Magnesium in PDB 1yd1: Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima Bound to Its Catalytic Divalent Cation: Magnesium

The structure of Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima Bound to Its Catalytic Divalent Cation: Magnesium, PDB code: 1yd1 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 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	55.246, 55.246, 108.630, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 20.2

The binding sites of Magnesium atom in the Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima Bound to Its Catalytic Divalent Cation: Magnesium (pdb code 1yd1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima Bound to Its Catalytic Divalent Cation: Magnesium, PDB code: 1yd1:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima Bound to Its Catalytic Divalent Cation: Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima Bound to Its Catalytic Divalent Cation: Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:24.8 occ:1.00 OE2 A:GLU76 2.0 20.3 1.0 O A:HOH2013 2.0 20.8 1.0 O A:HOH2026 2.1 24.9 1.0 O A:HOH2008 2.1 18.8 1.0 O A:HOH2017 2.1 22.6 1.0 O A:HOH2030 2.2 26.1 1.0 CD A:GLU76 3.0 20.4 1.0 OE1 A:GLU76 3.4 24.5 1.0 O A:HOH2042 4.0 30.6 1.0 CA A:GLY31 4.1 17.7 1.0 O A:HOH2031 4.2 29.1 1.0 O A:HOH2098 4.2 54.9 1.0 OH A:TYR29 4.3 21.8 1.0 O A:ILE30 4.3 17.8 1.0 CG A:GLU76 4.4 16.9 1.0 N A:LYS32 4.4 18.8 1.0 O A:HOH2080 4.4 48.3 1.0 O A:HOH2007 4.5 23.7 1.0 CD1 A:ILE80 4.6 19.9 1.0 C A:GLY31 4.8 17.2 1.0 CG A:LYS32 4.8 21.0 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Giy-Yig N-Terminal Endonuclease Domain of Uvrc From Thermotoga Maritima Bound to Its Catalytic Divalent Cation: Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:37.8 occ:1.00 CG A:ARG70 3.4 22.0 1.0 CB A:ASN68 3.6 19.1 1.0 CG A:ASN68 3.6 18.5 1.0 CD A:ARG70 3.7 21.8 1.0 OD1 A:ASN68 3.8 18.6 1.0 N A:ARG70 4.0 19.3 1.0 ND2 A:ASN68 4.1 19.1 1.0 CB A:ARG70 4.2 20.5 1.0 N A:GLU69 4.2 20.5 1.0 O A:HOH2043 4.6 41.6 1.0 CA A:ARG70 4.7 20.1 1.0 CA A:ASN68 4.8 18.9 1.0 C A:ASN68 4.8 19.8 1.0 CB A:GLU69 4.8 23.9 1.0 CA A:GLU69 4.9 21.9 1.0 C A:GLU69 4.9 20.3 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