Manganese in PDB 5o6g: Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi

The structure of Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi, PDB code: 5o6g was solved by R.Molina, M.J.Marcaida, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.18 / 2.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	107.280, 70.500, 107.150, 90.00, 119.89, 90.00
R / Rfree (%)	17.7 / 23.2

The structure of Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Manganese atom in the Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi (pdb code 5o6g). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi, PDB code: 5o6g:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:39.8 occ:1.00 OP1 B:DA14 2.2 37.3 1.0 O A:ALA116 2.3 40.1 1.0 OP2 C:DC16 2.4 39.9 1.0 OD2 A:ASP21 2.4 36.0 1.0 O A:HOH301 2.7 41.5 1.0 OD1 A:ASP21 2.9 39.2 1.0 CG A:ASP21 3.0 35.5 1.0 C A:ALA116 3.3 42.6 1.0 NZ A:LYS120 3.4 49.0 1.0 CA A:ALA116 3.6 42.1 1.0 P B:DA14 3.7 31.6 1.0 P C:DC16 3.7 57.0 1.0 O5' C:DC16 3.8 41.6 1.0 OE1 A:GLN42 3.9 42.1 1.0 O A:HOH302 3.9 41.0 1.0 O A:VAL115 4.0 49.7 1.0 CE A:LYS120 4.1 57.3 1.0 C5' B:DA14 4.2 36.5 1.0 NE2 A:GLN42 4.3 37.4 1.0 O3' B:DA13 4.3 40.7 1.0 CD A:GLN42 4.4 41.5 1.0 CB A:ASP21 4.4 37.2 1.0 O5' B:DA14 4.4 37.1 1.0 N A:GLU117 4.5 47.8 1.0 CB A:ALA116 4.5 32.1 1.0 C4' B:DA14 4.5 38.9 1.0 OP2 B:DA14 4.6 37.0 1.0 OP1 C:DC16 4.6 48.7 1.0 O3' C:DC15 4.7 45.5 1.0 N A:ALA116 4.7 38.4 1.0 C A:VAL115 4.8 41.0 1.0 CA A:GLU117 5.0 50.4 1.0

Manganese binding site 2 out of 6 in the Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:45.7 occ:1.00 OE2 A:GLU117 1.7 73.5 1.0 OP1 C:DC15 2.0 41.8 1.0 OP2 B:DG15 2.1 49.2 1.0 O A:GLY20 2.5 39.5 1.0 CD A:GLU117 2.6 45.8 1.0 OE1 A:GLU117 2.9 51.3 1.0 O A:HOH305 3.2 40.7 1.0 P C:DC15 3.4 38.3 1.0 P B:DG15 3.4 51.5 1.0 C A:GLY20 3.6 38.3 1.0 ND2 A:ASN129 3.7 35.9 1.0 O3' C:DA14 3.9 35.8 1.0 O A:ILE19 3.9 42.7 1.0 O5' B:DG15 3.9 44.6 1.0 CG A:GLU117 4.0 45.0 1.0 O A:HOH302 4.0 41.0 1.0 OP1 B:DG15 4.0 48.7 1.0 CA A:GLY20 4.0 38.7 1.0 C5' B:DG15 4.1 38.6 1.0 C5' C:DC15 4.2 43.3 1.0 C4' C:DC15 4.3 43.8 1.0 O5' C:DC15 4.3 42.0 1.0 OP2 C:DC15 4.3 37.1 1.0 O3' B:DA14 4.6 35.6 1.0 N A:ASP21 4.7 36.1 1.0 CG A:ASN129 4.8 39.6 1.0 C A:ILE19 4.9 37.3 1.0 N A:GLY20 5.0 39.2 1.0

Manganese binding site 3 out of 6 in the Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn201 b:42.1 occ:1.00 OP2 F:DC16 2.0 55.6 1.0 O D:HOH305 2.0 38.0 1.0 OP1 E:DA14 2.3 42.4 1.0 O D:ALA116 2.4 42.5 1.0 OD2 D:ASP21 2.4 40.8 1.0 OD1 D:ASP21 3.0 42.9 1.0 CG D:ASP21 3.0 39.7 1.0 P F:DC16 3.4 56.9 1.0 C D:ALA116 3.4 44.4 1.0 O D:HOH301 3.6 35.2 1.0 P E:DA14 3.7 37.6 1.0 CA D:ALA116 3.8 39.3 1.0 OP1 F:DC16 4.0 55.2 1.0 O5' F:DC16 4.1 46.8 1.0 C5' E:DA14 4.2 40.0 1.0 O3' E:DA13 4.2 38.0 1.0 NE2 D:GLN42 4.2 40.0 1.0 O D:VAL115 4.3 36.1 1.0 C4' E:DA14 4.4 38.3 1.0 C5' F:DC16 4.4 50.3 1.0 O5' E:DA14 4.5 42.1 1.0 CB D:ASP21 4.5 35.4 1.0 O3' F:DC15 4.5 43.2 1.0 NZ D:LYS120 4.5 53.4 1.0 CB D:ALA116 4.6 33.4 1.0 N D:GLU117 4.6 38.6 1.0 OE1 D:GLN42 4.6 43.1 1.0 OP2 E:DA14 4.7 42.9 1.0 CD D:GLN42 4.7 44.0 1.0 N D:ALA116 4.9 38.8 1.0 OE1 D:GLU117 4.9 43.3 1.0

Manganese binding site 4 out of 6 in the Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn202 b:41.4 occ:1.00 OP2 E:DG15 2.0 38.3 1.0 OE2 D:GLU117 2.1 43.0 1.0 OP1 F:DC15 2.1 35.5 1.0 O D:GLY20 2.2 37.5 1.0 O D:HOH302 2.5 39.5 1.0 O E:HOH105 2.5 48.1 1.0 CD D:GLU117 2.9 44.9 1.0 OE1 D:GLU117 3.2 43.3 1.0 P E:DG15 3.2 39.2 1.0 C D:GLY20 3.3 37.8 1.0 P F:DC15 3.5 41.1 1.0 O5' E:DG15 3.8 41.9 1.0 O D:ILE19 3.8 42.6 1.0 CA D:GLY20 3.9 38.3 1.0 ND2 D:ASN129 3.9 36.0 1.0 OP1 E:DG15 3.9 42.6 1.0 C5' F:DC15 3.9 42.4 1.0 O D:HOH301 3.9 35.2 1.0 O3' F:DA14 3.9 43.5 1.0 C5' E:DG15 4.0 34.9 1.0 O F:HOH105 4.0 39.2 1.0 O5' F:DC15 4.2 46.6 1.0 CG D:GLU117 4.2 41.5 1.0 C4' F:DC15 4.2 40.0 1.0 O3' E:DA14 4.4 39.4 1.0 N D:ASP21 4.5 34.0 1.0 OP2 F:DC15 4.6 38.8 1.0 C D:ILE19 4.7 39.8 1.0 OD1 D:ASP21 4.8 42.9 1.0 CA D:ASP21 4.8 36.4 1.0 N D:GLY20 4.8 36.8 1.0 CG D:ASN129 5.0 36.2 1.0

Manganese binding site 5 out of 6 in the Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn201 b:43.2 occ:1.00 OP2 I:DC16 2.1 49.0 1.0 OP1 H:DA14 2.1 56.4 1.0 O G:HOH303 2.2 29.6 1.0 O G:ALA116 2.3 43.4 1.0 OD2 G:ASP21 2.3 38.0 1.0 OD1 G:ASP21 3.0 46.1 1.0 CG G:ASP21 3.0 40.9 1.0 O I:HOH104 3.0 33.5 1.0 C G:ALA116 3.4 41.1 1.0 P I:DC16 3.4 54.8 1.0 P H:DA14 3.5 50.4 1.0 O G:HOH301 3.6 31.2 1.0 OP1 I:DC16 3.8 37.2 1.0 CA G:ALA116 3.9 42.0 1.0 C5' H:DA14 4.0 44.8 1.0 O3' H:DA13 4.0 45.3 1.0 O5' I:DC16 4.2 48.0 1.0 O5' H:DA14 4.3 52.4 1.0 C4' H:DA14 4.3 47.6 1.0 NZ G:LYS120 4.4 51.8 1.0 CB G:ASP21 4.4 36.5 1.0 O G:VAL115 4.4 42.3 1.0 OE1 G:GLN42 4.5 48.9 1.0 N G:GLU117 4.5 41.7 1.0 NE2 G:GLN42 4.5 47.2 1.0 OP2 H:DA14 4.5 50.6 1.0 O3' I:DC15 4.5 41.7 1.0 C5' I:DC16 4.6 42.9 1.0 CB G:ALA116 4.7 33.0 1.0 CD G:GLN42 4.8 53.9 1.0 CA G:GLU117 4.9 40.1 1.0 OE1 G:GLU117 5.0 42.0 1.0

Manganese binding site 6 out of 6 in the Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn202 b:45.3 occ:1.00 OP1 I:DC15 2.0 41.6 1.0 OP2 H:DG15 2.2 46.7 1.0 O G:GLY20 2.3 41.2 1.0 OE2 G:GLU117 2.4 33.5 1.0 O G:HOH305 2.6 38.2 1.0 OE1 G:GLU117 2.7 42.0 1.0 CD G:GLU117 2.9 38.5 1.0 O H:HOH102 2.9 45.4 1.0 P I:DC15 3.4 46.1 1.0 C G:GLY20 3.4 41.9 1.0 P H:DG15 3.4 43.9 1.0 O3' I:DA14 3.8 43.4 1.0 ND2 G:ASN129 3.9 37.1 1.0 OP1 H:DG15 3.9 39.3 1.0 CA G:GLY20 3.9 40.1 1.0 O5' H:DG15 4.0 42.9 1.0 O G:HOH301 4.0 31.2 1.0 O G:ILE19 4.0 39.5 1.0 C5' I:DC15 4.0 41.2 1.0 C5' H:DG15 4.1 38.9 1.0 O5' I:DC15 4.2 44.3 1.0 C4' I:DC15 4.3 38.3 1.0 CG G:GLU117 4.3 42.7 1.0 OP2 I:DC15 4.5 37.6 1.0 N G:ASP21 4.5 39.3 1.0 O3' H:DA14 4.6 47.5 1.0 OD1 G:ASP21 4.8 46.1 1.0 C G:ILE19 4.9 38.7 1.0 N G:GLY20 4.9 31.1 1.0 CA G:ASP21 4.9 38.4 1.0 CG G:ASN129 5.0 33.9 1.0

J.Alba, M.J.Marcaida, J.Prieto, G.Montoya, R.Molina, M.D'abramo. Structure and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi. J. Comput. Aided Mol. Des. V. 31 1063 2017.
ISSN: ESSN 1573-4951
PubMed: 29177929
DOI: 10.1007/S10822-017-0087-5