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Magnesium in PDB 4nca: Structure of Thermus Thermophilus Argonaute Bound to Guide Dna 19-Mer and Target Dna in the Presence of MN2+

Protein crystallography data

The structure of Structure of Thermus Thermophilus Argonaute Bound to Guide Dna 19-Mer and Target Dna in the Presence of MN2+, PDB code: 4nca 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) 48.16 / 2.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 110.950, 117.561, 160.380, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 24.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna 19-Mer and Target Dna in the Presence of MN2+ (pdb code 4nca). 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 19-Mer and Target Dna in the Presence of MN2+, PDB code: 4nca:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4nca

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Magnesium binding site 1 out of 6 in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna 19-Mer and Target Dna in the Presence of MN2+


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 19-Mer and Target Dna in the Presence of MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:43.3
occ:1.00
 OP3 D:DT10 2.0 59.0 1.0
OD2 A:ASP478 2.1 47.0 1.0
O A:HOH806 2.1 46.8 1.0
O A:HOH802 2.1 33.6 1.0
OD2 A:ASP546 2.1 44.6 1.0
O3' G:DC6 2.2 56.1 1.0
CG A:ASP478 3.1 43.5 1.0
CG A:ASP546 3.2 42.8 1.0
P D:DT10 3.3 53.9 1.0
OD1 A:ASP478 3.5 45.9 1.0
C3' G:DC6 3.5 52.0 1.0
OP1 D:DT10 3.6 54.0 1.0
MG D:MG101 3.7 67.2 1.0
O A:ALA479 3.7 44.6 1.0
CB A:ASP546 3.8 40.2 1.0
C4' G:DC6 3.9 53.5 1.0
O D:HOH202 4.0 46.3 1.0
C5' D:DT10 4.0 51.1 1.0
N A:ALA479 4.1 39.9 1.0
C2' G:DC6 4.1 54.7 1.0
OE2 A:GLU512 4.1 45.7 1.0
O5' D:DT10 4.1 61.6 1.0
OD1 A:ASP546 4.2 42.9 1.0
OP2 D:DT10 4.3 52.9 1.0
OE1 A:GLU512 4.3 45.7 1.0
O D:HOH201 4.3 43.2 1.0
CB A:ASP478 4.4 45.2 1.0
NZ A:LYS575 4.4 48.4 1.0
O A:ASP546 4.5 44.8 1.0
CD A:GLU512 4.6 37.4 1.0
C5' G:DC6 4.7 52.2 1.0
C A:ALA479 4.7 42.9 1.0
CA A:ASP478 4.7 43.2 1.0
C A:ASP546 4.7 42.9 1.0
NH2 A:ARG545 4.8 50.5 1.0
CA A:ALA479 4.9 37.9 1.0
CA A:ASP546 4.9 40.6 1.0
C A:ASP478 4.9 44.4 1.0

Magnesium binding site 2 out of 6 in 4nca

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Magnesium binding site 2 out of 6 in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna 19-Mer and Target Dna in the Presence of MN2+


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 19-Mer and Target Dna in the Presence of MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:44.5
occ:1.00
 OD2 B:ASP660 2.1 41.0 1.0
O B:HOH811 2.1 44.4 1.0
O B:HOH895 2.1 53.4 1.0
OD1 B:ASP478 2.1 42.8 1.0
OP2 F:DT10 2.2 46.3 1.0
OP1 F:DT10 2.2 53.2 1.0
P F:DT10 2.5 49.9 1.0
CG B:ASP478 3.0 41.0 1.0
CG B:ASP660 3.2 42.1 1.0
OD2 B:ASP478 3.3 43.1 1.0
MG B:MG703 3.5 51.5 1.0
OP3 F:DT10 3.7 52.3 1.0
O5' F:DT10 3.7 56.6 1.0
CB B:ASP660 3.8 34.2 1.0
C5' F:DT10 3.8 53.8 1.0
O B:ALA479 4.0 42.0 1.0
OD2 B:ASP546 4.0 46.0 1.0
O B:HOH868 4.0 62.0 1.0
OP2 F:DA11 4.1 66.3 1.0
CA B:ASP660 4.2 41.1 1.0
OD1 B:ASP660 4.2 44.2 1.0
CB B:ASP478 4.4 34.0 1.0
O3' H:DC9 4.4 48.8 1.0
CG B:ASP546 4.5 49.9 1.0
O B:HOH806 4.6 46.6 1.0
OD1 B:ASP546 4.8 48.1 1.0
NZ B:LYS664 4.9 61.6 1.0
CG2 B:VAL663 4.9 38.3 1.0
O B:ASP660 5.0 37.8 1.0
C B:ALA479 5.0 43.1 1.0

Magnesium binding site 3 out of 6 in 4nca

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Magnesium binding site 3 out of 6 in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna 19-Mer and Target Dna in the Presence of MN2+


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 19-Mer and Target Dna in the Presence of MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg703

b:51.5
occ:1.00
 OP2 F:DT10 2.0 46.3 1.0
O B:HOH806 2.1 46.6 1.0
OD2 B:ASP546 2.1 46.0 1.0
O B:HOH805 2.1 42.5 1.0
OD2 B:ASP478 2.1 43.1 1.0
O3' H:DC9 2.3 48.8 1.0
CG B:ASP478 3.2 41.0 1.0
CG B:ASP546 3.2 49.9 1.0
P F:DT10 3.4 49.9 1.0
MG B:MG702 3.5 44.5 1.0
C3' H:DC9 3.6 49.1 1.0
OD1 B:ASP478 3.6 42.8 1.0
O B:ALA479 3.7 42.0 1.0
C5' F:DT10 3.8 53.8 1.0
O5' F:DT10 3.9 56.6 1.0
CB B:ASP546 3.9 42.5 1.0
OE2 B:GLU512 4.0 45.2 1.0
N B:ALA479 4.0 39.6 1.0
OP3 F:DT10 4.0 52.3 1.0
C4' H:DC9 4.0 49.3 1.0
O B:HOH811 4.1 44.4 1.0
OD1 B:ASP546 4.2 48.1 1.0
O B:ASP546 4.2 45.6 1.0
C2' H:DC9 4.2 50.2 1.0
O B:HOH895 4.3 53.4 1.0
OE1 B:GLU512 4.4 53.6 1.0
CB B:ASP478 4.5 34.0 1.0
OP1 F:DT10 4.5 53.2 1.0
CD B:GLU512 4.6 53.2 1.0
C B:ASP546 4.6 44.5 1.0
NZ B:LYS575 4.7 41.3 1.0
C B:ALA479 4.7 43.1 1.0
CA B:ASP478 4.7 36.3 1.0
C5' H:DC9 4.8 45.1 1.0
CA B:ALA479 4.8 38.1 1.0
C B:ASP478 4.9 43.2 1.0
CA B:ASP546 4.9 45.0 1.0

Magnesium binding site 4 out of 6 in 4nca

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Magnesium binding site 4 out of 6 in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna 19-Mer and Target Dna in the Presence of MN2+


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 19-Mer and Target Dna in the Presence of MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg101

b:50.1
occ:1.00
 OP1 C:DA3 1.8 50.2 1.0
O A:VAL685 2.0 54.6 1.0
OP3 C:DT1 2.0 45.7 1.0
O C:HOH201 2.1 44.5 1.0
O A:HOH801 2.1 50.7 1.0
OXT A:VAL685 2.3 48.4 1.0
C A:VAL685 2.5 52.7 1.0
P C:DA3 3.2 46.8 1.0
P C:DT1 3.4 47.9 1.0
OP2 C:DT1 3.7 52.7 1.0
O3' C:DG2 3.9 46.6 1.0
OP2 C:DA3 3.9 57.6 1.0
NH2 A:ARG661 3.9 59.5 1.0
CA A:VAL685 4.0 52.5 1.0
OE1 A:GLN433 4.2 46.1 1.0
NZ A:LYS457 4.2 43.6 1.0
O5' C:DA3 4.3 46.0 1.0
OP1 C:DT1 4.3 42.6 1.0
NE2 A:GLN433 4.4 43.1 1.0
O5' C:DT1 4.4 49.8 1.0
O A:HOH812 4.5 44.1 1.0
C5' C:DA3 4.5 45.6 1.0
C5' C:DT1 4.5 50.8 1.0
O A:HOH853 4.6 56.0 1.0
CB A:VAL685 4.7 48.9 1.0
CD A:GLN433 4.7 46.9 1.0
CZ A:ARG661 4.7 57.8 1.0
N A:VAL685 4.8 45.0 1.0
CG2 A:VAL685 4.8 44.1 1.0
NH1 A:ARG661 4.9 50.6 1.0
CE A:LYS457 4.9 40.1 1.0

Magnesium binding site 5 out of 6 in 4nca

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Magnesium binding site 5 out of 6 in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna 19-Mer and Target Dna in the Presence of MN2+


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 19-Mer and Target Dna in the Presence of MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg101

b:67.2
occ:1.00
 OP1 D:DT10 1.4 54.0 1.0
OD2 A:ASP660 2.0 38.3 1.0
OD1 A:ASP478 2.1 45.9 1.0
O D:HOH202 2.1 46.3 1.0
O D:HOH201 2.1 43.2 1.0
P D:DT10 2.7 53.9 1.0
CG A:ASP660 3.1 40.3 1.0
OP3 D:DT10 3.1 59.0 1.0
CG A:ASP478 3.1 43.5 1.0
OD2 A:ASP478 3.5 47.0 1.0
CB A:ASP660 3.6 39.7 1.0
OP2 D:DT10 3.7 52.9 1.0
MG A:MG702 3.7 43.3 1.0
O A:HOH865 3.8 51.3 1.0
O5' D:DT10 3.8 61.6 1.0
CA A:ASP660 4.1 37.4 1.0
OD2 A:ASP546 4.1 44.6 1.0
OD1 A:ASP660 4.1 43.6 1.0
C5' D:DT10 4.2 51.1 1.0
OP2 D:DA11 4.2 66.1 1.0
O A:ALA479 4.3 44.6 1.0
O3' G:DC6 4.4 56.1 1.0
CB A:ASP478 4.4 45.2 1.0
CG A:ASP546 4.4 42.8 1.0
NZ A:LYS664 4.5 57.5 1.0
OD1 A:ASP546 4.6 42.9 1.0
O A:HOH806 4.8 46.8 1.0
O A:ASP660 4.8 40.7 1.0
C A:ASP660 4.9 39.9 1.0

Magnesium binding site 6 out of 6 in 4nca

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Magnesium binding site 6 out of 6 in the Structure of Thermus Thermophilus Argonaute Bound to Guide Dna 19-Mer and Target Dna in the Presence of MN2+


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 19-Mer and Target Dna in the Presence of MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg101

b:48.2
occ:1.00
 OP1 E:DA3 1.7 49.1 1.0
O B:VAL685 1.9 42.4 1.0
O B:HOH801 2.1 36.1 1.0
O E:HOH201 2.1 38.6 1.0
OP3 E:DT1 2.1 45.2 1.0
OXT B:VAL685 2.4 39.5 1.0
C B:VAL685 2.5 45.6 1.0
P E:DA3 3.1 47.4 1.0
P E:DT1 3.5 46.5 1.0
O3' E:DG2 3.8 42.6 1.0
OP2 E:DT1 3.8 45.4 1.0
OP2 E:DA3 3.9 45.4 1.0
CA B:VAL685 4.0 41.9 1.0
NZ B:LYS457 4.1 40.7 1.0
OE1 B:GLN433 4.1 37.9 1.0
NH2 B:ARG661 4.1 49.8 1.0
O5' E:DA3 4.1 46.3 1.0
C5' E:DA3 4.3 49.4 1.0
O B:HOH860 4.4 52.2 1.0
O B:HOH829 4.4 45.2 1.0
NE2 B:GLN433 4.4 37.4 1.0
OP1 E:DT1 4.4 45.2 1.0
O5' E:DT1 4.4 47.7 1.0
C5' E:DT1 4.5 44.8 1.0
NH1 B:ARG661 4.6 53.0 1.0
CB B:VAL685 4.7 36.4 1.0
CD B:GLN433 4.7 37.6 1.0
CZ B:ARG661 4.8 62.3 1.0
CG2 B:VAL685 4.9 39.3 1.0
N B:VAL685 4.9 37.1 1.0
CE B:LYS457 5.0 37.1 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 Aug 19 23:32:26 2024

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