Magnesium in PDB 6nhz: Mycobacterial Dna Ligase D Complexed with Atp and Mg

All present enzymatic activity of Mycobacterial Dna Ligase D Complexed with Atp and Mg:
6.5.1.1;

The structure of Mycobacterial Dna Ligase D Complexed with Atp and Mg, PDB code: 6nhz was solved by S.Shuman, M.Unciuleac, Y.Goldgur, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.49 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.618, 51.630, 72.874, 90.00, 99.57, 90.00
R / Rfree (%)	20.6 / 24.4

The binding sites of Magnesium atom in the Mycobacterial Dna Ligase D Complexed with Atp and Mg (pdb code 6nhz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Mycobacterial Dna Ligase D Complexed with Atp and Mg, PDB code: 6nhz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Mycobacterial Dna Ligase D Complexed with Atp and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mycobacterial Dna Ligase D Complexed with Atp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:38.8 occ:1.00 O A:HOH1023 2.5 37.9 1.0 O2B A:ATP801 2.6 32.4 1.0 O A:HOH1096 2.7 27.4 1.0 O3G A:ATP801 2.8 22.6 1.0 O3' A:ATP801 3.4 20.2 1.0 NH1 A:ARG501 3.4 30.0 1.0 PB A:ATP801 3.8 29.6 1.0 O3A A:ATP801 4.0 27.0 1.0 PG A:ATP801 4.1 24.2 1.0 O A:HOH968 4.2 31.6 1.0 O A:HOH1014 4.2 27.1 1.0 O3B A:ATP801 4.3 25.4 1.0 C4' A:ATP801 4.5 21.7 1.0 C3' A:ATP801 4.5 23.9 1.0 O A:HOH971 4.5 18.8 1.0 CZ A:ARG501 4.6 28.1 1.0 O A:HOH1084 4.7 33.3 1.0 O2G A:ATP801 4.8 21.6 1.0 MG A:MG803 5.0 68.7 1.0

Magnesium binding site 2 out of 2 in the Mycobacterial Dna Ligase D Complexed with Atp and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mycobacterial Dna Ligase D Complexed with Atp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:68.7 occ:1.00 O2A A:ATP801 2.5 23.5 1.0 O A:HOH1023 2.7 37.9 1.0 O A:HOH915 3.0 31.0 1.0 OE2 A:GLU613 3.2 30.5 1.0 NH2 A:ARG745 3.3 49.1 1.0 PA A:ATP801 3.6 25.0 1.0 O3A A:ATP801 3.6 27.0 1.0 O A:HOH947 3.7 39.9 1.0 C5' A:ATP801 3.8 24.0 1.0 NZ A:LYS637 3.8 31.2 1.0 CZ A:ARG745 3.9 48.9 1.0 C4' A:ATP801 4.0 21.7 1.0 OD1 A:ASP483 4.0 40.0 1.0 O A:HOH903 4.0 37.5 1.0 CD A:GLU613 4.1 31.2 1.0 O A:HOH944 4.2 41.3 1.0 O2B A:ATP801 4.2 32.4 1.0 OE1 A:GLU613 4.3 26.3 1.0 O5' A:ATP801 4.3 25.3 1.0 NE A:ARG745 4.3 49.6 1.0 PB A:ATP801 4.4 29.6 1.0 O4' A:ATP801 4.5 20.4 1.0 NH1 A:ARG745 4.7 47.2 1.0 O1B A:ATP801 4.7 33.9 1.0 CG A:ASP483 4.8 34.0 1.0 CE A:LYS637 4.9 26.5 1.0 O1A A:ATP801 4.9 25.1 1.0 MG A:MG802 5.0 38.8 1.0

M.C.Unciuleac, Y.Goldgur, S.Shuman. Structures of Atp-Bound Dna Ligase D in A Closed Domain Conformation Reveal A Network of Amino Acid and Metal Contacts to the Atp Phosphates. J. Biol. Chem. V. 294 5094 2019.
ISSN: ESSN 1083-351X
PubMed: 30718283
DOI: 10.1074/JBC.RA119.007445