Magnesium in PDB 2qnc: Crystal Structure of T4 Endonuclease VII N62D Mutant in Complex with A Dna Holliday Junction

All present enzymatic activity of Crystal Structure of T4 Endonuclease VII N62D Mutant in Complex with A Dna Holliday Junction:
3.1.22.4;

The structure of Crystal Structure of T4 Endonuclease VII N62D Mutant in Complex with A Dna Holliday Junction, PDB code: 2qnc was solved by C.Biertumpfel, W.Yang, D.Suck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.27 / 3.10
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.197, 99.197, 186.884, 90.00, 90.00, 90.00
R / Rfree (%)	25.8 / 27.8

The structure of Crystal Structure of T4 Endonuclease VII N62D Mutant in Complex with A Dna Holliday Junction also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of T4 Endonuclease VII N62D Mutant in Complex with A Dna Holliday Junction (pdb code 2qnc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of T4 Endonuclease VII N62D Mutant in Complex with A Dna Holliday Junction, PDB code: 2qnc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of T4 Endonuclease VII N62D Mutant in Complex with A Dna Holliday Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of T4 Endonuclease VII N62D Mutant in Complex with A Dna Holliday Junction within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg24 b:62.6 occ:1.00 OP1 F:DC13 2.2 91.2 1.0 O3' F:DC12 2.2 90.6 1.0 OD1 B:ASP40 2.2 78.4 1.0 O B:HOH161 2.3 39.6 1.0 P F:DC13 2.4 93.1 1.0 OP2 F:DC13 2.9 90.2 1.0 C3' F:DC12 3.0 87.2 1.0 OD1 B:ASP62 3.0 70.3 1.0 CG B:ASP40 3.4 77.8 1.0 NH2 B:ARG54 3.4 79.2 1.0 O B:HIS41 3.6 77.7 1.0 C4' F:DC12 3.7 84.5 1.0 O5' F:DC13 3.9 92.7 1.0 N B:HIS41 4.0 80.3 1.0 CB B:ASP40 4.1 80.2 1.0 CG B:ASP62 4.2 71.5 1.0 CA B:ASP40 4.3 82.3 1.0 O B:HOH162 4.3 43.0 1.0 C2' F:DC12 4.3 87.0 1.0 OD2 B:ASP40 4.4 74.9 1.0 C5' F:DC12 4.5 81.1 1.0 OE1 B:GLU65 4.6 50.8 1.0 C B:HIS41 4.6 78.4 1.0 NE2 B:HIS43 4.6 80.7 1.0 C B:ASP40 4.7 81.5 1.0 C5' F:DC13 4.7 97.7 1.0 OD2 B:ASP62 4.7 72.1 1.0 CZ B:ARG54 4.7 78.0 1.0 CD2 B:HIS43 4.7 80.5 1.0 O B:ASP62 4.8 67.8 1.0 CA B:HIS41 4.9 79.0 1.0 O4' F:DC12 4.9 85.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of T4 Endonuclease VII N62D Mutant in Complex with A Dna Holliday Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of T4 Endonuclease VII N62D Mutant in Complex with A Dna Holliday Junction within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg159 b:36.8 occ:1.00 OD1 A:ASP62 1.9 62.5 1.0 OD1 A:ASP40 2.1 71.8 1.0 O3' D:DC12 2.1 69.3 1.0 O A:HOH160 2.7 42.2 1.0 CG A:ASP40 2.9 71.7 1.0 C3' D:DC12 2.9 67.7 1.0 CG A:ASP62 3.0 62.9 1.0 C4' D:DC12 3.0 67.6 1.0 P D:DT13 3.3 71.8 1.0 O A:ASP62 3.3 58.8 1.0 OE1 A:GLU65 3.3 64.6 1.0 OP1 D:DT13 3.4 69.2 1.0 OD2 A:ASP40 3.6 70.3 1.0 OD2 A:ASP62 3.7 64.3 1.0 CB A:ASP40 3.8 71.6 1.0 NH2 A:ARG54 3.9 68.2 1.0 C5' D:DC12 3.9 69.8 1.0 C A:ASP62 4.0 59.0 1.0 OP2 D:DT13 4.1 70.7 1.0 CB A:ASP62 4.1 60.9 1.0 CA A:ASP62 4.2 60.0 1.0 O4' D:DC12 4.2 67.0 1.0 C2' D:DC12 4.3 67.9 1.0 O5' D:DT13 4.5 72.4 1.0 CA A:ASP40 4.5 71.6 1.0 CD A:GLU65 4.5 65.6 1.0 C1' D:DC12 4.7 65.8 1.0 N A:HIS41 4.9 73.0 1.0 O A:HIS41 5.0 74.6 1.0

C.Biertumpfel, W.Yang, D.Suck. Crystal Structure of T4 Endonuclease VII Resolving A Holliday Junction. Nature V. 449 616 2007.
ISSN: ISSN 0028-0836
PubMed: 17873859
DOI: 10.1038/NATURE06152