Magnesium in PDB 7r0t: Crystal Structure of Exonuclease EXNV1

The structure of Crystal Structure of Exonuclease EXNV1, PDB code: 7r0t was solved by M.Welin, A.Svensson, M.Hakansson, S.Al-Karadaghi, A.Jasilionis, J.A.Linares-Pasten, L.Wang, E.Nordberg Karlsson, J.Ahlqvist, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.78 / 2.19
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	42.279, 54.11, 171.732, 90, 90, 90
R / Rfree (%)	23.5 / 27.8

The structure of Crystal Structure of Exonuclease EXNV1 also contains other interesting chemical elements:

Terbium	(Tb)	1 atom
Chlorine	(Cl)	4 atoms

The binding sites of Magnesium atom in the Crystal Structure of Exonuclease EXNV1 (pdb code 7r0t). 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 Exonuclease EXNV1, PDB code: 7r0t:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Exonuclease EXNV1


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 Exonuclease EXNV1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:66.6 occ:1.00 OE2 A:GLU34 2.1 59.6 1.0 OD2 A:ASP32 2.1 54.6 1.0 OD2 A:ASP252 2.1 55.1 1.0 O2P A:TMP401 2.1 60.9 1.0 O1P A:TMP401 2.6 62.4 1.0 P A:TMP401 2.8 61.8 1.0 CG A:ASP32 3.1 53.4 1.0 CD A:GLU34 3.1 58.3 1.0 CG A:ASP252 3.1 53.3 1.0 O A:HOH506 3.4 40.5 1.0 OD1 A:ASP32 3.4 53.3 1.0 CB A:ASP252 3.5 48.7 1.0 OE1 A:GLU34 3.6 58.8 1.0 MG A:MG403 3.6 45.9 1.0 O3P A:TMP401 3.8 61.8 1.0 O5' A:TMP401 4.1 61.5 1.0 O A:THR33 4.1 53.0 1.0 CE2 A:TYR248 4.1 59.6 1.0 OH A:TYR248 4.2 62.2 1.0 OD1 A:ASP252 4.3 53.4 1.0 C5' A:TMP401 4.3 61.1 1.0 CG A:GLU34 4.4 53.3 1.0 CB A:ASP32 4.4 50.6 1.0 CZ A:TYR248 4.4 60.8 1.0 O A:HOH514 4.6 44.1 1.0 O A:HOH501 4.6 45.0 1.0 CA A:ALA249 4.7 52.3 1.0 O A:HOH519 4.8 40.8 1.0 NZ A:LYS140 4.8 64.5 1.0 O A:ALA249 4.8 51.7 1.0 C A:THR33 4.9 51.6 1.0 CD2 A:TYR248 5.0 58.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Exonuclease EXNV1


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 Exonuclease EXNV1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:45.9 occ:1.00 O A:HOH514 2.1 44.1 1.0 O A:HOH510 2.1 41.1 1.0 O2P A:TMP401 2.1 60.9 1.0 O A:HOH506 2.1 40.5 1.0 O A:HOH519 2.1 40.8 1.0 OD1 A:ASP32 2.1 53.3 1.0 CG A:ASP32 3.2 53.4 1.0 P A:TMP401 3.3 61.8 1.0 MG A:MG402 3.6 66.6 1.0 OD2 A:ASP32 3.6 54.6 1.0 O3P A:TMP401 3.7 61.8 1.0 C5' A:TMP401 3.9 61.1 1.0 O5' A:TMP401 3.9 61.5 1.0 OD1 A:ASP104 4.0 53.2 1.0 O A:THR33 4.0 53.0 1.0 O A:HOH525 4.1 48.4 1.0 O A:HOH507 4.1 32.2 1.0 O A:HOH501 4.2 45.0 1.0 OD2 A:ASP104 4.2 54.9 1.0 O A:HOH545 4.2 67.3 1.0 O A:HIS99 4.4 50.6 1.0 N A:THR33 4.5 51.0 1.0 CB A:ASP32 4.5 50.6 1.0 CG A:ASP104 4.5 52.8 1.0 O1P A:TMP401 4.6 62.4 1.0 CA A:ASP32 4.8 49.5 1.0 OD2 A:ASP252 4.8 55.1 1.0

J.Ahlqvist, J.A.Linares-Pasten, A.Jasilionis, M.Welin, M.Hakansson, L.A.Svensson, L.Wang, H.Watzlawick, A.Aevarsson, O.H.Fridjonsson, G.O.Hreggvidsson, B.Ketelsen Striberny, E.Glomsaker, O.Lanes, S.Al-Karadaghi, E.Nordberg Karlsson. Crystal Structure of Dna Polymerase I From Thermus Phage G20C. Acta Crystallogr D Struct V. 78 1384 2022BIOL.
PubMed: 36322421
DOI: 10.1107/S2059798322009895