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

Go back to Magnesium Binding Sites List in 6vcm
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 Dec 15 01:23:46 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy