Magnesium in PDB 9evp: SV40 Ltag Assembly with Dna in Presence of Amppnp and MG2+.

The binding sites of Magnesium atom in the SV40 Ltag Assembly with Dna in Presence of Amppnp and MG2+. (pdb code 9evp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the SV40 Ltag Assembly with Dna in Presence of Amppnp and MG2+., PDB code: 9evp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the SV40 Ltag Assembly with Dna in Presence of Amppnp and MG2+.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of SV40 Ltag Assembly with Dna in Presence of Amppnp and MG2+. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:53.4 occ:1.00 O1G A:ANP800 1.6 67.4 1.0 OG1 A:THR433 2.0 54.8 1.0 O1B A:ANP800 2.1 63.0 1.0 HG1 A:THR433 2.6 53.6 1.0 HB A:THR433 3.0 51.8 1.0 PG A:ANP800 3.0 71.2 1.0 CB A:THR433 3.1 53.4 1.0 HH22 B:ARG540 3.2 52.4 1.0 H A:THR433 3.3 49.9 1.0 PB A:ANP800 3.4 63.7 1.0 N3B A:ANP800 3.6 62.6 1.0 HH21 B:ARG540 3.7 51.0 1.0 NH2 B:ARG540 3.8 51.6 1.0 O1A A:ANP800 3.9 66.2 1.0 O3G A:ANP800 3.9 69.7 1.0 HB2 A:LYS432 3.9 50.7 1.0 N A:THR433 3.9 50.1 1.0 HE2 A:LYS432 3.9 54.3 1.0 HG23 A:THR433 3.9 56.6 1.0 O2G A:ANP800 3.9 60.4 1.0 HB2 A:ASP474 4.0 59.2 1.0 HZ1 B:LYS418 4.0 59.1 1.0 CA A:THR433 4.1 49.6 1.0 CG2 A:THR433 4.1 58.2 1.0 OE1 A:GLU473 4.1 72.4 1.0 OD2 B:ASP502 4.2 58.1 1.0 HZ3 B:LYS418 4.2 58.0 1.0 O3A A:ANP800 4.3 64.8 1.0 HNB1 A:ANP800 4.3 62.2 1.0 HA A:THR433 4.4 49.2 1.0 PA A:ANP800 4.5 66.8 1.0 O2B A:ANP800 4.5 61.8 1.0 HG22 A:THR433 4.5 55.7 1.0 NZ B:LYS418 4.6 60.4 1.0 HZ1 A:LYS432 4.6 59.6 1.0 CE A:LYS432 4.8 54.5 1.0 CB A:LYS432 4.8 50.5 1.0 O2A A:ANP800 4.8 55.3 1.0 HG21 A:THR433 4.9 55.3 1.0 CB A:ASP474 4.9 57.0 1.0 HZ3 A:LYS432 4.9 57.0 1.0 HE3 B:LYS418 4.9 49.0 1.0 OD2 A:ASP474 5.0 82.4 1.0 CG A:ASP474 5.0 70.6 1.0 NZ A:LYS432 5.0 60.4 1.0

Magnesium binding site 2 out of 6 in the SV40 Ltag Assembly with Dna in Presence of Amppnp and MG2+.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of SV40 Ltag Assembly with Dna in Presence of Amppnp and MG2+. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:50.6 occ:1.00 O2G B:ANP802 1.7 73.5 1.0 OG1 B:THR433 2.0 52.8 1.0 O1B B:ANP802 2.1 59.6 1.0 HG1 B:THR433 2.4 52.0 1.0 PG B:ANP802 3.0 66.9 1.0 CB B:THR433 3.1 50.6 1.0 HB B:THR433 3.2 49.4 1.0 H B:THR433 3.2 48.4 1.0 PB B:ANP802 3.3 59.0 1.0 HH22 C:ARG540 3.4 56.5 1.0 O1G B:ANP802 3.4 60.6 1.0 HE2 B:LYS432 3.4 48.8 1.0 N3B B:ANP802 3.4 54.5 1.0 HNB1 B:ANP802 3.6 57.4 1.0 OE2 B:GLU473 3.7 61.8 1.0 HB2 B:LYS432 3.7 47.4 1.0 HH21 C:ARG540 3.7 56.2 1.0 N B:THR433 3.8 48.9 1.0 O1A B:ANP802 3.8 54.2 1.0 NH2 C:ARG540 3.9 57.7 1.0 HG21 B:THR433 4.0 53.7 1.0 CA B:THR433 4.0 46.7 1.0 HZ3 C:LYS418 4.1 62.1 1.0 O3G B:ANP802 4.1 58.0 1.0 HZ1 C:LYS418 4.1 62.0 1.0 CG2 B:THR433 4.2 54.0 1.0 HZ2 B:LYS432 4.2 54.2 1.0 O3A B:ANP802 4.3 59.0 1.0 HB2 B:ASP474 4.3 53.7 1.0 CE B:LYS432 4.3 49.2 1.0 HA B:THR433 4.3 47.2 1.0 OD2 C:ASP502 4.4 65.3 1.0 O2B B:ANP802 4.4 62.6 1.0 HG1 B:THR527 4.4 51.6 1.0 CG B:ASP474 4.5 60.8 1.0 PA B:ANP802 4.5 60.7 1.0 OD1 B:ASP474 4.5 61.5 1.0 HG22 B:THR433 4.5 52.2 1.0 OD2 B:ASP474 4.6 77.4 1.0 NZ C:LYS418 4.6 64.8 1.0 NZ B:LYS432 4.6 55.8 1.0 CB B:LYS432 4.7 47.4 1.0 HZ1 B:LYS432 4.7 53.0 1.0 HE3 B:LYS432 4.7 49.1 1.0 O2A B:ANP802 4.8 55.4 1.0 HB B:THR527 4.8 45.9 1.0 CD B:GLU473 4.8 54.6 1.0 CB B:ASP474 4.9 52.3 1.0 C B:LYS432 4.9 47.0 1.0 HG23 B:THR433 5.0 52.1 1.0 OG1 B:THR527 5.0 54.1 1.0

Magnesium binding site 3 out of 6 in the SV40 Ltag Assembly with Dna in Presence of Amppnp and MG2+.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of SV40 Ltag Assembly with Dna in Presence of Amppnp and MG2+. within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg801 b:69.5 occ:1.00 O2G C:ANP800 1.8 79.8 1.0 O1B C:ANP800 1.9 74.0 1.0 OG1 C:THR433 2.1 60.9 1.0 O1G C:ANP800 2.2 82.8 1.0 PG C:ANP800 2.4 80.4 1.0 HG1 C:THR433 2.7 59.3 1.0 HB C:THR433 3.0 57.1 1.0 PB C:ANP800 3.0 73.7 1.0 CB C:THR433 3.1 58.5 1.0 H C:THR433 3.1 55.2 1.0 N3B C:ANP800 3.1 71.0 1.0 HNB1 C:ANP800 3.4 71.7 1.0 HH12 D:ARG540 3.7 83.9 1.0 HB2 C:LYS432 3.7 55.6 1.0 N C:THR433 3.7 54.1 1.0 O3G C:ANP800 3.7 69.0 1.0 O3A C:ANP800 3.9 70.5 1.0 HE2 C:LYS432 3.9 60.3 1.0 HZ2 C:LYS432 3.9 63.6 1.0 CA C:THR433 4.0 54.0 1.0 O2A C:ANP800 4.0 64.1 1.0 HG23 C:THR433 4.1 59.3 1.0 HH22 D:ARG540 4.2 83.6 1.0 CG2 C:THR433 4.2 60.5 1.0 O2B C:ANP800 4.2 70.0 1.0 HZ3 C:LYS432 4.2 62.7 1.0 OE1 C:GLU473 4.3 76.9 1.0 HA C:THR433 4.3 54.2 1.0 NZ C:LYS432 4.4 65.8 1.0 PA C:ANP800 4.4 71.4 1.0 NH1 D:ARG540 4.5 84.3 1.0 HB2 C:ASP474 4.6 63.7 1.0 CE C:LYS432 4.6 62.2 1.0 CB C:LYS432 4.7 54.5 1.0 HG22 C:THR433 4.7 58.4 1.0 O1A C:ANP800 4.8 61.8 1.0 C C:LYS432 4.8 53.3 1.0 HG21 C:THR433 4.9 58.8 1.0 NH2 D:ARG540 4.9 86.0 1.0 H C:LYS432 4.9 57.1 1.0

Magnesium binding site 4 out of 6 in the SV40 Ltag Assembly with Dna in Presence of Amppnp and MG2+.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of SV40 Ltag Assembly with Dna in Presence of Amppnp and MG2+. within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg801 b:98.4 occ:1.00 O1B D:ANP800 1.8 91.0 1.0 O2G D:ANP800 1.8 93.1 1.0 OG1 D:THR433 2.1 76.4 1.0 O1G D:ANP800 2.1 106.6 1.0 PG D:ANP800 2.4 96.8 1.0 HG1 D:THR433 2.6 72.5 1.0 PB D:ANP800 2.9 92.1 1.0 N3B D:ANP800 3.1 89.8 1.0 HB D:THR433 3.1 67.4 1.0 H D:THR433 3.1 72.1 1.0 CB D:THR433 3.2 67.8 1.0 HNB1 D:ANP800 3.4 90.7 1.0 HB2 D:LYS432 3.7 79.6 1.0 O3G D:ANP800 3.7 93.5 1.0 N D:THR433 3.8 69.9 1.0 HZ2 D:LYS432 3.8 94.5 1.0 HE2 D:LYS432 4.0 87.5 1.0 O2B D:ANP800 4.0 96.1 1.0 O3A D:ANP800 4.0 87.5 1.0 OE2 D:GLU473 4.0 89.3 1.0 CA D:THR433 4.0 66.5 1.0 HZ1 D:LYS432 4.1 92.7 1.0 HG21 D:THR433 4.2 66.7 1.0 CG2 D:THR433 4.3 65.6 1.0 NZ D:LYS432 4.3 96.9 1.0 HA D:THR433 4.4 67.4 1.0 O2A D:ANP800 4.5 84.5 1.0 HB2 D:ASP474 4.5 84.5 1.0 CB D:LYS432 4.6 78.2 1.0 HG1 D:THR527 4.6 78.8 1.0 CE D:LYS432 4.7 89.2 1.0 HG23 D:THR433 4.7 65.5 1.0 PA D:ANP800 4.7 88.3 1.0 C D:LYS432 4.8 69.0 1.0 HB3 D:LYS432 4.9 78.2 1.0 O1A D:ANP800 5.0 78.2 1.0 HB D:THR527 5.0 76.3 1.0

Magnesium binding site 5 out of 6 in the SV40 Ltag Assembly with Dna in Presence of Amppnp and MG2+.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of SV40 Ltag Assembly with Dna in Presence of Amppnp and MG2+. within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg801 b:62.9 occ:1.00 O2G E:ANP800 1.7 73.5 1.0 O1B E:ANP800 2.0 70.2 1.0 OG1 E:THR433 2.0 61.2 1.0 HG1 E:THR433 2.7 58.0 1.0 HB E:THR433 2.8 55.2 1.0 CB E:THR433 2.9 56.3 1.0 PG E:ANP800 3.0 80.9 1.0 PB E:ANP800 3.0 71.7 1.0 HNB1 E:ANP800 3.2 72.1 1.0 N3B E:ANP800 3.3 73.8 1.0 H E:THR433 3.3 53.6 1.0 O1G E:ANP800 3.7 80.6 1.0 HG21 E:THR433 3.7 57.9 1.0 O1A E:ANP800 3.8 69.5 1.0 O3A E:ANP800 3.8 68.5 1.0 N E:THR433 3.9 53.2 1.0 CG2 E:THR433 4.0 58.4 1.0 CA E:THR433 4.0 51.8 1.0 O3G E:ANP800 4.1 68.9 1.0 PA E:ANP800 4.2 70.6 1.0 O2B E:ANP800 4.3 64.5 1.0 HB2 E:LYS432 4.4 53.7 1.0 HA E:THR433 4.4 52.9 1.0 OD2 F:ASP499 4.5 85.8 1.0 HG23 E:THR433 4.5 56.8 1.0 OD1 F:ASP499 4.5 73.6 1.0 O2A E:ANP800 4.6 59.1 1.0 HG22 E:THR433 4.6 56.8 1.0 HB2 E:ASP474 4.7 71.8 1.0 HZ2 E:LYS432 4.9 63.8 1.0 HE2 E:LYS432 4.9 57.5 1.0 CG F:ASP499 5.0 73.8 1.0 HH11 F:ARG498 5.0 99.1 1.0

Magnesium binding site 6 out of 6 in the SV40 Ltag Assembly with Dna in Presence of Amppnp and MG2+.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of SV40 Ltag Assembly with Dna in Presence of Amppnp and MG2+. within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg801 b:140.2 occ:1.00 O1B F:ANP800 1.9 123.9 1.0 O1A F:ANP800 2.1 130.2 1.0 O2G F:ANP800 2.1 142.3 1.0 OG1 F:THR433 2.1 98.2 1.0 HB F:THR433 2.5 87.2 1.0 PB F:ANP800 2.6 134.9 1.0 HNB1 F:ANP800 2.7 130.6 1.0 CB F:THR433 2.8 88.4 1.0 N3B F:ANP800 2.8 134.2 1.0 HG1 F:THR433 2.8 91.3 1.0 H F:THR433 2.9 87.6 1.0 PA F:ANP800 2.9 125.3 1.0 PG F:ANP800 3.0 145.3 1.0 O3A F:ANP800 3.1 127.1 1.0 O2A F:ANP800 3.4 110.4 1.0 N F:THR433 3.6 85.8 1.0 CA F:THR433 3.8 82.0 1.0 O1G F:ANP800 3.8 132.3 1.0 HG22 F:THR433 3.8 80.2 1.0 CG2 F:THR433 3.9 78.5 1.0 HG3 F:LYS432 4.0 94.4 1.0 O2B F:ANP800 4.0 122.1 1.0 O3G F:ANP800 4.2 122.3 1.0 HG2 F:LYS432 4.3 95.3 1.0 O5' F:ANP800 4.3 129.9 1.0 H F:THR434 4.4 88.3 1.0 HA F:THR433 4.4 82.5 1.0 HG21 F:THR433 4.5 80.0 1.0 HG23 F:THR433 4.5 79.1 1.0 CG F:LYS432 4.6 95.7 1.0 HZ2 F:LYS432 4.6 104.5 1.0 H F:LYS432 4.6 96.1 1.0 H5'2 F:ANP800 4.6 127.7 1.0 H5'1 F:ANP800 4.8 127.8 1.0 C F:THR433 4.8 78.6 1.0 C F:LYS432 4.8 83.0 1.0 HE2 F:LYS432 4.8 101.7 1.0 C5' F:ANP800 4.9 130.4 1.0 N F:THR434 4.9 86.3 1.0 HZ3 F:LYS432 4.9 107.7 1.0 N F:LYS432 5.0 92.5 1.0 HG1 F:THR434 5.0 98.2 1.0 H F:GLY431 5.0 114.7 1.0 H F:ASP429 5.0 116.0 1.0

T.Shahid, A.U.Danazumi, M.Tehseen, L.Alhudhali, A.R.Clark, C.G.Savva, S.M.Hamdan, A.De Biasio. Structural Dynamics of Dna Unwinding By A Replicative Helicase Nature 2025.
ISSN: ESSN 1476-4687