Magnesium in PDB 6p5a: Drosophila P Element Transposase Strand Transfer Complex

The binding sites of Magnesium atom in the Drosophila P Element Transposase Strand Transfer Complex (pdb code 6p5a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Drosophila P Element Transposase Strand Transfer Complex, PDB code: 6p5a:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Drosophila P Element Transposase Strand Transfer Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Drosophila P Element Transposase Strand Transfer Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:32.2 occ:1.00 OD1 A:ASN440 1.9 34.8 1.0 O1B A:GTP601 2.4 39.1 1.0 O1G A:GTP601 2.8 39.1 1.0 O3A A:GTP601 2.8 39.1 1.0 CG A:ASN440 3.0 34.8 1.0 PB A:GTP601 3.1 39.1 1.0 ND2 A:ASN440 3.6 34.8 1.0 PG A:GTP601 3.9 39.1 1.0 O3B A:GTP601 4.0 39.1 1.0 CB A:ASN440 4.3 34.8 1.0 PA A:GTP601 4.3 39.1 1.0 O2B A:GTP601 4.4 39.1 1.0 O3G A:GTP601 4.4 39.1 1.0 N A:ASN410 4.7 39.9 1.0 O2A A:GTP601 4.7 39.1 1.0 O A:PHE408 4.8 33.1 1.0 CA A:SER409 4.8 37.3 1.0 O A:ASN440 4.8 34.8 1.0 CA A:ASN440 4.9 34.8 1.0 OD2 A:ASP444 4.9 32.8 1.0

Magnesium binding site 2 out of 4 in the Drosophila P Element Transposase Strand Transfer Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Drosophila P Element Transposase Strand Transfer Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:38.5 occ:1.00 O3' C:DA9 2.1 48.2 1.0 OD2 A:ASP303 2.1 38.2 1.0 OD1 A:ASP230 2.3 35.7 1.0 C3' C:DA9 2.9 48.2 1.0 OD2 A:ASP230 2.9 35.7 1.0 CG A:ASP230 3.0 35.7 1.0 CG A:ASP303 3.2 38.2 1.0 CB A:ASP303 3.9 38.2 1.0 C4' C:DA9 3.9 48.2 1.0 C2' C:DA9 4.0 48.2 1.0 OP2 K:DG1 4.0 49.7 1.0 OD1 A:ASP303 4.2 38.2 1.0 O A:GLU231 4.2 35.8 1.0 CB A:ASP230 4.5 35.7 1.0 N A:GLU231 4.5 35.8 1.0 CG A:GLU231 4.5 35.8 1.0 C5' C:DA9 4.6 48.2 1.0 NE2 A:GLN527 4.7 34.5 1.0 O3' K:DG-1 5.0 34.8 1.0

Magnesium binding site 3 out of 4 in the Drosophila P Element Transposase Strand Transfer Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Drosophila P Element Transposase Strand Transfer Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg601 b:38.5 occ:1.00 O3' I:DA9 2.1 48.2 1.0 OD2 G:ASP303 2.1 38.2 1.0 OD1 G:ASP230 2.3 35.7 1.0 C3' I:DA9 2.9 48.2 1.0 OD2 G:ASP230 2.9 35.7 1.0 CG G:ASP230 3.0 35.7 1.0 CG G:ASP303 3.2 38.2 1.0 CB G:ASP303 3.9 38.2 1.0 C4' I:DA9 3.9 48.2 1.0 OP2 E:DG1 4.0 49.7 1.0 C2' I:DA9 4.0 48.2 1.0 OD1 G:ASP303 4.2 38.2 1.0 O G:GLU231 4.2 35.8 1.0 CB G:ASP230 4.5 35.7 1.0 N G:GLU231 4.5 35.8 1.0 CG G:GLU231 4.5 35.8 1.0 C5' I:DA9 4.6 48.2 1.0 NE2 G:GLN527 4.7 34.5 1.0 O3' E:DG-1 5.0 34.8 1.0 P E:DG1 5.0 49.7 1.0

Magnesium binding site 4 out of 4 in the Drosophila P Element Transposase Strand Transfer Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Drosophila P Element Transposase Strand Transfer Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg603 b:32.2 occ:1.00 OD1 G:ASN440 1.9 34.8 1.0 O1B G:GTP602 2.4 39.1 1.0 O1G G:GTP602 2.8 39.1 1.0 O3A G:GTP602 2.8 39.1 1.0 CG G:ASN440 3.0 34.8 1.0 PB G:GTP602 3.1 39.1 1.0 ND2 G:ASN440 3.6 34.8 1.0 PG G:GTP602 3.9 39.1 1.0 O3B G:GTP602 4.0 39.1 1.0 PA G:GTP602 4.3 39.1 1.0 CB G:ASN440 4.3 34.8 1.0 O2B G:GTP602 4.4 39.1 1.0 O3G G:GTP602 4.4 39.1 1.0 N G:ASN410 4.7 39.9 1.0 O2A G:GTP602 4.7 39.1 1.0 O G:ASN440 4.8 34.8 1.0 O G:PHE408 4.8 33.1 1.0 CA G:SER409 4.8 37.3 1.0 CA G:ASN440 4.9 34.8 1.0 OD2 G:ASP444 4.9 32.8 1.0

G.E.Ghanim, E.H.Kellogg, E.Nogales, D.C.Rio. Structure of A P Element Transposase-Dna Complex Reveals Unusual Dna Structures and Gtp-Dna Contacts. Nat.Struct.Mol.Biol. V. 26 1013 2019.
ISSN: ESSN 1545-9985
PubMed: 31659330
DOI: 10.1038/S41594-019-0319-6