Magnesium in PDB 5th3: Restriction/Modification System-Type II R.Swai Cleaved Dna Complex

The structure of Restriction/Modification System-Type II R.Swai Cleaved Dna Complex, PDB code: 5th3 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 / 2.33
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	109.748, 57.072, 113.443, 90.00, 107.60, 90.00
R / Rfree (%)	19.8 / 23.9

The binding sites of Magnesium atom in the Restriction/Modification System-Type II R.Swai Cleaved Dna Complex (pdb code 5th3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Restriction/Modification System-Type II R.Swai Cleaved Dna Complex, PDB code: 5th3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Restriction/Modification System-Type II R.Swai Cleaved Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Restriction/Modification System-Type II R.Swai Cleaved Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:42.3 occ:1.00 O A:HOH414 2.0 49.0 1.0 OD1 A:ASP93 2.1 55.8 1.0 O A:HOH424 2.3 37.4 1.0 MG A:MG302 2.3 56.2 1.0 O A:PHE94 2.4 45.3 1.0 OD2 A:ASP76 2.4 45.5 1.0 CG A:ASP76 3.3 46.9 1.0 CG A:ASP93 3.3 47.3 1.0 OD1 A:ASP76 3.4 52.3 1.0 C A:PHE94 3.6 44.8 1.0 OP2 h:DA25 3.7 91.6 1.0 N A:PHE94 3.8 41.9 1.0 NZ A:LYS95 3.8 59.7 1.0 OD2 A:ASP93 3.9 52.7 1.0 C5' h:DA25 4.1 58.9 1.0 O h:HOH106 4.2 44.5 1.0 CA A:PHE94 4.2 44.0 1.0 C A:ASP93 4.3 40.3 1.0 OG A:SER41 4.4 54.9 1.0 CA A:ASP93 4.5 43.4 1.0 O3' H:DT14 4.5 48.5 1.0 CB A:ASP93 4.5 45.9 1.0 CE A:LYS95 4.5 52.6 1.0 P h:DA25 4.6 76.9 1.0 OP2 h:DA26 4.7 50.4 1.0 CB A:PHE94 4.7 44.5 1.0 N A:LYS95 4.7 45.0 1.0 O5' h:DA25 4.8 65.7 1.0 OP1 h:DA25 4.8 85.7 1.0 CD A:LYS95 4.8 48.6 1.0 CB A:ASP76 4.8 43.6 1.0 O h:HOH104 5.0 57.9 1.0

Magnesium binding site 2 out of 6 in the Restriction/Modification System-Type II R.Swai Cleaved Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Restriction/Modification System-Type II R.Swai Cleaved Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:56.2 occ:1.00 MG A:MG301 2.3 42.3 1.0 O A:HOH424 2.4 37.4 1.0 O3' H:DT14 2.4 48.5 1.0 OD1 A:ASP76 2.7 52.3 1.0 OP1 h:DA25 2.9 85.7 1.0 O h:HOH104 2.9 57.9 1.0 OP2 h:DA25 3.1 91.6 1.0 O A:HOH414 3.3 49.0 1.0 P h:DA25 3.4 76.9 1.0 OD2 A:ASP76 3.4 45.5 1.0 CG A:ASP76 3.4 46.9 1.0 OD1 A:ASP93 3.4 55.8 1.0 C5' h:DA25 3.5 58.9 1.0 C3' H:DT14 3.7 43.4 1.0 O5' h:DA25 3.9 65.7 1.0 CG A:ASP93 4.2 47.3 1.0 OD2 A:ASP93 4.4 52.7 1.0 O A:HOH401 4.6 61.0 1.0 C4' H:DT14 4.6 44.7 1.0 C2' H:DT14 4.7 43.4 1.0 O A:PHE94 4.7 45.3 1.0 OP3 h:DA25 4.8 86.2 1.0 CB A:ASP76 4.9 43.6 1.0 NZ A:LYS95 5.0 59.7 1.0 C4' h:DA25 5.0 55.8 1.0 C5' H:DT14 5.0 42.0 1.0

Magnesium binding site 3 out of 6 in the Restriction/Modification System-Type II R.Swai Cleaved Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Restriction/Modification System-Type II R.Swai Cleaved Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:51.0 occ:1.00 O i:HOH202 2.0 50.7 1.0 O B:PHE94 2.1 50.7 1.0 O B:HOH406 2.1 49.7 1.0 OD1 B:ASP93 2.2 54.4 1.0 OD2 B:ASP76 2.3 55.1 1.0 O B:HOH417 2.6 53.8 1.0 C B:PHE94 3.2 54.7 1.0 CG B:ASP76 3.3 55.1 1.0 CG B:ASP93 3.4 59.1 1.0 OD1 B:ASP76 3.5 63.5 1.0 N B:PHE94 3.5 48.7 1.0 OP3 i:DA25 3.6 79.3 1.0 CA B:PHE94 3.8 51.9 1.0 NZ B:LYS95 4.0 58.9 1.0 C B:ASP93 4.1 50.2 1.0 OG B:SER41 4.1 64.0 1.0 OD2 B:ASP93 4.2 63.8 1.0 C5' i:DA25 4.2 57.9 1.0 CB B:PHE94 4.3 51.8 1.0 N B:LYS95 4.4 53.9 1.0 CA B:ASP93 4.4 54.6 1.0 CB B:ASP93 4.6 57.3 1.0 CE B:LYS95 4.6 61.0 1.0 O B:HOH421 4.6 57.4 1.0 OP2 i:DA26 4.7 53.7 1.0 P i:DA25 4.7 68.3 1.0 CB B:ASP76 4.7 56.9 1.0 O3' I:DT14 4.7 66.0 1.0 CD B:LYS95 4.7 59.8 1.0 OP1 i:DA25 4.8 68.8 1.0 CA B:LYS95 4.8 53.5 1.0 O5' i:DA25 4.8 63.2 1.0 CB B:SER41 4.8 58.8 1.0 O B:ASP93 4.9 46.3 1.0

Magnesium binding site 4 out of 6 in the Restriction/Modification System-Type II R.Swai Cleaved Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Restriction/Modification System-Type II R.Swai Cleaved Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:50.7 occ:1.00 O C:HOH410 1.9 52.0 1.0 O j:HOH102 2.1 51.7 1.0 OD1 C:ASP93 2.1 56.0 1.0 O C:PHE94 2.2 60.2 1.0 OD2 C:ASP76 2.4 62.0 1.0 O C:HOH413 2.8 63.0 1.0 CG C:ASP76 3.3 60.0 1.0 C C:PHE94 3.4 53.0 1.0 CG C:ASP93 3.4 59.8 1.0 OD1 C:ASP76 3.5 62.4 1.0 N C:PHE94 3.6 50.8 1.0 OP3 j:DA25 3.7 80.7 1.0 NZ C:LYS95 3.9 60.3 1.0 CA C:PHE94 4.0 52.9 1.0 OD2 C:ASP93 4.1 64.0 1.0 C C:ASP93 4.1 50.5 1.0 OG C:SER41 4.2 61.3 1.0 C5' j:DA25 4.2 62.4 1.0 CB C:PHE94 4.4 55.0 1.0 CA C:ASP93 4.4 51.2 1.0 N C:LYS95 4.5 50.7 1.0 OP2 j:DA26 4.5 64.1 1.0 CB C:ASP93 4.6 55.0 1.0 CE C:LYS95 4.6 61.7 1.0 O C:HOH412 4.6 64.7 1.0 CB C:ASP76 4.7 59.9 1.0 CD C:LYS95 4.7 55.5 1.0 O3' J:DT14 4.7 60.8 1.0 P j:DA25 4.8 75.6 1.0 O5' j:DA25 4.8 73.6 1.0 CA C:LYS95 4.9 50.7 1.0 CB C:SER41 4.9 59.0 1.0 O C:ASP93 4.9 50.0 1.0

Magnesium binding site 5 out of 6 in the Restriction/Modification System-Type II R.Swai Cleaved Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Restriction/Modification System-Type II R.Swai Cleaved Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:52.3 occ:1.00 O D:HOH409 2.0 63.4 1.0 OD1 D:ASP93 2.1 66.0 1.0 MG D:MG302 2.3 63.2 1.0 O D:PHE94 2.3 46.5 1.0 OD2 D:ASP76 2.4 47.8 1.0 O D:HOH420 2.4 51.5 1.0 CG D:ASP76 3.3 48.0 1.0 CG D:ASP93 3.3 64.0 1.0 C D:PHE94 3.4 52.9 1.0 OD1 D:ASP76 3.4 52.4 1.0 OP2 k:DA25 3.5 82.0 1.0 N D:PHE94 3.6 52.6 1.0 NZ D:LYS95 3.9 55.2 1.0 OD2 D:ASP93 4.0 73.8 1.0 CA D:PHE94 4.1 53.0 1.0 C D:ASP93 4.2 53.6 1.0 C5' k:DA25 4.2 64.6 1.0 OG D:SER41 4.3 65.4 1.0 CA D:ASP93 4.4 53.0 1.0 CB D:ASP93 4.5 55.4 1.0 CB D:PHE94 4.5 55.4 1.0 CE D:LYS95 4.5 56.9 1.0 N D:LYS95 4.6 53.9 1.0 O3' K:DT14 4.6 48.0 1.0 CB D:ASP76 4.7 49.1 1.0 P k:DA25 4.7 73.5 1.0 CD D:LYS95 4.7 56.7 1.0 OP2 k:DA26 4.8 60.0 1.0 O5' k:DA25 4.8 70.3 1.0 CA D:LYS95 4.9 54.4 1.0 O D:ASP93 5.0 53.1 1.0

Magnesium binding site 6 out of 6 in the Restriction/Modification System-Type II R.Swai Cleaved Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Restriction/Modification System-Type II R.Swai Cleaved Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:63.2 occ:1.00 MG D:MG301 2.3 52.3 1.0 O D:HOH420 2.4 51.5 1.0 OP2 k:DA25 2.4 82.0 1.0 O3' K:DT14 2.5 48.0 1.0 OD1 D:ASP76 2.8 52.4 1.0 OD1 D:ASP93 3.2 66.0 1.0 O D:HOH413 3.2 65.6 1.0 O D:HOH409 3.3 63.4 1.0 OD2 D:ASP76 3.4 47.8 1.0 CG D:ASP76 3.5 48.0 1.0 P k:DA25 3.7 73.5 1.0 C5' k:DA25 3.7 64.6 1.0 C3' K:DT14 3.7 44.2 1.0 OP3 k:DA25 3.9 70.6 1.0 CG D:ASP93 4.0 64.0 1.0 O5' k:DA25 4.1 70.3 1.0 OD2 D:ASP93 4.2 73.8 1.0 O D:PHE94 4.5 46.5 1.0 NZ D:LYS95 4.7 55.2 1.0 C4' K:DT14 4.7 43.5 1.0 C2' K:DT14 4.8 43.9 1.0 O D:HOH401 4.9 67.7 1.0 CB D:ASP76 4.9 49.1 1.0 OP1 k:DA25 4.9 77.4 1.0 C5' K:DT14 5.0 44.8 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