Magnesium in PDB 7sp3: E. Coli Rpph Bound to AP4A

Protein crystallography data

The structure of E. Coli Rpph Bound to AP4A, PDB code: 7sp3 was solved by A.A.Serganov, N.Vasilyev, A.Nuthanakanti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.84 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 79.39, 36.384, 57.801, 90, 102.1, 90
R / Rfree (%) 18.3 / 22

Other elements in 7sp3:

The structure of E. Coli Rpph Bound to AP4A 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 E. Coli Rpph Bound to AP4A (pdb code 7sp3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the E. Coli Rpph Bound to AP4A, PDB code: 7sp3:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7sp3

Go back to Magnesium Binding Sites List in 7sp3
Magnesium binding site 1 out of 3 in the E. Coli Rpph Bound to AP4A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Coli Rpph Bound to AP4A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:17.4
occ:1.00
 OE1 A:GLU120 2.0 18.9 1.0
O A:GLN37 2.0 15.9 1.0
O1A A:B4P201 2.0 11.3 0.7
OE2 A:GLU57 2.1 15.7 1.0
O1B A:B4P201 2.1 19.1 0.7
O A:HOH363 2.1 15.8 1.0
CD A:GLU120 3.0 20.4 1.0
CD A:GLU57 3.0 15.8 1.0
MG A:MG203 3.1 15.3 1.0
C A:GLN37 3.3 15.7 1.0
OE1 A:GLU57 3.3 13.2 1.0
PA A:B4P201 3.3 20.3 0.7
OE2 A:GLU120 3.3 17.6 1.0
PB A:B4P201 3.4 27.8 0.7
O3A A:B4P201 3.6 20.7 0.7
O A:HOH396 3.9 34.7 1.0
C5E A:B4P201 4.0 19.4 0.3
CA A:GLY38 4.0 15.9 1.0
N A:GLN37 4.1 15.6 1.0
O5E A:B4P201 4.1 22.1 0.7
O A:HOH346 4.1 39.5 1.0
N A:GLY38 4.1 17.3 1.0
OE1 A:GLU53 4.2 16.9 1.0
CA A:GLN37 4.3 18.8 1.0
O A:HOH306 4.3 25.9 1.0
O2B A:B4P201 4.3 22.7 0.7
CG A:GLU120 4.3 19.6 1.0
CG A:GLU57 4.4 14.6 1.0
O3B A:B4P201 4.4 36.4 0.7
F A:F205 4.4 19.9 1.0
CG A:GLN37 4.4 19.5 1.0
O2A A:B4P201 4.5 18.0 0.7
CB A:GLU120 4.7 19.0 1.0
CB A:GLN37 5.0 17.7 1.0
O A:HOH321 5.0 15.8 1.0

Magnesium binding site 2 out of 3 in 7sp3

Go back to Magnesium Binding Sites List in 7sp3
Magnesium binding site 2 out of 3 in the E. Coli Rpph Bound to AP4A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E. Coli Rpph Bound to AP4A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:15.3
occ:1.00
 F A:F205 1.9 19.9 1.0
OE1 A:GLU53 2.1 16.9 1.0
OE2 A:GLU57 2.1 15.7 1.0
OE2 A:GLU120 2.1 17.6 1.0
O1A A:B4P201 2.1 11.3 0.7
O A:HOH321 2.1 15.8 1.0
CD A:GLU120 3.0 20.4 1.0
CD A:GLU57 3.1 15.8 1.0
CD A:GLU53 3.1 18.4 1.0
MG A:MG202 3.1 17.4 1.0
PA A:B4P201 3.2 20.3 0.7
OE1 A:GLU120 3.3 18.9 1.0
CG A:GLU57 3.4 14.6 1.0
OE2 A:GLU53 3.4 16.1 1.0
MG A:MG204 3.5 17.6 1.0
O2A A:B4P201 3.6 18.0 0.7
O5E A:B4P201 3.7 22.1 0.7
O A:HOH393 3.7 24.5 0.6
OE1 A:GLU56 3.9 19.8 1.0
O A:HOH322 4.0 25.9 1.0
O A:GLN37 4.0 15.9 1.0
O A:HOH318 4.2 18.2 1.0
OE1 A:GLU57 4.2 13.2 1.0
C5E A:B4P201 4.4 19.4 0.3
CG A:GLU120 4.4 19.6 1.0
O A:HOH351 4.4 27.9 1.0
CG A:GLU53 4.4 16.9 1.0
CA A:GLY38 4.4 15.9 1.0
O3A A:B4P201 4.6 20.7 0.7
O1B A:B4P201 4.7 19.1 0.7
CB A:GLU53 4.8 14.0 1.0
O A:HOH363 4.9 15.8 1.0
O A:HOH384 4.9 20.4 1.0
CB A:GLU57 4.9 12.7 1.0
C A:GLN37 4.9 15.7 1.0
C5E A:B4P201 4.9 26.8 0.7

Magnesium binding site 3 out of 3 in 7sp3

Go back to Magnesium Binding Sites List in 7sp3
Magnesium binding site 3 out of 3 in the E. Coli Rpph Bound to AP4A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E. Coli Rpph Bound to AP4A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:17.6
occ:1.00
 F A:F205 1.9 19.9 1.0
O2A A:B4P201 2.0 18.0 0.7
O A:HOH384 2.1 20.4 1.0
O A:HOH318 2.1 18.2 1.0
OE2 A:GLU53 2.2 16.1 1.0
O A:HOH343 2.2 20.9 1.0
PA A:B4P201 3.1 20.3 0.7
CD A:GLU53 3.2 18.4 1.0
MG A:MG203 3.5 15.3 1.0
O A:HOH393 3.5 24.5 0.6
OE1 A:GLU53 3.5 16.9 1.0
O5E A:B4P201 3.6 22.1 0.7
O1A A:B4P201 3.6 11.3 0.7
C5E A:B4P201 3.9 26.8 0.7
NH1 A:ARG52 3.9 15.7 1.0
N A:GLY39 4.0 17.1 1.0
OE1 A:GLU56 4.1 19.8 1.0
NH2 A:ARG8 4.1 27.1 1.0
O A:HOH391 4.2 31.4 1.0
O A:HOH393 4.2 25.0 0.4
O A:HOH321 4.4 15.8 1.0
O3A A:B4P201 4.5 20.7 0.7
O A:GLY39 4.5 21.0 1.0
CG A:GLU53 4.5 16.9 1.0
CA A:GLY38 4.6 15.9 1.0
C A:GLY38 4.8 14.7 1.0
OE2 A:GLU120 4.8 17.6 1.0
CA A:GLY39 4.8 19.4 1.0
CZ A:ARG52 4.9 13.2 1.0
NH2 A:ARG52 5.0 14.4 1.0

Reference:

R.Levenson-Palmer, D.J.Luciano, N.Vasilyev, A.Nuthanakanti, A.Serganov, J.G.Belasco. A Distinct Rna Recognition Mechanism Governs Np 4 Decapping By Rpph. Proc.Natl.Acad.Sci.Usa V. 119 2022.
ISSN: ESSN 1091-6490
PubMed: 35131855
DOI: 10.1073/PNAS.2117318119
Page generated: Thu Apr 6 22:10:50 2023

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