Chlorine in PDB 5tgq: Restriction-Modification System Type II R.Swai, Dna Free

The structure of Restriction-Modification System Type II R.Swai, Dna Free, PDB code: 5tgq was solved by B.W.Shen, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.01 / 1.88
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.386, 65.225, 67.567, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 27.9

The structure of Restriction-Modification System Type II R.Swai, Dna Free also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Chlorine atom in the Restriction-Modification System Type II R.Swai, Dna Free (pdb code 5tgq). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Restriction-Modification System Type II R.Swai, Dna Free, PDB code: 5tgq:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Restriction-Modification System Type II R.Swai, Dna Free


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Restriction-Modification System Type II R.Swai, Dna Free within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl302 b:33.2 occ:1.00 O A:HOH479 2.9 49.9 1.0 NE A:ARG199 3.2 33.1 1.0 NH1 A:ARG162 3.3 61.1 1.0 OG A:SER196 3.4 31.1 1.0 NH2 A:ARG199 3.5 32.5 1.0 CD A:PRO165 3.5 37.4 1.0 CG A:PRO165 3.7 36.9 1.0 CZ A:ARG199 3.8 33.7 1.0 O A:ILE163 3.8 30.6 1.0 CA A:SER196 3.9 34.7 1.0 CB A:SER196 3.9 32.0 1.0 O A:SER196 3.9 37.1 1.0 CA A:ASN164 4.0 31.4 1.0 N A:PRO165 4.1 35.4 1.0 CG A:GLN200 4.2 39.2 1.0 CB A:ARG199 4.2 36.1 1.0 C A:ASN164 4.3 34.2 1.0 CD A:ARG199 4.3 36.4 1.0 C A:SER196 4.4 38.0 1.0 CZ A:ARG162 4.4 57.2 1.0 NE2 A:GLN200 4.5 40.6 1.0 CD A:GLN200 4.7 38.6 1.0 C A:ILE163 4.7 28.0 1.0 CB A:ASN164 4.8 34.7 1.0 N A:ASN164 4.9 29.8 1.0 CG A:ARG199 4.9 36.7 1.0 NE A:ARG162 5.0 58.2 1.0 CA A:PRO165 5.0 35.5 1.0 CB A:PRO165 5.0 36.7 1.0

Chlorine binding site 2 out of 3 in the Restriction-Modification System Type II R.Swai, Dna Free


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Restriction-Modification System Type II R.Swai, Dna Free within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl303 b:44.8 occ:1.00 O A:HOH464 3.4 60.6 1.0 NZ A:LYS113 3.4 33.8 1.0 N A:THR110 3.4 28.7 1.0 CA A:GLY109 3.5 34.2 1.0 CG2 A:THR110 3.8 38.7 1.0 C A:GLY109 4.0 32.4 1.0 CE A:LYS113 4.0 32.7 1.0 CD A:LYS113 4.0 33.8 1.0 NE2 A:GLN168 4.4 39.6 1.0 O A:HOH469 4.5 62.2 1.0 CB A:THR110 4.5 34.5 1.0 CA A:THR110 4.5 31.5 1.0 N A:GLY109 4.8 30.5 1.0 CA A:PRO74 5.0 35.1 1.0 O A:LYS72 5.0 41.7 1.0 O A:ASN73 5.0 38.9 1.0

Chlorine binding site 3 out of 3 in the Restriction-Modification System Type II R.Swai, Dna Free


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Restriction-Modification System Type II R.Swai, Dna Free within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl304 b:49.2 occ:1.00 O A:HOH453 3.3 39.1 1.0 N A:ARG182 3.3 39.9 1.0 O A:HOH404 3.5 39.9 1.0 CB A:PHE3 3.8 45.6 1.0 CG A:ARG182 3.8 36.8 1.0 CD A:ARG182 3.8 37.2 1.0 CB A:THR181 3.8 43.2 1.0 CD2 A:PHE3 3.8 53.6 1.0 CB A:ARG182 3.8 38.2 1.0 CG A:PHE3 3.9 47.8 1.0 CA A:THR181 4.1 41.3 1.0 CA A:ARG182 4.1 38.6 1.0 C A:THR181 4.2 39.1 1.0 CG2 A:THR181 4.4 47.2 1.0 OH A:TYR179 4.5 48.1 1.0 CE2 A:PHE3 4.8 54.5 1.0 OG1 A:THR181 4.9 44.4 1.0 N A:GLU183 4.9 44.3 1.0

B.W.Shen, D.F.Heiter, K.D.Lunnen, G.G.Wilson, B.L.Stoddard. Dna Recognition By the Swai Restriction Endonuclease Involves Unusual Distortion of An 8 Base Pair A:T-Rich Target. Nucleic Acids Res. V. 45 1516 2017.
ISSN: ESSN 1362-4962
PubMed: 28180307
DOI: 10.1093/NAR/GKW1200