Manganese in PDB 8jkk: Crystal Structure of the Dioxygenase Cctet From Coprinopsis Cinerea Bound to 12BP 5-Methylcytosine (5MC) Containing Duplex Dna

The structure of Crystal Structure of the Dioxygenase Cctet From Coprinopsis Cinerea Bound to 12BP 5-Methylcytosine (5MC) Containing Duplex Dna, PDB code: 8jkk was solved by L.Zhang, L.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.98 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.569, 127.631, 212.236, 90, 90, 90
R / Rfree (%)	18.7 / 21.6

The binding sites of Manganese atom in the Crystal Structure of the Dioxygenase Cctet From Coprinopsis Cinerea Bound to 12BP 5-Methylcytosine (5MC) Containing Duplex Dna (pdb code 8jkk). 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 Cinerea Bound to 12BP 5-Methylcytosine (5MC) Containing Duplex Dna, PDB code: 8jkk:
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 Cinerea Bound to 12BP 5-Methylcytosine (5MC) 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 Cinerea Bound to 12BP 5-Methylcytosine (5MC) Containing Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:23.4 occ:1.00 O1 A:OGA502 2.1 25.0 1.0 O A:HOH655 2.2 25.7 1.0 NE2 A:HIS326 2.2 24.2 1.0 O2' A:OGA502 2.3 20.8 1.0 OD2 A:ASP328 2.3 23.4 1.0 NE2 A:HIS376 2.5 23.7 1.0 OD1 A:ASP328 2.7 28.9 1.0 CG A:ASP328 2.9 27.2 1.0 CE1 A:HIS326 2.9 23.9 1.0 C1 A:OGA502 2.9 25.9 1.0 C2 A:OGA502 2.9 24.3 1.0 CE1 A:HIS376 3.4 21.3 1.0 CD2 A:HIS326 3.4 21.9 1.0 CD2 A:HIS376 3.4 21.4 1.0 O A:HOH617 3.9 26.1 1.0 O2 A:OGA502 4.1 23.9 1.0 ND1 A:HIS326 4.1 21.6 1.0 N1 A:OGA502 4.3 22.1 1.0 CB A:ASP328 4.4 26.4 1.0 CG A:HIS326 4.4 25.5 1.0 ND1 A:HIS376 4.5 24.3 1.0 CG A:HIS376 4.6 22.8 1.0 NH1 A:ARG205 4.7 21.8 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of the Dioxygenase Cctet From Coprinopsis Cinerea Bound to 12BP 5-Methylcytosine (5MC) 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 Cinerea Bound to 12BP 5-Methylcytosine (5MC) Containing Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn501 b:21.2 occ:1.00 O D:HOH686 2.1 23.7 1.0 NE2 D:HIS326 2.2 25.9 1.0 O2 D:OGA502 2.3 38.6 1.0 NE2 D:HIS376 2.3 35.7 1.0 O2' D:OGA502 2.3 26.1 1.0 OD2 D:ASP328 2.4 28.2 1.0 OD1 D:ASP328 2.6 23.5 1.0 CG D:ASP328 2.8 24.3 1.0 CE1 D:HIS326 3.0 23.0 1.0 C1 D:OGA502 3.0 24.1 1.0 C2 D:OGA502 3.0 22.5 1.0 CE1 D:HIS376 3.2 21.9 1.0 CD2 D:HIS376 3.3 19.6 1.0 CD2 D:HIS326 3.4 22.2 1.0 O D:HOH608 3.8 23.8 1.0 ND1 D:HIS326 4.2 22.1 1.0 O1 D:OGA502 4.2 20.9 1.0 ND1 D:HIS376 4.3 22.9 1.0 CB D:ASP328 4.3 21.9 1.0 N1 D:OGA502 4.3 19.6 1.0 CG D:HIS376 4.4 21.6 1.0 CG D:HIS326 4.4 23.1 1.0 NH1 D:ARG205 4.7 21.0 1.0 N4 E:5CM6 4.8 22.5 1.0 N D:ASP328 4.9 20.8 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of the Dioxygenase Cctet From Coprinopsis Cinerea Bound to 12BP 5-Methylcytosine (5MC) 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 Cinerea Bound to 12BP 5-Methylcytosine (5MC) Containing Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn501 b:33.5 occ:1.00 OD2 G:ASP328 2.0 34.6 1.0 O1 G:OGA502 2.2 32.5 1.0 NE2 G:HIS326 2.2 36.6 1.0 O G:HOH658 2.2 33.0 1.0 NE2 G:HIS376 2.3 31.1 1.0 O2' G:OGA502 2.4 31.6 1.0 CG G:ASP328 2.8 34.5 1.0 CE1 G:HIS326 2.9 34.2 1.0 OD1 G:ASP328 2.9 31.2 1.0 C1 G:OGA502 3.0 33.4 1.0 C2 G:OGA502 3.0 33.0 1.0 CE1 G:HIS376 3.1 33.3 1.0 CD2 G:HIS376 3.4 32.0 1.0 CD2 G:HIS326 3.4 35.2 1.0 O G:HOH610 3.9 33.1 1.0 O G:HOH646 4.1 38.2 1.0 ND1 G:HIS326 4.1 35.4 1.0 O2 G:OGA502 4.2 30.0 1.0 ND1 G:HIS376 4.3 34.6 1.0 CB G:ASP328 4.3 35.5 1.0 N1 G:OGA502 4.4 32.3 1.0 CG G:HIS326 4.4 37.0 1.0 CG G:HIS376 4.4 35.9 1.0 NH1 G:ARG205 4.5 35.4 1.0 NH2 G:ARG205 5.0 38.5 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of the Dioxygenase Cctet From Coprinopsis Cinerea Bound to 12BP 5-Methylcytosine (5MC) 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 Cinerea Bound to 12BP 5-Methylcytosine (5MC) Containing Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn501 b:37.4 occ:1.00 OD2 J:ASP328 2.1 39.9 1.0 NE2 J:HIS326 2.2 39.1 1.0 O2' J:OGA502 2.3 40.8 1.0 O J:HOH633 2.3 38.5 1.0 O2 J:OGA502 2.3 44.1 1.0 NE2 J:HIS376 2.4 40.0 1.0 CG J:ASP328 2.9 41.8 1.0 OD1 J:ASP328 2.9 44.2 1.0 CE1 J:HIS326 3.0 39.5 1.0 C2 J:OGA502 3.0 40.1 1.0 C1 J:OGA502 3.0 42.7 1.0 CD2 J:HIS376 3.3 39.4 1.0 CE1 J:HIS376 3.4 39.2 1.0 CD2 J:HIS326 3.4 40.3 1.0 O J:HOH609 4.1 42.3 1.0 ND1 J:HIS326 4.2 39.0 1.0 O1 J:OGA502 4.2 44.7 1.0 N1 J:OGA502 4.3 36.4 1.0 CB J:ASP328 4.3 41.1 1.0 CG J:HIS326 4.4 41.6 1.0 CG J:HIS376 4.4 40.5 1.0 ND1 J:HIS376 4.4 41.1 1.0 NH1 J:ARG205 4.7 38.1 1.0 N4 K:5CM6 4.9 39.5 1.0

L.Zhang, Y.Mu, T.Li, J.Hu, H.Lin, L.Zhang. Molecular Basis of An Atypical Dsdna 5MC/6MA Bifunctional Dioxygenase Cctet From Coprinopsis Cinerea in Catalyzing Dsdna 5MC Demethylation. Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
PubMed: 38324471
DOI: 10.1093/NAR/GKAE066