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

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

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

Protein crystallography data

The structure of Crystal Structure of E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F-, PDB code: 6vcl 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) 30.00 / 2.06
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 162.444, 190.649, 51.336, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 22.7

Other elements in 6vcl:

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

Fluorine (F) 1 atom
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F- (pdb code 6vcl). 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 Pppgpp, MG2+ and F-, PDB code: 6vcl:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6vcl

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Magnesium binding site 1 out of 4 in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Pppgpp, 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 Pppgpp, MG2+ and F- within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:38.6
occ:1.00
 O B:HOH405 1.9 35.8 1.0
O B:HOH304 2.0 29.7 1.0
OE2 B:GLU53 2.0 31.7 1.0
O B:HOH307 2.1 35.3 1.0
O B:HOH446 2.2 39.4 1.0
O B:HOH357 2.3 38.1 1.0
MG B:MG204 3.0 34.3 1.0
CD B:GLU53 3.0 34.2 1.0
MG B:MG202 3.3 35.5 1.0
OE1 B:GLU53 3.5 30.9 1.0
F B:F208 3.6 32.9 1.0
O B:HOH425 3.7 42.1 1.0
N B:GLY39 3.8 32.0 1.0
O B:HOH437 3.9 51.9 1.0
NH2 B:ARG52 3.9 31.0 1.0
O B:GLY39 4.1 34.7 1.0
OE1 B:GLU56 4.1 39.8 1.0
O B:HOH313 4.3 49.8 1.0
O B:HOH325 4.3 34.5 1.0
CG B:GLU53 4.4 30.3 1.0
O2G B:0O2209 4.5 38.5 1.0
CA B:GLY38 4.6 31.9 1.0
CA B:GLY39 4.6 35.1 1.0
C B:GLY38 4.6 30.6 1.0
O B:HOH396 4.7 64.0 1.0
O B:HOH370 4.7 41.2 1.0
NH1 B:ARG52 4.8 32.4 1.0
CZ B:ARG52 4.8 38.0 1.0
C B:GLY39 4.8 34.7 1.0
NH1 B:ARG8 4.9 39.5 1.0
OE2 B:GLU120 4.9 32.3 1.0
OD1 B:ASN41 4.9 46.9 1.0

Magnesium binding site 2 out of 4 in 6vcl

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Magnesium binding site 2 out of 4 in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Pppgpp, 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 Pppgpp, MG2+ and F- within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:35.5
occ:1.00
 F B:F208 2.0 32.9 1.0
OE1 B:GLU53 2.0 30.9 1.0
O B:HOH405 2.1 35.8 1.0
O B:HOH325 2.1 34.5 1.0
OE2 B:GLU120 2.1 32.3 1.0
OE2 B:GLU57 2.4 35.5 1.0
CD B:GLU53 3.0 34.2 1.0
CD B:GLU120 3.1 40.2 1.0
MG B:MG204 3.2 34.3 1.0
MG B:MG203 3.3 34.7 1.0
OE2 B:GLU53 3.3 31.7 1.0
MG B:MG201 3.3 38.6 1.0
CD B:GLU57 3.3 32.9 1.0
OE1 B:GLU120 3.4 35.3 1.0
CG B:GLU57 3.6 32.3 1.0
O B:HOH370 3.7 41.2 1.0
O B:HOH304 3.7 29.7 1.0
OE1 B:GLU56 4.0 39.8 1.0
O B:HOH357 4.1 38.1 1.0
O B:GLN37 4.2 29.5 1.0
O B:HOH437 4.3 51.9 1.0
O B:HOH371 4.3 55.5 1.0
CG B:GLU53 4.4 30.3 1.0
CG B:GLU120 4.4 42.6 1.0
CA B:GLY38 4.5 31.9 1.0
OE1 B:GLU57 4.5 32.8 1.0
O2G B:0O2209 4.6 38.5 1.0
O1G B:0O2209 4.7 33.0 1.0
CB B:GLU53 4.8 25.6 1.0
O B:HOH387 4.9 45.0 1.0
O B:HOH446 4.9 39.4 1.0

Magnesium binding site 3 out of 4 in 6vcl

Go back to Magnesium Binding Sites List in 6vcl
Magnesium binding site 3 out of 4 in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Pppgpp, 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 Pppgpp, MG2+ and F- within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:34.7
occ:1.00
 O B:GLN37 1.9 29.5 1.0
F B:F208 2.0 32.9 1.0
O1G B:0O2209 2.1 33.0 1.0
OE2 B:GLU57 2.1 35.5 1.0
OE1 B:GLU120 2.1 35.3 1.0
O B:HOH361 2.3 31.5 1.0
CD B:GLU120 3.1 40.2 1.0
CD B:GLU57 3.1 32.9 1.0
C B:GLN37 3.1 30.0 1.0
MG B:MG202 3.3 35.5 1.0
PG B:0O2209 3.3 37.7 1.0
OE2 B:GLU120 3.4 32.3 1.0
OE1 B:GLU57 3.4 32.8 1.0
O2G B:0O2209 3.5 38.5 1.0
MG B:MG204 3.6 34.3 1.0
O B:HOH370 3.7 41.2 1.0
CA B:GLY38 3.8 31.9 1.0
O B:HOH306 3.9 45.8 1.0
N B:GLY38 3.9 32.9 1.0
O B:HOH340 4.0 36.6 1.0
N B:GLN37 4.1 24.8 1.0
O B:HOH400 4.1 37.7 1.0
OE1 B:GLU53 4.1 30.9 1.0
O3G B:0O2209 4.1 32.3 1.0
CA B:GLN37 4.2 28.0 1.0
CG B:GLN37 4.3 30.9 1.0
CG B:GLU120 4.4 42.6 1.0
O3B B:0O2209 4.4 41.9 1.0
CG B:GLU57 4.5 32.3 1.0
O B:HOH405 4.6 35.8 1.0
O B:HOH304 4.7 29.7 1.0
CB B:GLU120 4.8 35.0 1.0
CB B:GLN37 4.9 26.9 1.0
CD B:GLU53 5.0 34.2 1.0

Magnesium binding site 4 out of 4 in 6vcl

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Magnesium binding site 4 out of 4 in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Pppgpp, 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 Pppgpp, MG2+ and F- within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:34.3
occ:1.00
 F B:F208 1.9 32.9 1.0
O B:HOH304 1.9 29.7 1.0
O2G B:0O2209 1.9 38.5 1.0
O B:HOH370 2.1 41.2 1.0
O B:HOH405 2.4 35.8 1.0
O B:HOH425 2.5 42.1 1.0
MG B:MG201 3.0 38.6 1.0
MG B:MG202 3.2 35.5 1.0
PG B:0O2209 3.2 37.7 1.0
O1G B:0O2209 3.5 33.0 1.0
O B:HOH446 3.6 39.4 1.0
MG B:MG203 3.6 34.7 1.0
NH2 B:ARG8 3.8 40.3 1.0
O3B B:0O2209 3.8 41.9 1.0
OE2 B:GLU120 3.8 32.3 1.0
OE1 B:GLU120 3.9 35.3 1.0
CA B:GLY38 4.0 31.9 1.0
N B:GLY39 4.1 32.0 1.0
CD B:GLU120 4.2 40.2 1.0
OE2 B:GLU53 4.2 31.7 1.0
OE1 B:GLU53 4.3 30.9 1.0
O3G B:0O2209 4.4 32.3 1.0
NH1 B:ARG8 4.4 39.5 1.0
OE2 B:GLU57 4.5 35.5 1.0
CZ B:ARG8 4.5 48.6 1.0
O B:HOH307 4.6 35.3 1.0
CD B:GLU53 4.6 34.2 1.0
O B:GLN37 4.6 29.5 1.0
C B:GLY38 4.6 30.6 1.0
O B:HOH357 4.8 38.1 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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