Zinc in PDB 2er8: Crystal Structure of LEU3 Dna-Binding Domain Complexed with A 12MER Dna Duplex

The structure of Crystal Structure of LEU3 Dna-Binding Domain Complexed with A 12MER Dna Duplex, PDB code: 2er8 was solved by M.X.Fitzgerald, R.Marmorstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.53 / 2.85
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	107.500, 107.500, 218.900, 90.00, 90.00, 120.00
R / Rfree (%)	23.7 / 26.5

The binding sites of Zinc atom in the Crystal Structure of LEU3 Dna-Binding Domain Complexed with A 12MER Dna Duplex (pdb code 2er8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of LEU3 Dna-Binding Domain Complexed with A 12MER Dna Duplex, PDB code: 2er8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of LEU3 Dna-Binding Domain Complexed with A 12MER Dna Duplex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of LEU3 Dna-Binding Domain Complexed with A 12MER Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:50.6 occ:1.00 SG A:CYS60 2.1 71.2 1.0 SG A:CYS67 2.3 65.9 1.0 SG A:CYS57 2.4 63.0 1.0 SG A:CYS37 2.4 45.6 1.0 CB A:CYS60 2.9 74.5 1.0 CB A:CYS67 3.0 67.8 1.0 ZN A:ZN105 3.1 44.1 1.0 CB A:CYS37 3.2 45.1 1.0 CA A:CYS67 3.4 70.6 1.0 CB A:CYS57 3.4 69.1 1.0 N A:CYS57 4.0 79.5 1.0 CA A:CYS60 4.2 76.8 1.0 O A:HOH16 4.2 63.0 1.0 CA A:CYS57 4.2 74.0 1.0 C A:CYS67 4.2 70.1 1.0 N A:CYS60 4.3 73.9 1.0 N A:CYS67 4.5 73.6 1.0 SG A:CYS40 4.6 49.0 1.0 O A:CYS57 4.6 71.8 1.0 CA A:CYS37 4.7 46.0 1.0 N A:ILE68 4.7 66.7 1.0 CB A:GLU39 4.7 61.1 1.0 C A:CYS57 4.8 73.7 1.0 O A:CYS67 4.9 68.6 1.0 O A:PRO66 5.0 83.8 1.0 CB A:ALA49 5.0 70.4 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of LEU3 Dna-Binding Domain Complexed with A 12MER Dna Duplex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of LEU3 Dna-Binding Domain Complexed with A 12MER Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn105 b:44.1 occ:1.00 SG A:CYS57 2.4 63.0 1.0 SG A:CYS40 2.4 49.0 1.0 SG A:CYS47 2.5 52.7 1.0 SG A:CYS37 2.6 45.6 1.0 CB A:CYS47 2.9 57.6 1.0 CB A:CYS57 3.0 69.1 1.0 ZN A:ZN104 3.1 50.6 1.0 CB A:CYS40 3.2 48.0 1.0 CB A:CYS37 3.5 45.1 1.0 CA A:CYS47 3.6 61.6 1.0 N A:CYS37 4.0 48.9 1.0 N A:CYS40 4.3 49.9 1.0 CA A:CYS40 4.3 47.0 1.0 CA A:CYS37 4.3 46.0 1.0 C A:CYS47 4.4 63.5 1.0 CB A:ALA49 4.4 70.4 1.0 N A:ASP48 4.4 72.8 1.0 N A:ALA49 4.5 78.4 1.0 SG A:CYS60 4.5 71.2 1.0 CA A:CYS57 4.5 74.0 1.0 SG A:CYS67 4.5 65.9 1.0 O A:CYS37 4.6 45.7 1.0 N A:CYS47 4.7 62.0 1.0 CB A:LYS59 4.8 66.6 1.0 C A:CYS37 4.8 46.1 1.0 CA A:ALA49 4.9 80.8 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of LEU3 Dna-Binding Domain Complexed with A 12MER Dna Duplex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of LEU3 Dna-Binding Domain Complexed with A 12MER Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn104 b:56.8 occ:1.00 SG B:CYS60 2.2 70.7 1.0 SG B:CYS67 2.3 67.3 1.0 SG B:CYS37 2.4 56.4 1.0 SG B:CYS57 2.4 68.2 1.0 ZN B:ZN105 2.8 54.0 1.0 CB B:CYS60 3.0 76.8 1.0 CB B:CYS67 3.2 69.8 1.0 CB B:CYS57 3.4 73.9 1.0 CB B:CYS37 3.6 55.3 1.0 CA B:CYS67 3.7 72.1 1.0 N B:CYS57 4.0 79.5 1.0 N B:CYS60 4.1 83.7 1.0 CA B:CYS60 4.1 82.5 1.0 CA B:CYS57 4.2 78.4 1.0 SG B:CYS40 4.4 68.8 1.0 O B:CYS57 4.5 81.6 1.0 C B:CYS67 4.5 70.8 1.0 SG B:CYS47 4.6 60.6 1.0 CB B:ALA49 4.7 69.1 1.0 C B:CYS57 4.7 79.1 1.0 CB B:GLU39 4.9 64.8 1.0 N B:CYS67 4.9 75.1 1.0 N B:ILE68 5.0 70.4 1.0 CA B:CYS37 5.0 54.9 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of LEU3 Dna-Binding Domain Complexed with A 12MER Dna Duplex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of LEU3 Dna-Binding Domain Complexed with A 12MER Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn105 b:54.0 occ:1.00 SG B:CYS47 2.2 60.6 1.0 SG B:CYS40 2.4 68.8 1.0 SG B:CYS57 2.4 68.2 1.0 SG B:CYS37 2.6 56.4 1.0 ZN B:ZN104 2.8 56.8 1.0 CB B:CYS47 3.0 64.4 1.0 CB B:CYS40 3.3 59.2 1.0 CB B:CYS57 3.3 73.9 1.0 CB B:CYS37 3.5 55.3 1.0 CA B:CYS47 3.6 68.4 1.0 N B:CYS37 4.0 57.7 1.0 CB B:ALA49 4.3 69.1 1.0 N B:CYS40 4.3 53.6 1.0 CA B:CYS37 4.3 54.9 1.0 CA B:CYS40 4.4 52.0 1.0 SG B:CYS67 4.4 67.3 1.0 N B:ASP48 4.5 72.9 1.0 C B:CYS47 4.5 68.4 1.0 SG B:CYS60 4.5 70.7 1.0 N B:ALA49 4.6 76.5 1.0 N B:CYS47 4.8 72.1 1.0 CA B:CYS57 4.8 78.4 1.0 CB B:LYS59 4.9 79.8 1.0 C B:CYS37 4.9 52.5 1.0 O B:CYS37 4.9 52.5 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of LEU3 Dna-Binding Domain Complexed with A 12MER Dna Duplex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of LEU3 Dna-Binding Domain Complexed with A 12MER Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn105 b:51.4 occ:1.00 SG C:CYS60 2.2 72.0 1.0 SG C:CYS57 2.4 71.8 1.0 SG C:CYS67 2.5 67.6 1.0 SG C:CYS37 2.7 54.9 1.0 ZN C:ZN106 2.9 51.7 1.0 CB C:CYS60 3.0 71.2 1.0 CB C:CYS37 3.2 55.5 1.0 CB C:CYS57 3.2 76.4 1.0 CB C:CYS67 3.4 68.6 1.0 CA C:CYS67 3.8 70.1 1.0 N C:CYS57 3.9 83.1 1.0 N C:CYS60 4.0 72.4 1.0 CA C:CYS60 4.1 71.8 1.0 CA C:CYS57 4.1 78.9 1.0 O C:CYS57 4.4 74.1 1.0 SG C:CYS40 4.5 52.9 1.0 C C:CYS67 4.6 69.2 1.0 C C:CYS57 4.6 76.8 1.0 SG C:CYS47 4.6 52.6 1.0 CA C:CYS37 4.7 56.1 1.0 N C:CYS67 5.0 71.8 1.0 N C:ILE68 5.0 63.9 1.0 CB C:GLU39 5.0 64.0 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of LEU3 Dna-Binding Domain Complexed with A 12MER Dna Duplex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of LEU3 Dna-Binding Domain Complexed with A 12MER Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn106 b:51.7 occ:1.00 SG C:CYS40 2.3 52.9 1.0 SG C:CYS47 2.3 52.6 1.0 SG C:CYS57 2.5 71.8 1.0 SG C:CYS37 2.6 54.9 1.0 ZN C:ZN105 2.9 51.4 1.0 CB C:CYS40 3.1 48.8 1.0 CB C:CYS47 3.1 53.8 1.0 CB C:CYS57 3.3 76.4 1.0 CB C:CYS37 3.4 55.5 1.0 CA C:CYS47 3.7 57.6 1.0 N C:CYS37 4.1 56.0 1.0 N C:CYS40 4.2 49.5 1.0 CA C:CYS40 4.2 47.8 1.0 CA C:CYS37 4.3 56.1 1.0 N C:ASP48 4.5 66.9 1.0 SG C:CYS60 4.5 72.0 1.0 CB C:LYS59 4.6 88.0 1.0 C C:CYS47 4.6 59.6 1.0 CA C:CYS57 4.8 78.9 1.0 O C:CYS37 4.8 56.6 1.0 N C:CYS47 4.8 56.6 1.0 SG C:CYS67 4.8 67.6 1.0 C C:CYS37 4.9 55.2 1.0 N C:ALA49 4.9 73.8 1.0 CB C:ALA49 5.0 69.2 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of LEU3 Dna-Binding Domain Complexed with A 12MER Dna Duplex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of LEU3 Dna-Binding Domain Complexed with A 12MER Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn107 b:40.0 occ:1.00 SG D:CYS60 2.3 60.6 1.0 SG D:CYS67 2.4 52.5 1.0 SG D:CYS37 2.6 46.3 1.0 SG D:CYS57 2.7 66.5 1.0 CB D:CYS60 2.9 62.7 1.0 ZN D:ZN108 3.1 40.8 1.0 CB D:CYS67 3.2 48.0 1.0 CB D:CYS37 3.2 43.4 1.0 CB D:CYS57 3.4 67.0 1.0 CA D:CYS67 3.7 48.4 1.0 N D:CYS57 4.0 71.2 1.0 CA D:CYS60 4.1 64.4 1.0 N D:CYS60 4.2 65.6 1.0 CA D:CYS57 4.3 67.3 1.0 O D:CYS57 4.5 64.6 1.0 C D:CYS67 4.6 49.2 1.0 SG D:CYS40 4.7 49.6 1.0 SG D:CYS47 4.7 44.6 1.0 CA D:CYS37 4.7 43.7 1.0 C D:CYS57 4.8 65.9 1.0 N D:CYS67 4.8 50.8 1.0 CB D:GLU39 4.8 63.3 1.0 N D:ILE68 4.9 52.7 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of LEU3 Dna-Binding Domain Complexed with A 12MER Dna Duplex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of LEU3 Dna-Binding Domain Complexed with A 12MER Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn108 b:40.8 occ:1.00 SG D:CYS40 2.3 49.6 1.0 SG D:CYS47 2.3 44.6 1.0 SG D:CYS57 2.5 66.5 1.0 SG D:CYS37 2.5 46.3 1.0 ZN D:ZN107 3.1 40.0 1.0 CB D:CYS40 3.1 45.2 1.0 CB D:CYS47 3.1 45.9 1.0 CB D:CYS57 3.2 67.0 1.0 CB D:CYS37 3.5 43.4 1.0 CA D:CYS47 3.7 46.9 1.0 N D:CYS37 4.1 46.0 1.0 CA D:CYS40 4.2 44.9 1.0 N D:CYS40 4.2 48.5 1.0 CA D:CYS37 4.4 43.7 1.0 C D:CYS47 4.5 49.3 1.0 SG D:CYS60 4.5 60.6 1.0 CB D:LYS59 4.6 72.4 1.0 N D:ASP48 4.6 57.9 1.0 CG D:LYS59 4.6 78.3 1.0 CA D:CYS57 4.7 67.3 1.0 SG D:CYS67 4.8 52.5 1.0 O D:CYS37 4.9 39.8 1.0 N D:CYS47 4.9 46.4 1.0 C D:CYS37 4.9 43.0 1.0 N D:ALA49 4.9 62.5 1.0 CB D:ALA49 4.9 54.2 1.0

M.X.Fitzgerald, J.R.Rojas, J.M.Kim, G.B.Kohlhaw, R.Marmorstein. Structure of A LEU3-Dna Complex: Recognition of Everted Cgg Half-Sites By A ZN2CYS6 Binuclear Cluster Protein. Structure V. 14 725 2006.
ISSN: ISSN 0969-2126
PubMed: 16615914
DOI: 10.1016/J.STR.2005.11.025