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

Protein crystallography data

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

Magnesium Binding Sites:

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 5th3

Go back to Magnesium Binding Sites List in 5th3
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 5th3

Go back to Magnesium Binding Sites List in 5th3
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 5th3

Go back to Magnesium Binding Sites List in 5th3
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 5th3

Go back to Magnesium Binding Sites List in 5th3
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 5th3

Go back to Magnesium Binding Sites List in 5th3
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 5th3

Go back to Magnesium Binding Sites List in 5th3
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

Reference:

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
Page generated: Mon Dec 14 21:12:03 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy