Calcium in PDB 5tgx: Restriction/Modification System-Type II R-Swai Complexed with Partially Cleaved Dna

The structure of Restriction/Modification System-Type II R-Swai Complexed with Partially Cleaved Dna, PDB code: 5tgx 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)	49.00 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	109.856, 57.058, 112.785, 90.00, 108.22, 90.00
R / Rfree (%)	19.8 / 24.2

The binding sites of Calcium atom in the Restriction/Modification System-Type II R-Swai Complexed with Partially Cleaved Dna (pdb code 5tgx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Restriction/Modification System-Type II R-Swai Complexed with Partially Cleaved Dna, PDB code: 5tgx:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Restriction/Modification System-Type II R-Swai Complexed with Partially Cleaved Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Restriction/Modification System-Type II R-Swai Complexed with Partially Cleaved Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:42.2 occ:1.00 OD1 A:ASP93 2.2 43.7 1.0 O A:HOH439 2.2 38.4 1.0 OP1 H:DA25 2.3 30.9 0.5 O A:PHE94 2.4 36.5 1.0 O H:HOH202 2.5 30.4 1.0 OD2 A:ASP76 2.6 40.3 1.0 CG A:ASP76 3.3 40.8 1.0 OD1 A:ASP76 3.4 47.3 1.0 P H:DA25 3.4 35.9 0.5 CG A:ASP93 3.4 42.8 1.0 C A:PHE94 3.6 37.1 1.0 OP2 H:DA25 3.8 29.4 0.5 N A:PHE94 3.8 36.9 1.0 NZ A:LYS95 4.0 48.2 1.0 C5' H:DA25 4.1 39.4 0.5 OD2 A:ASP93 4.2 45.3 1.0 CA A:PHE94 4.2 36.5 1.0 C A:ASP93 4.3 39.1 1.0 OG A:SER41 4.3 51.4 1.0 O5' H:DA25 4.4 33.7 0.5 CA A:ASP93 4.4 41.4 1.0 O A:HOH428 4.4 35.3 1.0 O5' H:DA25 4.5 41.8 0.5 CE A:LYS95 4.5 46.4 1.0 CB A:ASP93 4.5 41.4 1.0 O3' H:DT14 4.6 34.3 0.5 O3' H:DT14 4.6 34.3 0.5 C5' H:DA25 4.6 35.6 0.5 CB A:PHE94 4.6 37.8 1.0 N A:LYS95 4.7 37.5 1.0 OP2 H:DA26 4.8 35.1 1.0 CD A:LYS95 4.8 44.3 1.0 P H:DA25 4.8 42.8 0.5 CB A:ASP76 4.8 38.1 1.0

Calcium binding site 2 out of 4 in the Restriction/Modification System-Type II R-Swai Complexed with Partially Cleaved Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Restriction/Modification System-Type II R-Swai Complexed with Partially Cleaved Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:49.0 occ:1.00 O B:HOH408 2.2 40.0 1.0 OD1 B:ASP93 2.3 48.7 1.0 O B:PHE94 2.3 43.5 1.0 OP1 I:DA25 2.4 42.2 0.5 OD2 B:ASP76 2.5 45.6 1.0 O B:HOH407 2.5 45.3 1.0 CG B:ASP76 3.3 47.0 1.0 P I:DA25 3.3 40.9 0.5 OD1 B:ASP76 3.4 49.0 1.0 C B:PHE94 3.5 43.6 1.0 CG B:ASP93 3.5 53.7 1.0 N B:PHE94 3.7 42.0 1.0 OP2 I:DA25 4.0 36.5 0.5 CA B:PHE94 4.0 43.5 1.0 OG B:SER41 4.1 57.5 1.0 NZ B:LYS95 4.2 51.2 1.0 C B:ASP93 4.2 44.3 1.0 C5' I:DA25 4.2 43.2 0.5 O5' I:DA25 4.3 39.3 0.5 OD2 B:ASP93 4.4 59.5 1.0 CA B:ASP93 4.4 48.0 1.0 O5' I:DA25 4.4 49.0 0.5 CB B:PHE94 4.4 43.8 1.0 O3' I:DT14 4.5 42.7 0.5 O B:HOH424 4.5 57.8 1.0 CB B:ASP93 4.6 51.4 1.0 N B:LYS95 4.6 43.4 1.0 P I:DA25 4.7 53.8 0.5 CE B:LYS95 4.7 50.7 1.0 CB B:ASP76 4.7 47.5 1.0 OP2 I:DA26 4.8 40.7 1.0 CD B:LYS95 4.9 47.4 1.0 C5' I:DA25 4.9 45.3 0.5 O B:ASP93 5.0 43.2 1.0

Calcium binding site 3 out of 4 in the Restriction/Modification System-Type II R-Swai Complexed with Partially Cleaved Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Restriction/Modification System-Type II R-Swai Complexed with Partially Cleaved Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:51.2 occ:1.00 O C:HOH413 2.0 46.7 1.0 OD1 C:ASP93 2.3 49.9 1.0 O C:HOH409 2.4 48.8 1.0 O C:PHE94 2.5 53.7 1.0 OD2 C:ASP76 2.5 52.9 1.0 OP1 J:DA25 2.5 47.8 0.5 OP2 J:DA25 3.1 63.6 0.5 CG C:ASP76 3.2 51.5 1.0 OD1 C:ASP76 3.2 51.3 1.0 CG C:ASP93 3.5 52.7 1.0 P J:DA25 3.5 44.8 0.5 C C:PHE94 3.6 52.7 1.0 N C:PHE94 3.7 48.4 1.0 P J:DA25 3.9 66.4 0.5 C5' J:DA25 4.0 45.8 0.5 OP2 J:DA25 4.0 42.1 0.5 O5' J:DA25 4.0 57.3 0.5 CA C:PHE94 4.2 51.9 1.0 NZ C:LYS95 4.2 53.3 1.0 OG C:SER41 4.2 56.5 1.0 O5' J:DA25 4.2 43.0 0.5 O J:HOH110 4.2 67.2 1.0 OP1 J:DA25 4.2 66.3 0.5 C C:ASP93 4.2 47.5 1.0 OD2 C:ASP93 4.3 57.2 1.0 CA C:ASP93 4.4 49.4 1.0 O3' J:DT14 4.5 45.5 0.5 CB C:PHE94 4.6 55.0 1.0 CB C:ASP93 4.6 50.9 1.0 CE C:LYS95 4.7 57.4 1.0 CB C:ASP76 4.7 51.4 1.0 OP2 J:DA26 4.7 45.8 1.0 N C:LYS95 4.8 52.3 1.0 CD C:LYS95 4.9 56.8 1.0

Calcium binding site 4 out of 4 in the Restriction/Modification System-Type II R-Swai Complexed with Partially Cleaved Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Restriction/Modification System-Type II R-Swai Complexed with Partially Cleaved Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:51.3 occ:1.00 OP1 K:DA25 2.0 36.7 0.5 O D:HOH421 2.1 50.6 1.0 OD1 D:ASP93 2.2 50.2 1.0 O D:PHE94 2.4 42.7 1.0 O D:HOH409 2.4 41.2 1.0 OD2 D:ASP76 2.5 45.1 1.0 P K:DA25 3.2 40.6 0.5 CG D:ASP76 3.3 43.5 1.0 OD1 D:ASP76 3.4 48.1 1.0 CG D:ASP93 3.4 50.9 1.0 C D:PHE94 3.5 44.1 1.0 N D:PHE94 3.7 44.0 1.0 OP2 K:DA25 3.9 36.5 0.5 NZ D:LYS95 4.0 43.5 1.0 C5' K:DA25 4.0 42.2 0.5 O5' K:DA25 4.0 40.5 0.5 CA D:PHE94 4.1 45.6 1.0 C D:ASP93 4.1 46.1 1.0 OD2 D:ASP93 4.2 51.7 1.0 O K:HOH112 4.3 61.7 1.0 OG D:SER41 4.3 53.8 1.0 CA D:ASP93 4.4 46.7 1.0 OP1 K:DA25 4.4 42.9 0.5 O3' K:DT14 4.5 42.2 0.5 CE D:LYS95 4.5 46.4 1.0 CB D:ASP93 4.5 47.6 1.0 O D:HOH427 4.5 50.5 1.0 O3' K:DT14 4.5 34.0 0.5 CB D:PHE94 4.6 47.1 1.0 N D:LYS95 4.6 47.0 1.0 P K:DA25 4.6 43.9 0.5 CD D:LYS95 4.8 46.3 1.0 CB D:ASP76 4.8 43.8 1.0 OP2 K:DA26 4.8 43.3 1.0 O D:ASP93 4.9 45.9 1.0 C5' K:DA25 5.0 40.8 0.5

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