Manganese in PDB 6dww: Hermes Transposase Deletion Dimer Complex with (A/T) Dna and MN2+

The structure of Hermes Transposase Deletion Dimer Complex with (A/T) Dna and MN2+, PDB code: 6dww was solved by F.Dyda, A.R.Voth, A.B.Hickman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.80 / 2.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	122.480, 136.460, 104.610, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 26.4

The binding sites of Manganese atom in the Hermes Transposase Deletion Dimer Complex with (A/T) Dna and MN2+ (pdb code 6dww). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Hermes Transposase Deletion Dimer Complex with (A/T) Dna and MN2+, PDB code: 6dww:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Hermes Transposase Deletion Dimer Complex with (A/T) Dna and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Hermes Transposase Deletion Dimer Complex with (A/T) Dna and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:43.2 occ:1.00 O A:HOH806 2.2 39.1 1.0 O A:HOH827 2.2 62.8 1.0 OP2 C:DG18 2.4 46.5 1.0 OD2 A:ASP248 2.5 42.4 1.0 OD1 A:ASP180 2.6 44.1 1.0 O3' D:DA7 2.6 50.7 1.0 OD2 A:ASP180 3.0 65.3 1.0 CG A:ASP248 3.0 48.5 1.0 OD1 A:ASP248 3.1 70.9 1.0 CG A:ASP180 3.1 52.3 1.0 C3' D:DA7 3.3 39.0 1.0 P C:DG18 3.8 46.3 1.0 C4' D:DA7 3.8 46.7 1.0 MN A:MN702 4.0 75.6 1.0 OP1 C:DG18 4.3 39.7 1.0 CB A:ASP248 4.3 44.0 1.0 C5' D:DA7 4.5 46.4 1.0 O5' C:DG18 4.5 53.4 1.0 CB A:ASP180 4.6 40.7 1.0 N A:LEU181 4.6 50.0 1.0 C5' C:DG18 4.6 37.3 1.0 C2' D:DA7 4.7 58.0 1.0 O A:LEU181 4.7 44.4 1.0 O3' C:DG17 4.8 53.0 1.0 NE2 A:HIS268 5.0 45.0 1.0

Manganese binding site 2 out of 3 in the Hermes Transposase Deletion Dimer Complex with (A/T) Dna and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Hermes Transposase Deletion Dimer Complex with (A/T) Dna and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:75.6 occ:1.00 O C:HOH204 2.2 52.1 1.0 OE1 A:GLU572 2.7 44.6 1.0 OP2 C:DG18 2.8 46.5 1.0 O3' C:DG17 2.9 53.0 1.0 OE2 A:GLU572 3.0 50.8 1.0 OD2 A:ASP180 3.0 65.3 1.0 CG A:ASP180 3.0 52.3 1.0 OD1 A:ASP180 3.1 44.1 1.0 CD A:GLU572 3.1 49.6 1.0 P C:DG18 3.4 46.3 1.0 CE1 A:PHE575 3.8 34.2 1.0 O A:LEU181 3.9 44.4 1.0 CB A:ASP180 3.9 40.7 1.0 MN A:MN701 4.0 43.2 1.0 O A:HOH806 4.1 39.1 1.0 C3' C:DG17 4.1 39.0 1.0 CD1 A:PHE575 4.3 35.1 1.0 C4' C:DG17 4.4 45.0 1.0 OP1 C:DG18 4.5 39.7 1.0 O5' C:DG18 4.5 53.4 1.0 C5' C:DG18 4.5 37.3 1.0 CG A:GLU572 4.6 48.9 1.0 C2' C:DG17 4.6 44.3 1.0 OP1 C:DG17 4.8 56.4 1.0 N A:LEU181 4.8 50.0 1.0 C A:LEU181 4.9 41.0 1.0 CZ A:PHE575 5.0 41.9 1.0

Manganese binding site 3 out of 3 in the Hermes Transposase Deletion Dimer Complex with (A/T) Dna and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Hermes Transposase Deletion Dimer Complex with (A/T) Dna and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn101 b:75.3 occ:1.00 O C:HOH203 2.2 42.7 1.0 OP2 C:DG17 2.4 49.0 1.0 N7 C:DG18 2.8 86.0 1.0 OP1 C:DT16 3.2 62.0 1.0 O6 C:DG18 3.3 99.4 1.0 OD1 A:ASN185 3.6 74.2 1.0 C5 C:DG18 3.6 80.8 1.0 P C:DG17 3.8 47.8 1.0 C6 C:DG18 3.8 98.1 1.0 C8 C:DG18 3.9 84.3 1.0 CG A:ASN185 4.4 64.5 1.0 NE1 A:TRP182 4.4 41.8 1.0 P C:DT16 4.4 50.5 1.0 ND2 A:ASN185 4.4 75.9 1.0 C5' C:DT16 4.5 38.8 1.0 OP1 C:DG17 4.5 56.4 1.0 O5' C:DG17 4.5 39.0 1.0 O A:THR183 4.5 43.6 1.0 O5' C:DT16 4.5 54.6 1.0 O A:HOH822 4.6 44.0 1.0 CD1 A:TRP182 4.8 50.3 1.0 O3' C:DT16 4.9 55.9 1.0 C4 C:DG18 4.9 62.0 1.0

A.B.Hickman, A.R.Voth, H.Ewis, X.Li, N.L.Craig, F.Dyda. Structural Insights Into the Mechanism of Double Strand Break Formation By Hermes, A Hat Family Eukaryotic Dna Transposase. Nucleic Acids Res. V. 46 10286 2018.
ISSN: ESSN 1362-4962
PubMed: 30239795
DOI: 10.1093/NAR/GKY838