Manganese in PDB 8sp5: Line-1 Retrotransposon Endonuclease Domain Complex with MN2+

All present enzymatic activity of Line-1 Retrotransposon Endonuclease Domain Complex with MN2+:
2.7.7.49;

The structure of Line-1 Retrotransposon Endonuclease Domain Complex with MN2+, PDB code: 8sp5 was solved by A.M.D'ordine, G.Jogl, J.M.Sedivy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.55 / 2.23
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	93.096, 122.378, 43.412, 90, 90, 90
R / Rfree (%)	20.3 / 25

The binding sites of Manganese atom in the Line-1 Retrotransposon Endonuclease Domain Complex with MN2+ (pdb code 8sp5). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Line-1 Retrotransposon Endonuclease Domain Complex with MN2+, PDB code: 8sp5:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Line-1 Retrotransposon Endonuclease Domain Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Line-1 Retrotransposon Endonuclease Domain Complex with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:28.9 occ:1.00 O A:HOH481 2.0 27.6 1.0 O A:HOH438 2.2 26.4 1.0 O A:HOH424 2.2 29.9 1.0 OD1 A:ASN16 2.3 28.6 1.0 OE1 A:GLU43 2.3 27.7 1.0 O A:HOH428 2.3 24.3 1.0 CD A:GLU43 3.1 27.1 1.0 CG A:ASN16 3.2 28.1 1.0 OE2 A:GLU43 3.2 30.0 1.0 CB A:ASN16 3.9 27.0 1.0 ND2 A:ASN16 4.1 28.6 1.0 CA A:ASN16 4.1 27.0 1.0 OD2 A:ASP229 4.2 27.2 1.0 O A:HOH472 4.2 29.2 1.0 OD1 A:ASP229 4.4 25.9 1.0 NE2 A:HIS45 4.4 31.5 1.0 CE1 A:HIS45 4.5 32.3 1.0 CG A:GLU43 4.5 26.7 1.0 OD1 A:ASN14 4.6 25.1 1.0 CG A:ASP229 4.7 26.8 1.0 CB A:GLU43 4.9 27.4 1.0

Manganese binding site 2 out of 2 in the Line-1 Retrotransposon Endonuclease Domain Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Line-1 Retrotransposon Endonuclease Domain Complex with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:37.7 occ:1.00 O B:HOH415 2.1 33.8 1.0 OD1 B:ASN16 2.1 36.8 1.0 OE1 B:GLU43 2.3 35.5 1.0 O B:HOH417 2.3 34.5 1.0 O B:HOH422 2.5 31.6 1.0 O B:HOH486 2.6 35.4 1.0 CG B:ASN16 3.0 35.1 1.0 CD B:GLU43 3.1 34.6 1.0 OE2 B:GLU43 3.1 33.1 1.0 CB B:ASN16 3.8 30.8 1.0 ND2 B:ASN16 3.9 35.1 1.0 O B:HOH431 4.0 30.8 1.0 CA B:ASN16 4.1 32.7 1.0 OD2 B:ASP229 4.3 30.1 1.0 OD1 B:ASP229 4.4 27.7 1.0 CE1 B:HIS45 4.4 37.4 1.0 NE2 B:HIS45 4.4 34.4 1.0 CG B:GLU43 4.5 30.6 1.0 OD1 B:ASN14 4.5 27.3 1.0 CG B:ASP229 4.8 30.2 1.0 CB B:GLU43 4.9 29.5 1.0 C B:ASN16 5.0 32.6 1.0

A.M.D'ordine, G.Jogl, J.M.Sedivy. Identification and Characterization of Small Molecule Inhibitors of the Line-1 Retrotransposon Endonuclease. Nat Commun V. 15 3883 2024.
ISSN: ESSN 2041-1723
PubMed: 38719805
DOI: 10.1038/S41467-024-48066-X