Magnesium in PDB 9kak: Cryoem Structure of Ltag Bound to SV40 at Half Origin Dna

All present enzymatic activity of Cryoem Structure of Ltag Bound to SV40 at Half Origin Dna:
5.6.2.4;

The binding sites of Magnesium atom in the Cryoem Structure of Ltag Bound to SV40 at Half Origin Dna (pdb code 9kak). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Cryoem Structure of Ltag Bound to SV40 at Half Origin Dna, PDB code: 9kak:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Cryoem Structure of Ltag Bound to SV40 at Half Origin Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryoem Structure of Ltag Bound to SV40 at Half Origin Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:55.6 occ:1.00 O3G A:ANP800 1.8 73.6 1.0 OG1 A:THR433 2.0 57.3 1.0 OD2 A:ASP474 2.1 68.6 1.0 OD1 A:ASP474 2.1 71.6 1.0 CG A:ASP474 2.4 69.9 1.0 HG1 A:THR433 2.5 55.7 1.0 O2B A:ANP800 2.5 61.9 1.0 PG A:ANP800 3.1 71.2 1.0 HH21 B:ARG540 3.2 56.8 1.0 CB A:THR433 3.3 57.3 1.0 HB A:THR433 3.4 55.1 1.0 H A:THR433 3.5 52.3 1.0 O2G A:ANP800 3.6 68.2 1.0 HE2 A:LYS432 3.6 51.0 1.0 OE2 A:GLU473 3.7 57.9 1.0 PB A:ANP800 3.7 61.1 1.0 HH22 B:ARG540 3.8 56.5 1.0 NH2 B:ARG540 3.8 56.9 1.0 N3B A:ANP800 3.9 60.3 1.0 HB2 A:LYS432 3.9 50.2 1.0 CB A:ASP474 3.9 58.6 1.0 HG21 A:THR433 4.1 59.8 1.0 N A:THR433 4.1 52.8 1.0 HZ1 B:LYS418 4.1 57.5 1.0 OD2 B:ASP502 4.1 64.6 1.0 HNB1 A:ANP800 4.2 61.3 1.0 O1G A:ANP800 4.2 61.5 1.0 CA A:THR433 4.2 49.8 1.0 CG2 A:THR433 4.3 61.4 1.0 HB3 A:ASP474 4.3 58.4 1.0 HB2 A:ASP474 4.3 59.1 1.0 HZ2 B:LYS418 4.4 58.4 1.0 HA A:THR433 4.4 49.8 1.0 HZ3 A:LYS432 4.4 57.1 1.0 O1A A:ANP800 4.5 62.1 1.0 CE A:LYS432 4.5 51.4 1.0 O3A A:ANP800 4.6 57.8 1.0 HA A:ASP474 4.6 59.9 1.0 CD A:GLU473 4.6 54.6 1.0 HG23 A:THR433 4.7 58.6 1.0 NZ B:LYS418 4.7 59.7 1.0 OG1 A:THR527 4.7 59.7 1.0 HB A:THR527 4.7 53.5 1.0 H A:ASP474 4.8 58.2 1.0 HG1 A:THR527 4.8 56.9 1.0 CA A:ASP474 4.8 57.8 1.0 O1B A:ANP800 4.8 63.2 1.0 HE3 A:LYS432 4.8 51.2 1.0 HG3 A:GLU473 4.8 54.4 1.0 NZ A:LYS432 4.9 57.5 1.0 CB A:LYS432 4.9 50.3 1.0 HZ2 A:LYS432 4.9 55.4 1.0 PA A:ANP800 5.0 64.5 1.0

Magnesium binding site 2 out of 6 in the Cryoem Structure of Ltag Bound to SV40 at Half Origin Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryoem Structure of Ltag Bound to SV40 at Half Origin Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:61.1 occ:1.00 O3G B:ANP802 1.9 70.4 1.0 OG1 B:THR433 2.0 60.1 1.0 OD2 B:ASP474 2.0 77.7 1.0 OD1 B:ASP474 2.1 74.0 1.0 CG B:ASP474 2.4 76.5 1.0 HG1 B:THR433 2.4 58.0 1.0 O2B B:ANP802 2.9 64.5 1.0 HH22 C:ARG540 3.3 60.2 1.0 CB B:THR433 3.3 57.9 1.0 PG B:ANP802 3.3 69.0 1.0 HB B:THR433 3.5 56.1 1.0 HH21 C:ARG540 3.5 60.8 1.0 OE2 B:GLU473 3.5 69.0 1.0 H B:THR433 3.7 53.2 1.0 NH2 C:ARG540 3.7 62.1 1.0 CB B:ASP474 3.9 62.6 1.0 HG21 B:THR433 3.9 57.6 1.0 HE2 B:LYS432 3.9 51.8 1.0 O2G B:ANP802 4.0 64.4 1.0 OD2 C:ASP502 4.1 67.3 1.0 PB B:ANP802 4.1 64.9 1.0 HG3 B:GLU473 4.1 59.7 1.0 HG1 B:THR527 4.1 59.9 1.0 N3B B:ANP802 4.1 60.5 1.0 CG2 B:THR433 4.2 58.1 1.0 HB2 B:LYS432 4.2 52.1 1.0 O1G B:ANP802 4.2 62.1 1.0 HB3 B:ASP474 4.2 63.8 1.0 N B:THR433 4.2 53.5 1.0 HB2 B:ASP474 4.3 62.5 1.0 CA B:THR433 4.3 52.1 1.0 O2A B:ANP802 4.4 61.3 1.0 CD B:GLU473 4.4 66.1 1.0 HG23 B:THR433 4.5 56.0 1.0 HA B:THR433 4.5 51.7 1.0 HA B:ASP474 4.6 64.8 1.0 HZ3 C:LYS418 4.6 63.4 1.0 HZ1 C:LYS418 4.6 64.2 1.0 OG1 B:THR527 4.7 59.3 1.0 HZ3 B:LYS432 4.7 56.3 1.0 H B:ASP474 4.7 62.7 1.0 CG B:GLU473 4.7 58.8 1.0 CA B:ASP474 4.7 61.6 1.0 HNB1 B:ANP802 4.8 60.0 1.0 CE B:LYS432 4.8 51.9 1.0 N B:ASP474 4.9 61.2 1.0 HB B:THR527 4.9 55.0 1.0 O3A B:ANP802 5.0 60.2 1.0 HG22 B:THR433 5.0 56.6 1.0

Magnesium binding site 3 out of 6 in the Cryoem Structure of Ltag Bound to SV40 at Half Origin Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryoem Structure of Ltag Bound to SV40 at Half Origin Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg801 b:58.9 occ:1.00 O2G C:ANP802 1.8 72.2 1.0 O2B C:ANP802 2.1 74.3 1.0 OG1 C:THR433 2.1 69.0 1.0 HG1 C:THR433 2.7 65.4 1.0 HB C:THR433 2.9 62.5 1.0 CB C:THR433 3.1 64.4 1.0 PG C:ANP802 3.1 78.5 1.0 PB C:ANP802 3.3 73.5 1.0 H C:THR433 3.3 58.4 1.0 N3B C:ANP802 3.4 71.8 1.0 HG21 C:THR433 3.8 64.2 1.0 O1G C:ANP802 3.9 74.8 1.0 O2A C:ANP802 3.9 66.8 1.0 N C:THR433 4.0 57.3 1.0 CG2 C:THR433 4.1 64.2 1.0 OD1 D:ASP499 4.1 77.8 1.0 CA C:THR433 4.1 57.5 1.0 O3A C:ANP802 4.1 68.3 1.0 HB2 C:LYS432 4.2 58.8 1.0 O3G C:ANP802 4.2 71.0 1.0 OE1 C:GLU473 4.2 69.2 1.0 HNB1 C:ANP802 4.3 69.7 1.0 HB2 C:ASP474 4.3 66.5 1.0 OD2 D:ASP499 4.4 82.0 1.0 O1B C:ANP802 4.4 68.6 1.0 HA C:THR433 4.5 58.2 1.0 PA C:ANP802 4.5 73.4 1.0 HE2 C:LYS432 4.5 59.7 1.0 HG23 C:THR433 4.6 61.8 1.0 CG D:ASP499 4.6 73.0 1.0 HG22 C:THR433 4.7 62.6 1.0 HZ2 C:LYS432 4.8 65.6 1.0

Magnesium binding site 4 out of 6 in the Cryoem Structure of Ltag Bound to SV40 at Half Origin Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryoem Structure of Ltag Bound to SV40 at Half Origin Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg801 b:69.1 occ:1.00 O2G D:ANP802 1.6 70.8 1.0 O2B D:ANP802 2.0 78.2 1.0 OG1 D:THR433 2.1 62.0 1.0 O1G D:ANP802 2.5 80.3 1.0 PG D:ANP802 2.5 81.8 1.0 HG1 D:THR433 2.6 59.2 1.0 HB D:THR433 3.1 57.1 1.0 CB D:THR433 3.1 57.9 1.0 PB D:ANP802 3.2 70.9 1.0 N3B D:ANP802 3.2 70.0 1.0 H D:THR433 3.3 55.0 1.0 HH12 E:ARG498 3.7 100.7 1.0 O3G D:ANP802 3.8 58.6 1.0 N D:THR433 3.9 54.4 1.0 OE2 D:GLU473 3.9 74.5 1.0 HNB1 D:ANP802 3.9 68.6 1.0 HG21 D:THR433 3.9 54.7 1.0 HB2 D:LYS432 3.9 55.3 1.0 NH1 E:ARG498 4.0 101.0 1.0 O3A D:ANP802 4.0 62.0 1.0 HZ3 D:LYS432 4.0 62.5 1.0 CA D:THR433 4.1 54.9 1.0 HB2 D:ASP474 4.1 62.3 1.0 CG2 D:THR433 4.1 54.5 1.0 HE2 D:LYS432 4.2 56.7 1.0 HH11 E:ARG498 4.3 96.4 1.0 O1B D:ANP802 4.3 66.2 1.0 HH22 E:ARG498 4.3 104.7 1.0 O2A D:ANP802 4.4 62.2 1.0 HA D:THR433 4.5 54.4 1.0 HZ2 D:LYS432 4.5 60.4 1.0 OD2 E:ASP499 4.6 61.5 1.0 CZ E:ARG498 4.6 101.5 1.0 NZ D:LYS432 4.6 63.6 1.0 HG22 D:THR433 4.6 53.1 1.0 PA D:ANP802 4.7 69.1 1.0 OD1 E:ASP499 4.7 71.3 1.0 NH2 E:ARG498 4.8 109.4 1.0 HG23 D:THR433 4.9 55.5 1.0 CB D:LYS432 4.9 55.1 1.0 CE D:LYS432 4.9 56.5 1.0 O1A D:ANP802 5.0 65.6 1.0

Magnesium binding site 5 out of 6 in the Cryoem Structure of Ltag Bound to SV40 at Half Origin Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryoem Structure of Ltag Bound to SV40 at Half Origin Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg801 b:104.3 occ:1.00 O2B E:ANP800 1.7 110.5 1.0 O1G E:ANP800 1.9 113.1 1.0 OG1 E:THR433 2.1 82.9 1.0 PB E:ANP800 2.7 111.7 1.0 HB E:THR433 2.7 74.4 1.0 HG1 E:THR433 2.8 78.5 1.0 O3A E:ANP800 2.8 94.2 1.0 CB E:THR433 2.9 76.2 1.0 PG E:ANP800 3.0 126.8 1.0 H E:THR433 3.0 71.1 1.0 N3B E:ANP800 3.2 109.5 1.0 O3G E:ANP800 3.6 112.1 1.0 PA E:ANP800 3.7 99.9 1.0 N E:THR433 3.7 66.8 1.0 O1A E:ANP800 3.8 91.5 1.0 HG21 E:THR433 3.9 73.3 1.0 CA E:THR433 3.9 67.2 1.0 HNB1 E:ANP800 4.0 102.5 1.0 O2A E:ANP800 4.0 98.3 1.0 O1B E:ANP800 4.0 103.0 1.0 CG2 E:THR433 4.0 72.8 1.0 O2G E:ANP800 4.2 109.8 1.0 HB2 E:LYS432 4.2 72.2 1.0 HE3 E:LYS432 4.2 79.2 1.0 HA E:THR433 4.4 68.4 1.0 HG23 E:THR433 4.6 70.7 1.0 HG22 E:THR433 4.7 70.5 1.0 H E:LYS432 4.8 81.1 1.0 C E:LYS432 4.9 69.1 1.0 HB2 E:ASP474 5.0 78.8 1.0

Magnesium binding site 6 out of 6 in the Cryoem Structure of Ltag Bound to SV40 at Half Origin Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryoem Structure of Ltag Bound to SV40 at Half Origin Dna within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg801 b:63.8 occ:1.00 O1G F:ANP800 1.8 80.9 1.0 OG1 F:THR433 2.0 84.9 1.0 OE2 F:GLU473 2.2 103.7 1.0 HG1 F:THR433 2.3 78.3 1.0 O2B F:ANP800 2.3 96.7 1.0 PG F:ANP800 3.1 110.2 1.0 CD F:GLU473 3.3 94.2 1.0 CB F:THR433 3.3 70.1 1.0 HH22 A:ARG540 3.3 64.0 1.0 HB F:THR433 3.5 70.2 1.0 O3G F:ANP800 3.6 104.5 1.0 PB F:ANP800 3.7 100.1 1.0 OE1 F:GLU473 3.8 94.2 1.0 HG21 F:THR433 3.8 65.4 1.0 HH21 A:ARG540 3.8 62.6 1.0 NH2 A:ARG540 3.9 67.2 1.0 N3B F:ANP800 3.9 96.2 1.0 HNB1 F:ANP800 3.9 90.4 1.0 HG3 F:LYS432 4.0 71.2 1.0 CG2 F:THR433 4.1 65.2 1.0 H F:THR433 4.1 67.1 1.0 OD2 A:ASP502 4.2 63.4 1.0 O2G F:ANP800 4.2 99.2 1.0 HB2 F:ASP474 4.3 84.3 1.0 HE2 F:LYS432 4.3 82.8 1.0 CA F:THR433 4.4 62.5 1.0 HG22 F:THR433 4.4 64.6 1.0 O3A F:ANP800 4.4 88.8 1.0 N F:THR433 4.4 64.7 1.0 O2A F:ANP800 4.4 85.0 1.0 CG F:GLU473 4.5 86.2 1.0 HG3 F:GLU473 4.5 86.0 1.0 HA F:THR433 4.6 65.4 1.0 HG2 F:GLU473 4.7 86.6 1.0 HB F:THR527 4.7 73.0 1.0 HG2 F:LYS432 4.8 74.2 1.0 O1B F:ANP800 4.8 92.2 1.0 HZ2 F:LYS432 4.8 87.2 1.0 OG1 F:THR527 4.8 79.3 1.0 CG F:LYS432 4.8 71.0 1.0 HZ3 F:LYS432 4.8 84.8 1.0 PA F:ANP800 4.8 94.4 1.0 H F:ASP474 4.9 81.7 1.0 HG23 F:THR433 4.9 65.6 1.0

A.U.Danazumi, T.Shahid, M.Tehseen, L.Alhudhali, A.Clark, C.G.Savva, S.M.Hamdan, A.De Biasio. Structural Visualisation of Fork Establishment and Traslocation Dynamics By A Replicative Helicase To Be Published.