Manganese in PDB 1yd3: Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation

The structure of Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation, PDB code: 1yd3 was solved by J.J.Truglio, B.Rhau, D.L.Croteau, L.Wang, M.Skorvaga, E.Karakas, M.J.Dellavecchia, H.Wang, B.Van Houten, C.Kisker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.60
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	56.094, 56.094, 111.491, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 19.4

The binding sites of Manganese atom in the Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation (pdb code 1yd3). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation, PDB code: 1yd3:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in the Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation


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 Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2001 b:21.8 occ:1.00 OE2 A:GLU76 2.2 19.2 1.0 O A:HOH2092 2.2 20.7 1.0 O A:HOH2035 2.2 24.4 1.0 O A:HOH2178 2.2 26.8 1.0 O A:HOH2045 2.2 25.5 1.0 O A:HOH2179 2.4 18.4 1.0 CD A:GLU76 3.2 19.0 1.0 OE1 A:GLU76 3.5 21.9 1.0 O A:HOH2138 4.3 57.0 1.0 O A:HOH2114 4.3 54.6 1.0 CA A:GLY31 4.4 16.3 1.0 O A:HOH2124 4.4 56.3 1.0 O A:HOH2031 4.4 29.3 1.0 O A:HOH2082 4.5 49.6 1.0 O A:ILE30 4.5 16.0 1.0 OH A:TYR29 4.5 19.1 1.0 CG A:GLU76 4.5 17.3 1.0 N A:LYS32 4.6 17.7 1.0 O A:HOH2015 4.7 24.0 1.0 CD1 A:ILE80 4.8 18.5 1.0 C A:GLY31 5.0 17.2 1.0

Manganese binding site 2 out of 5 in the Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation


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 Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2002 b:39.4 occ:1.00 O A:HOH2105 3.1 49.2 1.0 N A:LEU61 3.4 19.5 1.0 O A:LEU61 3.9 20.8 1.0 CA A:GLU60 3.9 20.8 1.0 C A:GLU60 4.1 19.9 1.0 CE A:LYS4 4.1 34.0 1.0 CG1 A:ILE5 4.2 23.2 1.0 CG A:LYS4 4.2 31.0 1.0 CA A:LEU61 4.3 19.6 1.0 CG A:GLU60 4.3 22.9 1.0 CD A:LYS4 4.4 31.4 1.0 CB A:LEU61 4.5 19.8 1.0 C A:LEU61 4.5 19.6 1.0 CB A:GLU60 4.6 21.2 1.0 O A:LYS4 4.6 26.0 1.0 CD A:LYS8 4.6 29.3 1.0 O A:HOH2118 4.7 61.0 1.0 NZ A:LYS4 4.7 36.5 1.0 C A:LYS4 4.7 26.0 1.0 N A:ILE5 4.8 24.4 1.0 CA A:ILE5 4.8 23.7 1.0 CB A:LYS4 4.8 28.1 1.0 O A:ASP59 4.8 22.5 1.0 N A:GLU60 4.9 21.1 1.0 O A:HOH2095 5.0 40.0 1.0

Manganese binding site 3 out of 5 in the Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation


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 Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2004 b:48.4 occ:1.00 O A:HOH2155 2.1 45.3 1.0 OE1 A:GLU49 2.2 29.5 1.0 O A:HOH2107 2.2 44.4 1.0 O A:HOH2112 2.2 46.1 1.0 O A:HOH2156 2.5 55.9 1.0 CD A:GLU49 3.1 29.7 1.0 OE2 A:GLU49 3.2 33.8 1.0 N A:GLU49 4.5 19.0 1.0 O A:HOH2154 4.5 51.4 1.0 CG A:GLU49 4.5 24.2 1.0 CA A:THR48 4.6 20.0 1.0 O A:HOH2011 4.7 23.2 1.0 CB A:THR48 5.0 20.5 1.0

Manganese binding site 4 out of 5 in the Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation


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 Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2005 b:46.7 occ:1.00 OE1 A:GLU60 2.2 29.3 1.0 O A:HOH2174 2.2 39.2 1.0 O A:HOH2132 2.3 46.5 1.0 O A:HOH2090 2.8 42.3 1.0 CD A:GLU60 3.2 24.0 1.0 OE2 A:GLU60 3.6 26.1 1.0 NZ A:LYS22 4.0 30.7 1.0 O A:HOH2108 4.5 52.9 1.0 CG A:GLU60 4.5 22.9 1.0 CD A:LYS22 4.7 23.3 1.0 OE1 A:GLU62 4.8 30.0 1.0 CE A:LYS22 4.8 27.6 1.0

Manganese binding site 5 out of 5 in the Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation


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 Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima: Point Mutant Y43F Bound to Its Catalytic Divalent Cation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2006 b:34.5 occ:1.00 NH2 A:ARG6 3.3 27.0 1.0 N A:MET1 3.4 23.5 1.0 O A:HOH2071 3.5 48.9 1.0 O A:HOH2040 3.6 33.4 1.0 O A:MET1 3.9 25.1 1.0 CB A:MET1 4.0 23.4 1.0 CA A:MET1 4.1 24.1 1.0 CZ A:ARG6 4.2 26.8 1.0 NE A:ARG6 4.3 26.4 1.0 C A:MET1 4.5 24.8 1.0 OE2 A:GLU56 4.8 23.0 1.0

J.J.Truglio, B.Rhau, D.L.Croteau, L.Wang, M.Skorvaga, E.Karakas, M.J.Dellavecchia, H.Wang, B.Van Houten, C.Kisker. Structural Insights Into the First Incision Reaction During Nucleotide Excision Repair Embo J. V. 24 885 2005.
ISSN: ISSN 0261-4189
PubMed: 15692561
DOI: 10.1038/SJ.EMBOJ.7600568