Manganese in PDB 7w5p: Crystal Structure of the Dioxygenase Cctet From Coprinopsis Cinereain Bound to 12BP N6-Methyldeoxyadenine (6MA) Containing Duplex Dna

The structure of Crystal Structure of the Dioxygenase Cctet From Coprinopsis Cinereain Bound to 12BP N6-Methyldeoxyadenine (6MA) Containing Duplex Dna, PDB code: 7w5p was solved by Y.J.Mu, L.Zhang, L.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.18 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.788, 105.198, 196.717, 90, 90, 90
R / Rfree (%)	22.8 / 25.7

The binding sites of Manganese atom in the Crystal Structure of the Dioxygenase Cctet From Coprinopsis Cinereain Bound to 12BP N6-Methyldeoxyadenine (6MA) Containing Duplex Dna (pdb code 7w5p). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of the Dioxygenase Cctet From Coprinopsis Cinereain Bound to 12BP N6-Methyldeoxyadenine (6MA) Containing Duplex Dna, PDB code: 7w5p:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of the Dioxygenase Cctet From Coprinopsis Cinereain Bound to 12BP N6-Methyldeoxyadenine (6MA) Containing Duplex Dna


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 the Dioxygenase Cctet From Coprinopsis Cinereain Bound to 12BP N6-Methyldeoxyadenine (6MA) Containing Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:28.8 occ:1.00 O A:HOH654 2.1 18.6 1.0 O1 A:OGA502 2.2 25.1 1.0 NE2 A:HIS326 2.2 20.8 1.0 O2' A:OGA502 2.3 21.0 1.0 NE2 A:HIS376 2.3 20.2 1.0 OD2 A:ASP328 2.4 21.5 1.0 OD1 A:ASP328 2.7 16.1 1.0 CE1 A:HIS326 2.8 15.5 1.0 CG A:ASP328 2.9 23.8 1.0 C1 A:OGA502 2.9 20.6 1.0 C2 A:OGA502 3.0 19.3 1.0 CE1 A:HIS376 3.1 18.2 1.0 CD2 A:HIS326 3.4 17.2 1.0 CD2 A:HIS376 3.4 16.3 1.0 O A:HOH705 3.8 19.5 1.0 ND1 A:HIS326 4.1 16.4 1.0 O2 A:OGA502 4.1 17.2 1.0 ND1 A:HIS376 4.3 19.4 1.0 N1 A:OGA502 4.3 24.6 1.0 CG A:HIS326 4.4 20.2 1.0 CB A:ASP328 4.4 18.1 1.0 CG A:HIS376 4.5 21.8 1.0 N1 B:6MA6 4.5 21.4 1.0 C1 B:6MA6 4.6 13.5 1.0 NH1 A:ARG205 4.6 14.7 1.0 N A:ASP328 4.9 16.2 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of the Dioxygenase Cctet From Coprinopsis Cinereain Bound to 12BP N6-Methyldeoxyadenine (6MA) Containing Duplex Dna


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 the Dioxygenase Cctet From Coprinopsis Cinereain Bound to 12BP N6-Methyldeoxyadenine (6MA) Containing Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn501 b:26.6 occ:1.00 O D:HOH645 2.0 20.8 1.0 O2 D:OGA502 2.1 28.9 1.0 OD2 D:ASP328 2.2 19.9 1.0 NE2 D:HIS326 2.3 19.2 1.0 O2' D:OGA502 2.4 23.8 1.0 NE2 D:HIS376 2.4 13.6 1.0 OD1 D:ASP328 2.6 17.4 1.0 CG D:ASP328 2.8 18.6 1.0 C1 D:OGA502 2.9 26.6 1.0 CE1 D:HIS326 2.9 15.4 1.0 C2 D:OGA502 3.0 22.6 1.0 CE1 D:HIS376 3.1 16.3 1.0 CD2 D:HIS326 3.5 16.2 1.0 CD2 D:HIS376 3.5 17.2 1.0 O D:HOH701 3.7 16.2 1.0 O1 D:OGA502 4.1 21.6 1.0 ND1 D:HIS326 4.1 15.5 1.0 CB D:ASP328 4.3 17.8 1.0 ND1 D:HIS376 4.3 16.4 1.0 N1 D:OGA502 4.4 22.5 1.0 CG D:HIS326 4.4 19.1 1.0 CG D:HIS376 4.5 14.8 1.0 N1 E:6MA6 4.6 18.1 1.0 C1 E:6MA6 4.6 17.0 1.0 NH1 D:ARG205 4.7 17.3 1.0 N D:ASP328 4.9 18.3 1.0 CD2 D:LEU339 4.9 17.2 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of the Dioxygenase Cctet From Coprinopsis Cinereain Bound to 12BP N6-Methyldeoxyadenine (6MA) Containing Duplex Dna


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 the Dioxygenase Cctet From Coprinopsis Cinereain Bound to 12BP N6-Methyldeoxyadenine (6MA) Containing Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn501 b:24.4 occ:1.00 O2 G:OGA502 2.1 21.1 1.0 NE2 G:HIS326 2.2 33.2 1.0 OD2 G:ASP328 2.2 25.7 1.0 O2' G:OGA502 2.3 22.8 1.0 NE2 G:HIS376 2.4 21.8 1.0 O G:HOH739 2.7 21.1 1.0 OD1 G:ASP328 2.8 28.4 1.0 C1 G:OGA502 2.8 23.7 1.0 CG G:ASP328 2.9 27.4 1.0 CE1 G:HIS326 2.9 28.6 1.0 C2 G:OGA502 2.9 19.0 1.0 CE1 G:HIS376 3.3 24.7 1.0 CD2 G:HIS326 3.4 26.7 1.0 CD2 G:HIS376 3.4 20.6 1.0 O G:HOH633 3.5 22.4 1.0 O1 G:OGA502 4.1 23.3 1.0 ND1 G:HIS326 4.1 30.4 1.0 N1 G:OGA502 4.3 14.8 1.0 CB G:ASP328 4.4 30.1 1.0 CG G:HIS326 4.4 34.0 1.0 ND1 G:HIS376 4.4 23.4 1.0 CG G:HIS376 4.5 25.8 1.0 O G:HOH769 4.5 35.4 1.0 NH1 G:ARG205 4.7 30.1 1.0 NH2 G:ARG205 4.9 32.1 1.0 CD2 G:LEU339 5.0 15.6 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of the Dioxygenase Cctet From Coprinopsis Cinereain Bound to 12BP N6-Methyldeoxyadenine (6MA) Containing Duplex Dna


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 the Dioxygenase Cctet From Coprinopsis Cinereain Bound to 12BP N6-Methyldeoxyadenine (6MA) Containing Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ H:Mn501 b:32.2 occ:1.00 OD2 H:ASP328 2.1 21.8 1.0 O1 H:OGA502 2.2 22.5 1.0 NE2 H:HIS376 2.3 30.4 1.0 NE2 H:HIS326 2.3 35.5 1.0 O2' H:OGA502 2.4 28.0 1.0 OD1 H:ASP328 2.6 32.4 1.0 CG H:ASP328 2.7 27.5 1.0 O H:HOH716 2.8 29.6 1.0 C1 H:OGA502 3.0 27.4 1.0 CE1 H:HIS326 3.0 31.9 1.0 C2 H:OGA502 3.1 31.0 1.0 CE1 H:HIS376 3.1 34.5 1.0 CD2 H:HIS376 3.3 22.6 1.0 CD2 H:HIS326 3.4 27.5 1.0 O H:HOH609 3.6 25.2 1.0 CB H:ASP328 4.2 32.3 1.0 O2 H:OGA502 4.2 23.6 1.0 ND1 H:HIS326 4.2 33.5 1.0 ND1 H:HIS376 4.3 27.2 1.0 N1 H:OGA502 4.4 25.0 1.0 CG H:HIS376 4.4 26.0 1.0 CG H:HIS326 4.4 36.9 1.0 NH1 H:ARG205 4.8 26.0 1.0 N H:ASP328 4.9 27.4 1.0 CA H:ASP328 4.9 36.0 1.0

Y.Mu, L.Zhang, J.Hu, J.Zhou, H.W.Lin, C.He, H.Z.Chen, L.Zhang. A Fungal Dioxygenase Cctet Serves As A Eukaryotic 6MA Demethylase on Duplex Dna. Nat.Chem.Biol. V. 18 733 2022.
ISSN: ESSN 1552-4469
PubMed: 35654845
DOI: 10.1038/S41589-022-01041-3