Magnesium in PDB 8e2l: Structure of Lates Calcarifer Twinkle Helicase with Atp and Dna

The binding sites of Magnesium atom in the Structure of Lates Calcarifer Twinkle Helicase with Atp and Dna (pdb code 8e2l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structure of Lates Calcarifer Twinkle Helicase with Atp and Dna, PDB code: 8e2l:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Structure of Lates Calcarifer Twinkle Helicase with Atp and Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Lates Calcarifer Twinkle Helicase with Atp and Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:125.6 occ:1.00 O1B C:ATP601 2.0 133.7 1.0 OE1 C:GLN325 2.1 139.4 1.0 O3G C:ATP601 2.1 133.7 1.0 OG1 C:THR302 2.7 124.6 1.0 PB C:ATP601 3.1 133.7 1.0 CD C:GLN325 3.3 139.4 1.0 PG C:ATP601 3.4 133.7 1.0 O3B C:ATP601 3.6 133.7 1.0 O2B C:ATP601 3.7 133.7 1.0 NE2 C:GLN325 3.9 139.4 1.0 CB C:THR302 4.0 124.6 1.0 OD2 C:ASP396 4.0 120.4 1.0 O1G C:ATP601 4.2 133.7 1.0 OD1 C:ASN397 4.2 129.9 1.0 CG C:GLN325 4.4 139.4 1.0 O3A C:ATP601 4.5 133.7 1.0 O2G C:ATP601 4.5 133.7 1.0 ND2 C:ASN397 4.5 129.9 1.0 O2A C:ATP601 4.6 133.7 1.0 CB C:GLN325 4.7 139.4 1.0 CG2 C:THR302 4.8 124.6 1.0 N C:THR302 4.8 124.6 1.0 CG C:ASN397 4.8 129.9 1.0 NH2 B:ARG489 4.9 131.7 1.0 CA C:THR302 4.9 124.6 1.0

Magnesium binding site 2 out of 5 in the Structure of Lates Calcarifer Twinkle Helicase with Atp and Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Lates Calcarifer Twinkle Helicase with Atp and Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:156.3 occ:1.00 OE1 B:GLN325 2.0 168.6 1.0 O1B B:ATP601 2.1 169.0 1.0 O3G B:ATP601 2.4 169.0 1.0 OG1 B:THR302 2.6 148.4 1.0 PB B:ATP601 3.1 169.0 1.0 CD B:GLN325 3.2 168.6 1.0 O2B B:ATP601 3.5 169.0 1.0 PG B:ATP601 3.6 169.0 1.0 O3B B:ATP601 3.7 169.0 1.0 NE2 B:GLN325 3.9 168.6 1.0 CB B:THR302 3.9 148.4 1.0 ND2 B:ASN397 4.1 144.5 1.0 O1G B:ATP601 4.2 169.0 1.0 CG B:GLN325 4.4 168.6 1.0 O3A B:ATP601 4.5 169.0 1.0 O2A B:ATP601 4.6 169.0 1.0 N B:THR302 4.6 148.4 1.0 CB B:GLN325 4.7 168.6 1.0 OD1 B:ASN397 4.7 144.5 1.0 CG2 B:THR302 4.8 148.4 1.0 CG B:ASN397 4.8 144.5 1.0 O2G B:ATP601 4.9 169.0 1.0 CA B:THR302 4.9 148.4 1.0 NH2 A:ARG489 4.9 216.4 1.0

Magnesium binding site 3 out of 5 in the Structure of Lates Calcarifer Twinkle Helicase with Atp and Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Lates Calcarifer Twinkle Helicase with Atp and Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:137.3 occ:1.00 O1B D:ATP601 2.0 129.5 1.0 O3G D:ATP601 2.0 129.5 1.0 OE1 D:GLN325 2.1 140.8 1.0 OG1 D:THR302 2.8 121.0 1.0 PB D:ATP601 3.0 129.5 1.0 CD D:GLN325 3.2 140.8 1.0 PG D:ATP601 3.3 129.5 1.0 O3B D:ATP601 3.5 129.5 1.0 O2B D:ATP601 3.6 129.5 1.0 NE2 D:GLN325 3.9 140.8 1.0 O1G D:ATP601 4.0 129.5 1.0 ND2 D:ASN397 4.0 138.4 1.0 OD1 D:ASP396 4.1 130.1 1.0 CB D:THR302 4.2 121.0 1.0 CG D:GLN325 4.4 140.8 1.0 O3A D:ATP601 4.5 129.5 1.0 O2G D:ATP601 4.5 129.5 1.0 O2A D:ATP601 4.6 129.5 1.0 NH2 C:ARG489 4.7 125.6 1.0 CB D:GLN325 4.8 140.8 1.0 N D:THR302 4.8 121.0 1.0 OD2 D:ASP396 4.9 130.1 1.0 CG D:ASP396 4.9 130.1 1.0 CG D:ASN397 4.9 138.4 1.0

Magnesium binding site 4 out of 5 in the Structure of Lates Calcarifer Twinkle Helicase with Atp and Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Lates Calcarifer Twinkle Helicase with Atp and Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg602 b:132.4 occ:1.00 O1B E:ATP601 2.1 131.6 1.0 O3G E:ATP601 2.1 131.6 1.0 OE1 E:GLN325 2.2 143.7 1.0 OG1 E:THR302 2.8 123.0 1.0 PB E:ATP601 3.1 131.6 1.0 CD E:GLN325 3.3 143.7 1.0 PG E:ATP601 3.3 131.6 1.0 O3B E:ATP601 3.6 131.6 1.0 O2B E:ATP601 3.7 131.6 1.0 ND2 E:ASN397 3.8 140.6 1.0 NE2 E:GLN325 3.9 143.7 1.0 O1G E:ATP601 4.0 131.6 1.0 CB E:THR302 4.1 123.0 1.0 OD1 E:ASP396 4.2 134.8 1.0 O3A E:ATP601 4.5 131.6 1.0 OD2 E:ASP396 4.5 134.8 1.0 CG E:GLN325 4.5 143.7 1.0 O2G E:ATP601 4.6 131.6 1.0 NH2 D:ARG489 4.6 120.6 1.0 O2A E:ATP601 4.6 131.6 1.0 CG E:ASN397 4.6 140.6 1.0 OD1 E:ASN397 4.6 140.6 1.0 N E:THR302 4.8 123.0 1.0 CG E:ASP396 4.8 134.8 1.0 CB E:GLN325 4.9 143.7 1.0

Magnesium binding site 5 out of 5 in the Structure of Lates Calcarifer Twinkle Helicase with Atp and Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Lates Calcarifer Twinkle Helicase with Atp and Dna within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg602 b:161.2 occ:1.00 O1B F:ATP601 2.1 161.7 1.0 O3G F:ATP601 2.1 161.7 1.0 OG1 F:THR302 2.6 156.6 1.0 OE1 F:GLN325 2.6 167.8 1.0 PB F:ATP601 2.7 161.7 1.0 O2B F:ATP601 2.9 161.7 1.0 PG F:ATP601 3.2 161.7 1.0 O3B F:ATP601 3.4 161.7 1.0 O1G F:ATP601 3.6 161.7 1.0 CD F:GLN325 3.8 167.8 1.0 CB F:THR302 3.9 156.6 1.0 O3A F:ATP601 4.2 161.7 1.0 OD2 F:ASP396 4.3 167.3 1.0 OD1 F:ASP396 4.3 167.3 1.0 ND2 F:ASN397 4.3 169.5 1.0 NE2 F:GLN325 4.4 167.8 1.0 N F:THR302 4.5 156.6 1.0 O2G F:ATP601 4.5 161.7 1.0 O2A F:ATP601 4.6 161.7 1.0 NH2 E:ARG489 4.6 137.1 1.0 CG F:ASP396 4.7 167.3 1.0 CA F:THR302 4.8 156.6 1.0 CG2 F:THR302 4.8 156.6 1.0 CG F:GLN325 4.8 167.8 1.0 PA F:ATP601 4.9 161.7 1.0

Z.Li, P.Kaur, C.Y.Lo, N.Chopra, J.Smith, H.Wang, Y.Gao. Structural and Dynamic Basis of Dna Capture and Translocation By Mitochondrial Twinkle Helicase. Nucleic Acids Res. V. 50 11965 2022.
ISSN: ESSN 1362-4962
PubMed: 36400570
DOI: 10.1093/NAR/GKAC1089