Atomistry » Magnesium » PDB 6vcl-6vno » 6vcl
Atomistry »
  Magnesium »
    PDB 6vcl-6vno »
      6vcl »

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

Go back to Magnesium Binding Sites List in 6vcl
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

Go back to Magnesium Binding Sites List in 6vcl
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

Go back to Magnesium Binding Sites List in 6vcl
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

Last articles

Zn in 1ELX
Zn in 1EKM
Zn in 1EKB
Zn in 1EJ6
Zn in 1EH8
Zn in 1EFZ
Zn in 1ED8
Zn in 1EH7
Zn in 1EH6
Zn in 1EF4
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy