Zinc in PDB 5yd0: Crystal Structure of Schlafen 13 (SLFN13) N'-Domain

The structure of Crystal Structure of Schlafen 13 (SLFN13) N'-Domain, PDB code: 5yd0 was solved by J.-Y.Yang, S.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.24 / 3.18
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	171.968, 134.065, 77.587, 90.00, 105.55, 90.00
R / Rfree (%)	20 / 24.7

The binding sites of Zinc atom in the Crystal Structure of Schlafen 13 (SLFN13) N'-Domain (pdb code 5yd0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Schlafen 13 (SLFN13) N'-Domain, PDB code: 5yd0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Schlafen 13 (SLFN13) N'-Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Schlafen 13 (SLFN13) N'-Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn900 b:0.1 occ:1.00 ND1 A:HIS281 2.1 0.7 1.0 CB A:CYS317 2.4 0.2 1.0 SG A:CYS318 2.5 0.8 1.0 CE1 A:HIS281 2.6 0.5 1.0 SG A:CYS283 2.9 0.2 1.0 CG A:HIS281 3.3 0.4 1.0 C A:CYS317 3.4 0.5 1.0 N A:CYS318 3.4 0.9 1.0 CA A:CYS317 3.4 96.6 1.0 CB A:CYS318 3.5 0.8 1.0 SG A:CYS317 3.7 0.3 1.0 NE2 A:HIS281 3.8 0.3 1.0 O A:CYS317 4.0 0.5 1.0 CB A:HIS281 4.0 0.2 1.0 CA A:CYS318 4.0 0.1 1.0 CD2 A:HIS281 4.2 0.8 1.0 CA A:HIS281 4.2 0.9 1.0 CB A:CYS283 4.3 0.9 1.0 N A:CYS317 4.3 0.1 1.0 N A:PHE282 4.5 0.6 1.0 N A:CYS283 4.5 0.1 1.0 O A:SER285 4.6 0.2 1.0 CE2 A:PHE316 4.8 96.2 1.0 C A:HIS281 4.9 0.2 1.0 CB A:SER285 4.9 0.9 1.0 CA A:CYS283 5.0 0.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Schlafen 13 (SLFN13) N'-Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Schlafen 13 (SLFN13) N'-Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn900 b:84.0 occ:1.00 ND1 B:HIS281 2.2 76.2 1.0 SG B:CYS317 2.2 69.4 1.0 SG B:CYS283 2.4 0.3 1.0 SG B:CYS318 2.5 78.8 1.0 CE1 B:HIS281 3.0 79.0 1.0 CG B:HIS281 3.3 79.7 1.0 CB B:CYS317 3.5 76.2 1.0 CB B:CYS318 3.5 84.2 1.0 CB B:HIS281 3.7 78.4 1.0 CB B:CYS283 3.7 98.0 1.0 N B:CYS318 3.8 68.2 1.0 CA B:HIS281 4.0 76.7 1.0 N B:CYS283 4.1 86.3 1.0 N B:PHE282 4.2 82.0 1.0 NE2 B:HIS281 4.2 80.3 1.0 C B:CYS317 4.2 71.7 1.0 CA B:CYS318 4.3 76.3 1.0 CD2 B:HIS281 4.3 80.9 1.0 CA B:CYS317 4.4 70.0 1.0 CA B:CYS283 4.4 92.5 1.0 C B:HIS281 4.6 81.1 1.0 CB B:SER285 4.6 0.3 1.0 O B:CYS317 4.9 77.4 1.0 CE2 B:PHE316 5.0 68.8 1.0 C B:PHE282 5.0 83.2 1.0 N B:CYS317 5.0 65.3 1.0 C B:CYS283 5.0 0.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Schlafen 13 (SLFN13) N'-Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Schlafen 13 (SLFN13) N'-Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn900 b:0.9 occ:1.00 ND1 C:HIS281 2.0 0.7 1.0 SG C:CYS317 2.3 0.6 1.0 SG C:CYS318 2.5 0.6 1.0 CB C:CYS317 2.9 0.8 1.0 CE1 C:HIS281 2.9 0.6 1.0 CG C:HIS281 3.0 0.0 1.0 OG C:SER285 3.2 0.1 1.0 SG C:CYS283 3.3 0.0 1.0 CB C:HIS281 3.3 0.3 1.0 CB C:CYS318 3.4 0.3 1.0 N C:CYS318 3.5 0.3 1.0 C C:CYS317 3.6 0.1 1.0 CA C:HIS281 3.7 0.5 1.0 CA C:CYS317 3.9 0.7 1.0 NE2 C:HIS281 4.0 0.9 1.0 CA C:CYS318 4.0 0.1 1.0 CD2 C:HIS281 4.1 0.3 1.0 O C:CYS317 4.1 0.0 1.0 N C:PHE282 4.2 0.2 1.0 C C:HIS281 4.4 0.5 1.0 N C:CYS283 4.5 0.8 1.0 CB C:SER285 4.6 0.7 1.0 CB C:CYS283 4.7 0.4 1.0 N C:CYS317 4.8 0.1 1.0 N C:HIS281 4.9 0.3 1.0 CE2 C:PHE316 5.0 0.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Schlafen 13 (SLFN13) N'-Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Schlafen 13 (SLFN13) N'-Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn900 b:0.0 occ:1.00 ND1 D:HIS281 2.1 0.8 1.0 SG D:CYS317 2.4 0.5 1.0 SG D:CYS318 2.4 0.9 1.0 CE1 D:HIS281 2.6 0.0 1.0 CB D:CYS317 2.6 0.4 1.0 SG D:CYS283 3.0 0.9 1.0 CG D:HIS281 3.3 0.6 1.0 N D:CYS318 3.4 0.7 1.0 CB D:CYS318 3.4 0.8 1.0 C D:CYS317 3.5 0.9 1.0 OG D:SER285 3.6 0.0 1.0 CA D:CYS317 3.6 0.8 1.0 NE2 D:HIS281 3.8 0.3 1.0 CA D:CYS318 4.0 0.1 1.0 CB D:HIS281 4.0 0.8 1.0 O D:CYS317 4.0 0.6 1.0 CD2 D:HIS281 4.2 0.7 1.0 CA D:HIS281 4.3 0.8 1.0 CB D:CYS283 4.5 0.4 1.0 N D:CYS317 4.5 0.4 1.0 N D:PHE282 4.6 0.8 1.0 N D:CYS283 4.8 0.1 1.0 O D:SER285 4.9 0.4 1.0 CE2 D:PHE316 4.9 0.9 1.0 C D:HIS281 5.0 0.1 1.0 CB D:SER285 5.0 0.5 1.0

J.Y.Yang, X.Y.Deng, Y.S.Li, X.C.Ma, J.X.Feng, B.Yu, Y.Chen, Y.L.Luo, X.Wang, M.L.Chen, Z.X.Fang, F.X.Zheng, Y.P.Li, Q.Zhong, T.B.Kang, L.B.Song, R.H.Xu, M.S.Zeng, W.Chen, H.Zhang, W.Xie, S.Gao. Structure of SCHLAFEN13 Reveals A New Class of Trna/Rrna- Targeting Rnase Engaged in Translational Control Nat Commun V. 9 1165 2018.
ISSN: ESSN 2041-1723
PubMed: 29563550
DOI: 10.1038/S41467-018-03544-X