Magnesium in PDB 7k33: Crystal Structure of Endonuclease Q Complex with 27-Mer Duplex Substrate with An Abasic Lesion at the Active Site

The structure of Crystal Structure of Endonuclease Q Complex with 27-Mer Duplex Substrate with An Abasic Lesion at the Active Site, PDB code: 7k33 was solved by K.Shi, N.M.Moeller, S.Banerjee, L.Yin, K.Orellana, H.Aihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	88.30 / 3.11
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	151.5, 151.5, 119.38, 90, 90, 120
R / Rfree (%)	19.1 / 23

The structure of Crystal Structure of Endonuclease Q Complex with 27-Mer Duplex Substrate with An Abasic Lesion at the Active Site also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Endonuclease Q Complex with 27-Mer Duplex Substrate with An Abasic Lesion at the Active Site (pdb code 7k33). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Endonuclease Q Complex with 27-Mer Duplex Substrate with An Abasic Lesion at the Active Site, PDB code: 7k33:

Magnesium binding site 1 out of 1 in the Crystal Structure of Endonuclease Q Complex with 27-Mer Duplex Substrate with An Abasic Lesion at the Active Site


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 Endonuclease Q Complex with 27-Mer Duplex Substrate with An Abasic Lesion at the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:116.2 occ:1.00 OH A:TYR299 2.0 159.6 1.0 OE2 A:GLU205 2.2 138.0 1.0 O A:LEU170 2.5 105.7 1.0 O A:GLY169 2.6 96.1 1.0 O A:ALA172 2.6 100.7 1.0 O A:LEU237 2.6 134.3 1.0 CD A:GLU205 3.2 120.5 1.0 C A:LEU170 3.3 96.2 1.0 CZ A:TYR299 3.3 135.5 1.0 N A:LEU237 3.5 108.0 1.0 CA A:LEU170 3.5 98.8 1.0 C A:LEU237 3.6 119.5 1.0 C A:GLY169 3.7 100.2 1.0 OE1 A:GLU205 3.7 124.6 1.0 C A:ALA172 3.8 105.8 1.0 CA A:LEU237 4.0 103.8 1.0 N A:LEU170 4.1 95.4 1.0 N A:ALA172 4.1 115.9 1.0 CE1 A:TYR299 4.1 130.8 1.0 C A:GLY236 4.1 116.6 1.0 CB A:LEU237 4.2 83.3 1.0 CE2 A:TYR299 4.3 129.7 1.0 CA A:GLY236 4.3 117.1 1.0 N A:SER171 4.5 88.0 1.0 CG A:GLU205 4.5 102.2 1.0 CA A:ALA172 4.6 101.1 1.0 N A:ASP173 4.8 120.7 1.0 N A:ASP238 4.8 98.7 1.0 N A:PRO239 4.8 110.2 1.0 CB A:LEU170 4.9 112.1 1.0 CA A:ASP173 4.9 96.5 1.0 C A:ASP238 4.9 100.0 1.0 C A:SER171 4.9 125.9 1.0 CA A:GLY169 5.0 95.1 1.0

K.Shi, N.H.Moeller, S.Banerjee, J.L.Mccann, M.A.Carpenter, L.Yin, R.Moorthy, K.Orellana, D.A.Harki, R.S.Harris, H.Aihara. Structural Basis For Recognition of Distinct Deaminated Dna Lesions By Endonuclease Q. Proc.Natl.Acad.Sci.Usa V. 118 2021.
ISSN: ESSN 1091-6490
PubMed: 33658373
DOI: 10.1073/PNAS.2021120118