Chlorine in PDB 6yjb: VCAM4I Restriction Endonuclease 5HMC-Ssdna Complex

The structure of VCAM4I Restriction Endonuclease 5HMC-Ssdna Complex, PDB code: 6yjb was solved by M.Pastor, H.Czapinska, T.Lutz, I.Helbrecht, S.Xu, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.77 / 1.55
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	128.685, 128.685, 110.895, 90.00, 90.00, 120.00
R / Rfree (%)	14.3 / 16.4

The binding sites of Chlorine atom in the VCAM4I Restriction Endonuclease 5HMC-Ssdna Complex (pdb code 6yjb). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the VCAM4I Restriction Endonuclease 5HMC-Ssdna Complex, PDB code: 6yjb:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the VCAM4I Restriction Endonuclease 5HMC-Ssdna Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of VCAM4I Restriction Endonuclease 5HMC-Ssdna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl414 b:39.5 occ:0.70 O A:HOH755 3.0 59.2 1.0 N A:SER68 3.0 20.0 0.5 N A:SER68 3.0 20.0 0.5 OG A:SER68 3.5 20.8 0.5 CA A:TYR67 3.6 19.9 1.0 O A:HOH1029 3.6 42.4 1.0 CB A:SER68 3.6 20.8 0.5 O A:HOH544 3.6 29.7 1.0 CB A:SER68 3.8 20.6 0.5 C A:TYR67 3.8 20.2 1.0 O A:HOH580 3.8 69.6 1.0 CA A:SER68 3.9 20.4 0.5 CA A:SER68 3.9 20.2 0.5 CB A:TYR67 3.9 20.1 1.0 O A:HOH691 4.3 46.9 1.0 CZ3 A:TRP87 4.5 24.0 1.0 O A:ALA66 4.7 22.8 1.0 O A:SER68 4.8 22.3 0.5 N A:TYR67 4.9 19.8 1.0 O A:HOH983 4.9 71.4 1.0 O A:SER68 4.9 21.6 0.5 C A:SER68 4.9 20.4 0.5 C A:SER68 4.9 20.3 0.5 O A:TYR67 5.0 19.6 1.0 OG A:SER68 5.0 21.4 0.5

Chlorine binding site 2 out of 2 in the VCAM4I Restriction Endonuclease 5HMC-Ssdna Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of VCAM4I Restriction Endonuclease 5HMC-Ssdna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl415 b:56.2 occ:1.00 O A:HOH968 2.9 66.6 1.0 N A:ASP122 3.1 29.7 1.0 O A:HOH832 3.4 42.6 1.0 CA A:GLN121 3.7 27.1 1.0 CB A:ASP122 3.8 36.5 1.0 CB A:GLN121 3.8 28.4 1.0 C A:GLN121 3.9 28.0 1.0 O A:HOH778 3.9 38.2 1.0 O A:HOH765 3.9 38.1 1.0 CG A:ASP122 4.0 41.8 1.0 CA A:ASP122 4.0 31.8 1.0 OD2 A:ASP122 4.3 49.3 1.0 CG A:GLN121 4.4 29.7 1.0 OD1 A:ASP122 4.4 45.5 1.0 O A:HOH875 4.9 68.4 1.0

M.Pastor, H.Czapinska, T.Lutz, I.Helbrecht, S.Xu, M.Bochtler. Crystal Structures of the Eve-Hnh Endonuclease VCAM4I in the Presence and Absence of Dna Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962
DOI: 10.1093/NAR/GKAA1218