Manganese in PDB 2vju: Crystal Structure of the IS608 Transposase in Complex with the Complete Right End 35-Mer Dna and Manganese

The structure of Crystal Structure of the IS608 Transposase in Complex with the Complete Right End 35-Mer Dna and Manganese, PDB code: 2vju was solved by O.Barabas, D.R.Ronning, C.Guynet, A.B.Hickman, B.Ton-Hoang, M.Chandler, F.Dyda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.04 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.550, 95.705, 98.561, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Manganese atom in the Crystal Structure of the IS608 Transposase in Complex with the Complete Right End 35-Mer Dna and Manganese (pdb code 2vju). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of the IS608 Transposase in Complex with the Complete Right End 35-Mer Dna and Manganese, PDB code: 2vju:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of the IS608 Transposase in Complex with the Complete Right End 35-Mer Dna and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the IS608 Transposase in Complex with the Complete Right End 35-Mer Dna and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1133 b:43.9 occ:1.00 NE2 A:HIS64 2.3 21.1 1.0 O3' C:DA-1 2.3 29.1 1.0 OE1 B:GLN131 2.4 66.4 1.0 NE2 A:HIS66 2.4 17.7 1.0 O A:HOH2045 2.8 55.9 1.0 O B:HOH2048 2.9 22.2 1.0 CE1 A:HIS64 3.1 20.8 1.0 CD B:GLN131 3.1 61.0 1.0 CD2 A:HIS66 3.3 17.2 1.0 CD2 A:HIS64 3.3 21.1 1.0 NE2 B:GLN131 3.4 53.5 1.0 CE1 A:HIS66 3.4 17.7 1.0 C3' C:DA-1 3.5 22.9 1.0 C4' C:DA-1 3.6 25.3 1.0 C2' C:DA-1 4.1 22.2 1.0 ND1 A:HIS64 4.2 20.6 1.0 OD2 A:ASP61 4.3 47.5 1.0 CG B:GLN131 4.3 45.9 1.0 CG A:HIS64 4.4 20.9 1.0 CG A:HIS66 4.4 17.0 1.0 C5' C:DA-1 4.5 28.2 1.0 ND1 A:HIS66 4.5 17.7 1.0 CB A:ASP61 4.6 37.1 1.0 O4' C:DA-1 4.8 23.7 1.0 CG A:ASP61 5.0 48.3 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of the IS608 Transposase in Complex with the Complete Right End 35-Mer Dna and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the IS608 Transposase in Complex with the Complete Right End 35-Mer Dna and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1000 b:32.7 occ:1.00 O C:HOH2031 2.2 32.8 1.0 O C:HOH2032 2.2 32.9 1.0 O C:HOH2034 2.2 32.5 1.0 O C:HOH2033 2.2 32.8 1.0 O C:HOH2030 2.2 32.7 1.0 O6 C:DG-13 2.2 30.6 1.0 C6 C:DG-13 3.3 31.3 1.0 N7 C:DG-13 3.7 33.4 1.0 C5 C:DG-13 3.8 32.2 1.0 OD1 B:ASN12 3.9 27.4 1.0 OP2 C:DT-32 4.0 24.9 1.0 O6 C:DG-14 4.0 26.3 1.0 O B:HIS11 4.2 28.7 1.0 N4 C:DC-29 4.2 47.0 1.0 O6 C:DG-12 4.2 32.5 1.0 ND2 A:ASN109 4.4 21.8 1.0 O C:HOH2006 4.4 39.2 1.0 O C:HOH2023 4.4 21.3 1.0 O B:HOH2009 4.4 42.1 1.0 N1 C:DG-13 4.5 32.2 1.0 N4 C:DC-30 4.7 32.8 1.0 CB B:HIS11 4.8 33.6 1.0 CG B:ASN12 4.8 24.1 1.0 C6 C:DG-14 4.9 25.0 1.0 C B:HIS11 4.9 30.3 1.0 C8 C:DG-13 5.0 30.5 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of the IS608 Transposase in Complex with the Complete Right End 35-Mer Dna and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the IS608 Transposase in Complex with the Complete Right End 35-Mer Dna and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1000 b:27.0 occ:1.00 O6 D:DG-13 2.1 21.6 1.0 O D:HOH2051 2.1 20.3 1.0 O D:HOH2052 2.2 27.1 1.0 O D:HOH2054 2.2 27.0 1.0 O D:HOH2053 2.2 27.1 1.0 O D:HOH2055 2.2 19.4 1.0 C6 D:DG-13 3.1 19.1 1.0 O6 D:DG-14 3.7 24.1 1.0 N7 D:DG-13 3.8 18.8 1.0 C5 D:DG-13 3.8 19.2 1.0 OD1 A:ASN12 3.8 27.4 1.0 N4 D:DC-29 4.0 23.3 1.0 OP2 D:DT-32 4.0 20.9 1.0 O D:HOH2014 4.1 28.1 1.0 O D:HOH2038 4.1 18.3 1.0 O6 D:DG-12 4.3 21.9 1.0 O D:HOH2037 4.3 20.1 1.0 N1 D:DG-13 4.3 17.1 1.0 ND2 B:ASN109 4.4 21.5 1.0 O A:HIS11 4.4 20.5 1.0 O D:HOH2011 4.6 27.9 1.0 C6 D:DG-14 4.7 18.9 1.0 N4 D:DC-30 4.7 17.5 1.0 CG A:ASN12 4.8 12.2 1.0 CB A:HIS11 4.8 19.6 1.0 N4 D:DC-28 4.9 22.7 1.0

O.Barabas, D.R.Ronning, C.Guynet, A.B.Hickman, B.Ton-Hoang, M.Chandler, F.Dyda. Mechanism of IS200/IS605 Family Dna Transposases: Activation and Transposon-Directed Target Site Selection. Cell(Cambridge,Mass.) V. 132 208 2008.
ISSN: ISSN 0092-8674
PubMed: 18243097
DOI: 10.1016/J.CELL.2007.12.029