Manganese in PDB 5akn: The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna Nicked in the Non-Coding Strand B 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 Non-Coding Strand B and in the Presence of 2MM Mn, PDB code: 5akn 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)	46.49 / 2.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	107.100, 70.340, 107.170, 90.00, 119.81, 90.00
R / Rfree (%)	17.5 / 23.6

The binding sites of Manganese atom in the The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna Nicked in the Non-Coding Strand B and in the Presence of 2MM Mn (pdb code 5akn). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna Nicked in the Non-Coding Strand B and in the Presence of 2MM Mn, PDB code: 5akn:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna Nicked in the Non-Coding Strand B 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 Non-Coding Strand B and in the Presence of 2MM Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1184 b:52.1 occ:1.00 O A:ALA116 2.0 45.1 1.0 OP1 E:DC16 2.2 33.3 1.0 OP1 B:DA14 2.2 43.5 1.0 OD2 A:ASP21 2.4 51.0 1.0 C A:ALA116 3.0 30.2 1.0 CG A:ASP21 3.2 47.0 1.0 OD1 A:ASP21 3.2 43.5 1.0 O A:HOH2039 3.3 31.1 1.0 CA A:ALA116 3.4 27.2 1.0 P E:DC16 3.5 45.5 1.0 P B:DA14 3.6 44.7 1.0 O5' E:DC16 3.7 42.8 1.0 O A:VAL115 3.8 55.2 1.0 N A:GLU117 4.1 17.5 1.0 O A:HOH2004 4.2 39.4 1.0 O3' B:DA13 4.2 43.9 1.0 OP3 E:DC16 4.3 41.6 1.0 OP2 B:DA14 4.3 50.2 1.0 CB A:ALA116 4.4 23.9 1.0 N A:ALA116 4.5 35.2 1.0 OP2 E:DC16 4.5 52.0 1.0 CA A:GLU117 4.5 30.5 1.0 C A:VAL115 4.6 41.9 1.0 CB A:ASP21 4.6 37.1 1.0 O A:HOH2003 4.6 18.5 1.0 C5' B:DA14 4.7 42.9 1.0 O5' B:DA14 4.7 51.9 1.0 C4' B:DA14 4.8 42.4 1.0 CE A:MET120 4.8 36.6 0.5 CB A:GLU117 5.0 24.5 1.0

Manganese binding site 2 out of 6 in the The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna Nicked in the Non-Coding Strand B 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 Non-Coding Strand B and in the Presence of 2MM Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1185 b:59.5 occ:1.00 OP1 D:DC15 2.4 29.2 1.0 OE1 A:GLU117 2.6 21.9 1.0 OP1 C:DG15 2.6 43.0 1.0 O A:GLY20 2.7 48.5 1.0 OE2 A:GLU117 3.0 42.1 1.0 CD A:GLU117 3.1 35.2 1.0 P C:DG15 3.3 48.3 1.0 O5' C:DG15 3.4 39.8 1.0 OP3 C:DG15 3.4 53.8 1.0 P D:DC15 3.5 34.1 1.0 C A:GLY20 3.6 45.8 1.0 O A:ILE19 3.6 30.8 1.0 O3' D:DA14 3.7 20.3 1.0 O C:HOH2001 3.9 52.6 1.0 CA A:GLY20 3.9 44.4 1.0 ND2 A:ASN129 4.0 31.2 1.0 O A:HOH2003 4.3 18.5 1.0 C4' D:DC15 4.5 33.0 1.0 OP2 D:DC15 4.5 36.3 1.0 C A:ILE19 4.6 29.6 1.0 O5' D:DC15 4.6 40.7 1.0 C5' C:DG15 4.6 34.5 1.0 CG A:GLU117 4.6 29.8 1.0 C5' D:DC15 4.7 34.7 1.0 OP2 C:DG15 4.7 53.4 1.0 N A:GLY20 4.8 32.6 1.0 N A:ASP21 4.8 36.7 1.0 CG A:ASN129 4.9 25.8 1.0

Manganese binding site 3 out of 6 in the The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna Nicked in the Non-Coding Strand B 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 Non-Coding Strand B and in the Presence of 2MM Mn within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn1189 b:56.2 occ:1.00 OP1 G:DA14 2.1 18.4 1.0 OP1 J:DC16 2.3 27.0 1.0 O F:ALA116 2.4 48.4 1.0 OD2 F:ASP21 2.4 31.2 1.0 OP3 J:DC16 3.0 47.3 1.0 P J:DC16 3.2 46.8 1.0 O F:HOH2032 3.3 41.3 1.0 CG F:ASP21 3.3 23.7 1.0 OD1 F:ASP21 3.4 21.7 1.0 C F:ALA116 3.4 37.5 1.0 P G:DA14 3.5 36.3 1.0 CA F:ALA116 3.9 21.4 1.0 O F:VAL115 4.0 38.9 1.0 C5' G:DA14 4.1 62.0 1.0 O5' J:DC16 4.1 36.6 1.0 OP2 G:DA14 4.1 40.8 1.0 O F:HOH2005 4.1 41.7 1.0 O3' G:DA13 4.2 26.2 1.0 O5' G:DA14 4.4 72.1 1.0 OP2 J:DC16 4.5 59.9 1.0 O F:HOH2004 4.6 17.2 1.0 O G:HOH2008 4.6 37.6 1.0 N F:GLU117 4.6 39.3 1.0 CB F:ASP21 4.6 29.8 1.0 C5' J:DC16 4.7 34.3 1.0 CE F:MET120 4.7 57.8 0.6 C4' G:DA14 4.7 46.7 1.0 CB F:ALA116 4.9 23.7 1.0 C F:VAL115 4.9 32.9 1.0 N F:ALA116 4.9 19.1 1.0 CA F:GLU117 4.9 39.0 1.0

Manganese binding site 4 out of 6 in the The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna Nicked in the Non-Coding Strand B 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 4 of The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna Nicked in the Non-Coding Strand B and in the Presence of 2MM Mn within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn1190 b:61.6 occ:1.00 O F:GLY20 2.4 49.6 1.0 OP1 H:DC1040 2.4 34.7 1.0 OE2 F:GLU117 2.5 31.0 1.0 OP1 H:DG15 2.5 47.9 1.0 O F:HOH2003 2.5 43.5 1.0 OE1 F:GLU117 2.7 47.0 1.0 CD F:GLU117 2.9 43.0 1.0 OP3 H:DG15 3.0 34.5 1.0 P H:DG15 3.2 44.5 1.0 C F:GLY20 3.3 41.8 1.0 O F:ILE19 3.5 22.7 1.0 CA F:GLY20 3.6 32.5 1.0 P H:DC1040 3.7 38.8 1.0 O5' H:DG15 3.8 32.4 1.0 ND2 F:ASN129 3.8 28.8 1.0 O3' H:DA1039 4.1 41.9 1.0 C5' H:DG15 4.4 34.9 1.0 C F:ILE19 4.4 24.7 1.0 CG F:GLU117 4.4 48.0 1.0 C4' H:DC1040 4.5 39.2 1.0 N F:GLY20 4.5 26.6 1.0 O F:HOH2027 4.5 27.0 1.0 O H:HOH2011 4.5 44.5 1.0 O F:HOH2004 4.6 17.2 1.0 N F:ASP21 4.6 35.0 1.0 OP2 H:DG15 4.6 55.7 1.0 C5' H:DC1040 4.6 35.4 1.0 OP2 H:DC1040 4.7 42.4 1.0 O5' H:DC1040 4.7 37.0 1.0 CG F:ASN129 4.8 33.7 1.0

Manganese binding site 5 out of 6 in the The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna Nicked in the Non-Coding Strand B 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 5 of The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna Nicked in the Non-Coding Strand B and in the Presence of 2MM Mn within 5.0Å range: probe atom residue distance (Å) B Occ K:Mn1188 b:71.1 occ:1.00 OE2 K:GLU117 2.0 48.5 1.0 O K:GLY20 2.4 36.4 1.0 OP1 M:DC1040 2.5 68.6 1.0 OP1 M:DG15 2.5 43.8 1.0 CD K:GLU117 2.7 42.0 1.0 OE1 K:GLU117 3.0 38.2 1.0 P M:DG15 3.2 45.5 1.0 OP2 M:DG15 3.2 40.1 1.0 C K:GLY20 3.3 30.9 1.0 P M:DC1040 3.5 50.7 1.0 CA K:GLY20 3.5 26.3 1.0 O5' M:DC1040 3.5 55.1 1.0 O K:ILE19 3.5 31.6 1.0 ND2 K:ASN129 3.8 37.4 1.0 O5' M:DG15 4.0 40.4 1.0 O3' M:DA1039 4.0 47.9 1.0 CG K:GLU117 4.1 38.6 1.0 C K:ILE19 4.4 33.1 1.0 N K:GLY20 4.4 27.6 1.0 O K:HOH2004 4.4 27.6 1.0 OP3 M:DG15 4.5 51.2 1.0 N K:ASP21 4.5 24.0 1.0 C5' M:DG15 4.5 31.0 1.0 C4' M:DC1040 4.6 42.1 1.0 C5' M:DC1040 4.7 46.5 1.0 OP2 M:DC1040 4.8 56.2 1.0 CG K:ASN129 4.8 42.2 1.0 O M:HOH2019 4.9 27.4 1.0 O K:HOH2003 4.9 38.5 1.0

Manganese binding site 6 out of 6 in the The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna Nicked in the Non-Coding Strand B 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 6 of The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna Nicked in the Non-Coding Strand B and in the Presence of 2MM Mn within 5.0Å range: probe atom residue distance (Å) B Occ K:Mn1189 b:49.3 occ:1.00 OP1 O:DC16 2.1 34.8 1.0 OP1 L:DA14 2.2 49.5 1.0 O K:ALA116 2.3 44.6 1.0 OD2 K:ASP21 2.5 41.6 1.0 P O:DC16 3.1 60.7 1.0 OP3 O:DC16 3.2 72.1 1.0 CG K:ASP21 3.2 37.6 1.0 C K:ALA116 3.2 31.5 1.0 OD1 K:ASP21 3.3 36.2 1.0 P L:DA14 3.5 46.2 1.0 O5' O:DC16 3.6 40.4 1.0 CA K:ALA116 3.6 30.3 1.0 O3' L:DA13 4.1 30.1 1.0 O K:VAL115 4.1 29.9 1.0 OP2 L:DA14 4.2 50.1 1.0 O O:HOH2001 4.2 46.4 1.0 OP2 O:DC16 4.4 71.0 1.0 N K:GLU117 4.4 23.6 1.0 CB K:ALA116 4.5 18.9 1.0 O K:HOH2004 4.5 27.6 1.0 O5' L:DA14 4.6 35.4 1.0 CB K:ASP21 4.6 29.4 1.0 C5' L:DA14 4.6 42.9 1.0 N K:ALA116 4.7 36.9 1.0 C4' L:DA14 4.8 45.3 1.0 C K:VAL115 4.9 35.5 1.0 CA K:GLU117 5.0 24.7 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