Chlorine 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:

Manganese

(Mn)

3 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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:Cl1181 b:90.7 occ:1.00 ND2 A:ASN131 3.8 53.3 1.0 NH2 A:ARG99 4.3 44.8 0.5 CG A:ASN131 4.8 45.0 1.0 OD1 A:ASN131 4.9 43.9 1.0 CB A:LEU134 4.9 34.5 1.0 CD1 A:ILE137 5.0 46.0 1.0 O A:HOH2042 5.0 60.4 1.0

Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl 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 B:Cl1015 b:0.7 occ:1.00 N3 D:DA22 3.4 79.2 1.0 C2 D:DA22 3.5 76.8 1.0 O4' B:DG6 3.6 50.2 1.0 O2 B:DT5 3.7 71.3 1.0 O B:HOH2003 3.7 60.9 1.0 C1' B:DG6 4.5 54.1 1.0 C4' B:DG6 4.5 52.8 1.0 N9 B:DG6 4.7 59.1 1.0 C4 D:DA22 4.7 80.1 1.0 O4' D:DG23 4.7 92.9 1.0 N1 D:DA22 4.7 72.2 1.0 C2 B:DT5 4.8 66.3 1.0 C1' B:DT5 4.9 61.5 1.0 C4 B:DG6 5.0 62.3 1.0 C5' B:DG6 5.0 56.0 1.0

Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl 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 E:Cl1181 b:89.2 occ:1.00 NH2 E:ARG99 3.9 62.0 0.5 ND2 E:ASN131 4.0 45.5 1.0 CD1 E:ILE137 4.2 57.4 1.0 CB E:LEU134 4.3 37.5 1.0 N E:LEU134 4.3 41.0 1.0 CA E:LEU134 4.4 43.5 1.0 OD1 E:ASN131 4.5 52.9 1.0 CG E:ASN131 4.6 47.3 1.0 C E:ALA133 4.7 42.1 1.0 CZ E:ARG99 4.8 54.0 0.5 CB E:ALA133 4.8 33.8 1.0 CD1 E:LEU134 4.8 33.5 1.0 NH1 E:ARG99 5.0 46.9 0.5

Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl1181 b:79.4 occ:1.00 ND2 I:ASN131 3.6 43.0 1.0 OD1 I:ASN131 4.1 42.9 1.0 CG I:ASN131 4.3 41.4 1.0 NH2 I:ARG99 4.4 49.4 0.6 N I:LEU134 4.4 32.9 1.0 CB I:LEU134 4.5 30.1 1.0 CA I:LEU134 4.7 31.5 1.0 CB I:ALA133 4.8 19.9 1.0 C I:ALA133 5.0 33.3 1.0 CD1 I:ILE137 5.0 40.8 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