Manganese in PDB 4cmq: Crystal Structure of Mn-Bound S.Pyogenes CAS9

The structure of Crystal Structure of Mn-Bound S.Pyogenes CAS9, PDB code: 4cmq was solved by M.Jinek, F.Jiang, D.W.Taylor, S.H.Sternberg, E.Kaya, E.Ma, C.Anders, M.Hauer, K.Zhou, S.Lin, M.Kaplan, A.T.Iavarone, E.Charpentier, E.Nogales, J.A.Doudna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.528 / 3.09
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	159.880, 210.120, 90.670, 90.00, 90.00, 90.00
R / Rfree (%)	24.93 / 27.71

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Mn-Bound S.Pyogenes CAS9 (pdb code 4cmq). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 13 binding sites of Manganese where determined in the Crystal Structure of Mn-Bound S.Pyogenes CAS9, PDB code: 4cmq:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 13 in the Crystal Structure of Mn-Bound S.Pyogenes CAS9


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Mn-Bound S.Pyogenes CAS9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2364 b:31.5 occ:1.00 OE1 A:GLU766 2.2 45.2 1.0 OE2 A:GLU766 2.2 50.8 1.0 OD2 A:ASP10 2.2 46.3 1.0 ND1 A:HIS983 2.2 26.2 1.0 CD A:GLU766 2.5 45.3 1.0 CE1 A:HIS983 2.8 25.3 1.0 CG A:ASP10 3.3 43.8 1.0 CG A:HIS983 3.4 24.8 1.0 MN A:MN2365 3.9 36.2 1.0 CB A:ASP10 3.9 36.8 1.0 CG A:GLU766 4.0 41.5 1.0 CB A:HIS983 4.0 21.6 1.0 CA A:HIS983 4.1 24.2 1.0 NE2 A:HIS983 4.1 22.9 1.0 OG A:SER15 4.1 24.0 1.0 CD2 A:HIS983 4.3 24.0 1.0 OD1 A:ASP10 4.4 48.7 1.0 OD2 A:ASP986 4.5 22.6 1.0 CB A:GLU766 4.7 41.5 1.0 N A:HIS983 4.9 26.0 1.0 CD2 A:HIS982 4.9 26.5 1.0

Manganese binding site 2 out of 13 in the Crystal Structure of Mn-Bound S.Pyogenes CAS9


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Mn-Bound S.Pyogenes CAS9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2365 b:36.2 occ:1.00 OD1 A:ASP10 2.1 48.7 1.0 OE1 A:GLU762 2.1 46.8 1.0 OE2 A:GLU766 2.2 50.8 1.0 OD2 A:ASP10 2.2 46.3 1.0 CG A:ASP10 2.5 43.8 1.0 CD A:GLU766 3.0 45.3 1.0 CD A:GLU762 3.3 43.9 1.0 CG A:GLU766 3.5 41.5 1.0 MN A:MN2364 3.9 31.5 1.0 OE2 A:GLU762 3.9 44.2 1.0 CB A:ASP10 4.0 36.8 1.0 OE1 A:GLU766 4.0 45.2 1.0 OD2 A:ASP986 4.1 22.6 1.0 O A:ALA764 4.4 43.1 1.0 CG A:GLU762 4.5 38.0 1.0 CA A:ASP10 4.6 32.1 1.0 O A:GLU762 4.7 35.8 1.0 O A:ILE11 4.7 28.5 1.0 N A:ALA764 4.7 38.5 1.0 N A:ILE11 4.8 26.9 1.0 CB A:GLU762 4.8 31.7 1.0

Manganese binding site 3 out of 13 in the Crystal Structure of Mn-Bound S.Pyogenes CAS9


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Mn-Bound S.Pyogenes CAS9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2366 b:53.9 occ:1.00 ND1 A:HIS511 2.1 56.6 1.0 OE2 A:GLU516 2.1 59.6 1.0 CE1 A:HIS511 2.8 58.2 1.0 CD A:GLU516 3.2 60.8 1.0 CG A:HIS511 3.2 52.0 1.0 OE1 A:GLU516 3.6 65.0 1.0 CB A:HIS511 3.7 46.4 1.0 OG1 A:THR593 3.8 42.0 1.0 NE2 A:HIS511 4.0 56.6 1.0 N A:THR593 4.2 41.2 1.0 CD2 A:HIS511 4.2 52.8 1.0 CA A:HIS511 4.2 42.0 1.0 CA A:GLY592 4.3 42.2 1.0 N A:GLY592 4.4 41.8 1.0 CG A:GLU516 4.5 56.7 1.0 C A:GLY592 4.6 41.1 1.0 O A:SER590 4.8 48.3 1.0 CB A:THR593 4.9 41.2 1.0

Manganese binding site 4 out of 13 in the Crystal Structure of Mn-Bound S.Pyogenes CAS9


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Mn-Bound S.Pyogenes CAS9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2367 b:84.6 occ:1.00 NE2 A:HIS1241 2.3 71.9 1.0 CD2 A:HIS1241 3.1 71.3 1.0 CE1 A:HIS1241 3.2 71.8 1.0 CG A:HIS1241 4.2 71.5 1.0 ND1 A:HIS1241 4.2 72.1 1.0 OH A:TYR1237 4.4 50.8 1.0 CE2 A:TYR1237 4.6 46.8 1.0 CZ A:TYR1237 4.8 48.7 1.0

Manganese binding site 5 out of 13 in the Crystal Structure of Mn-Bound S.Pyogenes CAS9


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Mn-Bound S.Pyogenes CAS9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2368 b:0.7 occ:1.00 OD2 A:ASP1328 2.2 96.6 1.0 OD1 A:ASP1328 2.2 95.9 1.0 NE2 A:HIS1297 2.3 92.4 1.0 CG A:ASP1328 2.5 95.4 1.0 CD2 A:HIS1297 2.9 91.8 1.0 CE1 A:HIS1297 3.5 92.1 1.0 CB A:ASP1328 4.0 92.6 1.0 CG A:HIS1297 4.2 90.6 1.0 ND1 A:HIS1297 4.4 91.3 1.0 N A:ASP1328 4.5 88.7 1.0 CA A:ASP1328 4.8 88.7 1.0 CB A:PHE1327 4.9 85.3 1.0

Manganese binding site 6 out of 13 in the Crystal Structure of Mn-Bound S.Pyogenes CAS9


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Mn-Bound S.Pyogenes CAS9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2369 b:0.0 occ:1.00 NE2 A:HIS1311 2.2 53.6 1.0 CE1 A:HIS1311 2.3 55.3 1.0 ND1 A:HIS1311 3.5 54.1 1.0 CD2 A:HIS1311 3.5 51.7 1.0 CG A:HIS1311 4.1 50.9 1.0 OE1 A:GLU1307 4.8 74.5 1.0 O A:GLU1307 5.0 59.0 1.0

Manganese binding site 7 out of 13 in the Crystal Structure of Mn-Bound S.Pyogenes CAS9


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Mn-Bound S.Pyogenes CAS9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2370 b:98.4 occ:1.00 NE2 A:HIS799 2.3 76.2 1.0 CE1 A:HIS799 2.6 75.8 1.0 CD2 A:HIS799 3.6 75.4 1.0 ND1 A:HIS799 3.8 76.1 1.0 CG A:HIS799 4.3 74.2 1.0 OE2 A:GLU827 4.5 88.0 1.0

Manganese binding site 8 out of 13 in the Crystal Structure of Mn-Bound S.Pyogenes CAS9


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Mn-Bound S.Pyogenes CAS9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2364 b:30.1 occ:1.00 OD2 B:ASP10 2.1 46.0 1.0 OE2 B:GLU766 2.2 48.1 1.0 ND1 B:HIS983 2.2 26.7 1.0 OE1 B:GLU766 2.2 46.9 1.0 CD B:GLU766 2.5 46.0 1.0 CE1 B:HIS983 2.8 25.3 1.0 CG B:ASP10 3.2 43.9 1.0 CG B:HIS983 3.4 26.5 1.0 OD1 B:ASP10 3.7 45.0 1.0 MN B:MN2365 3.9 38.5 1.0 CG B:GLU766 4.0 43.9 1.0 CB B:HIS983 4.0 27.7 1.0 CA B:HIS983 4.0 29.9 1.0 NE2 B:HIS983 4.0 22.6 1.0 OG B:SER15 4.1 29.1 1.0 OD2 B:ASP986 4.3 36.1 1.0 CD2 B:HIS983 4.3 23.3 1.0 CB B:ASP10 4.5 40.0 1.0 O B:ASP10 4.5 36.5 1.0 CB B:GLU766 4.8 44.1 1.0 N B:HIS983 4.8 31.0 1.0 CD2 B:HIS982 4.8 35.5 1.0 CB B:ASP986 4.9 28.8 1.0 CG B:ASP986 4.9 32.4 1.0

Manganese binding site 9 out of 13 in the Crystal Structure of Mn-Bound S.Pyogenes CAS9


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of Mn-Bound S.Pyogenes CAS9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2365 b:38.5 occ:1.00 OD1 B:ASP10 2.1 45.0 1.0 OE2 B:GLU766 2.1 48.1 1.0 OE1 B:GLU762 2.2 52.8 1.0 CD B:GLU766 3.1 46.0 1.0 CG B:ASP10 3.2 43.9 1.0 CD B:GLU762 3.3 48.2 1.0 CG B:GLU766 3.5 43.9 1.0 OD2 B:ASP10 3.5 46.0 1.0 OE2 B:GLU762 3.7 47.7 1.0 O B:ALA764 3.9 54.8 1.0 MN B:MN2364 3.9 30.1 1.0 OD2 B:ASP986 4.2 36.1 1.0 OE1 B:GLU766 4.2 46.9 1.0 O B:ILE11 4.4 33.5 1.0 CB B:ASP10 4.5 40.0 1.0 CG B:GLU762 4.5 45.1 1.0 N B:ALA764 4.7 38.9 1.0 O B:GLU762 4.7 41.7 1.0 C B:ALA764 4.9 56.4 1.0 CA B:ASP10 4.9 37.5 1.0 C B:GLU762 5.0 39.7 1.0 CB B:GLU766 5.0 44.1 1.0 CB B:GLU762 5.0 44.3 1.0 C B:ASP10 5.0 34.9 1.0

Manganese binding site 10 out of 13 in the Crystal Structure of Mn-Bound S.Pyogenes CAS9


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of Mn-Bound S.Pyogenes CAS9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2366 b:98.8 occ:1.00 O B:THR386 2.2 82.7 1.0 O B:LEU380 2.3 71.7 1.0 C B:LEU380 3.1 72.5 1.0 C B:THR386 3.2 84.5 1.0 N B:THR386 3.5 91.8 1.0 CA B:LEU380 3.6 68.4 1.0 CB B:LEU380 3.7 62.5 1.0 CA B:THR386 3.9 87.0 1.0 CD2 B:LEU380 4.1 54.7 1.0 CD1 B:LEU390 4.2 50.6 1.0 N B:GLU387 4.2 83.5 1.0 N B:GLY385 4.2 96.3 1.0 N B:GLU381 4.2 78.2 1.0 CA B:GLU387 4.4 80.7 1.0 CG B:LEU390 4.5 51.5 1.0 CG B:LEU380 4.5 56.4 1.0 C B:GLY385 4.6 94.7 1.0 N B:ASP384 4.6 0.6 1.0 CB B:MET383 4.7 0.9 1.0 OE1 B:GLU387 4.7 87.2 1.0 CA B:GLU381 4.7 84.2 1.0 CB B:THR386 4.7 84.3 1.0 CA B:GLY385 4.8 94.1 1.0 N B:LEU380 5.0 71.2 1.0

M.Jinek, F.Jiang, D.W.Taylor, S.H.Sternberg, E.Kaya, E.Ma, C.Anders, M.Hauer, K.Zhou, S.Lin, M.Kaplan, A.T.Iavarone, E.Charpentier, E.Nogales, J.A.Doudna. Structures of CAS9 Endonucleases Reveal Rna- Mediated Conformational Activation Science V. 343 47997 2014.
ISSN: ISSN 0036-8075
PubMed: 24505130
DOI: 10.1126/SCIENCE.1247997