Magnesium in PDB 6m0w: Crystal Structure of Streptococcus Thermophilus CAS9 in Complex with the Agaa Pam (original) (raw)
Protein crystallography data
The structure of Crystal Structure of Streptococcus Thermophilus CAS9 in Complex with the Agaa Pam, PDB code: 6m0wwas 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) | 48.87 / 2.76 |
|---|---|
| Space group | C 1 2 1 |
| Cell size a, b, c (Å), α, β, γ (°) | 321.708, 75.333, 70.300, 90.00, 93.47, 90.00 |
| R / Rfree (%) | 22 / 26 |
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Streptococcus Thermophilus CAS9 in Complex with the Agaa Pam (pdb code 6m0w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Streptococcus Thermophilus CAS9 in Complex with the Agaa Pam, PDB code: 6m0w:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;
Magnesium binding site 1 out of 5 in 6m0w
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Magnesium Binding Sites List in 6m0w
Magnesium binding site 1 out of 5 in the Crystal Structure of Streptococcus Thermophilus CAS9 in Complex with the Agaa Pam
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 Streptococcus Thermophilus CAS9 in Complex with the Agaa Pam within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:89.7 occ:1.00 O6 B:G40 2.3 48.2 1.0 C6 B:G40 3.5 52.5 1.0 OP2 B:A38 3.8 70.1 1.0 N7 B:A39 4.1 50.6 1.0 N6 B:A39 4.3 49.5 1.0 C5 B:G40 4.3 46.7 1.0 N7 B:G40 4.4 46.9 1.0 N1 B:G40 4.5 53.2 1.0 OP2 B:G27 4.6 49.6 1.0 C5 B:A39 5.0 51.0 1.0 | | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
Magnesium binding site 2 out of 5 in 6m0w
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Magnesium binding site 2 out of 5 in the Crystal Structure of Streptococcus Thermophilus CAS9 in Complex with the Agaa Pam
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 Streptococcus Thermophilus CAS9 in Complex with the Agaa Pam within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:78.7 occ:1.00 N3 D:DA5 4.1 42.2 1.0 OG A:SER940 4.1 53.7 1.0 O4' D:DA6 4.4 46.4 1.0 C5' D:DA6 4.4 45.8 1.0 O4' D:DA5 4.4 41.2 1.0 C4' D:DA6 4.5 45.4 1.0 C1' D:DA5 4.6 41.8 1.0 O2 C:DT6 4.6 40.0 1.0 N2 D:DG4 4.7 41.3 1.0 C2 D:DA5 4.8 42.5 1.0 C4 D:DA5 5.0 42.4 1.0 | | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
Magnesium binding site 3 out of 5 in 6m0w
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Magnesium binding site 3 out of 5 in the Crystal Structure of Streptococcus Thermophilus CAS9 in Complex with the Agaa Pam
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 Streptococcus Thermophilus CAS9 in Complex with the Agaa Pam within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1201 b:53.4 occ:1.00 OD1 A:ASP598 2.0 53.0 1.0 OP1 C:DC12 2.4 40.4 1.0 O3' C:DC11 2.6 40.5 1.0 OD1 A:ASN622 2.8 51.8 1.0 P C:DC12 3.0 39.7 1.0 CG A:ASP598 3.2 51.1 1.0 O A:ALA599 3.6 53.7 1.0 C3' C:DC11 3.8 39.0 1.0 CG A:ASN622 3.8 49.6 1.0 N A:ALA599 3.9 47.0 1.0 CB A:ASP598 4.0 50.0 1.0 O5' C:DC12 4.0 42.5 1.0 NZ A:LYS625 4.0 42.3 1.0 O A:GLY626 4.1 40.1 1.0 C4' C:DC11 4.1 38.8 1.0 OD2 A:ASP598 4.1 50.9 1.0 OP2 C:DC12 4.2 39.1 1.0 CA A:ASP598 4.2 48.6 1.0 ND2 A:ASN622 4.3 49.3 1.0 C5' C:DC11 4.4 38.5 1.0 O A:ASN622 4.4 44.3 1.0 C A:ALA599 4.4 50.7 1.0 C A:ASP598 4.5 46.5 1.0 CA A:ALA599 4.7 48.9 1.0 CD A:LYS625 4.7 43.1 1.0 C2' C:DC11 4.8 39.1 1.0 CB A:ALA599 4.9 49.6 1.0 | | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
Magnesium binding site 4 out of 5 in 6m0w
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Magnesium binding site 4 out of 5 in the Crystal Structure of Streptococcus Thermophilus CAS9 in Complex with the Agaa Pam
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 Streptococcus Thermophilus CAS9 in Complex with the Agaa Pam within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1202 b:75.2 occ:1.00 O A:LYS848 3.3 57.8 1.0 OP2 C:DT8 4.2 37.6 1.0 C A:LYS848 4.4 51.6 1.0 O C:HOH102 4.5 46.2 1.0 OH A:TYR937 4.7 47.9 1.0 N A:LYS848 4.9 47.8 1.0 | | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
Magnesium binding site 5 out of 5 in 6m0w
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Magnesium binding site 5 out of 5 in the Crystal Structure of Streptococcus Thermophilus CAS9 in Complex with the Agaa Pam
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 Streptococcus Thermophilus CAS9 in Complex with the Agaa Pam within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1203 b:98.7 occ:1.00 OD1 A:ASP824 2.9 41.6 1.0 O C:HOH101 3.1 37.8 1.0 OG A:SER961 3.2 38.5 1.0 CG A:ASP824 3.8 41.5 1.0 OD2 A:ASP824 3.8 42.8 1.0 CB A:SER961 4.0 38.2 1.0 O2 C:DT8 4.2 38.0 1.0 O4' C:DT8 4.9 37.3 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
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