Magnesium in PDB 8fcv: Cryo-Em Structure of Tnsc-Tniq-Dna Complex in Type I-B Cast System

The binding sites of Magnesium atom in the Cryo-Em Structure of Tnsc-Tniq-Dna Complex in Type I-B Cast System (pdb code 8fcv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Cryo-Em Structure of Tnsc-Tniq-Dna Complex in Type I-B Cast System, PDB code: 8fcv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Cryo-Em Structure of Tnsc-Tniq-Dna Complex in Type I-B Cast System


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Tnsc-Tniq-Dna Complex in Type I-B Cast System within 5.0Å range: probe atom residue distance (Å) B Occ Q:Mg601 b:197.9 occ:1.00 O3B Q:ATP600 2.0 204.4 1.0 OG1 Q:THR64 2.1 197.8 1.0 O1G Q:ATP600 2.4 204.4 1.0 O3A Q:ATP600 2.5 204.4 1.0 PG Q:ATP600 2.6 204.4 1.0 O5' Q:ATP600 2.9 204.4 1.0 PB Q:ATP600 2.9 204.4 1.0 PA Q:ATP600 3.0 204.4 1.0 CB Q:THR64 3.1 197.8 1.0 O2A Q:ATP600 3.1 204.4 1.0 O2G Q:ATP600 3.2 204.4 1.0 O2B Q:ATP600 3.9 204.4 1.0 C5' Q:ATP600 3.9 204.4 1.0 O1B Q:ATP600 3.9 204.4 1.0 O3G Q:ATP600 3.9 204.4 1.0 CG2 Q:THR64 4.0 197.8 1.0 N Q:THR64 4.1 197.8 1.0 CA Q:THR64 4.2 197.8 1.0 O1A Q:ATP600 4.5 204.4 1.0

Magnesium binding site 2 out of 7 in the Cryo-Em Structure of Tnsc-Tniq-Dna Complex in Type I-B Cast System


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Tnsc-Tniq-Dna Complex in Type I-B Cast System within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg601 b:161.4 occ:1.00 O3A R:ATP600 2.0 167.1 1.0 O3B R:ATP600 2.0 167.1 1.0 OG1 R:THR64 2.3 162.2 1.0 O2A R:ATP600 2.4 167.1 1.0 PA R:ATP600 2.5 167.1 1.0 PB R:ATP600 2.6 167.1 1.0 O3G R:ATP600 2.6 167.1 1.0 PG R:ATP600 2.7 167.1 1.0 O5' R:ATP600 2.8 167.1 1.0 O1G R:ATP600 3.2 167.1 1.0 CB R:THR64 3.3 162.2 1.0 O1B R:ATP600 3.4 167.1 1.0 N R:THR64 3.6 162.2 1.0 O2B R:ATP600 3.8 167.1 1.0 O1A R:ATP600 3.9 167.1 1.0 C5' R:ATP600 4.0 167.1 1.0 O2G R:ATP600 4.1 167.1 1.0 CA R:THR64 4.1 162.2 1.0 N R:LYS63 4.4 156.1 1.0 CG2 R:THR64 4.5 162.2 1.0 C R:LYS63 4.7 156.1 1.0 CB R:LYS63 4.8 156.1 1.0 CA R:LYS63 4.9 156.1 1.0 NH2 S:ARG223 4.9 155.8 1.0 NH1 S:ARG223 5.0 155.8 1.0

Magnesium binding site 3 out of 7 in the Cryo-Em Structure of Tnsc-Tniq-Dna Complex in Type I-B Cast System


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Tnsc-Tniq-Dna Complex in Type I-B Cast System within 5.0Å range: probe atom residue distance (Å) B Occ S:Mg601 b:147.3 occ:1.00 O3B S:ATP600 2.0 156.6 1.0 O3A S:ATP600 2.1 156.6 1.0 O1G S:ATP600 2.1 156.6 1.0 OG1 S:THR64 2.4 144.3 1.0 PG S:ATP600 2.5 156.6 1.0 PB S:ATP600 2.6 156.6 1.0 PA S:ATP600 3.0 156.6 1.0 O2A S:ATP600 3.0 156.6 1.0 O5' S:ATP600 3.2 156.6 1.0 O1B S:ATP600 3.3 156.6 1.0 CB S:THR64 3.5 144.3 1.0 O3G S:ATP600 3.5 156.6 1.0 O2G S:ATP600 3.7 156.6 1.0 N S:THR64 3.8 144.3 1.0 O2B S:ATP600 3.8 156.6 1.0 CA S:THR64 4.3 144.3 1.0 O1A S:ATP600 4.3 156.6 1.0 C5' S:ATP600 4.4 156.6 1.0 NH2 T:ARG224 4.6 147.3 1.0 CG2 S:THR64 4.6 144.3 1.0 N S:LYS63 4.7 144.0 1.0 CB S:LYS63 4.7 144.0 1.0 NH1 T:ARG223 4.8 142.8 1.0 C S:LYS63 4.8 144.0 1.0 CE S:LYS63 5.0 144.0 1.0 CA S:LYS63 5.0 144.0 1.0

Magnesium binding site 4 out of 7 in the Cryo-Em Structure of Tnsc-Tniq-Dna Complex in Type I-B Cast System


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Tnsc-Tniq-Dna Complex in Type I-B Cast System within 5.0Å range: probe atom residue distance (Å) B Occ T:Mg601 b:148.1 occ:1.00 O3B T:ATP600 2.0 160.3 1.0 O3A T:ATP600 2.1 160.3 1.0 O1G T:ATP600 2.3 160.3 1.0 OG1 T:THR64 2.3 144.8 1.0 PB T:ATP600 2.6 160.3 1.0 PG T:ATP600 2.6 160.3 1.0 O2A T:ATP600 2.7 160.3 1.0 PA T:ATP600 2.8 160.3 1.0 O5' T:ATP600 3.1 160.3 1.0 CB T:THR64 3.2 144.8 1.0 O1B T:ATP600 3.4 160.3 1.0 N T:THR64 3.6 144.8 1.0 O2G T:ATP600 3.7 160.3 1.0 O3G T:ATP600 3.7 160.3 1.0 O2B T:ATP600 3.8 160.3 1.0 CA T:THR64 4.0 144.8 1.0 O1A T:ATP600 4.2 160.3 1.0 C5' T:ATP600 4.3 160.3 1.0 CG2 T:THR64 4.4 144.8 1.0 N T:LYS63 4.6 144.1 1.0 C T:LYS63 4.7 144.1 1.0 CB T:LYS63 4.8 144.1 1.0 NH2 U:ARG223 4.8 152.9 1.0 CA T:LYS63 4.9 144.1 1.0

Magnesium binding site 5 out of 7 in the Cryo-Em Structure of Tnsc-Tniq-Dna Complex in Type I-B Cast System


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of Tnsc-Tniq-Dna Complex in Type I-B Cast System within 5.0Å range: probe atom residue distance (Å) B Occ U:Mg601 b:138.8 occ:1.00 O3B U:ATP600 2.0 151.8 1.0 O3A U:ATP600 2.0 151.8 1.0 OG1 U:THR64 2.3 146.0 1.0 PB U:ATP600 2.5 151.8 1.0 O1G U:ATP600 2.6 151.8 1.0 PG U:ATP600 2.8 151.8 1.0 PA U:ATP600 3.1 151.8 1.0 O2A U:ATP600 3.2 151.8 1.0 CB U:THR64 3.3 146.0 1.0 O5' U:ATP600 3.3 151.8 1.0 O1B U:ATP600 3.4 151.8 1.0 O3G U:ATP600 3.7 151.8 1.0 O2B U:ATP600 3.7 151.8 1.0 N U:THR64 3.8 146.0 1.0 O2G U:ATP600 4.0 151.8 1.0 CA U:THR64 4.2 146.0 1.0 O1A U:ATP600 4.4 151.8 1.0 CG2 U:THR64 4.4 146.0 1.0 C5' U:ATP600 4.5 151.8 1.0 NH2 V:ARG223 4.6 143.7 1.0 N U:LYS63 4.8 142.2 1.0 C U:LYS63 4.9 142.2 1.0

Magnesium binding site 6 out of 7 in the Cryo-Em Structure of Tnsc-Tniq-Dna Complex in Type I-B Cast System


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of Tnsc-Tniq-Dna Complex in Type I-B Cast System within 5.0Å range: probe atom residue distance (Å) B Occ V:Mg601 b:152.4 occ:1.00 O3A V:ATP600 2.0 168.4 1.0 O1G V:ATP600 2.0 168.4 1.0 O3B V:ATP600 2.1 168.4 1.0 O2A V:ATP600 2.2 168.4 1.0 PA V:ATP600 2.4 168.4 1.0 PG V:ATP600 2.5 168.4 1.0 OG1 V:THR64 2.5 150.8 1.0 PB V:ATP600 2.6 168.4 1.0 O5' V:ATP600 2.9 168.4 1.0 O2G V:ATP600 3.4 168.4 1.0 CB V:THR64 3.4 150.8 1.0 O1B V:ATP600 3.4 168.4 1.0 N V:THR64 3.4 150.8 1.0 O3G V:ATP600 3.7 168.4 1.0 O2B V:ATP600 3.8 168.4 1.0 O1A V:ATP600 3.8 168.4 1.0 C5' V:ATP600 3.9 168.4 1.0 CA V:THR64 4.0 150.8 1.0 N V:LYS63 4.1 153.4 1.0 NH2 W:ARG224 4.3 181.5 1.0 C V:LYS63 4.5 153.4 1.0 CB V:LYS63 4.6 153.4 1.0 CA V:LYS63 4.6 153.4 1.0 CG2 V:THR64 4.7 150.8 1.0 C V:GLY62 4.8 152.0 1.0 N V:GLY62 4.9 152.0 1.0 CA V:GLY62 5.0 152.0 1.0

Magnesium binding site 7 out of 7 in the Cryo-Em Structure of Tnsc-Tniq-Dna Complex in Type I-B Cast System


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of Tnsc-Tniq-Dna Complex in Type I-B Cast System within 5.0Å range: probe atom residue distance (Å) B Occ W:Mg601 b:207.5 occ:1.00 O3A W:ATP600 2.0 203.4 1.0 O3B W:ATP600 2.1 203.4 1.0 O1G W:ATP600 2.2 203.4 1.0 OG1 W:THR64 2.2 192.0 1.0 PB W:ATP600 2.4 203.4 1.0 PG W:ATP600 2.5 203.4 1.0 O2A W:ATP600 2.7 203.4 1.0 PA W:ATP600 2.8 203.4 1.0 O1B W:ATP600 3.0 203.4 1.0 O3G W:ATP600 3.1 203.4 1.0 CB W:THR64 3.3 192.0 1.0 O5' W:ATP600 3.3 203.4 1.0 N W:THR64 3.5 192.0 1.0 O2B W:ATP600 3.8 203.4 1.0 O2G W:ATP600 3.9 203.4 1.0 CA W:THR64 4.0 192.0 1.0 O1A W:ATP600 4.2 203.4 1.0 C5' W:ATP600 4.3 203.4 1.0 N W:LYS63 4.4 190.2 1.0 CG2 W:THR64 4.5 192.0 1.0 C W:LYS63 4.5 190.2 1.0 CB W:LYS63 4.6 190.2 1.0 CA W:LYS63 4.7 190.2 1.0 C W:GLY62 4.9 194.9 1.0

S.Wang, C.Gabel, R.Siddique, T.Klose, L.Chang. Cryo-Em Structure of Cascade-Dna Complex with 23 Bp Recognized in Type I-B Cast System Cell(Cambridge,Mass.) 2023.
ISSN: ISSN 0092-8674
DOI: 10.1016/J.CELL.2023.07.010