Zinc in PDB 4un7: The Crystal Structure of I-Dmoi in Complex with Its Target Dna Before Incubation in 5MM Mn (State 1)

The structure of The Crystal Structure of I-Dmoi in Complex with Its Target Dna Before Incubation in 5MM Mn (State 1), PDB code: 4un7 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)	46.195 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	106.570, 70.347, 106.601, 90.00, 119.89, 90.00
R / Rfree (%)	17.73 / 23.19

The binding sites of Zinc atom in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna Before Incubation in 5MM Mn (State 1) (pdb code 4un7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna Before Incubation in 5MM Mn (State 1), PDB code: 4un7:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna Before Incubation in 5MM Mn (State 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of I-Dmoi in Complex with Its Target Dna Before Incubation in 5MM Mn (State 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1188 b:87.3 occ:1.00 OP1 B:DA14 2.2 63.7 1.0 OP2 C:DC16 2.3 52.5 1.0 O A:ALA116 2.5 60.7 1.0 O A:HOH2005 2.6 42.9 1.0 OD2 A:ASP21 2.6 55.9 1.0 OD1 A:ASP21 2.8 55.6 1.0 CG A:ASP21 3.1 52.3 1.0 O A:HOH2004 3.4 36.9 1.0 C A:ALA116 3.5 55.3 1.0 P C:DC16 3.6 53.1 1.0 P B:DA14 3.7 58.5 1.0 CA A:ALA116 4.0 56.5 1.0 NZ A:LYS120 4.1 75.0 1.0 C5' B:DA14 4.2 53.6 1.0 O5' C:DC16 4.2 54.2 1.0 C4' B:DA14 4.2 53.0 1.0 OP1 C:DC16 4.3 51.9 1.0 O3' B:DA13 4.4 53.7 1.0 O5' B:DA14 4.4 63.7 1.0 NE2 A:GLN42 4.5 58.1 1.0 CB A:ASP21 4.6 47.4 1.0 C5' C:DC16 4.6 53.0 1.0 OP2 B:DA14 4.6 63.5 1.0 N A:GLU117 4.7 53.9 1.0 CB A:ALA116 4.7 50.9 1.0 O3' C:DC15 4.7 47.8 1.0 O A:VAL115 4.8 52.9 1.0 O3' B:DA14 4.8 49.9 1.0 OE1 A:GLU117 4.9 55.1 1.0 CD A:GLN42 5.0 58.1 1.0 C3' B:DA14 5.0 50.4 1.0

Zinc binding site 2 out of 3 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna Before Incubation in 5MM Mn (State 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of I-Dmoi in Complex with Its Target Dna Before Incubation in 5MM Mn (State 1) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1197 b:80.4 occ:1.00 OP2 F:DC16 2.4 50.9 1.0 O D:HOH2003 2.4 50.0 1.0 OP1 E:DA14 2.4 53.3 1.0 O D:ALA116 2.6 55.3 1.0 OD2 D:ASP21 2.6 44.8 1.0 O D:HOH2018 2.8 61.0 1.0 OD1 D:ASP21 3.0 53.6 1.0 CG D:ASP21 3.2 48.9 1.0 C D:ALA116 3.6 49.3 1.0 P F:DC16 3.6 49.0 1.0 P E:DA14 3.8 51.0 1.0 O D:HOH2002 3.9 40.5 1.0 NE2 D:GLN42 4.0 56.6 1.0 CA D:ALA116 4.0 47.0 1.0 NZ D:LYS120 4.1 80.9 1.0 O5' F:DC16 4.2 58.0 1.0 C5' F:DC16 4.3 54.4 1.0 OP1 F:DC16 4.3 54.4 1.0 O D:VAL115 4.3 52.0 1.0 O3' E:DA13 4.3 52.5 1.0 OE1 D:GLN42 4.4 55.2 1.0 C5' E:DA14 4.5 51.0 1.0 C4' E:DA14 4.5 52.0 1.0 CD D:GLN42 4.7 55.4 1.0 CB D:ASP21 4.7 49.4 1.0 O5' E:DA14 4.7 51.4 1.0 N D:GLU117 4.8 55.9 1.0 CE D:LYS120 4.8 92.6 1.0 O3' F:DC15 4.8 55.8 1.0 OP2 E:DA14 4.9 55.9 1.0 CB D:ALA116 4.9 48.0 1.0

Zinc binding site 3 out of 3 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna Before Incubation in 5MM Mn (State 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of I-Dmoi in Complex with Its Target Dna Before Incubation in 5MM Mn (State 1) within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1182 b:88.2 occ:1.00 OP2 I:DC16 2.3 52.2 1.0 O G:ALA116 2.4 55.6 1.0 OP1 H:DA14 2.4 58.8 1.0 OD2 G:ASP21 2.7 60.8 1.0 OD1 G:ASP21 2.7 59.9 1.0 O G:HOH2005 2.8 59.5 1.0 CG G:ASP21 3.1 60.0 1.0 C G:ALA116 3.4 57.5 1.0 O G:HOH2004 3.6 38.4 1.0 OE1 G:GLN42 3.7 69.7 1.0 P I:DC16 3.7 48.0 1.0 CA G:ALA116 3.8 52.2 1.0 P H:DA14 3.9 56.2 1.0 O5' I:DC16 4.4 44.8 1.0 C5' I:DC16 4.4 54.4 1.0 CB G:ALA116 4.4 48.6 1.0 C5' H:DA14 4.4 51.7 1.0 OP1 I:DC16 4.5 65.5 1.0 C4' H:DA14 4.5 49.2 1.0 CB G:ASP21 4.6 54.0 1.0 CD G:GLN42 4.6 67.3 1.0 N G:GLU117 4.6 54.7 1.0 O3' H:DA13 4.6 64.7 1.0 NZ G:LYS120 4.7 73.6 1.0 NE2 G:GLN42 4.7 71.5 1.0 O G:VAL115 4.7 49.0 1.0 O5' H:DA14 4.7 56.5 1.0 O3' I:DC15 4.8 52.0 1.0 OP2 H:DA14 4.8 52.8 1.0 O3' H:DA14 4.9 53.6 1.0 CA G:GLU117 5.0 59.5 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: ISSN 1545-9993
DOI: 10.1038/NSMB.2932