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Barium in PDB 6m0v: Crsytal Structure of Streptococcus Thermophilus CAS9 in Complex with the Ggaa Pam

Protein crystallography data

The structure of Crsytal Structure of Streptococcus Thermophilus CAS9 in Complex with the Ggaa Pam, PDB code: 6m0v was solved by Y.Zhang, H.Zhang, X.Xu, Y.Wang, W.Chen, Y.Wang, Z.Wu, N.Tang, Y.Wang, S.Zhao, J.Gan, Q.Ji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.82 / 3.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 321.839, 75.078, 70.109, 90.00, 93.21, 90.00
R / Rfree (%) 21.3 / 25.7

Other elements in 6m0v:

The structure of Crsytal Structure of Streptococcus Thermophilus CAS9 in Complex with the Ggaa Pam also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Barium Binding Sites:

The binding sites of Barium atom in the Crsytal Structure of Streptococcus Thermophilus CAS9 in Complex with the Ggaa Pam (pdb code 6m0v). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 10 binding sites of Barium where determined in the Crsytal Structure of Streptococcus Thermophilus CAS9 in Complex with the Ggaa Pam, PDB code: 6m0v:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 10 in 6m0v

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Barium binding site 1 out of 10 in the Crsytal Structure of Streptococcus Thermophilus CAS9 in Complex with the Ggaa Pam


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Crsytal Structure of Streptococcus Thermophilus CAS9 in Complex with the Ggaa Pam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba101

b:37.6
occ:1.00
 OP1 B:U50 2.7 41.5 1.0
N7 B:G53 2.9 37.5 1.0
O6 B:G53 3.2 35.8 1.0
C5 B:G53 3.6 24.9 1.0
C6 B:G53 3.7 24.3 1.0
C8 B:G53 4.0 26.3 1.0
P B:U50 4.2 22.9 1.0
N1 B:G64 4.6 22.0 1.0
OP1 B:A51 4.8 22.5 1.0
OP2 B:A52 4.8 21.1 1.0
O3' B:A49 4.8 25.5 1.0
N7 B:G54 4.9 24.6 1.0
C4 B:G53 4.9 24.2 1.0
O5' B:U50 5.0 24.3 1.0

Barium binding site 2 out of 10 in 6m0v

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Barium binding site 2 out of 10 in the Crsytal Structure of Streptococcus Thermophilus CAS9 in Complex with the Ggaa Pam


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Crsytal Structure of Streptococcus Thermophilus CAS9 in Complex with the Ggaa Pam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba102

b:86.0
occ:1.00
 O6 B:G40 2.6 46.2 1.0
O B:HOH203 2.7 38.5 1.0
C6 B:G40 3.7 35.4 1.0
N7 B:G40 4.2 35.1 1.0
OP2 B:A38 4.2 54.5 1.0
C5 B:G40 4.3 33.9 1.0
OP2 B:G27 4.5 57.9 1.0
N7 B:A39 4.7 33.1 1.0
N1 B:G40 4.8 34.8 1.0

Barium binding site 3 out of 10 in 6m0v

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Barium binding site 3 out of 10 in the Crsytal Structure of Streptococcus Thermophilus CAS9 in Complex with the Ggaa Pam


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Crsytal Structure of Streptococcus Thermophilus CAS9 in Complex with the Ggaa Pam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba103

b:0.8
occ:1.00
 O4 B:U2 2.8 72.5 1.0
C4 B:U2 3.8 72.8 1.0
C5 B:U2 4.4 73.1 1.0
O6 B:G1 4.7 84.3 1.0

Barium binding site 4 out of 10 in 6m0v

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Barium binding site 4 out of 10 in the Crsytal Structure of Streptococcus Thermophilus CAS9 in Complex with the Ggaa Pam


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Crsytal Structure of Streptococcus Thermophilus CAS9 in Complex with the Ggaa Pam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba104

b:0.9
occ:1.00
 O4 B:U22 4.5 27.6 1.0
N6 B:A49 4.5 24.0 1.0
N6 B:A47 4.7 26.2 1.0
NH2 A:ARG166 4.9 32.1 1.0

Barium binding site 5 out of 10 in 6m0v

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Barium binding site 5 out of 10 in the Crsytal Structure of Streptococcus Thermophilus CAS9 in Complex with the Ggaa Pam


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Crsytal Structure of Streptococcus Thermophilus CAS9 in Complex with the Ggaa Pam within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba101

b:0.4
occ:1.00
 O6 C:DG1 2.8 57.1 1.0
N7 C:DG1 3.6 52.8 1.0
C6 C:DG1 3.6 46.5 1.0
C5 C:DG1 4.0 45.3 1.0
NZ A:LYS1051 4.3 56.3 1.0
CE A:LYS1051 4.7 67.1 1.0
C8 C:DG1 4.8 44.7 1.0
NE2 A:GLN1052 4.9 44.6 1.0
N1 C:DG1 4.9 43.9 1.0

Barium binding site 6 out of 10 in 6m0v

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Barium binding site 6 out of 10 in the Crsytal Structure of Streptococcus Thermophilus CAS9 in Complex with the Ggaa Pam


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Crsytal Structure of Streptococcus Thermophilus CAS9 in Complex with the Ggaa Pam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1201

b:90.2
occ:1.00
 OG A:SER940 4.1 40.4 1.0
N2 D:DG3 4.5 42.2 1.0
CB A:SER940 4.5 37.6 1.0
O2 C:DC6 5.0 33.1 1.0
C4' C:DT7 5.0 32.9 1.0

Barium binding site 7 out of 10 in 6m0v

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Barium binding site 7 out of 10 in the Crsytal Structure of Streptococcus Thermophilus CAS9 in Complex with the Ggaa Pam


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of Crsytal Structure of Streptococcus Thermophilus CAS9 in Complex with the Ggaa Pam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1202

b:0.5
occ:1.00
 OP2 C:DT17 2.8 37.1 1.0
O A:GLY421 3.3 73.7 1.0
C A:GLY421 3.6 58.2 1.0
CA A:GLY421 3.8 58.3 1.0
P C:DT17 4.1 32.3 1.0
N A:LYS422 4.5 53.6 1.0
C7 C:DT17 4.6 32.8 1.0
OP1 C:DT16 4.6 40.4 1.0
O5' C:DT16 4.6 35.0 1.0
O3' C:DT16 4.7 35.9 1.0
OP2 C:DT16 4.7 38.7 1.0
N A:GLY423 4.7 49.1 1.0
NZ A:LYS560 4.8 67.3 1.0
OP1 C:DT17 4.8 45.1 1.0
P C:DT16 4.8 33.3 1.0
C3' C:DT16 4.9 35.0 1.0

Barium binding site 8 out of 10 in 6m0v

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Barium binding site 8 out of 10 in the Crsytal Structure of Streptococcus Thermophilus CAS9 in Complex with the Ggaa Pam


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of Crsytal Structure of Streptococcus Thermophilus CAS9 in Complex with the Ggaa Pam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1203

b:0.9
occ:1.00
 O A:LYS848 3.1 40.5 1.0
O C:HOH201 4.1 26.6 1.0
C A:LYS848 4.3 27.6 1.0
OP2 C:DT8 4.4 29.9 1.0
OP1 C:DT8 4.9 28.1 1.0
CA A:ILE849 5.0 29.1 1.0

Barium binding site 9 out of 10 in 6m0v

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Barium binding site 9 out of 10 in the Crsytal Structure of Streptococcus Thermophilus CAS9 in Complex with the Ggaa Pam


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of Crsytal Structure of Streptococcus Thermophilus CAS9 in Complex with the Ggaa Pam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1204

b:0.1
occ:1.00
 O A:THR514 3.4 83.8 1.0
C A:THR514 4.3 80.4 1.0
CA A:ASN515 4.5 81.5 1.0
N A:ASN515 4.8 79.0 1.0
OG1 A:THR514 5.0 99.2 1.0

Barium binding site 10 out of 10 in 6m0v

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Barium binding site 10 out of 10 in the Crsytal Structure of Streptococcus Thermophilus CAS9 in Complex with the Ggaa Pam


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 10 of Crsytal Structure of Streptococcus Thermophilus CAS9 in Complex with the Ggaa Pam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1205

b:67.0
occ:1.00
 OD1 A:ASP824 3.2 20.7 1.0
CB A:SER961 4.0 22.2 1.0
OG A:SER961 4.2 27.3 1.0
CG A:ASP824 4.3 19.6 1.0
OD2 A:ASP824 4.6 19.4 1.0
O4' D:DG3 4.6 24.0 1.0
O2 C:DT8 4.8 35.3 1.0
O A:SER961 4.8 21.6 1.0
C4' D:DG3 5.0 24.2 1.0

Reference:

Y.Zhang, H.Zhang, X.Xu, Y.Wang, W.Chen, Y.Wang, Z.Wu, N.Tang, Y.Wang, S.Zhao, J.Gan, Q.Ji. Catalytic-State Structure and Engineering of Streptococcus Thermophilus CAS9 Nat Catal 2020.
ISSN: ESSN 2520-1158
DOI: 10.1038/S41929-020-00506-9
Page generated: Wed Jul 10 15:58:24 2024

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