Magnesium in PDB 6pe2: Drosophila P Element Transposase Strand Transfer Complex

The binding sites of Magnesium atom in the Drosophila P Element Transposase Strand Transfer Complex (pdb code 6pe2). 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: 6pe2:
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:0.4 occ:1.00 O1G A:GTP601 2.1 0.3 1.0 O1B A:GTP601 2.1 0.3 1.0 O3A A:GTP601 2.1 0.3 1.0 OD1 A:ASN440 2.5 0.4 1.0 PB A:GTP601 2.5 0.3 1.0 PG A:GTP601 3.0 0.3 1.0 O3B A:GTP601 3.2 0.3 1.0 O3G A:GTP601 3.5 0.3 1.0 CG A:ASN440 3.6 0.4 1.0 PA A:GTP601 3.7 0.3 1.0 O2B A:GTP601 3.9 0.3 1.0 OD2 A:ASP444 4.0 1.0 1.0 OD1 A:ASP444 4.1 1.0 1.0 ND2 A:ASN440 4.1 0.4 1.0 O2A A:GTP601 4.1 0.3 1.0 O2G A:GTP601 4.4 0.3 1.0 CG A:ASP444 4.5 1.0 1.0 O1A A:GTP601 4.5 0.3 1.0 O5' A:GTP601 4.6 0.3 1.0 OG A:SER409 4.7 0.2 1.0 CA A:SER409 4.7 0.2 1.0 N A:ASN410 4.7 0.1 1.0 CB A:ASN440 4.9 0.4 1.0 O A:PHE408 4.9 0.2 1.0 CB A:SER409 4.9 0.2 1.0 CG2 A:THR405 5.0 0.3 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 C:Mg101 b:0.9 occ:1.00 C5' K:DG1 2.4 0.1 1.0 C2' C:DA9 2.4 0.7 1.0 O4' K:DG1 2.6 0.1 1.0 N9 C:DA9 2.8 0.7 1.0 C8 C:DA9 2.9 0.7 1.0 C4' K:DG1 3.0 0.1 1.0 C1' C:DA9 3.1 0.7 1.0 C4 C:DA9 3.3 0.7 1.0 C8 K:DG1 3.4 0.1 1.0 N7 C:DA9 3.5 0.7 1.0 O5' K:DG1 3.5 0.1 1.0 C5 C:DA9 3.7 0.7 1.0 C1' K:DG1 3.7 0.1 1.0 N9 K:DG1 3.7 0.1 1.0 C3' C:DA9 3.8 0.7 1.0 OP2 K:DG1 4.1 0.1 1.0 P K:DG1 4.1 0.1 1.0 N3 C:DA9 4.1 0.7 1.0 O4' C:DA9 4.1 0.7 1.0 OP1 K:DG1 4.1 0.1 1.0 N7 K:DG1 4.2 0.1 1.0 C3' K:DG1 4.3 0.1 1.0 O5' C:DA9 4.4 0.7 1.0 C2' K:DG1 4.4 0.1 1.0 C4' C:DA9 4.6 0.7 1.0 O3' C:DA9 4.8 0.7 1.0 C6 C:DA9 4.8 0.7 1.0 C4 K:DG1 4.8 0.1 1.0 C2 C:DA9 4.9 0.7 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:Mg602 b:0.1 occ:1.00 O1G G:GTP601 2.1 0.8 1.0 O1B G:GTP601 2.1 0.8 1.0 O3A G:GTP601 2.1 0.8 1.0 OD1 G:ASN441 2.2 0.3 1.0 PB G:GTP601 2.5 0.8 1.0 PG G:GTP601 3.0 0.8 1.0 CG G:ASN441 3.1 0.3 1.0 O3B G:GTP601 3.2 0.8 1.0 OD2 G:ASP445 3.4 0.9 1.0 ND2 G:ASN441 3.4 0.3 1.0 O3G G:GTP601 3.5 0.8 1.0 PA G:GTP601 3.7 0.8 1.0 O2B G:GTP601 3.9 0.8 1.0 O2A G:GTP601 4.1 0.8 1.0 CG G:ASP445 4.2 0.9 1.0 OD1 G:ASP445 4.3 0.9 1.0 O2G G:GTP601 4.4 0.8 1.0 O1A G:GTP601 4.5 0.8 1.0 N G:ASN411 4.5 0.5 1.0 CB G:ASN441 4.5 0.3 1.0 O5' G:GTP601 4.6 0.8 1.0 CA G:SER410 4.9 0.2 1.0 CB G:ASN411 5.0 0.5 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:0.6 occ:1.00 CB G:ASP231 2.4 0.2 1.0 CE2 G:PHE535 2.4 0.3 1.0 C G:ASP231 3.0 0.2 1.0 CA G:ASP231 3.1 0.2 1.0 CG G:ASP231 3.1 0.2 1.0 CD2 G:PHE535 3.2 0.3 1.0 N G:GLU232 3.3 0.5 1.0 CZ G:PHE535 3.3 0.3 1.0 O G:ASP231 3.4 0.2 1.0 CG1 G:VAL531 3.4 0.8 1.0 OD2 G:ASP231 3.5 0.2 1.0 N G:ASP231 3.7 0.2 1.0 O G:GLU232 3.8 0.5 1.0 OD1 G:ASP231 3.9 0.2 1.0 C G:GLU232 4.0 0.5 1.0 CA G:GLU232 4.1 0.5 1.0 CB G:VAL531 4.3 0.8 1.0 CG G:PHE535 4.4 0.3 1.0 CE1 G:PHE535 4.5 0.3 1.0 C G:PHE230 4.7 0.6 1.0 CG G:GLU532 4.8 0.5 1.0 N G:MET233 4.8 0.0 1.0 C G:VAL531 4.8 0.8 1.0 O G:VAL531 4.8 0.8 1.0 CD1 G:PHE535 5.0 0.3 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