Magnesium in PDB 7n8k: Line-1 Endonuclease Domain Complex with Mg

All present enzymatic activity of Line-1 Endonuclease Domain Complex with Mg:
2.7.7.49;

The structure of Line-1 Endonuclease Domain Complex with Mg, PDB code: 7n8k was solved by S.Korolev, I.Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.30 / 2.01
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.857, 126.776, 44.854, 90, 98.94, 90
R / Rfree (%)	19.2 / 23.6

The binding sites of Magnesium atom in the Line-1 Endonuclease Domain Complex with Mg (pdb code 7n8k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Line-1 Endonuclease Domain Complex with Mg, PDB code: 7n8k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Line-1 Endonuclease Domain Complex with Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Line-1 Endonuclease Domain Complex with Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:39.2 occ:1.00 O A:HOH475 2.0 36.6 1.0 O A:HOH430 2.2 39.4 1.0 O A:HOH445 2.2 29.6 1.0 OE1 A:GLU43 2.2 27.0 1.0 CD A:GLU43 3.0 35.2 1.0 OE2 A:GLU43 3.2 34.7 1.0 O A:HOH417 3.6 32.0 1.0 OD1 A:ASN16 3.8 33.9 1.0 ND2 A:ASN14 4.1 23.8 1.0 O A:HOH402 4.2 36.0 1.0 OD2 A:ASP229 4.2 31.2 1.0 OD1 A:ASN14 4.3 25.5 1.0 OD1 A:ASP229 4.4 26.3 1.0 NE2 A:HIS230 4.4 24.3 1.0 CG A:GLU43 4.4 28.6 1.0 CG A:ASN16 4.6 31.8 1.0 CG A:ASN14 4.6 26.1 1.0 CG A:ASP229 4.8 29.2 1.0 CD2 A:HIS230 4.8 24.1 1.0 OH A:TYR115 5.0 35.9 1.0 CB A:GLU43 5.0 28.6 1.0

Magnesium binding site 2 out of 2 in the Line-1 Endonuclease Domain Complex with Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Line-1 Endonuclease Domain Complex with Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:42.4 occ:1.00 O B:HOH491 2.0 36.9 1.0 O B:HOH406 2.1 33.7 1.0 OE1 B:GLU43 2.1 25.8 1.0 O B:HOH465 2.1 27.7 1.0 O B:HOH518 2.1 40.9 1.0 O B:HOH437 2.8 36.8 1.0 CD B:GLU43 2.9 30.1 1.0 OE2 B:GLU43 3.2 30.3 1.0 O B:HOH401 3.6 40.8 1.0 O B:HOH405 3.6 31.1 1.0 OD1 B:ASN16 4.0 30.6 1.0 ND2 B:ASN14 4.1 25.9 1.0 OD1 B:ASN14 4.2 21.6 1.0 CG B:GLU43 4.3 25.6 1.0 OD2 B:ASP229 4.3 31.5 1.0 NE2 B:HIS230 4.5 23.1 1.0 OD1 B:ASP229 4.5 31.6 1.0 CG B:ASN14 4.5 25.1 1.0 CG B:ASN16 4.6 33.3 1.0 OH B:TYR115 4.7 32.6 1.0 CD2 B:HIS230 4.8 24.5 1.0 CG B:ASP229 4.9 31.5 1.0 CB B:GLU43 4.9 22.8 1.0

I.Miller, M.Totrov, L.Korotchkina, D.N.Kazyulkin, A.V.Gudkov, S.Korolev. Structural Dissection of Sequence Recognition and Catalytic Mechanism of Human Line-1 Endonuclease. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 34554261
DOI: 10.1093/NAR/GKAB826