Magnesium in PDB 7sgl: Dna-Pk Complex of Dna End Processing

All present enzymatic activity of Dna-Pk Complex of Dna End Processing:
2.7.11.1;

The structure of Dna-Pk Complex of Dna End Processing also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Dna-Pk Complex of Dna End Processing (pdb code 7sgl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Dna-Pk Complex of Dna End Processing, PDB code: 7sgl:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Dna-Pk Complex of Dna End Processing


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna-Pk Complex of Dna End Processing within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4200 b:62.5 occ:1.00 OD1 A:ASN3927 2.1 48.6 1.0 OD2 A:ASP3941 2.1 52.1 1.0 O1B A:ATP4201 2.3 86.5 1.0 O1G A:ATP4201 2.6 86.5 1.0 CG A:ASP3941 3.0 52.1 1.0 CB A:ASP3941 3.2 52.1 1.0 CG A:ASN3927 3.2 48.6 1.0 PG A:ATP4201 3.4 86.5 1.0 O2G A:ATP4201 3.5 86.5 1.0 PB A:ATP4201 3.6 86.5 1.0 NE2 A:HIS3924 3.8 45.2 1.0 CE1 A:HIS3924 3.8 45.2 1.0 O3B A:ATP4201 3.8 86.5 1.0 ND2 A:ASN3927 3.9 48.6 1.0 OD1 A:ASP3941 4.1 52.1 1.0 O A:ASN3926 4.2 49.2 1.0 CB A:ASN3927 4.4 48.6 1.0 O1A A:ATP4201 4.5 86.5 1.0 O3A A:ATP4201 4.5 86.5 1.0 C A:ASN3926 4.5 49.2 1.0 CA A:ASN3927 4.5 48.6 1.0 N A:ASN3927 4.6 48.6 1.0 O2B A:ATP4201 4.7 86.5 1.0 CA A:ASP3941 4.8 52.1 1.0 NZ A:LYS4023 4.8 82.4 1.0 CB A:ASN3926 4.8 49.2 1.0 O3G A:ATP4201 4.8 86.5 1.0

Magnesium binding site 2 out of 3 in the Dna-Pk Complex of Dna End Processing


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dna-Pk Complex of Dna End Processing within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg801 b:67.8 occ:1.00 CD2 D:HIS38 2.1 50.9 1.0 OD1 D:ASP37 2.3 58.5 1.0 OD2 D:ASP37 2.4 58.5 1.0 NE2 D:HIS38 2.5 50.9 1.0 CG D:ASP37 2.6 58.5 1.0 OD2 D:ASP136 2.7 70.2 1.0 OP2 E:DA25 2.7 65.9 1.0 OP1 E:DA25 2.8 65.9 1.0 P E:DA25 3.1 65.9 1.0 CB D:HIS35 3.2 51.8 1.0 NE2 D:HIS33 3.3 42.6 1.0 ND1 D:HIS35 3.3 51.8 1.0 MG D:MG802 3.4 96.1 1.0 CG D:HIS38 3.4 50.9 1.0 O5' E:DA25 3.5 65.9 1.0 CG D:HIS35 3.7 51.8 1.0 CE1 D:HIS38 3.8 50.9 1.0 CG D:ASP136 3.9 70.2 1.0 CE1 D:HIS33 4.0 42.6 1.0 CB D:ASP37 4.1 58.5 1.0 ND1 D:HIS38 4.2 50.9 1.0 CD2 D:HIS33 4.3 42.6 1.0 N D:HIS38 4.3 50.9 1.0 CB D:HIS38 4.4 50.9 1.0 CA D:HIS35 4.5 51.8 1.0 CE1 D:HIS35 4.6 51.8 1.0 N D:ASP37 4.6 58.5 1.0 C5' E:DA25 4.6 65.9 1.0 C D:ASP37 4.7 58.5 1.0 CA D:ASP37 4.7 58.5 1.0 OD1 D:ASP136 4.7 70.2 1.0 O3' E:DT24 4.7 64.2 1.0 C D:HIS35 4.8 51.8 1.0 CB D:ASP136 4.8 70.2 1.0

Magnesium binding site 3 out of 3 in the Dna-Pk Complex of Dna End Processing


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dna-Pk Complex of Dna End Processing within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg802 b:96.1 occ:1.00 OP1 E:DA25 1.9 65.9 1.0 NE2 D:HIS115 2.2 96.1 1.0 OD2 D:ASP136 2.5 70.2 1.0 CE1 D:HIS115 2.6 96.1 1.0 ND1 D:HIS35 2.7 51.8 1.0 NE2 D:HIS33 2.8 42.6 1.0 CB D:ASP136 2.9 70.2 1.0 CE1 D:HIS35 3.1 51.8 1.0 CD2 D:HIS115 3.1 96.1 1.0 CG D:ASP136 3.1 70.2 1.0 P E:DA25 3.3 65.9 1.0 MG D:MG801 3.4 67.8 1.0 ND1 D:HIS115 3.5 96.1 1.0 CE1 D:HIS33 3.5 42.6 1.0 CD2 D:HIS33 3.6 42.6 1.0 CG D:HIS115 3.8 96.1 1.0 CE1 D:HIS319 3.8 44.5 1.0 OP2 E:DA25 3.9 65.9 1.0 CG D:HIS35 3.9 51.8 1.0 NE2 D:HIS319 4.2 44.5 1.0 O3' E:DT24 4.2 64.2 1.0 O5' E:DA25 4.3 65.9 1.0 OD1 D:ASP136 4.3 70.2 1.0 NE2 D:HIS35 4.3 51.8 1.0 NE2 D:HIS38 4.3 50.9 1.0 CA D:ASP136 4.4 70.2 1.0 O D:ASP136 4.5 70.2 1.0 ND1 D:HIS33 4.5 42.6 1.0 CG D:HIS33 4.6 42.6 1.0 CD2 D:HIS38 4.6 50.9 1.0 CB D:HIS35 4.6 51.8 1.0 C5' E:DA25 4.6 65.9 1.0 CD2 D:HIS35 4.8 51.8 1.0 ND1 D:HIS319 4.9 44.5 1.0 C D:ASP136 4.9 70.2 1.0

L.Liu, X.Chen, J.Li, H.Wang, C.J.Buehl, N.J.Goff, K.Meek, W.Yang, M.Gellert. Autophosphorylation Transforms Dna-Pk From Protecting to Processing Dna Ends. Mol.Cell V. 82 177 2022.
ISSN: ISSN 1097-2765
PubMed: 34936881
DOI: 10.1016/J.MOLCEL.2021.11.025