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Magnesium in PDB 8wd8: Cryo-Em Structure of Ttdago-Guide Dna-Target Dna Complex

Other elements in 8wd8:

The structure of Cryo-Em Structure of Ttdago-Guide Dna-Target Dna Complex also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Ttdago-Guide Dna-Target Dna Complex (pdb code 8wd8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Cryo-Em Structure of Ttdago-Guide Dna-Target Dna Complex, PDB code: 8wd8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8wd8

Go back to Magnesium Binding Sites List in 8wd8
Magnesium binding site 1 out of 6 in the Cryo-Em Structure of Ttdago-Guide Dna-Target Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Ttdago-Guide Dna-Target Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:30.0
occ:1.00
 O A:VAL750 2.1 18.0 1.0
OE1 A:GLN513 2.1 16.9 1.0
OP1 G:DA3 2.1 11.2 1.0
OP2 G:DG1 2.4 11.4 1.0
C A:VAL750 3.1 24.0 1.0
CD A:GLN513 3.3 18.4 1.0
P G:DA3 3.6 7.7 1.0
P G:DG1 3.6 15.6 1.0
NE2 A:GLN513 4.0 25.8 1.0
O5' G:DA3 4.2 9.6 1.0
C5' G:DA3 4.2 9.6 1.0
C5' G:DG1 4.3 12.9 1.0
O3' G:DG2 4.3 5.2 1.0
CA A:VAL750 4.4 15.6 1.0
CG A:GLN513 4.5 12.4 1.0
O5' G:DG1 4.5 14.4 1.0
CE A:LYS517 4.6 11.4 1.0
OP2 G:DA3 4.6 15.8 1.0
OP1 G:DG1 4.8 18.6 1.0
NZ A:LYS517 4.9 19.5 1.0
O A:PHE749 4.9 13.8 1.0

Magnesium binding site 2 out of 6 in 8wd8

Go back to Magnesium Binding Sites List in 8wd8
Magnesium binding site 2 out of 6 in the Cryo-Em Structure of Ttdago-Guide Dna-Target Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Ttdago-Guide Dna-Target Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:30.0
occ:1.00
 OD2 A:ASP538 2.1 17.4 1.0
OP1 T:DT6 2.2 9.9 1.0
ND1 A:HIS725 2.2 15.6 1.0
CE1 A:HIS725 2.9 9.9 1.0
CG A:ASP538 3.0 16.0 1.0
OD1 A:ASP538 3.1 23.1 1.0
P T:DT6 3.3 11.5 1.0
O5' T:DT6 3.4 5.0 1.0
CG A:HIS725 3.4 14.3 1.0
C5' T:DT6 3.6 1.2 1.0
CB A:HIS725 4.0 0.8 1.0
MG T:MG101 4.0 30.0 1.0
NE2 A:HIS725 4.1 5.0 1.0
O A:VAL539 4.1 19.8 1.0
OP2 T:DT6 4.2 3.1 1.0
NZ A:LYS637 4.2 22.4 1.0
OD2 A:ASP608 4.3 21.6 1.0
OD1 A:ASP608 4.4 21.6 1.0
CD2 A:HIS725 4.4 8.6 1.0
CG A:ASP608 4.4 22.6 1.0
CB A:ASP538 4.4 8.5 1.0
O3' T:DC5 4.5 4.3 1.0
CA A:HIS725 4.5 0.0 1.0
C4' T:DT6 4.8 1.3 1.0

Magnesium binding site 3 out of 6 in 8wd8

Go back to Magnesium Binding Sites List in 8wd8
Magnesium binding site 3 out of 6 in the Cryo-Em Structure of Ttdago-Guide Dna-Target Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Ttdago-Guide Dna-Target Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg101

b:30.0
occ:1.00
 O3' T:DC5 2.5 4.3 1.0
OD1 A:ASP538 2.6 23.1 1.0
OP1 T:DT6 2.7 9.9 1.0
OD1 A:ASP608 2.9 21.6 1.0
P T:DT6 3.1 11.5 1.0
O A:ASP608 3.2 27.6 1.0
O5' T:DT6 3.5 5.0 1.0
OE2 A:GLU576 3.6 23.2 1.0
CG A:ASP608 3.6 22.6 1.0
C3' T:DC5 3.7 3.5 1.0
CB A:ASP608 3.8 13.1 1.0
CG A:ASP538 3.8 16.0 1.0
C4' T:DC5 3.9 0.8 1.0
C A:ASP608 4.0 16.7 1.0
MG A:MG803 4.0 30.0 1.0
O A:VAL539 4.0 19.8 1.0
OD2 A:ASP538 4.3 17.4 1.0
N A:VAL539 4.4 9.2 1.0
C5' T:DC5 4.5 1.0 1.0
OP2 T:DT6 4.5 3.1 1.0
C2' T:DC5 4.5 1.2 1.0
CA A:ASP608 4.5 6.5 1.0
OD2 A:ASP608 4.6 21.6 1.0
CD A:GLU576 4.7 30.1 1.0
C5' T:DT6 4.8 1.2 1.0
N A:GLY609 4.9 7.2 1.0
NH1 A:ARG607 4.9 13.8 1.0
C A:VAL539 4.9 8.8 1.0
CB A:ASP538 5.0 8.5 1.0
CA A:ASP538 5.0 2.4 1.0

Magnesium binding site 4 out of 6 in 8wd8

Go back to Magnesium Binding Sites List in 8wd8
Magnesium binding site 4 out of 6 in the Cryo-Em Structure of Ttdago-Guide Dna-Target Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Ttdago-Guide Dna-Target Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg801

b:30.0
occ:1.00
 O B:VAL750 2.1 18.0 1.0
OE1 B:GLN513 2.1 16.9 1.0
OP1 H:DA3 2.1 11.2 1.0
OP2 H:DG1 2.4 11.4 1.0
C B:VAL750 3.1 24.0 1.0
CD B:GLN513 3.3 18.4 1.0
P H:DA3 3.6 7.7 1.0
P H:DG1 3.6 15.6 1.0
NE2 B:GLN513 4.0 25.8 1.0
O5' H:DA3 4.2 9.6 1.0
C5' H:DA3 4.2 9.6 1.0
C5' H:DG1 4.3 12.9 1.0
O3' H:DG2 4.3 5.2 1.0
CA B:VAL750 4.4 15.6 1.0
CG B:GLN513 4.5 12.4 1.0
O5' H:DG1 4.5 14.4 1.0
OP2 H:DA3 4.6 15.8 1.0
CE B:LYS517 4.7 11.4 1.0
OP1 H:DG1 4.8 18.6 1.0
NZ B:LYS517 4.9 19.5 1.0
O B:PHE749 4.9 13.8 1.0

Magnesium binding site 5 out of 6 in 8wd8

Go back to Magnesium Binding Sites List in 8wd8
Magnesium binding site 5 out of 6 in the Cryo-Em Structure of Ttdago-Guide Dna-Target Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of Ttdago-Guide Dna-Target Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:48.4
occ:1.00
 OP1 U:DT6 2.1 9.9 1.0
OD2 B:ASP538 2.1 17.4 1.0
ND1 B:HIS725 2.2 15.6 1.0
CE1 B:HIS725 2.9 9.9 1.0
CG B:ASP538 3.0 16.0 1.0
OD1 B:ASP538 3.1 23.1 1.0
P U:DT6 3.2 11.5 1.0
O5' U:DT6 3.3 5.0 1.0
CG B:HIS725 3.4 14.3 1.0
C5' U:DT6 3.6 1.2 1.0
CB B:HIS725 4.0 0.8 1.0
O B:VAL539 4.0 19.8 1.0
MG B:MG803 4.1 33.1 1.0
NE2 B:HIS725 4.1 5.0 1.0
OP2 U:DT6 4.1 3.1 1.0
NZ B:LYS637 4.3 22.4 1.0
CB B:ASP538 4.4 8.5 1.0
CD2 B:HIS725 4.4 8.6 1.0
O3' U:DC5 4.4 4.3 1.0
OD2 B:ASP608 4.5 21.6 1.0
CA B:HIS725 4.5 0.0 1.0
OD1 B:ASP608 4.5 21.6 1.0
CG B:ASP608 4.5 22.6 1.0
C4' U:DT6 4.9 1.3 1.0
CG2 B:VAL728 4.9 13.1 1.0

Magnesium binding site 6 out of 6 in 8wd8

Go back to Magnesium Binding Sites List in 8wd8
Magnesium binding site 6 out of 6 in the Cryo-Em Structure of Ttdago-Guide Dna-Target Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of Ttdago-Guide Dna-Target Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:33.1
occ:1.00
 O3' U:DC5 2.4 4.3 1.0
OD1 B:ASP538 2.7 23.1 1.0
OP1 U:DT6 2.8 9.9 1.0
OD1 B:ASP608 2.9 21.6 1.0
P U:DT6 3.1 11.5 1.0
O B:ASP608 3.2 27.6 1.0
CG B:ASP608 3.6 22.6 1.0
OE2 B:GLU576 3.6 23.2 1.0
O5' U:DT6 3.6 5.0 1.0
C3' U:DC5 3.6 3.5 1.0
C4' U:DC5 3.8 0.8 1.0
CB B:ASP608 3.8 13.1 1.0
CG B:ASP538 3.8 16.0 1.0
C B:ASP608 4.0 16.7 1.0
O B:VAL539 4.0 19.8 1.0
MG B:MG802 4.1 48.4 1.0
C5' U:DC5 4.2 1.0 1.0
OD2 B:ASP538 4.3 17.4 1.0
N B:VAL539 4.4 9.2 1.0
C2' U:DC5 4.4 1.2 1.0
OP2 U:DT6 4.5 3.1 1.0
CA B:ASP608 4.5 6.5 1.0
OD2 B:ASP608 4.6 21.6 1.0
CD B:GLU576 4.7 30.1 1.0
N B:GLY609 4.8 7.2 1.0
NH1 B:ARG607 4.9 13.8 1.0
C5' U:DT6 4.9 1.2 1.0
C B:VAL539 5.0 8.8 1.0
CB B:ASP538 5.0 8.5 1.0
CA B:ASP538 5.0 2.4 1.0

Reference:

L.Zhuang, L.Zhuang. N/A N/A.
ISSN: ISSN 1097-2765
DOI: 10.1016/J.MOLCEL.2024.01.004
Page generated: Fri Aug 15 18:42:58 2025

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