Zinc in PDB 6sei: 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: 6sei 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)	46.61 / 2.69
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.075, 92.700, 93.251, 90.00, 91.60, 90.00
R / Rfree (%)	20.8 / 26.6

The structure of Recognition and Processing of Branched Dna Substrates By SLX1-SLX4 Nuclease also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Recognition and Processing of Branched Dna Substrates By SLX1-SLX4 Nuclease (pdb code 6sei). 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: 6sei:
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 A:Zn401 b:24.7 occ:1.00 ND1 A:HIS256 2.3 20.8 1.0 SG A:CYS232 2.3 25.9 1.0 SG A:CYS229 2.4 24.4 1.0 SG A:CYS259 2.6 22.1 1.0 CB A:CYS232 3.1 26.0 1.0 CB A:CYS229 3.1 24.5 1.0 CG A:HIS256 3.1 20.4 1.0 CB A:CYS259 3.3 21.9 1.0 CB A:HIS256 3.3 20.4 1.0 CE1 A:HIS256 3.3 21.2 1.0 N A:CYS232 3.8 26.0 1.0 N A:HIS256 3.9 20.6 1.0 CA A:CYS232 4.0 25.9 1.0 O A:HOH526 4.1 35.9 1.0 CA A:HIS256 4.2 20.6 1.0 CD2 A:HIS256 4.3 20.7 1.0 NE2 A:HIS256 4.4 21.3 1.0 CA A:CYS229 4.6 24.5 1.0 CA A:CYS259 4.7 21.9 1.0 C A:CYS232 4.8 26.1 1.0 CB A:VAL231 4.8 25.0 1.0 NH1 B:ARG864 4.9 21.8 1.0 C A:VAL231 4.9 25.8 1.0 O A:HIS256 5.0 20.6 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 A:Zn402 b:28.5 occ:1.00 SG A:CYS246 2.3 25.7 1.0 SG A:CYS251 2.3 38.8 1.0 SG A:CYS280 2.4 30.5 1.0 SG A:CYS283 2.4 26.1 1.0 CB A:CYS280 3.0 31.0 1.0 CB A:CYS246 3.1 25.5 1.0 CB A:CYS251 3.3 40.4 1.0 CB A:CYS283 3.3 27.3 1.0 N A:CYS283 3.8 27.7 1.0 CA A:CYS283 4.2 28.3 1.0 CA A:CYS280 4.5 30.8 1.0 CA A:CYS246 4.5 25.7 1.0 N A:GLY253 4.7 32.0 1.0 CB A:ASN248 4.7 39.3 1.0 CA A:CYS251 4.7 41.1 1.0 CB A:LYS282 4.7 27.2 1.0 OD1 A:ASN248 4.8 39.3 1.0 C A:CYS283 4.9 29.4 1.0 CA A:GLY253 4.9 30.3 1.0 C A:LYS282 4.9 28.3 1.0 C A:CYS251 5.0 37.8 1.0 N A:GLY284 5.0 30.1 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 C:Zn401 b:26.0 occ:1.00 SG C:CYS232 2.2 46.6 1.0 ND1 C:HIS256 2.3 23.7 1.0 SG C:CYS259 2.3 21.3 1.0 SG C:CYS229 2.5 25.1 1.0 CB C:CYS232 3.1 44.5 1.0 CB C:CYS229 3.2 25.2 1.0 CB C:CYS259 3.2 20.6 1.0 CE1 C:HIS256 3.2 24.2 1.0 CG C:HIS256 3.3 23.4 1.0 CB C:HIS256 3.6 23.0 1.0 N C:CYS232 3.7 38.3 1.0 N C:HIS256 4.0 22.5 1.0 CA C:CYS232 4.0 41.3 1.0 O C:HOH515 4.3 16.4 1.0 NE2 C:HIS256 4.4 24.1 1.0 CA C:HIS256 4.4 22.6 1.0 CD2 C:HIS256 4.4 23.6 1.0 NH1 D:ARG864 4.6 28.6 1.0 CA C:CYS229 4.6 25.7 1.0 CA C:CYS259 4.7 21.6 1.0 CB C:VAL231 4.8 29.5 1.0 C C:CYS232 4.8 40.4 1.0 C C:VAL231 4.8 36.3 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 C:Zn402 b:32.7 occ:1.00 SG C:CYS246 2.3 29.9 1.0 SG C:CYS280 2.3 30.2 1.0 SG C:CYS251 2.5 36.3 1.0 SG C:CYS283 2.6 33.2 1.0 CB C:CYS283 3.1 33.7 1.0 CB C:CYS280 3.1 31.1 1.0 CB C:CYS246 3.1 29.1 1.0 CB C:CYS251 3.4 37.9 1.0 N C:CYS283 3.7 32.5 1.0 CA C:CYS283 3.9 34.0 1.0 CA C:CYS280 4.6 31.7 1.0 CA C:CYS246 4.6 29.1 1.0 CB C:LYS282 4.6 30.7 1.0 OD1 C:ASN248 4.7 44.9 1.0 C C:LYS282 4.8 32.5 1.0 CB C:ASN248 4.8 45.0 1.0 C C:CYS283 4.8 34.9 1.0 CA C:CYS251 4.8 38.9 1.0 N C:GLY253 4.9 29.2 1.0 N C:GLY284 5.0 33.9 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