Magnesium in PDB 1uut: The Nuclease Domain of Adeno-Associated Virus Rep Complexed with the Rbe' Stemloop of the Viral Inverted Terminal Repeat

The structure of The Nuclease Domain of Adeno-Associated Virus Rep Complexed with the Rbe' Stemloop of the Viral Inverted Terminal Repeat, PDB code: 1uut was solved by F.Dyda, A.B.Hickman, D.R.Ronning, Z.N.Perez, R.M.Kotin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.0 / 2.0
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.830, 78.705, 184.280, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 23.5

The structure of The Nuclease Domain of Adeno-Associated Virus Rep Complexed with the Rbe' Stemloop of the Viral Inverted Terminal Repeat also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the The Nuclease Domain of Adeno-Associated Virus Rep Complexed with the Rbe' Stemloop of the Viral Inverted Terminal Repeat (pdb code 1uut). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Nuclease Domain of Adeno-Associated Virus Rep Complexed with the Rbe' Stemloop of the Viral Inverted Terminal Repeat, PDB code: 1uut:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the The Nuclease Domain of Adeno-Associated Virus Rep Complexed with the Rbe' Stemloop of the Viral Inverted Terminal Repeat


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Nuclease Domain of Adeno-Associated Virus Rep Complexed with the Rbe' Stemloop of the Viral Inverted Terminal Repeat within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1196 b:45.7 occ:1.00 O A:HOH2110 2.1 43.2 1.0 O A:HOH2116 2.1 42.1 1.0 O A:HOH2117 2.1 49.2 1.0 OE1 A:GLU82 2.4 21.3 1.0 NE2 A:HIS89 2.5 27.9 1.0 NE2 A:HIS91 2.6 20.4 1.0 CE1 A:HIS91 3.4 20.2 1.0 CE1 A:HIS89 3.5 27.6 1.0 CD2 A:HIS89 3.6 27.5 1.0 CD A:GLU82 3.6 19.6 1.0 CD2 A:HIS91 3.7 19.9 1.0 OE2 A:GLU82 4.1 17.9 1.0 O A:HOH2109 4.2 38.5 1.0 OE2 A:GLU161 4.5 36.2 1.0 ND1 A:HIS91 4.6 20.1 1.0 CE A:LYS157 4.6 28.7 1.0 ND1 A:HIS89 4.7 27.5 1.0 CB A:GLU82 4.7 15.1 1.0 O A:HOH2171 4.7 35.7 1.0 CG A:GLU82 4.7 18.9 1.0 CG A:HIS89 4.7 26.3 1.0 CG A:HIS91 4.7 19.7 1.0

Magnesium binding site 2 out of 4 in the The Nuclease Domain of Adeno-Associated Virus Rep Complexed with the Rbe' Stemloop of the Viral Inverted Terminal Repeat


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Nuclease Domain of Adeno-Associated Virus Rep Complexed with the Rbe' Stemloop of the Viral Inverted Terminal Repeat within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1197 b:50.7 occ:1.00 O A:HOH2039 2.1 46.8 1.0 O A:HOH2038 2.1 46.9 1.0 O A:HOH2101 4.1 37.9 1.0 O A:HOH2105 4.4 34.5 1.0 CG A:LYS72 4.6 33.0 1.0 O A:LYS72 4.6 22.6 1.0 O A:HOH2037 4.7 40.2 1.0 CA A:LYS72 5.0 22.7 1.0

Magnesium binding site 3 out of 4 in the The Nuclease Domain of Adeno-Associated Virus Rep Complexed with the Rbe' Stemloop of the Viral Inverted Terminal Repeat


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Nuclease Domain of Adeno-Associated Virus Rep Complexed with the Rbe' Stemloop of the Viral Inverted Terminal Repeat within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1196 b:50.9 occ:1.00 O B:HOH2096 2.1 49.1 1.0 O B:HOH2102 2.1 50.4 1.0 O B:HOH2101 2.1 44.6 1.0 NE2 B:HIS89 2.3 35.3 1.0 OE1 B:GLU82 2.5 26.5 1.0 NE2 B:HIS91 2.8 27.8 1.0 CD2 B:HIS89 3.1 34.5 1.0 CE1 B:HIS89 3.4 35.4 1.0 CE1 B:HIS91 3.5 27.7 1.0 CD B:GLU82 3.6 20.4 1.0 CD2 B:HIS91 3.8 27.1 1.0 NZ B:LYS157 4.2 44.1 1.0 CG B:HIS89 4.3 33.4 1.0 CB B:GLU82 4.4 17.1 1.0 OE2 B:GLU82 4.4 24.1 1.0 ND1 B:HIS89 4.4 35.0 1.0 OE2 B:GLU161 4.5 37.0 1.0 CG B:GLU82 4.6 13.8 1.0 O B:HOH2095 4.6 63.8 1.0 ND1 B:HIS91 4.7 27.3 1.0 O B:HOH2030 4.7 41.5 1.0 CG B:HIS91 4.8 25.4 1.0

Magnesium binding site 4 out of 4 in the The Nuclease Domain of Adeno-Associated Virus Rep Complexed with the Rbe' Stemloop of the Viral Inverted Terminal Repeat


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Nuclease Domain of Adeno-Associated Virus Rep Complexed with the Rbe' Stemloop of the Viral Inverted Terminal Repeat within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1016 b:41.6 occ:1.00 O C:HOH2018 2.1 29.6 1.0 O C:HOH2016 2.1 41.4 1.0 O C:HOH2017 2.1 42.7 1.0 O C:HOH2005 2.1 49.9 1.0 OP1 C:DT9 2.5 33.9 1.0 O C:HOH2020 3.8 44.1 1.0 P C:DT9 3.9 31.5 1.0 O4' C:DA11 4.2 42.2 1.0 N2 C:DG10 4.4 18.0 1.0 N3 C:DG10 4.5 24.3 1.0 OP2 C:DT9 4.5 30.6 1.0 O3' C:DT8 4.6 29.4 1.0 C4' C:DA11 4.6 47.2 1.0 O4' C:DG10 4.7 40.8 1.0 C5' C:DA11 4.9 48.6 1.0 C2 C:DG10 4.9 22.5 1.0 O5' C:DT9 5.0 26.8 1.0

A.B.Hickman, D.R.Ronning, Z.N.Perez, R.M.Kotin, F.Dyda. The Nuclease Domain of Adeno-Associated Virus Rep Coordinates Replication Initiation Using Two Distinct Dna Recognition Interfaces Mol.Cell V. 13 403 2004.
ISSN: ISSN 1097-2765
PubMed: 14967147
DOI: 10.1016/S1097-2765(04)00023-1