Zinc in PDB 6wnl: Human Artemis/SNM1C Catalytic Domain, Crystal Form 2

The structure of Human Artemis/SNM1C Catalytic Domain, Crystal Form 2, PDB code: 6wnl was solved by F.Karim, S.Liu, A.R.Laciak, L.Volk, M.Rosenblum, R.Curtis, N.Huang, G.Carr, G.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.46 / 2.37
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.209, 105.675, 116.037, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 28

The binding sites of Zinc atom in the Human Artemis/SNM1C Catalytic Domain, Crystal Form 2 (pdb code 6wnl). 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 Artemis/SNM1C Catalytic Domain, Crystal Form 2, PDB code: 6wnl:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Human Artemis/SNM1C Catalytic Domain, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Artemis/SNM1C Catalytic Domain, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:24.2 occ:1.00 ND1 A:HIS254 2.1 20.3 1.0 ND1 A:HIS228 2.1 26.7 1.0 SG A:CYS256 2.2 26.0 1.0 SG A:CYS272 2.4 23.9 1.0 CE1 A:HIS228 2.9 26.8 1.0 CE1 A:HIS254 2.9 20.2 1.0 CG A:HIS254 3.1 20.1 1.0 CG A:HIS228 3.2 26.2 1.0 CB A:CYS272 3.2 25.4 1.0 CB A:CYS256 3.2 24.9 1.0 CB A:HIS254 3.5 20.3 1.0 CB A:HIS228 3.6 25.5 1.0 NE2 A:HIS228 4.1 26.5 1.0 NE2 A:HIS254 4.1 20.2 1.0 CD2 A:HIS254 4.2 20.4 1.0 CD2 A:HIS228 4.2 26.6 1.0 N A:CYS272 4.2 24.8 1.0 CA A:CYS272 4.3 25.2 1.0 CA A:CYS256 4.5 24.1 1.0 CA A:HIS254 4.5 20.9 1.0 N A:CYS256 4.6 23.1 1.0 CB A:LEU270 4.7 23.3 1.0 CD1 A:LEU270 4.9 24.4 1.0 CA A:HIS228 4.9 25.7 1.0 O A:HIS228 4.9 25.8 1.0

Zinc binding site 2 out of 4 in the Human Artemis/SNM1C Catalytic Domain, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Artemis/SNM1C Catalytic Domain, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:27.7 occ:1.00 NE2 A:HIS115 2.1 22.9 1.0 OD2 A:ASP136 2.1 24.9 1.0 O A:HOH547 2.2 25.4 1.0 NE2 A:HIS33 2.3 23.6 1.0 O A:HOH559 2.3 30.5 1.0 ND1 A:HIS35 2.4 27.6 1.0 CE1 A:HIS115 2.9 23.6 1.0 CD2 A:HIS33 3.1 22.8 1.0 CG A:ASP136 3.2 24.2 1.0 CD2 A:HIS115 3.2 22.6 1.0 CE1 A:HIS33 3.3 23.8 1.0 CE1 A:HIS35 3.3 27.0 1.0 CG A:HIS35 3.4 27.4 1.0 CB A:ASP136 3.6 23.3 1.0 CB A:HIS35 3.6 27.4 1.0 O A:HOH570 3.8 31.9 1.0 ND1 A:HIS115 4.0 23.3 1.0 CE1 A:HIS38 4.1 31.6 1.0 ND1 A:HIS38 4.1 31.2 1.0 CG A:HIS115 4.2 22.7 1.0 CG A:HIS33 4.2 23.3 1.0 O A:HOH594 4.3 26.8 1.0 ND1 A:HIS33 4.3 23.3 1.0 OD1 A:ASP136 4.3 24.6 1.0 NE2 A:HIS35 4.5 28.6 1.0 CD2 A:HIS35 4.5 27.1 1.0 CE1 A:HIS319 4.6 24.0 1.0

Zinc binding site 3 out of 4 in the Human Artemis/SNM1C Catalytic Domain, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Artemis/SNM1C Catalytic Domain, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:24.1 occ:1.00 ND1 B:HIS254 1.9 23.2 1.0 ND1 B:HIS228 2.1 28.1 1.0 SG B:CYS272 2.2 23.4 1.0 SG B:CYS256 2.2 22.7 1.0 CE1 B:HIS254 2.7 23.5 1.0 CE1 B:HIS228 2.9 28.9 1.0 CG B:HIS254 3.1 23.3 1.0 CB B:CYS272 3.1 24.7 1.0 CB B:CYS256 3.2 23.6 1.0 CG B:HIS228 3.2 27.7 1.0 CB B:HIS254 3.6 23.5 1.0 CB B:HIS228 3.7 27.5 1.0 NE2 B:HIS254 3.9 23.0 1.0 NE2 B:HIS228 4.1 28.4 1.0 CD2 B:HIS254 4.1 23.0 1.0 N B:CYS272 4.2 24.5 1.0 CD2 B:HIS228 4.3 28.1 1.0 CA B:CYS272 4.3 24.6 1.0 CA B:CYS256 4.5 24.6 1.0 N B:CYS256 4.5 25.3 1.0 CA B:HIS254 4.6 22.9 1.0 CB B:LEU270 4.7 23.8 1.0 CD1 B:LEU270 4.7 23.7 1.0 CG B:ARG249 4.8 45.7 1.0 O B:HIS228 4.9 33.1 1.0

Zinc binding site 4 out of 4 in the Human Artemis/SNM1C Catalytic Domain, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Artemis/SNM1C Catalytic Domain, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:32.4 occ:1.00 O B:HOH535 2.0 28.0 1.0 ND1 B:HIS35 2.1 30.5 1.0 OD2 B:ASP136 2.2 20.1 1.0 O B:HOH526 2.3 28.9 1.0 NE2 B:HIS115 2.3 27.3 1.0 NE2 B:HIS33 2.3 22.9 1.0 CE1 B:HIS35 3.0 31.0 1.0 CE1 B:HIS115 3.1 27.5 1.0 CG B:HIS35 3.1 31.4 1.0 CD2 B:HIS33 3.2 23.1 1.0 CG B:ASP136 3.3 21.5 1.0 CD2 B:HIS115 3.3 27.5 1.0 CE1 B:HIS33 3.4 23.8 1.0 CB B:HIS35 3.5 30.7 1.0 O B:HOH564 3.6 23.0 1.0 CB B:ASP136 3.7 22.0 1.0 NE2 B:HIS38 3.8 30.4 1.0 CD2 B:HIS38 3.9 31.0 1.0 NE2 B:HIS35 4.2 32.2 1.0 ND1 B:HIS115 4.2 28.4 1.0 CD2 B:HIS35 4.2 31.2 1.0 O B:HOH598 4.3 36.0 1.0 CG B:HIS115 4.4 27.6 1.0 OD1 B:ASP136 4.4 22.6 1.0 CG B:HIS33 4.4 23.6 1.0 ND1 B:HIS33 4.4 23.3 1.0 CE1 B:HIS319 4.8 28.6 1.0 CE1 B:HIS38 5.0 30.4 1.0 CA B:HIS35 5.0 31.4 1.0

M.F.Karim, S.Liu, A.R.Laciak, L.Volk, M.Koszelak-Rosenblum, M.R.Lieber, M.Wu, R.Curtis, N.N.Huang, G.Carr, G.Zhu. Structural Analysis of the Catalytic Domain of Artemis Endonuclease/SNM1C Reveals Distinct Structural Features. J.Biol.Chem. V. 295 12368 2020.
ISSN: ESSN 1083-351X
PubMed: 32576658
DOI: 10.1074/JBC.RA120.014136