Zinc in PDB 5yj3: Crystal Structure of Tzap and Telomeric Dna Complex

The structure of Crystal Structure of Tzap and Telomeric Dna Complex, PDB code: 5yj3 was solved by F.Li, Y.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.28 / 2.85
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	56.713, 56.713, 226.229, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 26.8

The binding sites of Zinc atom in the Crystal Structure of Tzap and Telomeric Dna Complex (pdb code 5yj3). 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 Tzap and Telomeric Dna Complex, PDB code: 5yj3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Tzap and Telomeric Dna Complex


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 Tzap and Telomeric Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn701 b:66.8 occ:1.00 NE2 C:HIS596 1.9 78.1 1.0 NE2 C:HIS600 2.1 90.2 1.0 SG C:CYS583 2.2 86.0 1.0 SG C:CYS580 2.2 92.2 1.0 CE1 C:HIS596 2.8 74.8 1.0 CD2 C:HIS600 2.9 80.4 1.0 CD2 C:HIS596 2.9 78.0 1.0 CB C:CYS580 3.1 70.7 1.0 CE1 C:HIS600 3.2 77.8 1.0 CB C:CYS583 3.3 85.0 1.0 N C:CYS583 3.6 76.8 1.0 ND1 C:HIS596 3.9 73.5 1.0 CA C:CYS583 4.0 75.3 1.0 CG C:HIS596 4.0 81.4 1.0 CG C:HIS600 4.1 77.3 1.0 ND1 C:HIS600 4.2 86.4 1.0 CB C:GLU582 4.3 89.7 1.0 C C:GLU582 4.5 81.1 1.0 CA C:CYS580 4.6 72.9 1.0 C C:CYS583 4.6 76.6 1.0 CA C:GLU582 4.8 82.9 1.0 N C:GLU582 4.8 82.0 1.0 N C:GLY584 4.8 73.9 1.0 SD C:MET597 4.8 89.7 1.0 CB C:TYR585 4.9 60.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Tzap and Telomeric Dna Complex


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 Tzap and Telomeric Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn702 b:0.8 occ:1.00 SG C:CYS555 2.4 0.7 1.0 NE2 C:HIS568 2.8 0.1 1.0 CD2 C:HIS572 3.0 0.6 1.0 SG C:CYS552 3.1 0.0 1.0 CD2 C:HIS568 3.3 0.1 1.0 NE2 C:HIS572 3.3 0.4 1.0 CB C:CYS555 3.9 0.1 1.0 CE1 C:HIS568 4.1 0.7 1.0 N C:CYS555 4.1 0.7 1.0 CB C:CYS552 4.2 0.0 1.0 CG C:HIS572 4.2 0.1 1.0 CE1 C:HIS572 4.6 0.7 1.0 CA C:CYS555 4.6 0.3 1.0 CG C:HIS568 4.6 0.9 1.0 CB C:ILE554 4.6 0.8 1.0 N C:GLY556 4.8 0.7 1.0 CB C:VAL569 4.9 0.4 1.0 ND1 C:HIS568 4.9 0.5 1.0 C C:ILE554 5.0 0.2 1.0 N C:ILE554 5.0 1.0 1.0 ND1 C:HIS572 5.0 0.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Tzap and Telomeric Dna Complex


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 Tzap and Telomeric Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn701 b:65.3 occ:1.00 NE2 D:HIS596 1.9 81.4 1.0 NE2 D:HIS600 2.0 0.4 1.0 SG D:CYS580 2.3 65.7 1.0 SG D:CYS583 2.3 77.7 1.0 CD2 D:HIS600 2.5 97.6 1.0 CD2 D:HIS596 2.7 82.4 1.0 CE1 D:HIS596 3.1 77.3 1.0 CE1 D:HIS600 3.1 99.0 1.0 CB D:CYS583 3.3 64.6 1.0 CB D:CYS580 3.3 60.7 1.0 N D:CYS583 3.6 64.7 1.0 CG D:HIS600 3.7 97.3 1.0 CG D:HIS596 3.9 76.2 1.0 ND1 D:HIS600 4.0 96.4 1.0 CA D:CYS583 4.0 70.7 1.0 ND1 D:HIS596 4.1 74.1 1.0 CB D:GLU582 4.2 59.0 1.0 C D:GLU582 4.5 74.7 1.0 N D:GLY584 4.6 70.5 1.0 C D:CYS583 4.7 64.8 1.0 CA D:CYS580 4.7 62.9 1.0 CG D:GLU582 4.7 75.7 1.0 CA D:GLU582 4.8 60.4 1.0 CB D:TYR585 4.9 63.2 1.0 N D:TYR585 4.9 63.9 1.0 N D:GLU582 4.9 71.1 1.0 CD2 D:TYR606 5.0 95.1 1.0 CB D:HIS600 5.0 91.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Tzap and Telomeric Dna Complex


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 Tzap and Telomeric Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn702 b:0.7 occ:1.00 NE2 D:HIS572 2.1 0.7 1.0 SG D:CYS555 2.5 97.3 1.0 NE2 D:HIS568 2.6 0.9 1.0 CD2 D:HIS572 2.9 0.5 1.0 CB D:CYS555 3.1 99.9 1.0 N D:CYS555 3.2 0.6 1.0 SG D:CYS552 3.2 0.2 1.0 CE1 D:HIS572 3.2 1.0 1.0 CD2 D:HIS568 3.3 99.6 1.0 CA D:CYS555 3.7 0.5 1.0 CE1 D:HIS568 3.7 0.4 1.0 CB D:ILE554 4.1 99.4 1.0 CG D:HIS572 4.1 0.4 1.0 ND1 D:HIS572 4.2 0.2 1.0 C D:ILE554 4.3 0.7 1.0 N D:GLY556 4.4 0.2 1.0 CG D:HIS568 4.5 0.3 1.0 CA D:ILE554 4.6 0.1 1.0 N D:ILE554 4.6 0.3 1.0 C D:CYS555 4.6 0.9 1.0 CB D:CYS552 4.7 0.3 1.0 ND1 D:HIS568 4.7 0.0 1.0

Y.Zhao, G.Zhang, C.He, Y.Mei, Y.Shi, F.Li. The 11TH C2H2 Zinc Finger and An Adjacent C-Terminal Arm Are Responsible For Tzap Recognition of Telomeric Dna. Cell Res. V. 28 130 2018.
ISSN: ISSN 1748-7838
PubMed: 29134956
DOI: 10.1038/CR.2017.141