Zinc in PDB 8xuf: CDF1 Dof Domain in Palindromic-Bound Complex with Dna Duplex

The structure of CDF1 Dof Domain in Palindromic-Bound Complex with Dna Duplex, PDB code: 8xuf was solved by H.Furihata, M.Tanokura, T.Miyakawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.53 / 2.30
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.442, 79.442, 93.729, 90, 90, 90
R / Rfree (%)	22.9 / 24.9

The binding sites of Zinc atom in the CDF1 Dof Domain in Palindromic-Bound Complex with Dna Duplex (pdb code 8xuf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the CDF1 Dof Domain in Palindromic-Bound Complex with Dna Duplex, PDB code: 8xuf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the CDF1 Dof Domain in Palindromic-Bound Complex with Dna Duplex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of CDF1 Dof Domain in Palindromic-Bound Complex with Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:63.5 occ:1.00 SG C:CYS81 2.3 67.2 1.0 SG C:CYS84 2.3 62.1 1.0 SG C:CYS56 2.3 63.4 1.0 SG C:CYS59 2.3 77.5 1.0 CB C:CYS56 3.1 66.8 1.0 CB C:CYS81 3.1 71.5 1.0 CB C:CYS59 3.1 60.7 1.0 CB C:CYS84 3.2 68.0 1.0 N C:CYS59 3.6 68.3 1.0 N C:CYS84 3.7 74.6 1.0 CA C:CYS59 3.9 63.1 1.0 CA C:CYS84 4.0 70.8 1.0 C C:CYS59 4.5 68.3 1.0 CA C:CYS56 4.5 66.3 1.0 CA C:CYS81 4.5 68.3 1.0 CB C:ARG58 4.5 63.4 1.0 CB C:SER61 4.6 66.2 1.0 N C:ASN60 4.6 74.0 1.0 N C:SER61 4.7 66.0 1.0 CB C:ALA83 4.7 75.5 1.0 C C:ARG58 4.7 70.5 1.0 O C:CYS81 4.8 71.7 1.0 NH2 C:ARG86 4.8 71.5 1.0 C C:ALA83 4.9 76.2 1.0 C C:CYS56 4.9 67.1 1.0 C C:CYS84 4.9 68.1 1.0 C C:CYS81 5.0 71.9 1.0 O C:CYS56 5.0 68.0 1.0

Zinc binding site 2 out of 2 in the CDF1 Dof Domain in Palindromic-Bound Complex with Dna Duplex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of CDF1 Dof Domain in Palindromic-Bound Complex with Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:76.2 occ:1.00 SG D:CYS81 2.0 76.8 1.0 SG D:CYS84 2.1 71.8 1.0 SG D:CYS59 2.1 75.6 1.0 SG D:CYS56 2.3 70.0 1.0 CB D:CYS81 2.5 72.8 1.0 CB D:CYS56 2.9 70.8 1.0 CB D:CYS84 3.3 77.5 1.0 CB D:CYS59 3.6 69.4 1.0 N D:CYS84 3.7 68.1 1.0 CA D:CYS81 4.0 71.2 1.0 CA D:CYS84 4.1 73.0 1.0 N D:CYS59 4.1 72.9 1.0 O D:CYS81 4.3 74.1 1.0 CA D:CYS56 4.4 71.0 1.0 CA D:CYS59 4.4 73.5 1.0 C D:CYS81 4.4 73.3 1.0 CB D:ALA83 4.7 74.8 1.0 C D:ALA83 4.8 79.2 1.0 CB D:SER61 4.8 76.6 1.0 N D:CYS81 4.9 71.6 1.0 NH2 D:ARG86 5.0 76.8 1.0 C D:CYS84 5.0 74.2 1.0 N D:SER61 5.0 75.5 1.0 C D:CYS59 5.0 78.2 1.0

H.Furihata, Z.Zhu, K.Nishida, Y.Sakuraba, A.Tsuji, H.Yamashita, S.Nosaki, R.Tachibana, A.Yamagami, Y.Ikeda, M.Abe, T.Sawasaki, T.Nakano, S.Yanagisawa, M.Tanokura, T.Miyakawa. Structural Insights Into CDF1 Accumulation on the Constans Promoter Via A Plant-Specific Dna-Binding Domain to Regulate Gene Expression To Be Published.