Manganese in PDB 4dm0: TN5 Transposase: 20MER Outside End 2 Mn Complex

The structure of TN5 Transposase: 20MER Outside End 2 Mn Complex, PDB code: 4dm0 was solved by V.A.Klenchin, S.Lovell, I.Y.Goryshin, W.R.Reznikoff, I.Rayment, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.86 / 2.50
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	112.378, 112.378, 232.783, 90.00, 90.00, 120.00
R / Rfree (%)	17 / 20.3

The binding sites of Manganese atom in the TN5 Transposase: 20MER Outside End 2 Mn Complex (pdb code 4dm0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the TN5 Transposase: 20MER Outside End 2 Mn Complex, PDB code: 4dm0:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the TN5 Transposase: 20MER Outside End 2 Mn Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of TN5 Transposase: 20MER Outside End 2 Mn Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:45.4 occ:0.75 O A:HOH601 2.0 29.1 1.0 OD2 A:ASP97 2.2 34.1 1.0 OE2 A:GLU326 2.6 52.6 1.0 OE1 A:GLU326 2.7 53.5 1.0 MN A:MN502 3.0 41.8 0.5 CD A:GLU326 3.0 50.9 1.0 CG A:ASP97 3.1 26.5 1.0 O B:HOH202 3.2 39.8 1.0 OD1 A:ASP97 3.4 23.5 1.0 OP2 B:DA121 3.5 0.0 1.0 O A:HOH603 3.7 55.8 1.0 C5' B:DG120 4.0 60.8 1.0 NH1 A:ARG322 4.1 23.6 1.0 OP1 B:DG120 4.2 43.3 1.0 OD2 A:ASP188 4.2 53.3 1.0 O A:THR98 4.2 17.6 1.0 O3' B:DG120 4.4 88.9 1.0 CB A:ASP97 4.4 16.1 1.0 NH2 A:ARG322 4.5 27.5 1.0 CG A:GLU326 4.5 40.9 1.0 P B:DA121 4.5 97.0 1.0 O B:HOH201 4.6 27.4 1.0 CZ A:ARG322 4.8 25.0 1.0 O5' B:DG120 4.8 52.4 1.0 C4' B:DG120 4.8 72.1 1.0 C3' B:DG120 4.9 80.5 1.0

Manganese binding site 2 out of 3 in the TN5 Transposase: 20MER Outside End 2 Mn Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of TN5 Transposase: 20MER Outside End 2 Mn Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:41.8 occ:0.50 O B:HOH201 2.2 27.4 1.0 O A:HOH602 2.2 40.6 1.0 OD1 A:ASP97 2.5 23.5 1.0 OD2 A:ASP188 2.5 53.3 1.0 O B:HOH202 2.5 39.8 1.0 MN A:MN501 3.0 45.4 0.8 CG A:ASP97 3.3 26.5 1.0 O A:HOH603 3.3 55.8 1.0 OD2 A:ASP97 3.3 34.1 1.0 OP2 B:DA121 3.4 0.0 1.0 CG A:ASP188 3.4 37.0 1.0 OD1 A:ASP188 3.6 37.9 1.0 O A:HOH601 4.1 29.1 1.0 O C:HOH313 4.5 37.7 1.0 P B:DA121 4.6 97.0 1.0 O A:HOH744 4.6 27.1 1.0 CG A:GLU190 4.6 53.5 1.0 NH1 A:ARG322 4.7 23.6 1.0 CB A:ASP97 4.7 16.1 1.0 CB A:ASP188 4.7 25.6 1.0 OP1 B:DA121 4.9 98.5 1.0 O A:THR98 4.9 17.6 1.0 N A:THR98 4.9 19.2 1.0 O A:HOH645 5.0 34.8 1.0

Manganese binding site 3 out of 3 in the TN5 Transposase: 20MER Outside End 2 Mn Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of TN5 Transposase: 20MER Outside End 2 Mn Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:35.1 occ:0.30 O A:HOH881 2.3 48.1 1.0 OG A:SER181 2.7 38.0 1.0 O A:SER178 2.7 24.7 1.0 C A:SER178 3.8 25.4 1.0 CB A:SER181 3.9 30.7 1.0 O A:HOH629 4.2 47.1 1.0 CB A:SER178 4.3 29.3 1.0 CA A:SER178 4.4 27.0 1.0 N A:SER181 4.9 26.9 1.0 N A:MET179 4.9 21.2 1.0 CA A:SER181 4.9 29.5 1.0

S.Lovell, I.Y.Goryshin, W.R.Reznikoff, I.Rayment. Two-Metal Active Site Binding of A TN5 Transposase Synaptic Complex Nat.Struct.Biol. V. 9 278 2002.
ISSN: ISSN 1072-8368
PubMed: 11896402