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Magnesium in PDB 4ncb: Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 19- Mer Target Dna with MG2+

Protein crystallography data

The structure of Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 19- Mer Target Dna with MG2+, PDB code: 4ncb was solved by G.Sheng, H.Zhao, J.Wang, Y.Rao, Y.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.22 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.736, 105.363, 92.058, 90.00, 94.25, 90.00
R / Rfree (%) 17.5 / 23

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 19- Mer Target Dna with MG2+ (pdb code 4ncb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 19- Mer Target Dna with MG2+, PDB code: 4ncb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4ncb

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Magnesium binding site 1 out of 6 in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 19- Mer Target Dna with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 19- Mer Target Dna with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:27.5
occ:1.00
 OP1 D:DT10 2.1 28.8 0.5
O D:HOH202 2.1 14.7 1.0
O D:HOH201 2.1 23.3 1.0
O D:HOH203 2.1 51.9 0.5
OD2 A:ASP478 2.1 18.4 1.0
OD1 A:ASP660 2.2 20.3 1.0
O3T D:DT10 2.4 24.8 0.5
OP2 D:DT10 2.5 23.0 0.5
P D:DT10 3.0 28.1 0.5
CG A:ASP660 3.0 24.8 1.0
CG A:ASP478 3.3 18.3 1.0
CB A:ASP660 3.4 13.1 1.0
P D:DT10 3.4 29.8 0.5
O A:HOH893 3.7 34.6 1.0
CA A:ASP660 3.8 13.0 1.0
OD1 A:ASP478 3.8 17.6 1.0
OP1 D:DT10 3.9 30.5 0.5
MG D:MG101 3.9 24.6 1.0
OD2 A:ASP660 4.0 28.9 1.0
O5' D:DT10 4.0 32.3 0.5
OP2 D:DA11 4.1 23.2 1.0
NZ A:LYS664 4.2 26.9 1.0
OP2 D:DT10 4.2 31.0 0.5
O5' D:DT10 4.2 33.6 0.5
C5' D:DT10 4.3 33.9 0.5
O A:ASP660 4.4 13.9 1.0
O A:ALA479 4.4 20.5 1.0
C A:ASP660 4.5 14.2 1.0
CB A:ASP478 4.5 17.4 1.0
C5' D:DT10 4.6 35.1 0.5
O3' D:DC9 4.6 26.9 0.5
OD1 A:ASP546 4.6 28.6 1.0
CG2 A:VAL663 4.8 17.3 1.0
O A:HOH802 4.9 17.3 1.0
CG A:ASP546 5.0 29.1 1.0
N A:ASP660 5.0 12.6 1.0

Magnesium binding site 2 out of 6 in 4ncb

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Magnesium binding site 2 out of 6 in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 19- Mer Target Dna with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 19- Mer Target Dna with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:24.3
occ:1.00
 OD1 B:ASP660 2.0 18.9 1.0
O B:HOH802 2.0 20.1 1.0
O B:HOH958 2.0 21.3 1.0
OD2 B:ASP478 2.1 14.7 1.0
OP2 F:DT10 2.3 20.1 1.0
OP1 F:DT10 2.4 22.7 1.0
P F:DT10 2.7 27.1 1.0
CG B:ASP660 3.1 19.6 1.0
CG B:ASP478 3.2 18.9 1.0
OD1 B:ASP478 3.5 17.3 1.0
CB B:ASP660 3.6 13.6 1.0
MG B:MG703 3.7 25.4 1.0
OP3 F:DT10 3.7 25.2 1.0
O5' F:DT10 4.0 18.5 1.0
CA B:ASP660 4.1 10.8 1.0
OD2 B:ASP546 4.1 19.6 1.0
OD2 B:ASP660 4.2 15.4 1.0
OP2 F:DA11 4.2 20.8 1.0
C5' F:DT10 4.3 19.0 1.0
O B:ALA479 4.3 15.0 1.0
CB B:ASP478 4.5 12.9 1.0
CG B:ASP546 4.6 29.9 1.0
O B:HOH803 4.6 19.4 1.0
O3' H:DC9 4.6 39.1 1.0
OD1 B:ASP546 4.7 38.0 1.0
O B:ASP660 4.8 17.3 1.0
NZ B:LYS664 4.8 38.5 1.0
C B:ASP660 4.9 10.5 1.0
CE B:LYS664 4.9 37.5 1.0
CG2 B:VAL663 5.0 17.1 1.0

Magnesium binding site 3 out of 6 in 4ncb

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Magnesium binding site 3 out of 6 in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 19- Mer Target Dna with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 19- Mer Target Dna with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg703

b:25.4
occ:1.00
 OP2 F:DT10 2.0 20.1 1.0
O3' H:DC9 2.1 39.1 1.0
O B:HOH804 2.1 29.0 1.0
OD1 B:ASP478 2.1 17.3 1.0
O B:HOH803 2.1 19.4 1.0
OD2 B:ASP546 2.2 19.6 1.0
CG B:ASP478 3.2 18.9 1.0
CG B:ASP546 3.3 29.9 1.0
P F:DT10 3.3 27.1 1.0
C3' H:DC9 3.5 40.0 1.0
OD2 B:ASP478 3.6 14.7 1.0
MG B:MG702 3.7 24.3 1.0
OP3 F:DT10 3.8 25.2 1.0
C5' F:DT10 3.8 19.0 1.0
O5' F:DT10 3.9 18.5 1.0
CB B:ASP546 3.9 29.4 1.0
O B:ALA479 3.9 15.0 1.0
O B:HOH802 4.1 20.1 1.0
C4' H:DC9 4.1 40.6 1.0
OE2 B:GLU512 4.1 35.6 1.0
N B:ALA479 4.2 14.7 1.0
OD1 B:ASP546 4.2 38.0 1.0
OE1 B:GLU512 4.3 45.1 1.0
C2' H:DC9 4.3 42.3 1.0
O B:HOH958 4.4 21.3 1.0
O B:ASP546 4.4 22.9 1.0
NZ B:LYS575 4.5 36.1 1.0
OP1 F:DT10 4.5 22.7 1.0
CB B:ASP478 4.5 12.9 1.0
CD B:GLU512 4.6 43.9 1.0
C B:ASP546 4.8 22.6 1.0
CA B:ASP478 4.8 13.9 1.0
C5' H:DC9 4.8 31.9 1.0
C B:ALA479 4.8 18.8 1.0
CA B:ALA479 5.0 15.2 1.0
CA B:ASP546 5.0 25.7 1.0

Magnesium binding site 4 out of 6 in 4ncb

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Magnesium binding site 4 out of 6 in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 19- Mer Target Dna with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 19- Mer Target Dna with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg101

b:24.6
occ:1.00
 O3T D:DT10 2.0 24.8 0.5
O A:HOH801 2.1 15.1 1.0
O3' P:DC9 2.1 33.0 0.5
O A:HOH802 2.1 17.3 1.0
OD1 A:ASP546 2.1 28.6 1.0
O3' D:DC9 2.2 26.9 0.5
OD1 A:ASP478 2.2 17.6 1.0
OP1 D:DT10 2.5 28.8 0.5
P D:DT10 2.9 29.8 0.5
CG A:ASP478 3.2 18.3 1.0
P D:DT10 3.2 28.1 0.5
CG A:ASP546 3.3 29.1 1.0
C3' D:DC9 3.4 28.1 0.5
OD2 A:ASP478 3.4 18.4 1.0
C3' P:DC9 3.5 35.8 0.5
OP1 D:DT10 3.5 30.5 0.5
C4' D:DC9 3.7 29.8 0.5
C5' D:DT10 3.7 33.9 0.5
O5' D:DT10 3.8 32.3 0.5
O5' D:DT10 3.8 33.6 0.5
C5' D:DT10 3.8 35.1 0.5
MG A:MG702 3.9 27.5 1.0
O D:HOH201 3.9 23.3 1.0
O A:ALA479 4.0 20.5 1.0
CB A:ASP546 4.1 13.7 1.0
OP2 D:DT10 4.1 31.0 0.5
C4' P:DC9 4.1 37.2 0.5
OE2 A:GLU512 4.1 32.8 1.0
OD2 A:ASP546 4.2 34.6 1.0
C2' P:DC9 4.2 42.1 0.5
C2' D:DC9 4.3 32.9 0.5
NZ A:LYS575 4.3 19.2 1.0
C5' D:DC9 4.3 29.4 0.5
OP2 D:DT10 4.4 23.0 0.5
N A:ALA479 4.4 14.0 1.0
O A:ASP546 4.4 22.6 1.0
OE1 A:GLU512 4.5 37.1 1.0
CB A:ASP478 4.5 17.4 1.0
O D:HOH202 4.6 14.7 1.0
C5' P:DC9 4.7 33.2 0.5
CD A:GLU512 4.7 35.5 1.0
C A:ASP546 4.8 21.0 1.0
CA A:ASP478 4.9 20.5 1.0

Magnesium binding site 5 out of 6 in 4ncb

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Magnesium binding site 5 out of 6 in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 19- Mer Target Dna with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 19- Mer Target Dna with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg101

b:20.8
occ:1.00
 OP3 C:DT1 1.9 16.7 1.0
OP1 C:DA3 2.0 19.5 1.0
O C:HOH221 2.0 25.2 1.0
O A:HOH803 2.1 17.8 1.0
O A:VAL685 2.1 37.6 1.0
OXT A:VAL685 2.4 27.3 1.0
C A:VAL685 2.6 40.0 1.0
P C:DT1 3.2 18.9 1.0
P C:DA3 3.4 19.8 1.0
OP2 C:DT1 3.4 18.1 1.0
NZ A:LYS457 3.7 30.0 1.0
OE1 A:GLN433 4.0 18.2 1.0
O3' C:DG2 4.0 22.4 1.0
OP2 C:DA3 4.1 18.2 1.0
O C:HOH223 4.1 33.0 1.0
O A:HOH971 4.1 32.9 1.0
OP1 C:DT1 4.1 19.3 1.0
NH2 A:ARG661 4.2 31.2 1.0
CA A:VAL685 4.2 29.2 1.0
O5' C:DT1 4.2 29.4 1.0
NE2 A:GLN433 4.3 17.2 1.0
CE A:LYS457 4.4 15.9 1.0
C5' C:DT1 4.5 20.2 1.0
O5' C:DA3 4.5 28.8 1.0
CD A:GLN433 4.6 17.1 1.0
C5' C:DA3 4.8 28.6 1.0
O A:HOH809 4.8 16.5 1.0
N A:VAL685 4.9 22.0 1.0
O A:HOH882 4.9 36.6 1.0
O A:PHE684 4.9 26.6 1.0
CZ A:ARG661 4.9 41.7 1.0
CB A:VAL685 5.0 13.9 1.0

Magnesium binding site 6 out of 6 in 4ncb

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Magnesium binding site 6 out of 6 in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 19- Mer Target Dna with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Thermus Thermophilus Argonaute Bound to Guide Dna and 19- Mer Target Dna with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg101

b:24.6
occ:1.00
 OP3 E:DT1 2.0 21.2 1.0
OP1 E:DA3 2.0 23.6 1.0
O E:HOH202 2.0 15.4 1.0
O E:HOH208 2.1 9.3 1.0
O B:VAL685 2.2 25.3 1.0
OXT B:VAL685 2.3 25.9 1.0
C B:VAL685 2.7 29.0 1.0
P E:DT1 3.2 17.4 1.0
P E:DA3 3.3 16.6 1.0
OP2 E:DT1 3.4 18.6 1.0
O E:HOH218 3.8 18.0 1.0
O3' E:DG2 3.9 13.3 1.0
NZ B:LYS457 3.9 9.8 1.0
OP2 E:DA3 4.0 10.4 1.0
OP1 E:DT1 4.2 13.6 1.0
OE1 B:GLN433 4.2 13.5 1.0
O B:HOH805 4.2 32.0 1.0
CA B:VAL685 4.2 24.9 1.0
NH2 B:ARG661 4.2 28.6 1.0
O5' E:DT1 4.3 14.5 1.0
NE2 B:GLN433 4.5 10.1 1.0
C5' E:DT1 4.5 6.0 1.0
O5' E:DA3 4.5 20.1 1.0
NH1 B:ARG661 4.5 35.3 1.0
CE B:LYS457 4.7 12.9 1.0
O B:HOH807 4.7 38.6 1.0
O B:HOH801 4.8 13.7 1.0
CD B:GLN433 4.8 14.9 1.0
C5' E:DA3 4.8 12.7 1.0
CZ B:ARG661 4.8 25.5 1.0
O B:PHE684 4.8 18.8 1.0
N B:VAL685 5.0 9.2 1.0

Reference:

G.Sheng, H.Zhao, J.Wang, Y.Rao, W.Tian, D.C.Swarts, J.Van Der Oost, D.J.Patel, Y.Wang. Structure-Based Cleavage Mechanism of Thermus Thermophilus Argonaute Dna Guide Strand-Mediated Dna Target Cleavage. Proc.Natl.Acad.Sci.Usa V. 111 652 2014.
ISSN: ISSN 0027-8424
PubMed: 24374628
DOI: 10.1073/PNAS.1321032111
Page generated: Mon Dec 14 19:14:00 2020

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