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Magnesium in PDB 5xvn: E. Far CAS1-CAS2/Prespacer Binary Complex

Protein crystallography data

The structure of E. Far CAS1-CAS2/Prespacer Binary Complex, PDB code: 5xvn was solved by Y.Xiao, S.Ng, K.H.Nam, A.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.41 / 3.25
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 160.711, 160.711, 187.965, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 24.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Far CAS1-CAS2/Prespacer Binary Complex (pdb code 5xvn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the E. Far CAS1-CAS2/Prespacer Binary Complex, PDB code: 5xvn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5xvn

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Magnesium binding site 1 out of 4 in the E. Far CAS1-CAS2/Prespacer Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Far CAS1-CAS2/Prespacer Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg201

b:45.7
occ:1.00
 OD1 E:ASP13 2.2 72.6 1.0
OG E:SER43 2.2 76.5 1.0
OP1 H:DC15 2.5 52.4 1.0
O E:PHE12 2.7 60.1 1.0
CB E:SER43 2.8 71.5 1.0
CG E:ASP13 3.4 63.3 1.0
NE2 F:GLN41 3.6 60.1 1.0
C E:PHE12 3.8 58.4 1.0
P H:DC15 3.9 67.2 1.0
OD2 E:ASP13 4.1 59.3 1.0
N F:PHE42 4.1 49.9 1.0
CB F:PHE42 4.1 65.5 1.0
CG F:GLN41 4.3 57.4 1.0
CA E:SER43 4.3 62.5 1.0
CA E:ASP13 4.4 59.9 1.0
CD F:GLN41 4.4 60.8 1.0
N E:ASP13 4.4 59.2 1.0
CB E:ASP13 4.5 61.9 1.0
CA F:PHE42 4.5 59.1 1.0
N F:SER43 4.5 62.8 1.0
O3' H:DC14 4.5 64.5 1.0
O E:SER43 4.6 63.1 1.0
C5' H:DC15 4.6 59.0 1.0
O E:PHE42 4.6 63.6 1.0
C E:SER43 4.7 57.6 1.0
CD2 F:PHE42 4.8 65.9 1.0
O5' H:DC15 4.8 61.5 1.0
C F:GLN41 4.9 52.7 1.0
CG F:PHE42 4.9 67.9 1.0
CB F:GLN41 4.9 58.2 1.0
OP2 H:DC15 4.9 62.4 1.0
N E:PHE12 5.0 55.1 1.0

Magnesium binding site 2 out of 4 in 5xvn

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Magnesium binding site 2 out of 4 in the E. Far CAS1-CAS2/Prespacer Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E. Far CAS1-CAS2/Prespacer Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg201

b:43.7
occ:1.00
 OD1 F:ASP13 2.0 64.0 1.0
OG F:SER43 2.2 66.7 1.0
O F:PHE12 2.4 54.0 1.0
CB F:SER43 2.5 69.9 1.0
OP1 G:DC15 2.5 58.1 1.0
CG F:ASP13 3.3 56.5 1.0
C F:PHE12 3.6 57.0 1.0
O E:PHE42 3.6 63.6 1.0
OE1 E:GLN41 3.6 63.8 1.0
CA F:SER43 3.9 63.8 1.0
OD2 F:ASP13 4.0 60.1 1.0
P G:DC15 4.0 61.8 1.0
CG E:GLN41 4.1 59.1 1.0
CA F:ASP13 4.2 55.3 1.0
N F:ASP13 4.2 56.8 1.0
CB F:ASP13 4.3 55.7 1.0
CD E:GLN41 4.3 61.9 1.0
N E:PHE42 4.4 59.5 1.0
O F:SER43 4.4 74.3 1.0
CB E:PHE42 4.5 67.4 1.0
C F:SER43 4.5 64.8 1.0
C E:PHE42 4.6 58.7 1.0
N F:SER43 4.6 62.8 1.0
O3' G:DC14 4.6 59.5 1.0
C5' G:DC15 4.7 54.1 1.0
CA F:PHE12 4.7 56.6 1.0
N F:PHE12 4.7 56.9 1.0
CA E:PHE42 4.8 63.3 1.0
CB E:GLN41 4.9 59.0 1.0
O5' G:DC15 4.9 54.3 1.0

Magnesium binding site 3 out of 4 in 5xvn

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Magnesium binding site 3 out of 4 in the E. Far CAS1-CAS2/Prespacer Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E. Far CAS1-CAS2/Prespacer Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg201

b:51.9
occ:1.00
 OG M:SER43 2.0 54.8 1.0
OD1 M:ASP13 2.2 58.6 1.0
OP1 P:DC15 2.5 36.6 1.0
CB M:SER43 2.6 52.4 1.0
O M:PHE12 2.7 57.4 1.0
CG M:ASP13 3.4 54.2 1.0
NE2 N:GLN41 3.7 49.3 1.0
C M:PHE12 3.8 57.1 1.0
P P:DC15 4.0 44.5 1.0
CA M:SER43 4.1 47.7 1.0
CB N:PHE42 4.1 45.5 1.0
OD2 M:ASP13 4.2 53.9 1.0
N N:PHE42 4.2 44.8 1.0
CG N:GLN41 4.4 51.0 1.0
CA M:ASP13 4.4 54.9 1.0
N M:ASP13 4.4 56.6 1.0
O M:PHE42 4.5 56.0 1.0
CB M:ASP13 4.5 54.6 1.0
O M:SER43 4.5 49.4 1.0
O3' P:DC14 4.5 42.6 1.0
CD N:GLN41 4.6 52.9 1.0
N N:SER43 4.6 50.9 1.0
CA N:PHE42 4.6 46.1 1.0
C5' P:DC15 4.6 40.8 1.0
C M:SER43 4.7 45.9 1.0
CD2 N:PHE42 4.7 41.0 1.0
O5' P:DC15 4.8 39.5 1.0
CG N:PHE42 4.9 40.5 1.0
OP2 P:DC15 5.0 43.5 1.0

Magnesium binding site 4 out of 4 in 5xvn

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Magnesium binding site 4 out of 4 in the E. Far CAS1-CAS2/Prespacer Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of E. Far CAS1-CAS2/Prespacer Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:31.7
occ:1.00
 OD1 N:ASP13 2.1 75.9 1.0
OG N:SER43 2.3 62.4 1.0
OP1 O:DC15 2.4 43.5 1.0
CB N:SER43 2.5 60.6 1.0
O N:PHE12 2.6 50.5 1.0
CG N:ASP13 3.3 65.8 1.0
O M:PHE42 3.4 56.0 1.0
C N:PHE12 3.7 55.5 1.0
P O:DC15 3.9 51.4 1.0
OE1 M:GLN41 3.9 57.1 1.0
CA N:SER43 4.0 53.7 1.0
OD2 N:ASP13 4.0 63.8 1.0
CB M:PHE42 4.2 48.3 1.0
CG M:GLN41 4.2 52.7 1.0
N M:PHE42 4.2 46.1 1.0
CA N:ASP13 4.2 58.9 1.0
N N:ASP13 4.3 58.4 1.0
C M:PHE42 4.3 49.6 1.0
CB N:ASP13 4.4 60.0 1.0
O3' O:DC14 4.5 56.5 1.0
C5' O:DC15 4.5 47.1 1.0
CA M:PHE42 4.5 47.0 1.0
N N:SER43 4.5 50.9 1.0
CD M:GLN41 4.5 55.5 1.0
O N:SER43 4.6 62.8 1.0
C N:SER43 4.6 55.1 1.0
CD2 M:PHE42 4.7 51.5 1.0
O5' O:DC15 4.7 45.8 1.0
CG M:PHE42 4.9 48.9 1.0
CB M:GLN41 4.9 52.0 1.0
OP2 O:DC15 4.9 45.0 1.0
CA N:PHE12 4.9 54.7 1.0
C M:GLN41 5.0 48.8 1.0
N N:PHE12 5.0 54.6 1.0

Reference:

Y.Xiao, S.Ng, K.Hyun Nam, A.Ke. How Type II Crispr-Cas Establish Immunity Through CAS1-CAS2-Mediated Spacer Integration. Nature V. 550 137 2017.
ISSN: ESSN 1476-4687
PubMed: 28869593
DOI: 10.1038/NATURE24020
Page generated: Wed Aug 13 00:27:46 2025

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