Magnesium in PDB 9bw1: Tnsabcd-Dna Transpososome

The structure of Tnsabcd-Dna Transpososome also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Magnesium atom in the Tnsabcd-Dna Transpososome (pdb code 9bw1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Tnsabcd-Dna Transpososome, PDB code: 9bw1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in the Tnsabcd-Dna Transpososome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tnsabcd-Dna Transpososome within 5.0Å range: probe atom residue distance (Å) B Occ 4:Mg101 b:33.7 occ:1.00 OP1 4:DA-1 2.8 50.6 1.0 O N:GLU522 3.3 58.8 1.0 OD1 N:ASP524 3.4 71.7 1.0 OP1 4:DT1 3.5 63.5 1.0 OD2 N:ASP524 3.5 69.3 1.0 OG1 N:THR521 3.6 58.4 1.0 CG N:ASP524 3.7 71.4 1.0 P 4:DA-1 3.9 45.8 1.0 OD1 N:ASN631 3.9 56.8 1.0 ND2 N:ASN631 4.0 52.7 1.0 CG2 N:THR521 4.0 55.1 1.0 C N:GLU522 4.2 53.5 1.0 OP2 4:DA-1 4.2 53.7 1.0 CG N:ASN631 4.4 48.0 1.0 CB N:THR521 4.4 56.9 1.0 N N:ASP524 4.5 65.1 1.0 CA N:LEU523 4.5 50.6 1.0 O3' 4:DC-2 4.6 39.8 1.0 N N:LEU523 4.7 47.9 1.0 N N:GLU522 4.8 54.5 1.0 CD2 N:LEU523 4.9 50.5 1.0 P 4:DT1 4.9 73.3 1.0 C N:LEU523 4.9 54.2 1.0

Magnesium binding site 2 out of 11 in the Tnsabcd-Dna Transpososome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tnsabcd-Dna Transpososome within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg201 b:51.2 occ:1.00 OP1 I:DG16 2.0 80.8 1.0 OP2 I:DA14 2.5 69.3 1.0 OP1 I:DA14 3.1 75.2 1.0 P I:DA14 3.2 71.0 1.0 P I:DG16 3.4 91.1 1.0 OD1 M:ASP524 3.8 69.0 1.0 C5' I:DG16 3.8 76.7 1.0 OD2 M:ASP524 4.0 73.7 1.0 O5' I:DG16 4.1 81.0 1.0 OP2 I:DG16 4.1 80.5 1.0 O5' I:DA14 4.2 63.3 1.0 CG M:ASP524 4.3 72.2 1.0 OP2 I:DC13 4.3 66.7 1.0 OE2 M:GLU522 4.3 69.5 1.0 OP1 I:DC13 4.3 64.1 1.0 O5' I:DC13 4.4 65.3 1.0 NH2 N:ARG649 4.4 68.3 1.0 O3' I:DC15 4.5 82.3 1.0 P I:DC13 4.5 66.8 1.0 OP1 I:DT17 4.5 77.5 1.0 O3' I:DC13 4.6 64.2 1.0 C5' I:DA14 4.8 62.8 1.0 NH2 M:ARG538 4.9 49.8 1.0 C4' I:DG16 4.9 73.8 1.0 O M:GLU522 5.0 62.8 1.0

Magnesium binding site 3 out of 11 in the Tnsabcd-Dna Transpososome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tnsabcd-Dna Transpososome within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg202 b:85.3 occ:1.00 O M:HIS520 2.1 69.8 1.0 C5' I:DC15 2.4 80.2 1.0 C M:HIS520 3.2 59.3 1.0 C4' I:DC15 3.2 80.1 1.0 O5' I:DC15 3.5 81.0 1.0 OP2 I:DC15 3.6 80.2 1.0 O3' 6:DA20 3.6 91.5 1.0 O3' I:DA14 3.8 70.8 1.0 P I:DC15 3.9 80.7 1.0 CA M:THR521 4.0 62.6 1.0 N M:THR521 4.0 63.9 1.0 O4' I:DC15 4.1 80.0 1.0 CA M:HIS520 4.2 48.9 1.0 N M:HIS520 4.3 51.8 1.0 CB M:THR521 4.3 63.3 1.0 C3' 6:DA20 4.4 92.5 1.0 C3' I:DC15 4.5 79.4 1.0 CB M:HIS520 4.6 47.0 1.0 O3' I:DC15 4.7 82.3 1.0 OG1 M:THR521 4.7 65.9 1.0 C2' 6:DA20 4.8 89.2 1.0 OE2 M:GLU624 4.9 72.9 1.0 O5' I:DA14 5.0 63.3 1.0

Magnesium binding site 4 out of 11 in the Tnsabcd-Dna Transpososome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tnsabcd-Dna Transpososome within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg901 b:42.5 occ:1.00 OD1 M:ASP104 2.0 80.0 1.0 CG M:ASP104 2.8 80.5 1.0 OP1 2:DA-2 3.3 75.8 1.0 C5' 2:DA-2 3.4 78.5 1.0 OD2 M:ASP104 3.4 79.8 1.0 OE1 M:GLU57 3.7 71.0 1.0 CD M:GLU57 3.8 76.1 1.0 CB M:ASP104 3.8 81.0 1.0 OE2 M:GLU57 4.1 79.0 1.0 O3' 2:DA-3 4.1 85.4 1.0 P 2:DA-2 4.1 88.2 1.0 O5' 2:DA-2 4.2 81.0 1.0 CG M:GLU57 4.2 73.3 1.0 O M:CYS118 4.4 80.1 1.0 CA M:ASP104 4.4 77.4 1.0 CB M:GLU57 4.6 60.3 1.0 C4' 2:DA-2 4.6 77.3 1.0

Magnesium binding site 5 out of 11 in the Tnsabcd-Dna Transpososome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tnsabcd-Dna Transpososome within 5.0Å range: probe atom residue distance (Å) B Occ Q:Mg601 b:72.6 occ:1.00 OG1 Q:THR64 2.0 66.6 1.0 O3B Q:ATP600 2.0 69.5 1.0 PB Q:ATP600 2.9 58.5 1.0 O1B Q:ATP600 2.9 69.8 1.0 O1G Q:ATP600 2.9 70.1 1.0 PG Q:ATP600 3.0 62.7 1.0 CB Q:THR64 3.4 69.0 1.0 O3A Q:ATP600 3.4 63.8 1.0 O3G Q:ATP600 4.0 68.9 1.0 O2G Q:ATP600 4.1 56.6 1.0 CG2 Q:THR64 4.1 71.9 1.0 N Q:THR64 4.2 77.3 1.0 O2B Q:ATP600 4.2 71.2 1.0 O2A Q:ATP600 4.3 63.4 1.0 PA Q:ATP600 4.3 75.0 1.0 CA Q:THR64 4.4 69.9 1.0 O5' Q:ATP600 4.4 73.5 1.0 OE2 Q:GLU172 4.5 74.3 1.0 NH1 R:ARG224 4.9 62.9 1.0 NZ Q:LYS63 5.0 78.4 1.0

Magnesium binding site 6 out of 11 in the Tnsabcd-Dna Transpososome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Tnsabcd-Dna Transpososome within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg601 b:27.9 occ:1.00 OG1 R:THR64 2.0 52.9 1.0 O3G R:ATP600 2.1 53.2 1.0 O1B R:ATP600 3.0 63.6 1.0 CB R:THR64 3.2 51.6 1.0 PG R:ATP600 3.3 61.4 1.0 O2A R:ATP600 3.4 55.1 1.0 OE2 R:GLU172 3.5 43.9 1.0 O1G R:ATP600 3.7 56.3 1.0 CG2 R:THR64 3.8 50.9 1.0 O3B R:ATP600 3.8 48.9 1.0 PB R:ATP600 3.9 55.5 1.0 OD2 R:ASP171 4.1 56.3 1.0 O3A R:ATP600 4.4 61.0 1.0 CA R:THR64 4.4 48.3 1.0 PA R:ATP600 4.4 59.2 1.0 CD R:GLU172 4.5 52.0 1.0 N R:THR64 4.5 52.6 1.0 O2G R:ATP600 4.6 59.9 1.0 NH2 S:ARG224 4.7 58.2 1.0 OD1 S:ASN197 4.7 57.0 1.0 O1A R:ATP600 4.8 55.4 1.0 OE1 R:GLU172 4.9 56.7 1.0 CG R:ASP171 5.0 53.2 1.0

Magnesium binding site 7 out of 11 in the Tnsabcd-Dna Transpososome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Tnsabcd-Dna Transpososome within 5.0Å range: probe atom residue distance (Å) B Occ S:Mg601 b:63.9 occ:1.00 O S:HOH701 2.0 35.1 1.0 O S:HOH702 2.0 63.2 1.0 O S:HOH705 2.1 45.1 1.0 O1G S:ATP600 2.1 47.7 1.0 OG1 S:THR64 2.5 40.8 1.0 O1B S:ATP600 2.7 58.0 1.0 PG S:ATP600 3.2 48.3 1.0 O3B S:ATP600 3.4 28.6 1.0 PB S:ATP600 3.6 35.8 1.0 OD1 S:ASP171 3.7 57.8 1.0 OE2 S:GLU172 3.7 49.3 1.0 OD2 S:ASP171 3.7 40.9 1.0 CB S:THR64 3.9 38.8 1.0 NH2 T:ARG224 3.9 49.4 1.0 CG S:ASP171 4.0 48.6 1.0 O S:HOH704 4.1 41.0 1.0 O3G S:ATP600 4.2 43.9 1.0 CD S:GLU172 4.3 49.7 1.0 O2G S:ATP600 4.3 58.0 1.0 O3A S:ATP600 4.5 38.0 1.0 N S:THR64 4.6 39.3 1.0 CG S:GLU172 4.6 44.6 1.0 O2A S:ATP600 4.7 45.2 1.0 CG2 S:THR64 4.7 41.9 1.0 CA S:THR64 4.7 34.8 1.0 O2B S:ATP600 4.8 49.8 1.0 NE2 T:GLN220 4.9 44.2 1.0

Magnesium binding site 8 out of 11 in the Tnsabcd-Dna Transpososome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Tnsabcd-Dna Transpososome within 5.0Å range: probe atom residue distance (Å) B Occ T:Mg601 b:25.2 occ:1.00 O1G T:ATP600 2.1 29.6 1.0 OG1 T:THR64 3.1 32.4 1.0 PG T:ATP600 3.3 30.4 1.0 OE2 T:GLU172 3.4 58.1 1.0 O1B T:ATP600 3.6 44.5 1.0 O3G T:ATP600 3.7 32.0 1.0 O3B T:ATP600 4.1 23.0 1.0 CD T:GLU172 4.4 58.4 1.0 PB T:ATP600 4.4 9.6 1.0 CB T:THR64 4.4 36.3 1.0 OD1 T:ASP171 4.4 46.7 1.0 OD2 T:ASP171 4.5 53.0 1.0 ND2 U:ASN197 4.5 46.4 1.0 CG T:GLU172 4.5 52.3 1.0 O2G T:ATP600 4.5 36.1 1.0 CG T:ASP171 4.6 43.5 1.0 NH1 U:ARG224 4.7 47.5 1.0 NE2 U:GLN220 4.7 57.2 1.0 O3A T:ATP600 4.9 2.4 1.0 CG2 T:THR64 4.9 41.4 1.0

Magnesium binding site 9 out of 11 in the Tnsabcd-Dna Transpososome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Tnsabcd-Dna Transpososome within 5.0Å range: probe atom residue distance (Å) B Occ U:Mg601 b:28.2 occ:1.00 OG1 U:THR64 1.9 36.4 1.0 O3G U:ATP600 2.4 48.7 1.0 O3B U:ATP600 2.9 36.5 1.0 PG U:ATP600 3.2 44.8 1.0 CB U:THR64 3.3 43.3 1.0 O3A U:ATP600 3.8 40.5 1.0 O1G U:ATP600 3.9 52.2 1.0 CG2 U:THR64 4.0 45.7 1.0 PB U:ATP600 4.1 51.4 1.0 NH2 V:ARG224 4.2 41.8 1.0 CA U:THR64 4.3 44.9 1.0 N U:THR64 4.3 45.9 1.0 O2G U:ATP600 4.5 46.7 1.0 OD2 U:ASP171 4.5 60.8 1.0 OE2 U:GLU172 4.8 59.4 1.0 O2A U:ATP600 4.8 56.4 1.0 NH1 V:ARG224 4.8 38.6 1.0 O1B U:ATP600 4.8 49.0 1.0 CG U:ASP171 5.0 58.4 1.0 CZ V:ARG224 5.0 42.2 1.0

Magnesium binding site 10 out of 11 in the Tnsabcd-Dna Transpososome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Tnsabcd-Dna Transpososome within 5.0Å range: probe atom residue distance (Å) B Occ V:Mg601 b:5.7 occ:1.00 O1G V:ATP600 1.9 52.3 1.0 O1B V:ATP600 2.1 60.3 1.0 OG1 V:THR64 2.3 37.4 1.0 PG V:ATP600 3.0 49.9 1.0 PB V:ATP600 3.2 66.0 1.0 O3B V:ATP600 3.2 44.8 1.0 O3G V:ATP600 3.7 62.4 1.0 CB V:THR64 3.8 37.5 1.0 O2A V:ATP600 3.8 50.1 1.0 OD1 V:ASP171 4.0 23.5 1.0 O3A V:ATP600 4.1 57.1 1.0 N V:THR64 4.3 39.8 1.0 O2G V:ATP600 4.3 58.1 1.0 O2B V:ATP600 4.4 52.6 1.0 PA V:ATP600 4.5 57.0 1.0 CG2 V:THR64 4.5 43.3 1.0 CA V:THR64 4.6 35.8 1.0 NH2 W:ARG224 4.7 55.2 1.0 CG V:GLU172 4.7 48.3 1.0 CG V:ASP171 4.8 35.9 1.0 OD2 V:ASP171 4.8 42.2 1.0 OE1 V:GLU172 4.9 55.7 1.0 CE V:LYS63 4.9 34.2 1.0 CD V:GLU172 4.9 54.3 1.0

S.Wang, R.Siddique, M.C.Hall, P.A.Rice, L.Chang. Structure of Tnsabcd Transpososome Reveals Mechanisms of Targeted Dna Transposition. Cell 2024.
ISSN: ISSN 1097-4172
PubMed: 39383864
DOI: 10.1016/J.CELL.2024.09.023