Magnesium in PDB 6vck: Crystal Structure of E.Coli Rpph-Dapf in Complex with Gdp, MG2+ and F-

All present enzymatic activity of Crystal Structure of E.Coli Rpph-Dapf in Complex with Gdp, MG2+ and F-:
5.1.1.7;

The structure of Crystal Structure of E.Coli Rpph-Dapf in Complex with Gdp, MG2+ and F-, PDB code: 6vck was solved by A.Gao, N.Vasilyev, A.Kaushik, W.Duan, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.93 / 2.69
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	161.840, 193.601, 51.037, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 26.8

The structure of Crystal Structure of E.Coli Rpph-Dapf in Complex with Gdp, MG2+ and F- also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Gdp, MG2+ and F- (pdb code 6vck). 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 Rpph-Dapf in Complex with Gdp, MG2+ and F-, PDB code: 6vck:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Gdp, MG2+ and F-


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 Rpph-Dapf in Complex with Gdp, MG2+ and F- within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:91.2 occ:1.00 O B:HOH313 2.1 76.7 1.0 F B:F206 2.2 0.5 1.0 O3B B:GDP204 2.3 94.6 1.0 OE2 B:GLU53 2.4 75.5 1.0 O B:HOH353 3.1 93.6 1.0 PB B:GDP204 3.4 97.6 1.0 O2B B:GDP204 3.5 89.9 1.0 CD B:GLU53 3.5 71.8 1.0 NH2 B:ARG52 3.9 66.4 1.0 MG B:MG202 3.9 89.0 1.0 OE1 B:GLU53 3.9 72.5 1.0 O1B B:GDP204 4.0 95.9 1.0 N B:GLY39 4.1 73.1 1.0 O B:GLY39 4.1 74.5 1.0 OE1 B:GLU56 4.4 77.6 1.0 NH1 B:ARG52 4.4 81.3 1.0 CZ B:ARG52 4.6 80.5 1.0 CA B:GLY39 4.7 71.4 1.0 O3A B:GDP204 4.8 0.6 1.0 CG B:GLU53 4.8 71.4 1.0 C B:GLY39 4.8 78.9 1.0 OD1 B:ASN41 4.9 87.6 1.0 CA B:GLY38 5.0 72.4 1.0 C B:GLY38 5.0 71.6 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Gdp, MG2+ and F-


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 Rpph-Dapf in Complex with Gdp, MG2+ and F- within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:89.0 occ:1.00 O2B B:GDP204 2.0 89.9 1.0 OE2 B:GLU57 2.0 79.0 0.4 F B:F206 2.2 0.5 1.0 OE1 B:GLU120 2.3 89.0 1.0 OE1 B:GLU53 2.3 72.5 1.0 CD B:GLU57 3.1 70.4 0.4 MG B:MG203 3.2 86.1 1.0 CD B:GLU53 3.3 71.8 1.0 PB B:GDP204 3.4 97.6 1.0 CG B:GLU57 3.5 68.5 0.4 CD B:GLU120 3.6 95.5 1.0 OE2 B:GLU53 3.6 75.5 1.0 CG B:GLU57 3.7 72.4 0.6 MG B:MG201 3.9 91.2 1.0 O1B B:GDP204 4.0 95.9 1.0 O3B B:GDP204 4.0 94.6 1.0 OE1 B:GLU57 4.1 74.3 0.6 O B:HOH342 4.2 96.5 1.0 OE1 B:GLU57 4.2 64.5 0.4 O B:HOH353 4.3 93.6 1.0 CD B:GLU57 4.3 72.8 0.6 OE2 B:GLU120 4.3 0.5 1.0 OE1 B:GLU56 4.3 77.6 1.0 O B:GLN37 4.4 75.9 1.0 O3A B:GDP204 4.5 0.6 1.0 CG B:GLU120 4.5 87.4 1.0 CA B:GLY38 4.6 72.4 1.0 CG B:GLU53 4.7 71.4 1.0 CB B:GLU57 5.0 61.8 0.6 CB B:GLU53 5.0 61.0 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Gdp, MG2+ and F-


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 Rpph-Dapf in Complex with Gdp, MG2+ and F- within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:86.1 occ:1.00 O B:GLN37 2.0 75.9 1.0 OE2 B:GLU57 2.1 79.0 0.4 O1A B:GDP204 2.7 97.8 1.0 OE1 B:GLU120 2.7 89.0 1.0 OE2 B:GLU120 2.8 0.5 1.0 CD B:GLU57 2.9 70.4 0.4 O2B B:GDP204 2.9 89.9 1.0 CD B:GLU120 3.0 95.5 1.0 OE1 B:GLU57 3.0 64.5 0.4 C B:GLN37 3.2 66.0 1.0 MG B:MG202 3.2 89.0 1.0 O3A B:GDP204 3.8 0.6 1.0 PA B:GDP204 3.9 0.4 1.0 PB B:GDP204 3.9 97.6 1.0 N B:GLN37 3.9 58.5 1.0 CA B:GLY38 4.0 72.4 1.0 N B:GLY38 4.0 73.7 1.0 OE1 B:GLU53 4.1 72.5 1.0 CA B:GLN37 4.2 62.5 1.0 CG B:GLU57 4.2 68.5 0.4 CG B:GLU120 4.4 87.4 1.0 CG B:GLU57 4.4 72.4 0.6 O1B B:GDP204 4.6 95.9 1.0 CB B:GLU120 4.6 70.2 1.0 CZ B:PHE121 4.7 74.2 1.0 CE2 B:PHE121 4.7 72.8 1.0 CG B:GLN37 4.7 60.5 1.0 O2A B:GDP204 4.9 86.4 1.0 O5' B:GDP204 4.9 0.1 1.0 C B:PRO36 5.0 52.5 1.0 CD B:GLU53 5.0 71.8 1.0

A.Gao, N.Vasilyev, A.Kaushik, W.Duan, A.Serganov. Principles of Rna and Nucleotide Discrimination By the Rna Processing Enzyme Rpph. Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962
PubMed: 31960065
DOI: 10.1093/NAR/GKAA024