Manganese in PDB 4ut0: The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 10 Days Incubation in 5MM Mn (State 7)

The structure of The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 10 Days Incubation in 5MM Mn (State 7), PDB code: 4ut0 was solved by R.Molina, S.Stella, P.Redondo, H.Gomez, M.J.Marcaida, M.Orozco, J.Prieto, G.Montoya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.489 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	106.984, 70.387, 107.154, 90.00, 119.81, 90.00
R / Rfree (%)	18.29 / 22.82

The binding sites of Manganese atom in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 10 Days Incubation in 5MM Mn (State 7) (pdb code 4ut0). 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 in Complex with Its Target Dna at 10 Days Incubation in 5MM Mn (State 7), PDB code: 4ut0:
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 in Complex with Its Target Dna at 10 Days Incubation in 5MM Mn (State 7)


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 in Complex with Its Target Dna at 10 Days Incubation in 5MM Mn (State 7) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1188 b:45.4 occ:1.00 O A:HOH2004 1.9 38.5 1.0 OP1 B:DA14 1.9 49.2 1.0 OD2 A:ASP21 2.2 42.1 1.0 OP3 E:DC16 2.2 47.6 1.0 O A:ALA116 2.3 41.0 1.0 OP1 E:DC16 2.6 50.1 1.0 P E:DC16 2.9 60.5 1.0 CG A:ASP21 3.0 42.3 1.0 OD1 A:ASP21 3.1 47.0 1.0 C A:ALA116 3.3 41.2 1.0 P B:DA14 3.4 47.4 1.0 O A:HOH2019 3.8 47.9 1.0 CA A:ALA116 3.8 41.9 1.0 O3' B:DA13 3.9 48.5 1.0 O5' E:DC16 4.0 53.3 1.0 O A:HOH2003 4.0 32.5 1.0 OP2 E:DC16 4.1 51.7 1.0 NE2 A:GLN42 4.1 41.4 1.0 C5' B:DA14 4.2 46.7 1.0 C4' B:DA14 4.2 49.8 1.0 O5' B:DA14 4.3 53.5 1.0 O A:VAL115 4.4 43.6 1.0 OP2 B:DA14 4.4 51.9 1.0 CB A:ASP21 4.4 37.6 1.0 N A:GLU117 4.5 30.0 1.0 OE1 A:GLN42 4.6 60.8 1.0 O3' B:DA14 4.6 48.2 1.0 CB A:ALA116 4.6 32.4 1.0 CD A:GLN42 4.7 53.5 1.0 C3' B:DA14 4.8 41.9 1.0 C5' E:DC16 4.8 46.6 1.0 CA A:GLU117 4.9 30.0 1.0 N A:ALA116 4.9 37.5 1.0

Manganese binding site 2 out of 6 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 10 Days Incubation in 5MM Mn (State 7)


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 in Complex with Its Target Dna at 10 Days Incubation in 5MM Mn (State 7) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1189 b:47.0 occ:1.00 OP1 C:DG15 2.0 47.9 1.0 OP1 D:DC15 2.1 37.5 1.0 O A:HOH2002 2.3 36.2 1.0 O A:GLY20 2.3 42.9 1.0 OE2 A:GLU117 2.4 20.0 1.0 OE1 A:GLU117 2.7 20.0 1.0 CD A:GLU117 2.9 20.0 1.0 P C:DG15 3.0 42.8 1.0 OP3 C:DG15 3.0 45.1 1.0 C A:GLY20 3.4 40.2 1.0 P D:DC15 3.5 41.2 1.0 O A:HOH2029 3.6 43.2 1.0 ND2 A:ASN129 3.6 37.0 1.0 CA A:GLY20 3.8 39.4 1.0 O3' D:DA14 3.9 40.4 1.0 O5' C:DG15 3.9 45.3 1.0 O A:HOH2003 3.9 32.5 1.0 O A:ILE19 4.0 36.9 1.0 OP2 C:DG15 4.1 40.5 1.0 C5' D:DC15 4.4 40.7 1.0 C4' D:DC15 4.4 43.4 1.0 C5' C:DG15 4.4 40.8 1.0 O5' D:DC15 4.4 42.1 1.0 CG A:GLU117 4.4 20.0 1.0 OP2 D:DC15 4.5 42.9 1.0 N A:ASP21 4.6 36.9 1.0 CG A:ASN129 4.8 41.3 1.0 OD1 A:ASP21 4.8 47.0 1.0 N A:GLY20 4.8 36.4 1.0 C A:ILE19 4.9 37.7 1.0 CA A:ASP21 5.0 39.7 1.0

Manganese binding site 3 out of 6 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 10 Days Incubation in 5MM Mn (State 7)


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 in Complex with Its Target Dna at 10 Days Incubation in 5MM Mn (State 7) within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn1196 b:45.2 occ:1.00 OP1 G:DA14 2.0 45.1 1.0 O F:HOH2003 2.0 41.5 1.0 OD2 F:ASP21 2.2 40.0 1.0 OP2 J:DC16 2.2 52.3 1.0 O F:ALA116 2.4 46.5 1.0 OP3 J:DC16 2.5 52.0 1.0 P J:DC16 2.8 57.5 1.0 CG F:ASP21 3.0 39.2 1.0 OD1 F:ASP21 3.2 43.7 1.0 C F:ALA116 3.4 51.5 1.0 P G:DA14 3.4 39.4 1.0 OE1 F:GLN42 3.7 56.6 1.0 NZ F:LYS120 3.7 59.1 1.0 CA F:ALA116 3.8 44.0 1.0 OP1 J:DC16 3.9 57.3 1.0 O5' J:DC16 3.9 57.1 1.0 O F:HOH2002 4.0 32.6 1.0 O3' G:DA13 4.0 46.6 1.0 C5' G:DA14 4.1 43.4 1.0 C4' G:DA14 4.2 43.4 1.0 O5' G:DA14 4.3 44.8 1.0 O F:VAL115 4.3 47.6 1.0 NE2 F:GLN42 4.3 65.9 1.0 CD F:GLN42 4.3 50.4 1.0 OP2 G:DA14 4.3 42.7 1.0 CB F:ASP21 4.4 38.4 1.0 N F:GLU117 4.6 47.1 1.0 CB F:ALA116 4.7 39.6 1.0 O3' G:DA14 4.8 41.2 1.0 C5' J:DC16 4.8 53.5 1.0 CE F:LYS120 4.8 61.8 1.0 C3' G:DA14 4.9 40.2 1.0 N F:ALA116 4.9 44.1 1.0

Manganese binding site 4 out of 6 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 10 Days Incubation in 5MM Mn (State 7)


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 in Complex with Its Target Dna at 10 Days Incubation in 5MM Mn (State 7) within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn1197 b:47.9 occ:1.00 OE2 F:GLU117 1.3 56.6 1.0 OP2 H:DG15 2.1 48.7 1.0 CD F:GLU117 2.2 56.5 1.0 OP1 I:DC15 2.3 55.8 1.0 O F:GLY20 2.4 41.8 1.0 O F:HOH2001 2.4 41.3 1.0 OE1 F:GLU117 2.5 62.5 1.0 OP3 H:DG15 3.0 52.3 1.0 P H:DG15 3.1 44.8 1.0 C F:GLY20 3.4 41.0 1.0 P I:DC15 3.6 45.3 1.0 CA F:GLY20 3.8 41.6 1.0 CG F:GLU117 3.8 45.9 1.0 ND2 F:ASN129 3.8 46.0 1.0 O F:HOH2002 3.9 32.6 1.0 O F:ILE19 3.9 39.8 1.0 O5' H:DG15 3.9 39.5 1.0 O5' I:DC15 4.0 56.2 1.0 O3' I:DA14 4.1 46.4 1.0 OP1 H:DG15 4.4 46.2 1.0 O F:HOH2023 4.5 46.6 1.0 C5' H:DG15 4.5 40.6 1.0 N F:ASP21 4.6 39.8 1.0 C4' I:DC15 4.6 51.8 1.0 OD1 F:ASP21 4.7 43.7 1.0 C F:ILE19 4.8 38.0 1.0 N F:GLY20 4.8 36.3 1.0 CB F:GLU117 4.8 56.8 1.0 OP2 I:DC15 4.8 57.0 1.0 CG F:ASN129 4.8 46.7 1.0 C5' I:DC15 4.9 53.8 1.0

Manganese binding site 5 out of 6 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 10 Days Incubation in 5MM Mn (State 7)


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 in Complex with Its Target Dna at 10 Days Incubation in 5MM Mn (State 7) within 5.0Å range: probe atom residue distance (Å) B Occ K:Mn1183 b:44.0 occ:1.00 OP1 M:DG15 2.0 45.4 1.0 OE2 K:GLU117 2.1 51.0 1.0 OP1 N:DC15 2.1 36.7 1.0 O K:GLY20 2.2 34.3 1.0 OE1 K:GLU117 2.4 48.8 1.0 O K:HOH2002 2.5 33.7 1.0 CD K:GLU117 2.6 44.5 1.0 OP3 M:DG15 2.9 43.9 1.0 P M:DG15 3.0 41.1 1.0 C K:GLY20 3.3 39.9 1.0 P N:DC15 3.5 41.5 1.0 O M:HOH2001 3.7 51.2 1.0 O K:HOH2003 3.7 35.2 1.0 CA K:GLY20 3.8 38.3 1.0 O K:ILE19 3.8 42.5 1.0 O5' M:DG15 3.9 45.3 1.0 ND2 K:ASN129 3.9 42.5 1.0 O3' N:DA14 3.9 39.9 1.0 CG K:GLU117 4.1 51.2 1.0 OP2 M:DG15 4.2 47.9 1.0 C4' N:DC15 4.4 42.6 1.0 C5' M:DG15 4.4 42.9 1.0 N K:ASP21 4.4 36.4 1.0 C5' N:DC15 4.4 40.7 1.0 O K:HOH2019 4.5 40.6 1.0 O5' N:DC15 4.5 49.8 1.0 OP2 N:DC15 4.5 40.2 1.0 OD1 K:ASP21 4.6 38.6 1.0 O N:HOH2002 4.6 46.8 1.0 C K:ILE19 4.7 42.8 1.0 N K:GLY20 4.7 39.6 1.0 CA K:ASP21 4.8 37.8 1.0 CG K:ASN129 5.0 45.0 1.0 CB K:GLU117 5.0 48.8 1.0

Manganese binding site 6 out of 6 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 10 Days Incubation in 5MM Mn (State 7)


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 in Complex with Its Target Dna at 10 Days Incubation in 5MM Mn (State 7) within 5.0Å range: probe atom residue distance (Å) B Occ K:Mn1184 b:44.3 occ:1.00 OP3 O:DC16 1.9 46.8 1.0 O K:HOH2004 2.0 39.2 1.0 OP2 L:DA14 2.1 43.6 1.0 O K:ALA116 2.2 36.1 1.0 OD2 K:ASP21 2.3 40.0 1.0 OP1 O:DC16 2.6 45.6 1.0 P O:DC16 2.7 61.8 1.0 CG K:ASP21 3.1 41.5 1.0 OD1 K:ASP21 3.2 38.6 1.0 C K:ALA116 3.3 42.2 1.0 P L:DA14 3.5 45.7 1.0 CA K:ALA116 3.7 40.8 1.0 OP2 O:DC16 3.8 54.8 1.0 O5' O:DC16 3.9 51.9 1.0 O K:HOH2003 4.0 35.2 1.0 NZ K:LYS120 4.1 52.4 1.0 O3' L:DA13 4.1 45.9 1.0 NE2 K:GLN42 4.2 51.0 1.0 O K:VAL115 4.3 43.7 1.0 C5' L:DA14 4.3 41.3 1.0 C4' L:DA14 4.4 43.0 1.0 N K:GLU117 4.4 41.9 1.0 OP1 L:DA14 4.5 44.6 1.0 O5' L:DA14 4.5 45.1 1.0 CB K:ALA116 4.5 38.9 1.0 CB K:ASP21 4.6 37.7 1.0 OE1 K:GLN42 4.6 55.0 1.0 CD K:GLN42 4.7 53.0 1.0 C5' O:DC16 4.8 41.8 1.0 CA K:GLU117 4.8 46.8 1.0 O3' L:DA14 4.9 38.6 1.0 N K:ALA116 4.9 40.1 1.0 C3' L:DA14 5.0 43.3 1.0

R.Molina, S.Stella, P.Redondo, H.Gomez, M.J.Marcaida, M.Orozco, J.Prieto, G.Montoya. Visualizing Phosphodiester-Bond Hydrolysis By An Endonuclease. Nat.Struct.Mol.Biol. 2014.
ISSN: ESSN 1545-9985
PubMed: 25486305
DOI: 10.1038/NSMB.2932