Zinc in PDB 5egb: Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence II

All present enzymatic activity of Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence II:
2.1.1.43;

The structure of Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence II, PDB code: 5egb was solved by A.Patel, J.R.Horton, G.G.Wilson, X.Zhang, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.64 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	34.575, 79.221, 68.415, 90.00, 95.42, 90.00
R / Rfree (%)	19.3 / 22

The binding sites of Zinc atom in the Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence II (pdb code 5egb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence II, PDB code: 5egb:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence II


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence II within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:26.3 occ:1.00 NE2 A:HIS741 2.0 29.4 1.0 NE2 A:HIS737 2.0 24.3 1.0 SG A:CYS721 2.2 24.3 1.0 SG A:CYS724 2.2 24.2 1.0 CD2 A:HIS741 2.9 28.8 1.0 CD2 A:HIS737 3.0 20.8 1.0 CE1 A:HIS737 3.0 23.6 1.0 CE1 A:HIS741 3.0 29.3 1.0 CB A:CYS721 3.1 25.4 1.0 CB A:CYS724 3.3 27.9 1.0 N A:CYS724 3.7 25.8 1.0 CA A:CYS724 4.1 23.5 1.0 ND1 A:HIS737 4.1 23.8 1.0 CG A:HIS737 4.1 22.6 1.0 CG A:HIS741 4.1 30.8 1.0 ND1 A:HIS741 4.1 34.2 1.0 CB A:GLU723 4.4 30.2 1.0 CA A:CYS721 4.5 26.4 1.0 C A:GLU723 4.5 28.9 1.0 NH1 A:ARG726 4.8 41.1 1.0 C A:CYS724 4.8 23.7 1.0 CA A:GLU723 4.8 23.3 1.0 HD1 A:HIS737 4.9 28.6 1.0 N A:GLU723 4.9 22.3 1.0 C A:CYS721 4.9 29.2 1.0 HD1 A:HIS741 4.9 41.0 1.0 CB A:ARG726 5.0 23.6 1.0

Zinc binding site 2 out of 4 in the Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence II


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence II within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:25.3 occ:1.00 NE2 A:HIS769 2.2 27.8 1.0 NE2 A:HIS765 2.2 23.1 1.0 SG A:CYS749 2.2 23.5 1.0 SG A:CYS752 2.3 25.1 1.0 CD2 A:HIS769 2.9 26.1 1.0 CD2 A:HIS765 3.0 23.7 1.0 CB A:CYS749 3.1 23.4 1.0 CE1 A:HIS765 3.2 26.9 1.0 CB A:CYS752 3.2 29.1 1.0 CE1 A:HIS769 3.3 28.5 1.0 N A:CYS752 3.6 27.9 1.0 CA A:CYS752 4.0 29.0 1.0 CG A:HIS769 4.2 28.6 1.0 CG A:HIS765 4.2 24.1 1.0 ND1 A:HIS765 4.3 23.9 1.0 ND1 A:HIS769 4.3 28.8 1.0 CB A:GLU751 4.5 28.0 1.0 C A:GLU751 4.5 26.9 1.0 CA A:CYS749 4.5 25.6 1.0 C A:CYS752 4.7 24.2 1.0 N A:GLY753 4.8 25.6 1.0 O A:HOH1183 4.8 38.0 1.0 CA A:GLU751 4.9 24.2 1.0 CB A:ARG754 4.9 34.2 1.0 N A:GLU751 5.0 26.0 1.0 N A:ARG754 5.0 24.9 1.0 O A:HOH1125 5.0 32.1 1.0 O A:HOH1186 5.0 43.6 1.0

Zinc binding site 3 out of 4 in the Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence II


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence II within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:31.6 occ:1.00 NE2 A:HIS793 2.1 32.7 1.0 NE2 A:HIS797 2.1 34.8 1.0 SG A:CYS780 2.2 30.8 1.0 SG A:CYS777 2.2 25.5 1.0 CD2 A:HIS797 2.9 25.9 1.0 CE1 A:HIS793 3.0 28.4 1.0 CB A:CYS777 3.1 27.7 1.0 CD2 A:HIS793 3.1 22.6 1.0 CE1 A:HIS797 3.3 32.5 1.0 CB A:CYS780 3.3 31.0 1.0 N A:CYS780 3.6 31.4 1.0 CA A:CYS780 4.0 25.1 1.0 CG A:HIS797 4.1 35.2 1.0 ND1 A:HIS793 4.1 30.5 1.0 CG A:HIS793 4.2 26.3 1.0 O A:HOH1157 4.3 43.9 1.0 ND1 A:HIS797 4.3 34.5 1.0 CA A:CYS777 4.6 26.1 1.0 CB A:GLU779 4.6 34.2 1.0 C A:GLU779 4.6 29.7 1.0 C A:CYS780 4.7 27.4 1.0 N A:GLY781 4.8 25.3 1.0 HD1 A:HIS793 4.9 36.6 1.0 N A:GLU779 4.9 26.5 1.0 C A:CYS777 5.0 25.8 1.0 CA A:GLU779 5.0 26.9 1.0

Zinc binding site 4 out of 4 in the Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence II


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence II within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:64.3 occ:1.00 CB A:CYS808 2.2 52.5 1.0 SG A:CYS808 2.2 71.7 1.0 NE2 A:HIS821 2.3 59.3 1.0 SG A:CYS805 2.3 54.7 1.0 NE2 A:HIS825 2.4 65.2 1.0 CD2 A:HIS821 3.0 53.1 1.0 CB A:CYS805 3.2 55.4 1.0 CA A:CYS808 3.2 63.4 1.0 N A:CYS808 3.2 67.3 1.0 CE1 A:HIS825 3.4 69.2 1.0 CD2 A:HIS825 3.4 69.1 1.0 CE1 A:HIS821 3.4 61.8 1.0 CG A:HIS821 4.3 55.4 1.0 CG A:GLU807 4.4 73.2 1.0 ND1 A:HIS821 4.4 54.7 1.0 C A:CYS808 4.4 65.1 1.0 ND1 A:HIS825 4.5 72.6 1.0 C A:GLU807 4.5 69.4 1.0 CG A:HIS825 4.5 69.9 1.0 CA A:CYS805 4.6 56.4 1.0 N A:GLY809 4.8 63.6 1.0 CB A:GLU807 5.0 65.2 1.0 CB A:ARG810 5.0 54.7 1.0

A.Patel, J.R.Horton, G.G.Wilson, X.Zhang, X.Cheng. Structural Basis For Human PRDM9 Action at Recombination Hot Spots. Genes Dev. V. 30 257 2016.
ISSN: ISSN 0890-9369
PubMed: 26833727
DOI: 10.1101/GAD.274928.115