1.0 CG2 A:THR43 3.6 34.5 1.0 CA A:VAL42 3.6 30.0 1.0 C A:VAL42 3.7 33.3 1.0 N A:VAL42 3.7 30.3 1.0 CB A:THR43 3.8 34.9 1.0 N A:THR116 3.9 29.6 1.0 CA A:ALA115 4.1 29.6 1.0 CG2 A:ILE114 4.1 30.4 1.0 N A:ALA115 4.2 31.0 1.0 CA A:THR43 4.2 36.2 1.0 CG A:PHE41 4.2 32.7 1.0 CE2 A:PHE41 4.3 30.4 1.0 CB A:PHE41 4.3 28.3 1.0 CB A:ILE114 4.3 31.4 1.0 CA A:PHE41 4.3 28.8 1.0 C A:ALA115 4.4 30.2 1.0 CA A:ILE114 4.5 30.9 1.0 CB A:THR116 4.5 31.8 1.0 O A:VAL42 4.6 30.8 1.0 CA A:THR116 4.8 29.6 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