Manganese in PDB 2j6v: Crystal Structure of the Dna Repair Enzyme Uv Damage Endonuclease

The structure of Crystal Structure of the Dna Repair Enzyme Uv Damage Endonuclease, PDB code: 2j6v was solved by K.Paspaleva, E.A.J.Thomassen, N.S.Pannu, N.Goossen, J.P.Abrahams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.55
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	47.352, 48.700, 68.763, 106.14, 94.36, 114.20
R / Rfree (%)	18.2 / 21.2

The binding sites of Manganese atom in the Crystal Structure of the Dna Repair Enzyme Uv Damage Endonuclease (pdb code 2j6v). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of the Dna Repair Enzyme Uv Damage Endonuclease, PDB code: 2j6v:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Crystal Structure of the Dna Repair Enzyme Uv Damage Endonuclease


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 Dna Repair Enzyme Uv Damage Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1278 b:18.8 occ:1.00 OD2 A:ASP200 2.1 14.9 1.0 OE2 A:GLU175 2.1 18.4 1.0 O3 A:PO41281 2.2 34.2 1.0 OE1 A:GLU269 2.2 17.6 1.0 ND1 A:HIS231 2.3 14.0 1.0 O1 A:PO41281 2.5 39.4 1.0 P A:PO41281 2.9 43.1 1.0 CD A:GLU269 3.1 20.3 1.0 CD A:GLU175 3.1 19.0 1.0 CG A:ASP200 3.2 14.9 1.0 CG A:HIS231 3.3 14.6 1.0 CE1 A:HIS231 3.3 16.5 1.0 OE2 A:GLU269 3.3 21.6 1.0 OE1 A:GLU175 3.5 21.1 1.0 CB A:HIS231 3.5 12.8 1.0 CB A:ASP200 3.7 12.2 1.0 O2 A:PO41281 3.8 40.5 1.0 MN A:MN1279 3.8 65.6 1.0 CE1 A:HIS203 3.9 20.3 1.0 MN A:MN1280 4.0 71.0 1.0 O4 A:PO41281 4.1 43.2 1.0 O A:HOH2184 4.1 28.0 1.0 OD1 A:ASP200 4.2 16.0 1.0 ND1 A:HIS203 4.3 17.6 1.0 CG A:GLU175 4.4 13.9 1.0 NE2 A:HIS231 4.4 15.2 1.0 CD2 A:HIS231 4.4 16.6 1.0 CG A:GLU269 4.5 15.2 1.0 NE2 A:HIS203 4.7 20.2 1.0 CA A:ASP200 4.9 12.4 1.0 NE2 A:HIS244 5.0 25.6 1.0 CE1 A:HIS244 5.0 25.1 1.0

Manganese binding site 2 out of 6 in the Crystal Structure of the Dna Repair Enzyme Uv Damage Endonuclease


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 Dna Repair Enzyme Uv Damage Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1279 b:65.6 occ:1.00 OE1 A:GLU175 2.2 21.1 1.0 NE2 A:HIS101 2.2 21.5 1.0 NE2 A:HIS143 2.3 29.4 1.0 O1 A:PO41281 2.4 39.4 1.0 O2 A:PO41281 2.6 40.5 1.0 CE1 A:HIS101 2.9 22.7 1.0 CE1 A:HIS143 2.9 29.8 1.0 CD2 A:HIS143 2.9 27.8 1.0 CD A:GLU175 3.0 19.0 1.0 P A:PO41281 3.0 43.1 1.0 OE2 A:GLU175 3.2 18.4 1.0 CD2 A:HIS101 3.2 20.3 1.0 ND1 A:HIS143 3.8 29.4 1.0 CG A:HIS143 3.8 24.1 1.0 MN A:MN1278 3.8 18.8 1.0 O3 A:PO41281 4.0 34.2 1.0 ND1 A:HIS101 4.0 19.8 1.0 O4 A:PO41281 4.1 43.2 1.0 CG A:HIS101 4.2 18.2 1.0 CG A:GLU175 4.3 13.9 1.0 CE1 A:HIS231 4.5 16.5 1.0 CB A:GLU175 4.6 12.6 1.0 CE1 A:HIS203 4.6 20.3 1.0 ND1 A:HIS231 4.7 14.0 1.0 CG1 A:VAL141 5.0 13.6 1.0

Manganese binding site 3 out of 6 in the Crystal Structure of the Dna Repair Enzyme Uv Damage Endonuclease


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 Dna Repair Enzyme Uv Damage Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1280 b:71.0 occ:1.00 O3 A:PO41281 1.9 34.2 1.0 O A:HOH2184 2.4 28.0 1.0 NE2 A:HIS203 2.4 20.2 1.0 NE2 A:HIS244 2.6 25.6 1.0 P A:PO41281 2.9 43.1 1.0 CE1 A:HIS203 3.0 20.3 1.0 CE1 A:HIS244 3.2 25.1 1.0 O2 A:PO41281 3.2 40.5 1.0 O4 A:PO41281 3.3 43.2 1.0 CD2 A:HIS203 3.4 19.1 1.0 CD2 A:HIS244 3.7 23.6 1.0 O A:GLY242 3.8 17.8 1.0 OD2 A:ASP200 3.9 14.9 1.0 MN A:MN1278 4.0 18.8 1.0 ND1 A:HIS203 4.0 17.6 1.0 O1 A:PO41281 4.3 39.4 1.0 CG A:HIS203 4.3 15.6 1.0 OE1 A:GLU269 4.3 17.6 1.0 ND1 A:HIS244 4.4 22.7 1.0 CG A:ASP200 4.5 14.9 1.0 OD1 A:ASP200 4.6 16.0 1.0 CG A:HIS244 4.6 20.2 1.0 C A:GLY242 4.8 17.7 1.0 OE2 A:GLU175 4.9 18.4 1.0

Manganese binding site 4 out of 6 in the Crystal Structure of the Dna Repair Enzyme Uv Damage Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the Dna Repair Enzyme Uv Damage Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1278 b:18.3 occ:1.00 OD2 B:ASP200 1.9 15.2 1.0 O3 B:PO41281 1.9 31.9 1.0 OE2 B:GLU175 2.0 17.1 1.0 OE1 B:GLU269 2.0 17.9 1.0 ND1 B:HIS231 2.1 18.3 1.0 O4 B:PO41281 2.7 36.7 1.0 P B:PO41281 2.9 42.9 1.0 CD B:GLU269 3.0 16.9 1.0 CD B:GLU175 3.1 16.2 1.0 CE1 B:HIS231 3.1 16.6 1.0 CG B:ASP200 3.1 14.9 1.0 CG B:HIS231 3.1 16.2 1.0 OE2 B:GLU269 3.2 21.6 1.0 CB B:HIS231 3.5 13.3 1.0 OE1 B:GLU175 3.5 20.7 1.0 CB B:ASP200 3.7 12.5 1.0 MN B:MN1279 3.7 72.8 1.0 O2 B:PO41281 3.9 38.4 1.0 CE1 B:HIS203 3.9 24.4 1.0 O1 B:PO41281 4.0 39.4 1.0 MN B:MN1280 4.1 77.7 1.0 OD1 B:ASP200 4.2 14.2 1.0 NE2 B:HIS231 4.2 15.9 1.0 ND1 B:HIS203 4.2 22.3 1.0 CD2 B:HIS231 4.3 16.8 1.0 CG B:GLU175 4.3 14.8 1.0 O B:HOH2172 4.4 32.7 1.0 CG B:GLU269 4.4 15.1 1.0 NE2 B:HIS203 4.8 23.0 1.0 CA B:ASP200 4.9 12.3 1.0 CE1 B:HIS101 5.0 22.0 1.0 CE1 B:HIS244 5.0 24.5 1.0 CA B:HIS231 5.0 12.4 1.0

Manganese binding site 5 out of 6 in the Crystal Structure of the Dna Repair Enzyme Uv Damage Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of the Dna Repair Enzyme Uv Damage Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1279 b:72.8 occ:1.00 NE2 B:HIS143 2.2 26.7 1.0 OE1 B:GLU175 2.2 20.7 1.0 O4 B:PO41281 2.3 36.7 1.0 CE1 B:HIS101 2.3 22.0 1.0 O2 B:PO41281 2.6 38.4 1.0 NE2 B:HIS101 2.8 24.1 1.0 CD B:GLU175 2.9 16.2 1.0 P B:PO41281 2.9 42.9 1.0 CE1 B:HIS143 2.9 26.9 1.0 CD2 B:HIS143 3.0 26.0 1.0 OE2 B:GLU175 3.0 17.1 1.0 ND1 B:HIS101 3.4 23.1 1.0 O3 B:PO41281 3.7 31.9 1.0 MN B:MN1278 3.7 18.3 1.0 ND1 B:HIS143 3.9 27.0 1.0 CG B:HIS143 3.9 21.5 1.0 CD2 B:HIS101 4.1 17.2 1.0 O1 B:PO41281 4.2 39.4 1.0 CG B:GLU175 4.2 14.8 1.0 CE1 B:HIS231 4.4 16.6 1.0 CG B:HIS101 4.4 17.2 1.0 CE1 B:HIS203 4.5 24.4 1.0 ND1 B:HIS231 4.5 18.3 1.0 CB B:GLU175 4.7 12.8 1.0 OE2 B:GLU269 4.8 21.6 1.0

Manganese binding site 6 out of 6 in the Crystal Structure of the Dna Repair Enzyme Uv Damage Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of the Dna Repair Enzyme Uv Damage Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1280 b:77.7 occ:1.00 O B:HOH2172 2.3 32.7 1.0 NE2 B:HIS244 2.3 23.1 1.0 O3 B:PO41281 2.5 31.9 1.0 NE2 B:HIS203 2.5 23.0 1.0 CE1 B:HIS203 3.0 24.4 1.0 CE1 B:HIS244 3.1 24.5 1.0 P B:PO41281 3.3 42.9 1.0 CD2 B:HIS244 3.4 22.2 1.0 CD2 B:HIS203 3.4 20.7 1.0 O2 B:PO41281 3.5 38.4 1.0 O1 B:PO41281 3.5 39.4 1.0 O B:GLY242 3.7 17.7 1.0 OD2 B:ASP200 3.8 15.2 1.0 ND1 B:HIS203 4.0 22.3 1.0 MN B:MN1278 4.1 18.3 1.0 CG B:HIS203 4.2 17.1 1.0 ND1 B:HIS244 4.2 21.1 1.0 OE1 B:GLU269 4.3 17.9 1.0 CG B:HIS244 4.4 19.5 1.0 CG B:ASP200 4.4 14.9 1.0 OD1 B:ASP200 4.4 14.2 1.0 O4 B:PO41281 4.7 36.7 1.0 C B:GLY242 4.8 17.8 1.0 CD2 B:LEU202 5.0 11.3 1.0

K.Paspaleva, E.A.J.Thomassen, N.S.Pannu, S.Iwai, G.F.Moolenaar, N.Goosen, J.P.Abrahams. Crystal Structure of the Dna Repair Enzyme Ultraviolet Damage Endonuclease. Structure V. 15 1316 2007.
ISSN: ISSN 0969-2126
PubMed: 17937920
DOI: 10.1016/J.STR.2007.05.010