Zinc in PDB 7abs: Structure of Human DCLRE1C/Artemis in Complex with Dna - Re-Evaluation of 6WO0

The structure of Structure of Human DCLRE1C/Artemis in Complex with Dna - Re-Evaluation of 6WO0, PDB code: 7abs was solved by J.A.Newman, Y.Yosaatmadja, F.Von Delft, C.H.Arrowsmith, A.Edwards, C.Bountra, O.Gileadi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.54 / 1.97
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	72.69, 111.01, 55.16, 90, 90, 90
R / Rfree (%)	21.5 / 27.6

The binding sites of Zinc atom in the Structure of Human DCLRE1C/Artemis in Complex with Dna - Re-Evaluation of 6WO0 (pdb code 7abs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of Human DCLRE1C/Artemis in Complex with Dna - Re-Evaluation of 6WO0, PDB code: 7abs:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of Human DCLRE1C/Artemis in Complex with Dna - Re-Evaluation of 6WO0


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human DCLRE1C/Artemis in Complex with Dna - Re-Evaluation of 6WO0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:42.9 occ:1.00 ND1 A:HIS228 2.0 42.3 1.0 ND1 A:HIS254 2.0 45.5 1.0 SG A:CYS256 2.3 39.6 1.0 SG A:CYS272 2.3 44.5 1.0 CE1 A:HIS228 2.7 45.8 1.0 CE1 A:HIS254 2.9 48.4 1.0 CG A:HIS254 3.1 44.5 1.0 CB A:CYS256 3.2 36.5 1.0 CB A:CYS272 3.2 44.1 1.0 CG A:HIS228 3.2 43.6 1.0 CB A:HIS254 3.6 44.5 1.0 CB A:HIS228 3.8 43.1 1.0 NE2 A:HIS228 4.0 43.1 1.0 NE2 A:HIS254 4.1 47.0 1.0 CD2 A:HIS254 4.2 41.8 1.0 CD2 A:HIS228 4.2 51.4 1.0 N A:CYS272 4.2 41.2 1.0 CA A:CYS272 4.3 45.0 1.0 CA A:CYS256 4.5 39.3 1.0 CA A:HIS254 4.5 42.1 1.0 N A:CYS256 4.6 43.3 1.0 CB A:LEU270 4.6 34.3 1.0 CG A:ARG249 4.6 55.5 1.0 CD1 A:LEU270 4.8 40.9 1.0

Zinc binding site 2 out of 3 in the Structure of Human DCLRE1C/Artemis in Complex with Dna - Re-Evaluation of 6WO0


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human DCLRE1C/Artemis in Complex with Dna - Re-Evaluation of 6WO0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:46.9 occ:1.00 NE2 A:HIS33 2.1 34.9 1.0 OP1 E:DA1 2.2 28.0 0.5 NE2 A:HIS115 2.2 36.8 1.0 OD2 A:ASP136 2.2 43.2 1.0 ND1 A:HIS35 2.3 46.1 1.0 O E:HOH202 2.4 51.3 1.0 CD2 A:HIS33 3.0 35.4 1.0 CE1 A:HIS115 3.1 37.1 1.0 CE1 A:HIS33 3.1 35.7 1.0 CE1 A:HIS35 3.2 44.5 1.0 CD2 A:HIS115 3.2 41.0 1.0 CG A:ASP136 3.3 41.0 1.0 CG A:HIS35 3.3 47.0 1.0 P E:DA1 3.4 46.7 0.5 CB A:HIS35 3.6 45.1 1.0 CB A:ASP136 3.6 38.1 1.0 OP2 E:DA1 4.0 52.0 0.5 ZN E:ZN101 4.0 81.1 0.5 O5' E:DA1 4.1 44.6 0.5 CG A:HIS33 4.2 38.1 1.0 ND1 A:HIS115 4.2 41.0 1.0 ND1 A:HIS33 4.2 36.1 1.0 CD2 A:HIS38 4.3 42.4 1.0 CG A:HIS115 4.3 41.7 1.0 NE2 A:HIS35 4.3 50.5 1.0 CD2 A:HIS35 4.4 49.5 1.0 OD1 A:ASP136 4.4 42.9 1.0 NE2 A:HIS38 4.4 38.8 1.0 CE1 A:HIS319 4.7 44.1 1.0 O3' E:DC0 4.7 35.5 0.5 O A:HOH540 5.0 57.7 1.0

Zinc binding site 3 out of 3 in the Structure of Human DCLRE1C/Artemis in Complex with Dna - Re-Evaluation of 6WO0


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human DCLRE1C/Artemis in Complex with Dna - Re-Evaluation of 6WO0 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn101 b:81.1 occ:0.50 OP2 E:DA1 2.2 52.0 0.5 O A:HOH540 2.3 57.7 1.0 O E:HOH202 2.7 51.3 1.0 P E:DA1 2.9 46.7 0.5 OP1 E:DA1 3.1 28.0 0.5 OD2 A:ASP37 3.1 88.5 1.0 OD2 A:ASP136 3.1 43.2 1.0 O3' E:DC0 3.4 35.5 0.5 O A:HOH542 3.5 46.8 1.0 CG A:ASP37 4.0 71.5 1.0 CG A:ASP136 4.0 41.0 1.0 ZN A:ZN402 4.0 46.9 1.0 NE2 A:HIS38 4.0 38.8 1.0 CE1 A:HIS319 4.0 44.1 1.0 OD1 A:ASP136 4.0 42.9 1.0 NE2 A:HIS319 4.2 38.4 1.0 CB A:ASP37 4.2 62.3 1.0 CD2 A:HIS38 4.4 42.4 1.0 O5' E:DA1 4.4 44.6 0.5 OD1 A:ASP37 5.0 81.6 1.0

J.A.Newman, Y.Yosaatmadja, F.Von Delft, C.H.Arrowsmith, A.Edwards, C.Bountra, O.Gileadi. Structural and Mechanistic Insights Into the Artemis Endonuclease and Strategies For Its Inhibition Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962