Magnesium in PDB 6wug: Crystal Structure of S. Pombe RAI1 in Complex with 3'-Fadp

Protein crystallography data

The structure of Crystal Structure of S. Pombe RAI1 in Complex with 3'-Fadp, PDB code: 6wug was solved by S.K.Doamekpor, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.66 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.594, 59.978, 72.545, 90.00, 104.67, 90.00
R / Rfree (%) 19.1 / 22.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of S. Pombe RAI1 in Complex with 3'-Fadp (pdb code 6wug). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of S. Pombe RAI1 in Complex with 3'-Fadp, PDB code: 6wug:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6wug

Go back to Magnesium Binding Sites List in 6wug
Magnesium binding site 1 out of 2 in the Crystal Structure of S. Pombe RAI1 in Complex with 3'-Fadp


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 S. Pombe RAI1 in Complex with 3'-Fadp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:22.8
occ:1.00
O A:HOH546 2.1 35.2 1.0
OE2 A:GLU150 2.2 33.6 1.0
OE2 A:GLU239 2.2 31.8 1.0
OD2 A:ASP201 2.3 27.7 1.0
O A:LEU240 2.4 26.2 1.0
O52 A:UBG403 2.9 40.6 1.0
CG A:ASP201 3.2 32.3 1.0
CD A:GLU239 3.3 28.5 1.0
OD1 A:ASP201 3.4 34.0 1.0
CD A:GLU150 3.4 33.7 1.0
C A:LEU240 3.6 30.5 1.0
N A:LEU240 3.9 25.5 1.0
O3B A:UBG403 4.0 37.8 1.0
OE1 A:GLU239 4.0 27.8 1.0
P51 A:UBG403 4.1 40.0 1.0
CG A:GLU150 4.2 26.1 1.0
O A:HOH629 4.2 35.8 1.0
O A:HOH584 4.2 35.1 1.0
CA A:LEU240 4.2 23.6 1.0
O A:HOH563 4.2 31.0 1.0
CG A:GLU239 4.3 28.5 1.0
O A:HOH622 4.3 30.9 1.0
OE1 A:GLU150 4.4 35.5 1.0
CD A:LYS241 4.4 37.1 1.0
CB A:LEU240 4.5 23.0 1.0
CB A:ASP201 4.6 25.9 1.0
N A:LYS241 4.7 29.4 1.0
CE A:LYS241 4.7 31.4 1.0
NZ A:LYS241 4.7 35.4 1.0
C A:GLU239 4.9 24.2 1.0
CA A:LYS241 4.9 29.6 1.0

Magnesium binding site 2 out of 2 in 6wug

Go back to Magnesium Binding Sites List in 6wug
Magnesium binding site 2 out of 2 in the Crystal Structure of S. Pombe RAI1 in Complex with 3'-Fadp


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 S. Pombe RAI1 in Complex with 3'-Fadp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:31.6
occ:1.00
OE2 A:GLU199 2.0 31.3 1.0
O A:HOH565 2.0 31.6 1.0
O A:HOH584 2.0 35.1 1.0
O A:HOH567 2.1 29.9 1.0
O A:HOH550 2.1 30.9 1.0
O A:HOH515 2.2 38.7 1.0
CD A:GLU199 3.0 35.8 1.0
OE1 A:GLU199 3.3 29.7 1.0
OE1 A:GLU150 3.8 35.5 1.0
OD1 A:ASP201 4.0 34.0 1.0
O2B A:UBG403 4.2 39.8 1.0
O A:HOH556 4.2 28.8 1.0
O A:PRO177 4.2 31.9 1.0
CG A:GLU199 4.3 29.2 1.0
CD A:GLU150 4.4 33.7 1.0
O A:HOH546 4.5 35.2 1.0
CG A:GLN180 4.5 32.0 1.0
O A:HOH560 4.5 33.8 1.0
O A:GLU179 4.5 34.8 1.0
OE2 A:GLU150 4.6 33.6 1.0
O A:HOH625 4.7 32.8 1.0
CA A:PRO177 4.9 33.0 1.0
O A:HOH583 5.0 31.7 1.0

Reference:

S.K.Doamekpor, E.Grudzien-Nogalska, A.Mlynarska-Cieslak, J.Kowalska, M.Kiledjian, L.Tong. Dxo/RAI1 Enzymes Remove 5'-End Fad and Dephospho-Coa Caps on Rnas. Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962
PubMed: 32374864
DOI: 10.1093/NAR/GKAA297
Page generated: Tue Dec 15 01:37:43 2020

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