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Magnesium in PDB 5ng6: Crystal Structure of FNCAS12A Bound to A Crrna

Protein crystallography data

The structure of Crystal Structure of FNCAS12A Bound to A Crrna, PDB code: 5ng6 was solved by D.C.Swarts, J.Van Der Oost, M.Jinek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.24 / 3.34
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 214.684, 277.061, 135.636, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 25.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of FNCAS12A Bound to A Crrna (pdb code 5ng6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of FNCAS12A Bound to A Crrna, PDB code: 5ng6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5ng6

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Magnesium binding site 1 out of 8 in the Crystal Structure of FNCAS12A Bound to A Crrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of FNCAS12A Bound to A Crrna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1401

b:57.0
occ:1.00
 O A:HOH1502 1.7 26.9 1.0
O A:HOH1504 1.8 0.8 1.0
O B:HOH305 1.9 0.3 1.0
O A:ARG800 2.1 54.4 1.0
OP2 B:A-3 2.1 56.2 1.0
O B:HOH302 2.2 79.7 1.0
OP2 B:U-4 3.2 55.4 1.0
C A:ARG800 3.3 54.6 1.0
P B:A-3 3.6 57.3 1.0
N A:ARG800 3.8 56.2 1.0
OD1 A:ASP792 4.0 52.9 1.0
CA A:ARG800 4.1 55.7 1.0
N A:PRO801 4.2 54.1 1.0
P B:U-4 4.3 56.6 1.0
OP1 B:A-3 4.3 58.3 1.0
C A:GLY799 4.3 56.9 1.0
O5' B:A-3 4.3 56.8 1.0
CA A:PRO801 4.4 53.3 1.0
C3' B:U-4 4.5 57.3 1.0
OP1 B:U-4 4.5 57.7 1.0
O3' B:U-4 4.5 57.9 1.0
CB A:ARG800 4.6 56.0 1.0
C A:PRO801 4.6 52.8 1.0
O5' B:U-4 4.7 57.1 1.0
O A:GLY799 4.8 56.5 1.0
CA A:GLY799 4.9 57.7 1.0
OD1 A:ASN802 4.9 51.7 1.0
OP2 B:G-2 4.9 54.7 1.0
N A:ASN802 4.9 52.1 1.0
CG A:ASP792 5.0 52.4 1.0
O A:PRO801 5.0 53.0 1.0

Magnesium binding site 2 out of 8 in 5ng6

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Magnesium binding site 2 out of 8 in the Crystal Structure of FNCAS12A Bound to A Crrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of FNCAS12A Bound to A Crrna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg200

b:62.0
occ:1.00
 O B:HOH306 1.7 62.0 1.0
O B:HOH309 1.7 62.0 1.0
O B:HOH308 1.8 62.0 1.0
O A:HOH1505 1.9 62.0 1.0
O B:HOH307 1.9 62.0 1.0
O B:HOH310 1.9 72.4 1.0
O B:HOH301 3.7 17.6 1.0
OP2 B:A-17 4.1 50.8 1.0
O4 B:U-16 4.2 49.3 1.0
OP2 B:A-11 4.3 47.7 1.0
O A:HOH1503 4.6 17.6 1.0
OP1 B:A-17 4.6 53.1 1.0
OP2 B:U-12 4.7 45.3 1.0
C5 B:C-10 4.8 52.3 1.0
P B:A-17 4.9 50.7 1.0
N7 B:A-11 5.0 50.2 1.0

Magnesium binding site 3 out of 8 in 5ng6

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Magnesium binding site 3 out of 8 in the Crystal Structure of FNCAS12A Bound to A Crrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of FNCAS12A Bound to A Crrna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1401

b:57.0
occ:1.00
 O C:ARG800 2.0 70.7 1.0
OP2 D:A-3 2.3 75.3 1.0
C C:ARG800 3.2 71.2 1.0
OP2 D:U-4 3.6 81.2 1.0
P D:A-3 3.7 75.6 1.0
N C:ARG800 3.8 72.8 1.0
OD1 C:ASP792 3.8 70.6 1.0
CA C:ARG800 4.0 72.2 1.0
C C:GLY799 4.1 84.1 1.0
N C:PRO801 4.2 71.1 1.0
CA C:PRO801 4.3 70.4 1.0
OP1 D:A-3 4.4 76.6 1.0
O5' D:A-3 4.4 73.9 1.0
O C:GLY799 4.5 84.7 1.0
C C:PRO801 4.5 69.4 1.0
CB C:ARG800 4.6 71.8 1.0
CA C:GLY799 4.6 91.2 1.0
C3' D:U-4 4.7 76.4 1.0
CG C:ASP792 4.7 70.2 1.0
OD1 C:ASN802 4.7 67.4 1.0
O3' D:U-4 4.7 76.5 1.0
OP2 D:G-2 4.7 70.8 1.0
P D:U-4 4.8 79.7 1.0
O5' D:U-4 4.8 78.8 1.0
OD2 C:ASP792 4.8 69.4 1.0
N C:ASN802 4.8 68.8 1.0
O C:PRO801 4.9 69.2 1.0

Magnesium binding site 4 out of 8 in 5ng6

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Magnesium binding site 4 out of 8 in the Crystal Structure of FNCAS12A Bound to A Crrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of FNCAS12A Bound to A Crrna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg200

b:62.0
occ:1.00
 O D:HOH306 1.8 62.0 1.0
O D:HOH304 1.9 62.0 1.0
O D:HOH303 1.9 62.0 1.0
O D:HOH302 1.9 64.4 1.0
O D:HOH301 2.0 64.4 1.0
O D:HOH305 2.0 65.7 1.0
OP2 D:A-11 3.9 62.1 1.0
O4 D:U-16 4.1 70.0 1.0
OP2 D:A-17 4.2 73.0 1.0
N7 D:A-11 4.7 66.1 1.0
OP2 D:U-12 4.7 62.2 1.0
C5 D:C-10 4.8 70.5 1.0
OP1 D:A-17 4.9 73.5 1.0

Magnesium binding site 5 out of 8 in 5ng6

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Magnesium binding site 5 out of 8 in the Crystal Structure of FNCAS12A Bound to A Crrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of FNCAS12A Bound to A Crrna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1401

b:78.2
occ:1.00
 O E:HOH1505 1.9 0.3 1.0
O F:HOH303 1.9 0.1 1.0
O E:HOH1502 2.0 0.2 1.0
O E:ARG800 2.0 60.2 1.0
O F:HOH308 2.1 17.6 1.0
OP2 F:A-3 2.1 56.0 1.0
C E:ARG800 3.2 60.1 1.0
P F:A-3 3.5 56.5 1.0
N E:ARG800 3.9 60.8 1.0
OP2 F:U-4 4.0 56.1 1.0
CA E:ARG800 4.1 60.2 1.0
O E:HOH1504 4.1 20.9 1.0
OD1 E:ASP792 4.2 59.7 1.0
OP1 F:A-3 4.2 57.3 1.0
N E:PRO801 4.2 59.9 1.0
O5' F:A-3 4.2 55.9 1.0
CA E:PRO801 4.3 59.9 1.0
O E:HOH1503 4.3 17.6 1.0
C E:PRO801 4.4 60.1 1.0
C E:GLY799 4.4 95.2 1.0
OD1 E:ASN802 4.5 60.6 1.0
CB E:ARG800 4.5 60.5 1.0
OP1 F:U-4 4.5 57.7 1.0
OP2 F:G-2 4.5 54.3 1.0
O3' F:U-4 4.6 57.1 1.0
P F:U-4 4.6 57.1 1.0
C3' F:U-4 4.7 56.7 1.0
O E:PRO801 4.7 60.4 1.0
N E:ASN802 4.7 60.2 1.0
O E:GLY799 4.9 0.5 1.0
O5' F:U-4 5.0 57.2 1.0

Magnesium binding site 6 out of 8 in 5ng6

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Magnesium binding site 6 out of 8 in the Crystal Structure of FNCAS12A Bound to A Crrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of FNCAS12A Bound to A Crrna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg200

b:62.4
occ:1.00
 O F:HOH307 1.7 62.0 1.0
O F:HOH306 1.7 62.0 1.0
O F:HOH310 1.7 62.0 1.0
O F:HOH304 1.8 62.0 1.0
O F:HOH309 1.8 62.0 1.0
O F:HOH302 1.8 62.0 1.0
OP2 F:A-11 3.9 48.9 1.0
O4 F:U-16 4.1 50.9 1.0
O E:HOH1501 4.2 58.7 1.0
OP2 F:A-17 4.4 52.2 1.0
N7 F:A-11 4.6 51.0 1.0
OP2 F:U-12 4.7 47.6 1.0
C5 F:C-10 4.8 52.8 1.0
OP1 F:A-17 5.0 51.4 1.0

Magnesium binding site 7 out of 8 in 5ng6

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Magnesium binding site 7 out of 8 in the Crystal Structure of FNCAS12A Bound to A Crrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of FNCAS12A Bound to A Crrna within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1401

b:57.0
occ:1.00
 O H:HOH302 1.8 0.1 1.0
O G:HOH1501 1.8 0.8 1.0
O G:ARG800 2.0 58.6 1.0
OP2 H:A-3 2.1 57.7 1.0
O G:HOH1502 2.1 93.1 1.0
C G:ARG800 3.2 58.6 1.0
P H:A-3 3.5 58.0 1.0
OP2 H:U-4 3.7 59.0 1.0
N G:ARG800 3.8 60.1 1.0
CA G:ARG800 4.0 59.6 1.0
N G:PRO801 4.2 58.0 1.0
OP1 H:A-3 4.2 57.5 1.0
OP1 H:U-4 4.2 58.7 1.0
O5' H:A-3 4.2 57.8 1.0
OD1 G:ASP792 4.3 56.8 1.0
C G:GLY799 4.3 93.8 1.0
P H:U-4 4.4 59.4 1.0
CA G:PRO801 4.4 57.2 1.0
CB G:ARG800 4.4 60.2 1.0
C3' H:U-4 4.5 60.0 1.0
C G:PRO801 4.5 57.0 1.0
O3' H:U-4 4.5 59.3 1.0
OP2 H:G-2 4.7 55.2 1.0
O5' H:U-4 4.7 60.3 1.0
O G:PRO801 4.8 57.4 1.0
O G:GLY799 4.8 0.9 1.0
OD1 G:ASN802 4.8 56.6 1.0
N G:ASN802 4.9 56.4 1.0
CA G:GLY799 4.9 93.4 1.0

Magnesium binding site 8 out of 8 in 5ng6

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Magnesium binding site 8 out of 8 in the Crystal Structure of FNCAS12A Bound to A Crrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of FNCAS12A Bound to A Crrna within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg200

b:62.0
occ:1.00
 O H:HOH305 1.7 62.0 1.0
O G:HOH1503 1.8 62.0 1.0
O H:HOH304 1.9 62.0 1.0
O H:HOH303 1.9 62.0 1.0
O H:HOH306 1.9 65.0 1.0
O H:HOH301 2.0 62.0 1.0
O4 H:U-16 4.1 59.9 1.0
OP2 H:A-17 4.2 60.2 1.0
OP2 H:A-11 4.4 60.5 1.0
OP2 H:U-12 4.6 59.9 1.0
OP1 H:A-17 4.6 60.1 1.0
C5 H:C-10 4.9 63.8 1.0
P H:A-17 5.0 59.8 1.0

Reference:

D.C.Swarts, J.Van Der Oost, M.Jinek. Structural Basis For Guide Rna Processing and Seed-Dependent Dna Targeting By Crispr-CAS12A. Mol. Cell V. 66 221 2017.
ISSN: ISSN 1097-4164
PubMed: 28431230
DOI: 10.1016/J.MOLCEL.2017.03.016
Page generated: Sun Sep 29 23:16:23 2024

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