Manganese in PDB 4kpy: Dna Binding Protein and Dna Complex Structure

The structure of Dna Binding Protein and Dna Complex Structure, PDB code: 4kpy was solved by G.Sheng, H.Zhao, J.Wang, Y.Rao, Y.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.31 / 2.41
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	111.329, 118.362, 160.873, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 23.5

The binding sites of Manganese atom in the Dna Binding Protein and Dna Complex Structure (pdb code 4kpy). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Dna Binding Protein and Dna Complex Structure, PDB code: 4kpy:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Dna Binding Protein and Dna Complex Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dna Binding Protein and Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:33.0 occ:1.00 OP1 D:DT10 2.1 48.9 1.0 OD1 A:ASP660 2.1 27.2 1.0 OD2 A:ASP478 2.2 27.1 1.0 O A:HOH822 2.2 28.0 1.0 O D:HOH107 2.2 30.5 1.0 OP3 D:DT10 2.4 39.1 1.0 P D:DT10 2.8 34.4 1.0 CG A:ASP660 3.2 29.0 1.0 CG A:ASP478 3.2 27.0 1.0 OD1 A:ASP478 3.5 24.0 1.0 MN A:MN703 3.6 32.2 1.0 CB A:ASP660 3.7 19.9 1.0 O5' D:DT10 3.8 50.2 1.0 OP2 D:DT10 3.9 32.8 1.0 O A:HOH879 4.0 35.3 1.0 C5' D:DT10 4.1 43.3 1.0 OD2 A:ASP546 4.1 38.0 1.0 CA A:ASP660 4.1 20.2 1.0 OD2 A:ASP660 4.2 27.9 1.0 OP2 D:DA11 4.3 56.7 1.0 O A:ALA479 4.3 30.6 1.0 NZ A:LYS664 4.3 66.3 1.0 CG A:ASP546 4.5 35.5 1.0 CB A:ASP478 4.6 17.2 1.0 O3' N:DC9 4.6 41.6 1.0 OD1 A:ASP546 4.7 44.0 1.0 O A:HOH806 4.8 28.5 1.0 O A:ASP660 4.9 27.7 1.0 C A:ASP660 5.0 24.0 1.0

Manganese binding site 2 out of 6 in the Dna Binding Protein and Dna Complex Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dna Binding Protein and Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn703 b:32.2 occ:1.00 OP3 D:DT10 2.0 39.1 1.0 OD2 A:ASP546 2.1 38.0 1.0 O A:HOH803 2.2 32.1 1.0 O A:HOH806 2.2 28.5 1.0 O3' N:DC9 2.2 41.6 1.0 OD1 A:ASP478 2.2 24.0 1.0 CG A:ASP546 3.2 35.5 1.0 CG A:ASP478 3.3 27.0 1.0 P D:DT10 3.4 34.4 1.0 MN A:MN702 3.6 33.0 1.0 C3' N:DC9 3.6 43.3 1.0 OD2 A:ASP478 3.6 27.1 1.0 CB A:ASP546 3.7 28.7 1.0 O A:ALA479 3.9 30.6 1.0 C5' D:DT10 3.9 43.3 1.0 OP2 D:DT10 4.0 32.8 1.0 O A:HOH822 4.1 28.0 1.0 O5' D:DT10 4.1 50.2 1.0 C4' N:DC9 4.1 38.1 0.8 OD1 A:ASP546 4.2 44.0 1.0 OP1 D:DT10 4.3 48.9 1.0 N A:ALA479 4.4 23.1 1.0 C2' N:DC9 4.4 41.6 1.0 NZ A:LYS575 4.4 37.8 1.0 OE2 A:GLU512 4.4 37.8 1.0 OE1 A:GLU512 4.4 27.6 1.0 O A:ASP546 4.5 29.8 1.0 O D:HOH107 4.5 30.5 1.0 CB A:ASP478 4.6 17.2 1.0 C A:ASP546 4.6 36.1 1.0 C5' N:DC9 4.7 32.9 1.0 CA A:ASP546 4.8 30.5 1.0 CD A:GLU512 4.8 34.7 1.0 CA A:ASP478 4.8 17.7 1.0 C A:ALA479 4.9 25.7 1.0

Manganese binding site 3 out of 6 in the Dna Binding Protein and Dna Complex Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Dna Binding Protein and Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn702 b:32.5 occ:1.00 OP3 F:DT10 2.1 19.7 1.0 OD2 B:ASP546 2.1 37.2 1.0 O B:HOH936 2.2 35.4 1.0 OD1 B:ASP478 2.2 27.3 1.0 O3' M:DC9 2.2 48.4 1.0 O B:HOH801 2.2 22.7 1.0 CG B:ASP546 3.2 30.4 1.0 CG B:ASP478 3.2 30.5 1.0 P F:DT10 3.5 47.8 1.0 OD2 B:ASP478 3.6 38.0 1.0 C3' M:DC9 3.6 40.3 1.0 MN B:MN703 3.6 35.0 1.0 CB B:ASP546 3.7 21.2 1.0 O B:HOH823 3.8 30.9 1.0 OP2 F:DT10 3.8 30.6 1.0 O B:ALA479 3.9 38.6 1.0 C5' F:DT10 3.9 40.2 1.0 C4' M:DC9 4.1 36.4 1.0 O5' F:DT10 4.1 52.1 1.0 OD1 B:ASP546 4.1 41.0 1.0 NZ B:LYS575 4.3 34.9 1.0 OE2 B:GLU512 4.3 29.7 1.0 N B:ALA479 4.3 30.5 1.0 O B:HOH867 4.3 34.4 1.0 C2' M:DC9 4.4 45.9 1.0 O B:ASP546 4.5 29.1 1.0 OP1 F:DT10 4.6 37.6 1.0 CB B:ASP478 4.6 28.4 1.0 C5' M:DC9 4.6 30.5 1.0 OE1 B:GLU512 4.6 41.9 1.0 C B:ASP546 4.7 28.0 1.0 CA B:ASP546 4.9 28.6 1.0 CA B:ASP478 4.9 23.1 1.0 CD B:GLU512 4.9 31.9 1.0 C B:ALA479 4.9 33.1 1.0

Manganese binding site 4 out of 6 in the Dna Binding Protein and Dna Complex Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Dna Binding Protein and Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn703 b:35.0 occ:1.00 OD1 B:ASP660 2.1 25.4 1.0 OD2 B:ASP478 2.2 38.0 1.0 O B:HOH823 2.2 30.9 1.0 O B:HOH867 2.2 34.4 1.0 OP3 F:DT10 2.2 19.7 1.0 OP1 F:DT10 2.5 37.6 1.0 P F:DT10 2.9 47.8 1.0 CG B:ASP660 3.1 30.9 1.0 CG B:ASP478 3.2 30.5 1.0 CB B:ASP660 3.5 24.5 1.0 OD1 B:ASP478 3.5 27.3 1.0 MN B:MN702 3.6 32.5 1.0 OP2 F:DT10 3.9 30.6 1.0 O B:HOH879 3.9 30.8 1.0 CA B:ASP660 4.0 21.8 1.0 O5' F:DT10 4.0 52.1 1.0 O F:HOH106 4.2 51.7 1.0 OD2 B:ASP546 4.2 37.2 1.0 OD2 B:ASP660 4.2 48.1 1.0 C5' F:DT10 4.3 40.2 1.0 O B:ALA479 4.3 38.6 1.0 NZ B:LYS664 4.3 51.7 1.0 OP2 F:DA11 4.3 77.2 1.0 CB B:ASP478 4.5 28.4 1.0 CG B:ASP546 4.5 30.4 1.0 O3' M:DC9 4.7 48.4 1.0 OD1 B:ASP546 4.7 41.0 1.0 O B:ASP660 4.8 22.2 1.0 C B:ASP660 4.8 26.4 1.0 O B:HOH936 4.9 35.4 1.0

Manganese binding site 5 out of 6 in the Dna Binding Protein and Dna Complex Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Dna Binding Protein and Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn101 b:28.2 occ:1.00 OP1 C:DA3 2.0 23.4 1.0 OP3 C:DT1 2.1 30.7 1.0 O A:HOH824 2.2 28.5 1.0 O C:HOH202 2.2 28.7 1.0 OXT A:VAL685 2.3 32.8 1.0 O A:VAL685 2.4 27.5 1.0 C A:VAL685 2.7 33.6 1.0 P C:DA3 3.3 25.7 1.0 P C:DT1 3.5 26.3 1.0 OP2 C:DT1 3.7 24.4 1.0 O3' C:DG2 3.8 21.9 1.0 NZ A:LYS457 4.0 28.8 1.0 OP2 C:DA3 4.1 28.9 1.0 O C:HOH214 4.1 40.8 1.0 OE1 A:GLN433 4.1 28.4 1.0 CA A:VAL685 4.2 20.0 1.0 NE2 A:GLN433 4.3 19.4 1.0 O5' C:DT1 4.4 27.2 1.0 O A:HOH802 4.4 28.8 1.0 O5' C:DA3 4.5 28.8 1.0 C5' C:DT1 4.5 22.6 1.0 OP1 C:DT1 4.5 34.0 1.0 O A:HOH827 4.6 27.0 1.0 CD A:GLN433 4.6 22.8 1.0 CE A:LYS457 4.7 19.8 1.0 C5' C:DA3 4.7 26.2 1.0 O A:HOH897 4.9 42.6 1.0 CB A:VAL685 4.9 29.8 1.0 CG2 A:VAL685 5.0 22.5 1.0

Manganese binding site 6 out of 6 in the Dna Binding Protein and Dna Complex Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Dna Binding Protein and Dna Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn101 b:33.2 occ:1.00 OP1 E:DA3 2.0 34.9 1.0 OP3 E:DT1 2.0 34.3 1.0 OXT B:VAL685 2.1 38.6 1.0 O E:HOH203 2.2 26.4 1.0 O B:HOH838 2.2 27.3 1.0 O B:VAL685 2.4 29.2 1.0 C B:VAL685 2.6 39.5 1.0 P E:DA3 3.2 32.1 1.0 P E:DT1 3.3 32.5 1.0 OP2 E:DT1 3.5 30.3 1.0 O3' E:DG2 3.8 37.6 1.0 NZ B:LYS457 4.0 25.6 1.0 OP2 E:DA3 4.0 35.2 1.0 OE1 B:GLN433 4.0 28.7 1.0 CA B:VAL685 4.2 35.8 1.0 NE2 B:GLN433 4.2 22.4 1.0 OP1 E:DT1 4.3 33.6 1.0 O E:HOH206 4.3 41.9 1.0 NH2 B:ARG661 4.3 33.6 0.5 O5' E:DT1 4.3 43.4 1.0 C5' E:DT1 4.4 37.6 1.0 O5' E:DA3 4.4 26.3 1.0 O B:HOH841 4.5 35.7 1.0 CD B:GLN433 4.6 37.4 1.0 O B:HOH885 4.6 30.5 1.0 O B:HOH881 4.6 28.7 1.0 C5' E:DA3 4.7 25.9 1.0 CE B:LYS457 4.7 21.6 1.0 CB B:VAL685 4.8 21.1 1.0 CG2 B:VAL685 4.9 20.4 1.0 CZ B:ARG661 4.9 33.1 0.5 N B:VAL685 5.0 25.3 1.0 NH1 B:ARG661 5.0 20.8 0.5

G.Sheng, H.Zhao, J.Wang, Y.Rao, W.Tian, D.C.Swarts, J.Van Der Oost, D.J.Patel, Y.Wang. Structure-Based Cleavage Mechanism of Thermus Thermophilus Argonaute Dna Guide Strand-Mediated Dna Target Cleavage. Proc.Natl.Acad.Sci.Usa V. 111 652 2014.
ISSN: ISSN 0027-8424
PubMed: 24374628
DOI: 10.1073/PNAS.1321032111