Zinc in PDB 6seh: Recognition and Processing of Branched Dna Substrates By SLX1-SLX4 Nuclease

The structure of Recognition and Processing of Branched Dna Substrates By SLX1-SLX4 Nuclease, PDB code: 6seh was solved by V.Gaur, W.Zajko, S.Nirwal, A.Szlachcic, M.Gapinska, M.Nowotny, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.74 / 3.15
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	180.322, 63.410, 103.687, 90.00, 116.70, 90.00
R / Rfree (%)	20.2 / 25.4

The binding sites of Zinc atom in the Recognition and Processing of Branched Dna Substrates By SLX1-SLX4 Nuclease (pdb code 6seh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Recognition and Processing of Branched Dna Substrates By SLX1-SLX4 Nuclease, PDB code: 6seh:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Recognition and Processing of Branched Dna Substrates By SLX1-SLX4 Nuclease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Recognition and Processing of Branched Dna Substrates By SLX1-SLX4 Nuclease within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:0.1 occ:1.00 SG C:CYS232 2.4 0.5 1.0 CD2 C:HIS256 2.5 85.9 1.0 SG C:CYS259 2.8 95.4 1.0 SG C:CYS229 2.9 97.2 1.0 CG C:HIS256 3.2 90.0 1.0 CB C:HIS256 3.3 87.8 1.0 CB C:CYS229 3.4 91.0 1.0 CB C:CYS232 3.4 0.8 1.0 CB C:CYS259 3.7 87.2 1.0 NE2 C:HIS256 3.7 91.9 1.0 N C:HIS256 3.9 89.7 1.0 CA C:HIS256 4.2 79.7 1.0 N C:CYS232 4.2 98.0 1.0 NH1 D:ARG864 4.4 0.2 1.0 CA C:CYS232 4.5 0.8 1.0 ND1 C:HIS256 4.5 92.0 1.0 CE1 C:HIS256 4.7 91.0 1.0 CA C:CYS229 5.0 87.8 1.0

Zinc binding site 2 out of 4 in the Recognition and Processing of Branched Dna Substrates By SLX1-SLX4 Nuclease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Recognition and Processing of Branched Dna Substrates By SLX1-SLX4 Nuclease within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:0.2 occ:1.00 SG C:CYS280 2.4 86.3 1.0 SG C:CYS251 2.5 87.8 1.0 SG C:CYS246 2.6 0.1 1.0 SG C:CYS283 2.7 97.8 1.0 CB C:CYS283 3.3 97.2 1.0 CB C:CYS280 3.3 87.6 1.0 CB C:CYS251 3.4 94.6 1.0 CB C:CYS246 3.5 87.2 1.0 N C:CYS283 3.9 97.7 1.0 CA C:CYS283 4.1 93.9 1.0 OD1 C:ASN248 4.7 0.1 1.0 CA C:CYS280 4.7 85.5 1.0 CB C:LYS282 4.8 87.5 1.0 CA C:CYS251 4.9 0.6 1.0 C C:CYS283 4.9 85.8 1.0 CB C:ASN248 4.9 0.1 1.0 C C:LYS282 5.0 0.4 1.0 N C:GLY284 5.0 79.7 1.0

Zinc binding site 3 out of 4 in the Recognition and Processing of Branched Dna Substrates By SLX1-SLX4 Nuclease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Recognition and Processing of Branched Dna Substrates By SLX1-SLX4 Nuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:0.5 occ:1.00 SG A:CYS232 2.4 98.6 1.0 SG A:CYS259 2.4 89.3 1.0 ND1 A:HIS256 2.5 74.1 1.0 SG A:CYS229 2.5 69.6 1.0 CB A:CYS232 2.9 96.0 1.0 CB A:CYS259 3.2 86.8 1.0 CB A:CYS229 3.2 71.5 1.0 CE1 A:HIS256 3.3 77.7 1.0 CG A:HIS256 3.4 74.8 1.0 N A:CYS232 3.6 69.8 1.0 CB A:HIS256 3.8 65.2 1.0 CA A:CYS232 3.9 86.3 1.0 N A:HIS256 4.3 81.3 1.0 NH1 B:ARG864 4.4 0.7 1.0 NE2 A:HIS256 4.4 77.5 1.0 CD2 A:HIS256 4.5 77.0 1.0 CA A:HIS256 4.7 73.0 1.0 CA A:CYS259 4.7 85.8 1.0 NH2 B:ARG864 4.7 0.2 1.0 C A:CYS232 4.7 93.3 1.0 CA A:CYS229 4.7 74.8 1.0 C A:VAL231 4.8 71.3 1.0 CB A:VAL231 4.8 64.0 1.0 N A:ARG233 4.9 76.9 1.0 CZ B:ARG864 4.9 0.2 1.0

Zinc binding site 4 out of 4 in the Recognition and Processing of Branched Dna Substrates By SLX1-SLX4 Nuclease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Recognition and Processing of Branched Dna Substrates By SLX1-SLX4 Nuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:95.8 occ:1.00 SG A:CYS251 2.4 0.8 1.0 SG A:CYS280 2.5 76.8 1.0 SG A:CYS283 2.6 99.9 1.0 SG A:CYS246 2.6 73.4 1.0 CB A:CYS283 2.7 90.2 1.0 N A:CYS283 3.3 79.9 1.0 CB A:CYS251 3.3 0.2 1.0 CB A:CYS280 3.4 86.9 1.0 CB A:CYS246 3.5 62.6 1.0 CA A:CYS283 3.6 81.4 1.0 C A:LYS282 4.5 82.7 1.0 C A:CYS283 4.6 80.0 1.0 CB A:LYS282 4.7 62.2 1.0 CA A:CYS251 4.7 0.6 1.0 N A:GLY284 4.8 78.2 1.0 N A:GLY253 4.8 90.2 1.0 CA A:CYS280 4.9 84.1 1.0 N A:LYS282 4.9 71.6 1.0 CA A:LYS282 4.9 66.5 1.0 CA A:GLY253 4.9 84.6 1.0 CA A:CYS246 5.0 66.0 1.0 OD1 A:ASN248 5.0 87.2 1.0

V.Gaur, W.Zajko, S.Nirwal, A.Szlachcic, M.Gapinska, M.Nowotny. Recognition and Processing of Branched Dna Substrates By SLX1-SLX4 Nuclease. Nucleic Acids Res. 2019.
ISSN: ESSN 1362-4962
PubMed: 31584081
DOI: 10.1093/NAR/GKZ842