Manganese in PDB 5a0w: The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna and in the Presence of 2MM Mn

The structure of The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna and in the Presence of 2MM Mn, PDB code: 5a0w was solved by R.Molina, N.Besker, J.Prieto, G.Montoya, M.D'abramo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.220 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	106.928, 69.770, 106.985, 90.00, 120.06, 90.00
R / Rfree (%)	17.06 / 20.79

The structure of The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna and in the Presence of 2MM Mn also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

The binding sites of Manganese atom in the The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna and in the Presence of 2MM Mn (pdb code 5a0w). 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 E117A in Complex with Its Target Dna and in the Presence of 2MM Mn, PDB code: 5a0w:
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 E117A in Complex with Its Target Dna 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 E117A in Complex with Its Target Dna and in the Presence of 2MM Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1189 b:26.9 occ:1.00 OP1 B:DA14 2.1 27.0 1.0 O A:HOH2008 2.1 28.8 1.0 OD2 A:ASP21 2.2 22.4 1.0 O A:ALA116 2.2 24.9 1.0 OP1 C:DC16 2.2 41.7 1.0 OD1 A:ASP21 2.4 19.2 1.0 CG A:ASP21 2.6 18.8 1.0 P C:DC16 3.1 35.1 1.0 OP2 C:DC16 3.2 38.7 1.0 C A:ALA116 3.3 23.7 1.0 P B:DA14 3.5 34.6 1.0 O A:HOH2065 3.8 39.3 1.0 O A:HOH2007 3.8 13.9 1.0 CA A:ALA116 3.8 17.9 1.0 O3' B:DA13 4.1 31.1 1.0 O3' C:DC15 4.1 39.6 1.0 CB A:ASP21 4.1 17.2 1.0 C4' B:DA14 4.2 31.9 1.0 C5' B:DA14 4.2 27.4 1.0 NE2 A:GLN42 4.3 45.4 1.0 OE1 A:GLN42 4.3 48.9 1.0 O5' C:DC16 4.3 31.3 1.0 NZ A:LYS120 4.3 50.7 1.0 O5' B:DA14 4.4 29.9 1.0 O A:VAL115 4.4 25.9 1.0 N A:ALA117 4.5 21.4 1.0 O A:HOH2061 4.5 37.1 1.0 OP2 B:DA14 4.5 34.4 1.0 CB A:ALA116 4.6 20.1 1.0 CD A:GLN42 4.6 49.0 1.0 C5' C:DC16 4.9 29.6 1.0 CA A:ALA117 4.9 21.9 1.0 C3' B:DA14 4.9 34.5 1.0 O3' B:DA14 4.9 38.1 1.0 O A:GLY20 5.0 27.1 1.0 N A:ALA116 5.0 22.5 1.0

Manganese binding site 2 out of 6 in the The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna 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 E117A in Complex with Its Target Dna and in the Presence of 2MM Mn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1026 b:45.5 occ:1.00 OP2 C:DC15 2.1 47.5 1.0 OP1 B:DG15 2.1 28.4 1.0 O B:HOH2018 2.1 37.2 1.0 O B:HOH2043 2.4 43.6 1.0 O B:HOH2019 2.5 56.7 1.0 O B:HOH2020 2.6 47.9 1.0 P B:DG15 3.4 30.1 1.0 P C:DC15 3.4 40.4 1.0 OP2 B:DG15 3.8 27.4 1.0 O3' C:DA14 4.0 68.8 1.0 C4' B:DG15 4.0 34.5 1.0 O4' B:DG15 4.1 36.2 1.0 O C:HOH2009 4.1 50.9 1.0 OP1 C:DC15 4.3 44.5 1.0 O2 C:DT13 4.4 50.3 1.0 O3' B:DA14 4.4 38.1 1.0 O5' B:DG15 4.5 33.2 1.0 O5' C:DC15 4.5 40.7 1.0 O A:HOH2002 4.6 42.5 1.0 N3 B:DA14 4.6 33.8 1.0 C5' C:DC15 4.6 33.0 1.0 C5' B:DG15 4.7 27.5 1.0 C1' B:DG15 4.8 32.0 1.0 O B:HOH2021 4.8 44.5 1.0 C4' C:DA14 5.0 58.0 1.0

Manganese binding site 3 out of 6 in the The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna 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 E117A in Complex with Its Target Dna and in the Presence of 2MM Mn within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1197 b:31.3 occ:1.00 OP1 E:DA14 2.1 37.6 1.0 O D:HOH2007 2.2 24.2 1.0 OP1 F:DC16 2.2 47.2 1.0 O D:ALA116 2.3 30.2 1.0 OD2 D:ASP21 2.3 26.4 1.0 OD1 D:ASP21 2.5 20.1 1.0 CG D:ASP21 2.7 17.3 1.0 P F:DC16 3.0 36.9 1.0 OP2 F:DC16 3.0 39.8 1.0 C D:ALA116 3.3 35.1 1.0 P E:DA14 3.6 32.0 1.0 O D:HOH2006 3.8 16.0 1.0 CA D:ALA116 3.8 30.2 1.0 NE2 D:GLN42 4.0 34.0 1.0 O D:HOH2057 4.1 41.1 1.0 O3' F:DC15 4.1 51.9 1.0 O3' E:DA13 4.2 33.8 1.0 CB D:ASP21 4.2 16.2 1.0 O5' F:DC16 4.2 45.6 1.0 C5' E:DA14 4.3 27.6 1.0 OE1 D:GLN42 4.3 51.3 1.0 C4' E:DA14 4.3 26.1 1.0 O D:HOH2056 4.4 52.6 1.0 O D:VAL115 4.4 35.1 1.0 O5' E:DA14 4.5 33.8 1.0 N D:ALA117 4.5 29.0 1.0 OP2 E:DA14 4.5 30.0 1.0 CD D:GLN42 4.5 38.6 1.0 CB D:ALA116 4.6 19.4 1.0 C5' F:DC16 4.7 35.7 1.0 CA D:ALA117 4.9 26.6 1.0 O3' E:DA14 4.9 33.8 1.0 O D:GLY20 4.9 32.5 1.0 C3' E:DA14 5.0 25.3 1.0 N D:ALA116 5.0 26.4 1.0

Manganese binding site 4 out of 6 in the The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna 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 E117A in Complex with Its Target Dna and in the Presence of 2MM Mn within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn1028 b:45.5 occ:1.00 OP1 F:DC15 2.1 58.5 1.0 OP1 E:DG15 2.2 26.7 1.0 O E:HOH2006 2.2 32.5 1.0 O E:HOH2007 2.2 49.0 1.0 O E:HOH2008 2.7 55.4 1.0 O F:HOH2006 3.0 59.8 1.0 P F:DC15 3.5 56.8 1.0 P E:DG15 3.5 32.7 1.0 O3' F:DA14 3.9 65.5 1.0 OP2 E:DG15 4.1 36.4 1.0 C4' E:DG15 4.2 35.4 1.0 O2 F:DT13 4.3 60.2 1.0 O4' E:DG15 4.4 34.0 1.0 OP2 F:DC15 4.4 64.0 1.0 O5' F:DC15 4.5 54.8 1.0 O3' E:DA14 4.5 33.8 1.0 O D:HOH2002 4.5 54.0 1.0 O5' E:DG15 4.5 36.0 1.0 N3 E:DA14 4.6 33.9 1.0 C5' F:DC15 4.6 46.7 1.0 C5' E:DG15 4.7 30.9 1.0 O E:HOH2009 4.9 48.6 1.0

Manganese binding site 5 out of 6 in the The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna 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 E117A in Complex with Its Target Dna and in the Presence of 2MM Mn within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn1183 b:32.5 occ:1.00 OP1 H:DA14 2.1 42.7 1.0 OP2 I:DC16 2.2 37.1 1.0 OD2 G:ASP21 2.3 27.0 1.0 O G:ALA116 2.3 24.1 1.0 O G:HOH2007 2.3 33.0 1.0 OD1 G:ASP21 2.5 23.8 1.0 CG G:ASP21 2.7 27.6 1.0 P I:DC16 3.1 32.1 1.0 OP1 I:DC16 3.3 32.7 1.0 C G:ALA116 3.3 28.2 1.0 P H:DA14 3.5 36.3 1.0 CA G:ALA116 3.7 27.2 1.0 O G:HOH2006 3.7 15.1 1.0 O3' H:DA13 4.1 37.6 1.0 O G:HOH2051 4.2 53.7 1.0 O3' I:DC15 4.2 46.6 1.0 CB G:ASP21 4.2 24.6 1.0 NE2 G:GLN42 4.2 47.4 1.0 C5' H:DA14 4.3 32.0 1.0 C4' H:DA14 4.3 32.6 1.0 O5' I:DC16 4.3 35.4 1.0 O5' H:DA14 4.4 38.9 1.0 OP2 H:DA14 4.4 40.8 1.0 OE1 G:GLN42 4.5 50.0 1.0 CB G:ALA116 4.5 23.2 1.0 O G:VAL115 4.5 31.9 1.0 N G:ALA117 4.5 31.1 1.0 NZ G:LYS120 4.5 52.6 1.0 CD G:GLN42 4.7 43.6 1.0 C5' I:DC16 4.8 30.8 1.0 CA G:ALA117 4.9 31.6 1.0 N G:ALA116 4.9 33.9 1.0 O3' H:DA14 5.0 29.8 1.0 O G:GLY20 5.0 29.2 1.0

Manganese binding site 6 out of 6 in the The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna 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 E117A in Complex with Its Target Dna and in the Presence of 2MM Mn within 5.0Å range: probe atom residue distance (Å) B Occ H:Mn1027 b:43.5 occ:1.00 OP1 I:DC15 2.1 52.1 1.0 OP1 H:DG15 2.1 31.4 1.0 O H:HOH2008 2.2 41.7 1.0 O H:HOH2010 2.3 40.0 1.0 O H:HOH2019 2.4 45.1 1.0 O H:HOH2009 2.4 52.9 1.0 P H:DG15 3.4 33.6 1.0 P I:DC15 3.4 45.3 1.0 O3' I:DA14 3.9 58.4 1.0 OP2 H:DG15 3.9 33.9 1.0 C4' H:DG15 4.1 32.8 1.0 O2 I:DT13 4.3 55.1 1.0 O4' H:DG15 4.3 36.5 1.0 OP2 I:DC15 4.4 47.1 1.0 O3' H:DA14 4.4 29.8 1.0 O5' I:DC15 4.5 49.9 1.0 O5' H:DG15 4.5 30.9 1.0 N3 H:DA14 4.6 33.4 1.0 OXT I:ACT1026 4.6 68.4 1.0 C5' I:DC15 4.6 40.9 1.0 O G:HOH2003 4.6 49.5 1.0 C5' H:DG15 4.7 28.5 1.0 C1' H:DG15 4.8 36.2 1.0 O H:HOH2012 4.9 43.8 1.0 C1' H:DA14 4.9 33.9 1.0 C4' I:DA14 4.9 62.3 1.0 C2' H:DA14 5.0 25.3 1.0

R.Molina, N.Besker, J.Prieto, G.Montoya, M.D'abramo. Structural and Dynamical Characterization of the I- Dmo Catalytic Activity To Be Published.