Zinc in PDB 2ere: Crystal Structure of A LEU3 Dna-Binding Domain Complexed with A 15MER Dna Duplex

The structure of Crystal Structure of A LEU3 Dna-Binding Domain Complexed with A 15MER Dna Duplex, PDB code: 2ere 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)	32.12 / 3.00
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	66.565, 66.565, 122.768, 90.00, 90.00, 120.00
R / Rfree (%)	27.7 / 27.7

The binding sites of Zinc atom in the Crystal Structure of A LEU3 Dna-Binding Domain Complexed with A 15MER Dna Duplex (pdb code 2ere). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of A LEU3 Dna-Binding Domain Complexed with A 15MER Dna Duplex, PDB code: 2ere:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of A LEU3 Dna-Binding Domain Complexed with A 15MER 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 A LEU3 Dna-Binding Domain Complexed with A 15MER Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:97.0 occ:1.00 SG A:CYS57 2.1 88.1 1.0 SG A:CYS60 2.4 0.5 1.0 SG A:CYS67 2.5 0.8 1.0 SG A:CYS37 2.6 82.8 1.0 CB A:CYS57 3.0 88.1 1.0 CB A:CYS37 3.1 82.8 1.0 ZN A:ZN105 3.2 91.0 1.0 CB A:CYS60 3.3 0.5 1.0 CB A:CYS67 3.3 0.8 1.0 N A:CYS57 3.7 91.3 1.0 CA A:CYS57 3.9 91.3 1.0 CA A:CYS67 3.9 83.1 1.0 N A:CYS60 4.4 0.1 1.0 CA A:CYS60 4.4 0.1 1.0 C A:CYS57 4.5 91.3 1.0 O A:CYS57 4.5 91.3 1.0 CA A:CYS37 4.6 0.9 1.0 C A:CYS67 4.7 83.1 1.0 SG A:CYS47 4.7 91.6 1.0 SG A:CYS40 4.7 86.2 1.0 C A:PRO56 4.8 0.6 1.0 CB A:GLU39 4.9 0.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of A LEU3 Dna-Binding Domain Complexed with A 15MER 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 A LEU3 Dna-Binding Domain Complexed with A 15MER Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn105 b:91.0 occ:1.00 SG A:CYS47 2.2 91.6 1.0 SG A:CYS37 2.2 82.8 1.0 SG A:CYS40 2.3 86.2 1.0 SG A:CYS57 2.4 88.1 1.0 CB A:CYS57 2.8 88.1 1.0 CB A:CYS47 3.0 91.6 1.0 ZN A:ZN104 3.2 97.0 1.0 CB A:CYS40 3.3 86.2 1.0 CB A:CYS37 3.5 82.8 1.0 CA A:CYS47 3.6 98.4 1.0 N A:CYS37 4.3 0.9 1.0 N A:ASP48 4.3 0.0 1.0 C A:CYS47 4.3 98.4 1.0 CA A:CYS57 4.4 91.3 1.0 CA A:CYS37 4.4 0.9 1.0 CA A:CYS40 4.5 71.0 1.0 N A:CYS40 4.5 71.0 1.0 N A:CYS47 4.9 98.4 1.0 SG A:CYS60 4.9 0.5 1.0 C A:CYS57 4.9 91.3 1.0 CB A:LYS59 4.9 0.8 1.0 O A:CYS37 4.9 0.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of A LEU3 Dna-Binding Domain Complexed with A 15MER 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 A LEU3 Dna-Binding Domain Complexed with A 15MER Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn104 b:99.0 occ:1.00 SG B:CYS57 2.2 70.2 1.0 SG B:CYS67 2.4 0.9 1.0 SG B:CYS60 2.5 0.1 1.0 SG B:CYS37 2.6 86.5 1.0 CB B:CYS37 3.0 86.5 1.0 CB B:CYS57 3.1 70.2 1.0 ZN B:ZN105 3.2 96.7 1.0 CB B:CYS67 3.3 0.9 1.0 CB B:CYS60 3.3 0.1 1.0 N B:CYS57 3.7 90.2 1.0 CA B:CYS67 3.9 82.5 1.0 CA B:CYS57 3.9 90.2 1.0 N B:CYS60 4.5 0.5 1.0 CA B:CYS60 4.5 0.5 1.0 CA B:CYS37 4.5 0.8 1.0 C B:CYS57 4.5 90.2 1.0 O B:CYS57 4.6 90.2 1.0 C B:CYS67 4.6 82.5 1.0 SG B:CYS47 4.7 95.7 1.0 SG B:CYS40 4.8 95.8 1.0 C B:PRO56 4.8 0.8 1.0 CB B:GLU39 4.9 0.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of A LEU3 Dna-Binding Domain Complexed with A 15MER 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 A LEU3 Dna-Binding Domain Complexed with A 15MER Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn105 b:96.7 occ:1.00 SG B:CYS37 2.2 86.5 1.0 SG B:CYS40 2.2 95.8 1.0 SG B:CYS47 2.2 95.7 1.0 SG B:CYS57 2.4 70.2 1.0 CB B:CYS57 2.9 70.2 1.0 CB B:CYS47 3.0 95.7 1.0 ZN B:ZN104 3.2 99.0 1.0 CB B:CYS40 3.3 95.8 1.0 CB B:CYS37 3.5 86.5 1.0 CA B:CYS47 3.6 0.2 1.0 N B:CYS37 4.3 0.8 1.0 N B:ASP48 4.3 0.2 1.0 C B:CYS47 4.4 0.2 1.0 CA B:CYS57 4.4 90.2 1.0 CA B:CYS40 4.4 75.8 1.0 N B:CYS40 4.4 75.8 1.0 CA B:CYS37 4.4 0.8 1.0 N B:CYS47 4.8 0.2 1.0 SG B:CYS60 4.9 0.1 1.0 CB B:LYS59 4.9 0.5 1.0 O B:CYS37 4.9 0.8 1.0 C B:CYS57 4.9 90.2 1.0 O B:LYS46 5.0 76.7 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