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

Enzymatic activity of Crystal Structure of E.Coli Rpph-Dapf in Complex with Gtp, MG2+ and F-

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

Protein crystallography data

The structure of Crystal Structure of E.Coli Rpph-Dapf in Complex with Gtp, MG2+ and F-, PDB code: 6vcm 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) 29.90 / 2.35
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 162.357, 192.948, 51.100, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 23.5

Other elements in 6vcm:

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

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Gtp, MG2+ and F- (pdb code 6vcm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Gtp, MG2+ and F-, PDB code: 6vcm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6vcm

Go back to Magnesium Binding Sites List in 6vcm
Magnesium binding site 1 out of 4 in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Gtp, 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 Gtp, MG2+ and F- within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:79.4
occ:1.00
 OE2 B:GLU53 2.3 55.0 1.0
MG B:MG205 2.8 69.6 1.0
N B:GLY39 3.4 51.9 1.0
CD B:GLU53 3.5 55.3 1.0
F B:F207 3.6 76.5 1.0
O B:GLY39 3.6 55.0 1.0
OE1 B:GLU53 4.0 42.0 1.0
CA B:GLY39 4.0 46.0 1.0
MG B:MG203 4.1 80.5 1.0
NH2 B:ARG52 4.2 46.6 1.0
C B:GLY39 4.2 50.3 1.0
C B:GLY38 4.2 44.4 1.0
CA B:GLY38 4.3 49.3 1.0
NH1 B:ARG52 4.5 48.4 1.0
CG B:GLU53 4.7 46.0 1.0
O2G B:GTP206 4.7 73.0 0.6
CZ B:ARG52 4.8 54.6 1.0
OD1 B:ASN41 4.9 67.0 1.0

Magnesium binding site 2 out of 4 in 6vcm

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Magnesium binding site 2 out of 4 in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Gtp, 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 Gtp, MG2+ and F- within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:80.5
occ:1.00
 F B:F207 2.0 76.5 1.0
OE1 B:GLU53 2.6 42.0 1.0
MG B:MG204 3.2 81.8 1.0
CD B:GLU53 3.6 55.3 1.0
MG B:MG205 3.6 69.6 1.0
CG B:GLU57 3.6 51.3 1.0
OE2 B:GLU53 3.7 55.0 1.0
CG B:GLU120 3.8 80.2 1.0
OE1 B:GLU57 4.0 71.6 1.0
CD B:GLU57 4.0 65.7 1.0
MG B:MG202 4.1 79.4 1.0
O B:GLN37 4.4 46.6 1.0
CB B:GLU120 4.6 63.1 1.0
CA B:GLY38 4.7 49.3 1.0
CD B:GLU120 4.8 87.4 1.0
OE2 B:GLU57 4.9 65.8 1.0
CG B:GLU53 5.0 46.0 1.0
O2G B:GTP206 5.0 73.0 0.6

Magnesium binding site 3 out of 4 in 6vcm

Go back to Magnesium Binding Sites List in 6vcm
Magnesium binding site 3 out of 4 in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Gtp, 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 Gtp, MG2+ and F- within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:81.8
occ:1.00
 O B:GLN37 2.0 46.6 1.0
F B:F207 2.4 76.5 1.0
O3G B:GTP206 2.6 68.4 0.6
MG B:MG203 3.2 80.5 1.0
C B:GLN37 3.3 47.8 1.0
PG B:GTP206 3.8 64.3 0.6
CA B:GLY38 4.0 49.3 1.0
O2G B:GTP206 4.1 73.0 0.6
N B:GLN37 4.1 36.8 1.0
N B:GLY38 4.1 46.2 1.0
MG B:MG205 4.2 69.6 1.0
OE1 B:GLU53 4.2 42.0 1.0
CG B:GLU120 4.3 80.2 1.0
CA B:GLN37 4.3 37.1 1.0
CB B:GLU120 4.3 63.1 1.0
CZ B:PHE121 4.4 59.5 1.0
CE2 B:PHE121 4.4 62.9 1.0
O1G B:GTP206 4.4 54.5 0.6
CG B:GLN37 4.6 41.8 1.0
CG B:GLU57 4.8 51.3 1.0
O1B B:GTP206 4.9 84.9 0.6

Magnesium binding site 4 out of 4 in 6vcm

Go back to Magnesium Binding Sites List in 6vcm
Magnesium binding site 4 out of 4 in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Gtp, MG2+ and F-


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of E.Coli Rpph-Dapf in Complex with Gtp, MG2+ and F- within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg205

b:69.6
occ:1.00
 O2G B:GTP206 2.2 73.0 0.6
F B:F207 2.2 76.5 1.0
MG B:MG202 2.8 79.4 1.0
N B:GLY39 3.5 51.9 1.0
PG B:GTP206 3.5 64.3 0.6
MG B:MG203 3.6 80.5 1.0
CA B:GLY38 3.8 49.3 1.0
O3G B:GTP206 3.9 68.4 0.6
OE2 B:GLU53 4.0 55.0 1.0
NH1 B:ARG8 4.1 82.9 1.0
C B:GLY38 4.2 44.4 1.0
MG B:MG204 4.2 81.8 1.0
NH2 B:ARG8 4.3 0.1 1.0
O1G B:GTP206 4.4 54.5 0.6
CA B:GLY39 4.5 46.0 1.0
O3B B:GTP206 4.6 72.2 0.6
OE1 B:GLU53 4.6 42.0 1.0
CZ B:ARG8 4.7 91.0 1.0
O B:GLN37 4.7 46.6 1.0
CD B:GLU53 4.7 55.3 1.0

Reference:

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
Page generated: Tue Oct 1 21:59:10 2024

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