Zinc in PDB 1m55: Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein

The structure of Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein, PDB code: 1m55 was solved by A.B.Hickman, D.R.Ronning, R.M.Kotin, F.Dyda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.888, 73.455, 65.560, 90.00, 94.49, 90.00
R / Rfree (%)	17.8 / 19.6

The structure of Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein (pdb code 1m55). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein, PDB code: 1m55:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:9.8 occ:1.00 NE2 A:HIS91 2.0 7.9 1.0 NE2 A:HIS89 2.1 7.6 1.0 OE1 A:GLU82 2.1 10.3 1.0 CD2 A:HIS91 3.0 7.9 1.0 CE1 A:HIS89 3.0 7.8 1.0 CE1 A:HIS91 3.1 7.8 1.0 CD2 A:HIS89 3.1 7.7 1.0 CD A:GLU82 3.1 10.9 1.0 OE2 A:GLU82 3.7 10.7 1.0 NZ A:LYS157 3.9 11.7 1.0 CB A:GLU82 4.1 7.8 1.0 CG A:GLU82 4.1 9.1 1.0 CG A:HIS91 4.1 7.8 1.0 ND1 A:HIS91 4.2 7.9 1.0 ND1 A:HIS89 4.2 7.8 1.0 CG A:HIS89 4.2 7.4 1.0 OE2 A:GLU161 4.5 19.7 1.0

Zinc binding site 2 out of 6 in the Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:27.5 occ:1.00 OE2 A:GLU95 2.2 15.2 1.0 OE1 A:GLN73 2.3 22.5 1.0 O A:HOH1011 2.4 22.1 1.0 O A:HOH1211 2.4 30.0 1.0 CD A:GLU95 3.0 23.6 1.0 OE1 A:GLU95 3.1 30.1 1.0 CD A:GLN73 3.4 21.6 1.0 NE2 A:GLN73 3.9 23.8 1.0 CG A:LYS76 4.2 15.2 1.0 CG A:GLU95 4.3 17.5 1.0 N A:LYS76 4.4 9.1 1.0 O A:GLU74 4.5 10.2 1.0 O B:HOH2153 4.5 30.5 1.0 CA A:SER75 4.6 9.5 1.0 CG A:GLN73 4.7 16.0 1.0 CB A:LYS76 4.9 12.0 1.0 CB A:SER97 5.0 21.6 1.0 C A:SER75 5.0 9.8 1.0

Zinc binding site 3 out of 6 in the Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:9.3 occ:1.00 NE2 B:HIS91 2.0 8.4 1.0 NE2 B:HIS89 2.0 7.4 1.0 OE1 B:GLU82 2.1 10.1 1.0 CD2 B:HIS91 2.9 8.2 1.0 CE1 B:HIS89 3.0 7.9 1.0 CE1 B:HIS91 3.1 8.4 1.0 CD B:GLU82 3.1 11.3 1.0 CD2 B:HIS89 3.1 7.4 1.0 OE2 B:GLU82 3.7 11.6 1.0 NZ B:LYS157 3.9 10.2 1.0 CG B:GLU82 4.1 8.9 1.0 CG B:HIS91 4.1 7.9 1.0 CB B:GLU82 4.1 6.7 1.0 ND1 B:HIS91 4.2 8.4 1.0 ND1 B:HIS89 4.2 7.7 1.0 CG B:HIS89 4.2 7.2 1.0 OE2 B:GLU161 4.5 20.9 1.0 O B:HOH1254 4.9 24.8 1.0 O B:HOH1248 5.0 13.4 1.0

Zinc binding site 4 out of 6 in the Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:25.8 occ:1.00 OE2 B:GLU16 2.1 22.3 1.0 O B:HOH1376 2.4 25.2 1.0 CD B:GLU16 2.8 22.0 1.0 OE1 B:GLU16 2.9 23.1 1.0 O B:HOH2123 3.7 48.9 1.0 CG B:GLU16 4.2 18.2 1.0 O B:HOH2122 4.6 51.2 1.0 O B:HOH1381 4.8 24.6 1.0

Zinc binding site 5 out of 6 in the Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:20.8 occ:1.00 OE2 B:GLU95 2.2 11.7 1.0 O B:HOH1058 2.2 16.7 1.0 O B:HOH1059 2.2 21.1 1.0 OE1 B:GLN73 2.2 17.6 1.0 O B:HOH1057 2.3 24.7 1.0 O B:HOH1329 2.3 18.9 1.0 CD B:GLU95 3.0 21.3 1.0 OE1 B:GLU95 3.2 24.4 1.0 CD B:GLN73 3.3 16.4 1.0 NE2 B:GLN73 3.8 20.1 1.0 CG B:LYS76 4.2 10.9 1.0 O B:HOH1061 4.3 22.4 1.0 CG B:GLU95 4.4 13.6 1.0 N B:LYS76 4.4 7.8 1.0 O B:GLU74 4.4 7.4 1.0 O B:HOH1060 4.5 36.2 1.0 CG B:GLN73 4.6 11.9 1.0 OG B:SER97 4.6 27.3 1.0 CA B:SER75 4.7 7.9 1.0 CB B:SER97 4.8 16.6 1.0 CB B:LYS76 4.9 8.3 1.0

Zinc binding site 6 out of 6 in the Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Catalytic Domain of the Adeno Associated Virus Type 5 Rep Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn206 b:27.3 occ:1.00 OD1 B:ASP146 2.2 17.7 1.0 OD2 B:ASP146 2.3 25.8 1.0 CG B:ASP146 2.6 18.6 1.0 O B:HOH1088 3.7 46.2 1.0 CB B:ASP146 4.1 17.2 1.0 CA B:GLY148 4.3 10.4 1.0 N B:GLY148 4.4 10.9 1.0 C B:GLY148 4.9 10.9 1.0 CA B:ASP146 5.0 14.8 1.0

A.B.Hickman, D.R.Ronning, R.M.Kotin, F.Dyda. Structural Unity Among Viral Origin Binding Proteins: Crystal Structure of the Nuclease Domain of Adeno-Associated Virus Rep. Mol.Cell V. 10 327 2002.
ISSN: ISSN 1097-2765
PubMed: 12191478
DOI: 10.1016/S1097-2765(02)00592-0