Manganese in PDB 5akf: The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna Nicked in the Coding Strand A and in the Presence of 2MM Mn

The structure of The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna Nicked in the Coding Strand A and in the Presence of 2MM Mn, PDB code: 5akf was solved by R.Molina, M.J.Marcaida, P.Redondo, M.Marenchino, M.D'abramo, G.Montoya, J.Prieto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.65 / 2.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	106.820, 70.470, 107.100, 90.00, 119.88, 90.00
R / Rfree (%)	17.6 / 23

The structure of The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna Nicked in the Coding Strand A and in the Presence of 2MM Mn also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Manganese atom in the The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna Nicked in the Coding Strand A and in the Presence of 2MM Mn (pdb code 5akf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna Nicked in the Coding Strand A and in the Presence of 2MM Mn, PDB code: 5akf:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna Nicked in the Coding Strand A and in the Presence of 2MM Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna Nicked in the Coding Strand A and in the Presence of 2MM Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1185 b:49.4 occ:1.00 OP2 D:DC16 2.3 33.2 1.0 OP1 B:DA14 2.3 41.0 1.0 O A:ALA116 2.4 39.5 1.0 OD2 A:ASP21 2.5 36.9 1.0 O A:HOH2007 2.5 37.2 1.0 O A:HOH2055 2.7 40.0 1.0 OD1 A:ASP21 2.8 44.6 1.0 CG A:ASP21 3.0 40.7 1.0 P D:DC16 3.5 43.5 1.0 C A:ALA116 3.5 39.4 1.0 P B:DA14 3.7 49.9 1.0 O A:HOH2005 3.8 23.0 1.0 OP1 D:DC16 4.1 48.2 1.0 CA A:ALA116 4.1 36.2 1.0 O5' D:DC16 4.1 38.2 1.0 C5' B:DA14 4.2 52.1 1.0 C4' B:DA14 4.3 53.5 1.0 O3' B:DA13 4.3 55.6 1.0 O5' B:DA14 4.4 65.2 1.0 C5' D:DC16 4.4 42.8 1.0 CB A:ASP21 4.5 31.5 1.0 O A:HOH2006 4.5 48.0 1.0 N A:GLU117 4.7 36.5 1.0 O3' B:DA14 4.7 56.9 1.0 CB A:ALA116 4.7 29.3 1.0 O3' D:DC15 4.7 41.2 1.0 O A:VAL115 4.7 52.7 1.0 C3' B:DA14 4.8 55.4 1.0 OP2 B:DA14 4.8 61.5 1.0

Manganese binding site 2 out of 3 in the The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna Nicked in the Coding Strand A and in the Presence of 2MM Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna Nicked in the Coding Strand A and in the Presence of 2MM Mn within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn1182 b:48.8 occ:1.00 OP1 F:DA14 2.3 34.6 1.0 OP2 H:DC16 2.4 35.2 1.0 O E:ALA116 2.4 41.6 1.0 OD2 E:ASP21 2.6 31.6 1.0 O E:HOH2046 2.8 47.4 1.0 OD1 E:ASP21 2.8 26.4 1.0 CG E:ASP21 3.1 27.7 1.0 C E:ALA116 3.5 35.8 1.0 P H:DC16 3.6 39.0 1.0 P F:DA14 3.7 33.9 1.0 O E:HOH2005 3.9 25.9 1.0 CA E:ALA116 3.9 33.1 1.0 O5' H:DC16 4.2 42.3 1.0 O E:HOH2039 4.2 54.4 1.0 OP1 H:DC16 4.3 35.3 1.0 C4' F:DA14 4.3 38.6 1.0 C5' H:DC16 4.3 39.6 1.0 C5' F:DA14 4.3 36.2 1.0 O3' F:DA13 4.4 48.0 1.0 O F:HOH2010 4.4 44.6 1.0 O E:VAL115 4.5 37.8 1.0 O E:HOH2007 4.6 31.1 1.0 CB E:ASP21 4.6 27.2 1.0 O5' F:DA14 4.6 45.1 1.0 N E:GLU117 4.6 37.3 1.0 CB E:ALA116 4.7 26.7 1.0 OP2 F:DA14 4.7 43.5 1.0 O3' F:DA14 4.8 35.4 1.0 O3' H:DC15 4.8 45.5 1.0 C3' F:DA14 4.9 37.9 1.0

Manganese binding site 3 out of 3 in the The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna Nicked in the Coding Strand A and in the Presence of 2MM Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna Nicked in the Coding Strand A and in the Presence of 2MM Mn within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1180 b:47.4 occ:1.00 OP1 J:DA14 2.2 37.2 1.0 OP2 L:DC16 2.3 38.0 1.0 O I:ALA116 2.4 39.6 1.0 OD2 I:ASP21 2.6 39.9 1.0 OD1 I:ASP21 2.8 33.3 1.0 CG I:ASP21 3.1 40.5 1.0 C I:ALA116 3.4 37.2 1.0 O I:HOH2057 3.6 62.6 1.0 P L:DC16 3.6 41.8 1.0 P J:DA14 3.7 41.9 1.0 O I:HOH2011 3.9 35.0 1.0 CA I:ALA116 3.9 36.1 1.0 O5' L:DC16 4.2 28.0 1.0 OP1 L:DC16 4.3 50.5 1.0 O3' J:DA13 4.4 39.3 1.0 C5' L:DC16 4.4 36.1 1.0 C5' J:DA14 4.5 37.3 1.0 C4' J:DA14 4.5 41.1 1.0 O I:VAL115 4.6 41.9 1.0 OP2 J:DA14 4.6 41.1 1.0 N I:GLU117 4.6 35.3 1.0 O I:HOH2012 4.6 38.3 1.0 O5' J:DA14 4.6 41.3 1.0 CB I:ASP21 4.6 29.7 1.0 O J:HOH2009 4.6 48.5 1.0 CB I:ALA116 4.7 22.7 1.0 O3' L:DC15 4.8 28.7 1.0 O3' J:DA14 4.9 43.1 1.0 CA I:GLU117 5.0 41.5 1.0

R.Molina, M.J.Marcaida, P.Redondo, M.Marenchino, P.Duchateau, M.D'abramo, G.Montoya, J.Prieto. Engineering A Nickase on the Homing Endonuclease I-Dmoi Scaffold. J.Biol.Chem. V. 290 18534 2015.
ISSN: ISSN 0021-9258
PubMed: 26045557
DOI: 10.1074/JBC.M115.658666