Zinc in PDB 2erg: Crystal Structure of LEU3 Dna-Binding Domain with A Single H50C Mutation Complexed with A 15MER Dna Duplex

The structure of Crystal Structure of LEU3 Dna-Binding Domain with A Single H50C Mutation Complexed with A 15MER Dna Duplex, PDB code: 2erg 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)	42.09 / 3.15
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	66.768, 66.768, 122.745, 90.00, 90.00, 120.00
R / Rfree (%)	27.3 / 27.7

The binding sites of Zinc atom in the Crystal Structure of LEU3 Dna-Binding Domain with A Single H50C Mutation Complexed with A 15MER Dna Duplex (pdb code 2erg). 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 LEU3 Dna-Binding Domain with A Single H50C Mutation Complexed with A 15MER Dna Duplex, PDB code: 2erg:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of LEU3 Dna-Binding Domain with A Single H50C Mutation 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 LEU3 Dna-Binding Domain with A Single H50C Mutation Complexed with A 15MER Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:96.8 occ:1.00 CB A:CYS57 2.1 95.0 1.0 SG A:CYS57 2.2 95.0 1.0 SG A:CYS67 2.3 91.5 1.0 SG A:CYS37 2.3 66.5 1.0 SG A:CYS60 2.5 94.3 1.0 CB A:CYS37 2.6 66.5 1.0 ZN A:ZN105 3.0 87.5 1.0 CB A:CYS60 3.2 94.3 1.0 CA A:CYS57 3.3 80.1 1.0 N A:CYS57 3.5 80.1 1.0 CB A:CYS67 3.6 91.5 1.0 C A:CYS57 4.1 80.1 1.0 SG A:CYS47 4.1 73.0 1.0 CA A:CYS37 4.2 81.1 1.0 O A:CYS57 4.2 80.1 1.0 CA A:CYS67 4.2 66.4 1.0 CA A:CYS60 4.4 82.6 1.0 N A:CYS60 4.4 82.6 1.0 C A:PRO56 4.7 1.0 1.0 SG A:CYS40 4.7 73.3 1.0 N A:CYS37 4.8 81.1 1.0 C A:CYS37 4.8 81.1 1.0 C A:CYS67 5.0 66.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of LEU3 Dna-Binding Domain with A Single H50C Mutation 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 LEU3 Dna-Binding Domain with A Single H50C Mutation Complexed with A 15MER Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn105 b:87.5 occ:1.00 SG A:CYS47 2.1 73.0 1.0 SG A:CYS37 2.2 66.5 1.0 SG A:CYS40 2.3 73.3 1.0 SG A:CYS57 2.5 95.0 1.0 CB A:CYS47 2.7 73.0 1.0 CB A:CYS57 2.7 95.0 1.0 ZN A:ZN104 3.0 96.8 1.0 CB A:CYS40 3.1 73.3 1.0 CA A:CYS47 3.1 60.7 1.0 CB A:CYS37 3.4 66.5 1.0 C A:CYS47 4.0 60.7 1.0 N A:ASP48 4.0 99.6 1.0 N A:CYS37 4.1 81.1 1.0 CA A:CYS57 4.2 80.1 1.0 CA A:CYS40 4.3 43.2 1.0 CA A:CYS37 4.4 81.1 1.0 N A:CYS40 4.4 43.2 1.0 N A:CYS47 4.4 60.7 1.0 SG A:CYS60 4.6 94.3 1.0 O A:CYS37 4.7 81.1 1.0 C A:CYS57 4.8 80.1 1.0 O A:LYS46 4.8 91.0 1.0 C A:CYS37 5.0 81.1 1.0 O A:CYS47 5.0 60.7 1.0 SG A:CYS67 5.0 91.5 1.0 CB A:LYS59 5.0 0.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of LEU3 Dna-Binding Domain with A Single H50C Mutation 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 LEU3 Dna-Binding Domain with A Single H50C Mutation Complexed with A 15MER Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn104 b:84.8 occ:1.00 CB B:CYS57 2.1 95.3 1.0 SG B:CYS57 2.2 95.3 1.0 SG B:CYS67 2.3 97.5 1.0 SG B:CYS37 2.4 72.1 1.0 SG B:CYS60 2.5 95.6 1.0 CB B:CYS37 2.6 72.1 1.0 ZN B:ZN105 3.0 83.9 1.0 CB B:CYS60 3.2 95.6 1.0 CA B:CYS57 3.3 78.7 1.0 N B:CYS57 3.4 78.7 1.0 CB B:CYS67 3.5 97.5 1.0 O B:HOH6 3.8 94.8 1.0 C B:CYS57 4.1 78.7 1.0 SG B:CYS47 4.1 81.8 1.0 CA B:CYS37 4.2 66.1 1.0 O B:CYS57 4.2 78.7 1.0 CA B:CYS67 4.2 76.0 1.0 CA B:CYS60 4.4 93.8 1.0 N B:CYS60 4.4 93.8 1.0 C B:PRO56 4.7 0.2 1.0 SG B:CYS40 4.7 94.0 1.0 N B:CYS37 4.8 66.1 1.0 C B:CYS37 4.8 66.1 1.0 C B:CYS67 5.0 76.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of LEU3 Dna-Binding Domain with A Single H50C Mutation 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 LEU3 Dna-Binding Domain with A Single H50C Mutation Complexed with A 15MER Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn105 b:83.9 occ:1.00 SG B:CYS47 2.1 81.8 1.0 SG B:CYS37 2.2 72.1 1.0 SG B:CYS40 2.3 94.0 1.0 SG B:CYS57 2.5 95.3 1.0 CB B:CYS47 2.7 81.8 1.0 CB B:CYS57 2.7 95.3 1.0 ZN B:ZN104 3.0 84.8 1.0 CB B:CYS40 3.1 94.0 1.0 CA B:CYS47 3.1 70.1 1.0 CB B:CYS37 3.5 72.1 1.0 C B:CYS47 4.0 70.1 1.0 N B:ASP48 4.0 0.1 1.0 N B:CYS37 4.1 66.1 1.0 CA B:CYS57 4.2 78.7 1.0 CA B:CYS40 4.3 46.8 1.0 CA B:CYS37 4.4 66.1 1.0 N B:CYS47 4.4 70.1 1.0 N B:CYS40 4.4 46.8 1.0 O B:HOH7 4.6 92.2 1.0 SG B:CYS60 4.6 95.6 1.0 O B:CYS37 4.7 66.1 1.0 C B:CYS57 4.7 78.7 1.0 O B:LYS46 4.8 0.2 1.0 CB B:LYS59 5.0 99.5 1.0 C B:CYS37 5.0 66.1 1.0 SG B:CYS67 5.0 97.5 1.0 O B:CYS47 5.0 70.1 1.0 N B:THR58 5.0 88.2 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