Manganese in PDB 7vpn: Crystal Structure of the Dioxygenase Cctet From Coprinopsis Cinereain in Complex with Mn(II) and N-Oxalylglycine

The structure of Crystal Structure of the Dioxygenase Cctet From Coprinopsis Cinereain in Complex with Mn(II) and N-Oxalylglycine, PDB code: 7vpn 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)	49.16 / 2.60
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	219.804, 219.804, 77.751, 90, 90, 120
R / Rfree (%)	21.7 / 26.6

The binding sites of Manganese atom in the Crystal Structure of the Dioxygenase Cctet From Coprinopsis Cinereain in Complex with Mn(II) and N-Oxalylglycine (pdb code 7vpn). 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 in Complex with Mn(II) and N-Oxalylglycine, PDB code: 7vpn:
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 in Complex with Mn(II) and N-Oxalylglycine


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 in Complex with Mn(II) and N-Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1001 b:59.8 occ:1.00 O1 A:OGA1002 1.8 15.4 1.0 O2' A:OGA1002 1.8 15.8 1.0 O A:HOH1143 2.4 46.0 1.0 NE2 A:HIS376 2.4 41.6 1.0 C1 A:OGA1002 2.4 15.6 1.0 C2 A:OGA1002 2.5 20.4 1.0 OD1 A:ASP328 2.7 56.6 1.0 NE2 A:HIS326 3.0 38.0 1.0 CE1 A:HIS376 3.0 34.6 1.0 OD2 A:ASP328 3.0 52.0 1.0 CG A:ASP328 3.2 50.7 1.0 CE1 A:HIS326 3.3 32.4 1.0 O2 A:OGA1002 3.6 15.0 1.0 CD2 A:HIS376 3.6 32.0 1.0 N1 A:OGA1002 3.9 18.9 1.0 CD2 A:HIS326 4.1 35.1 1.0 O A:HOH1163 4.2 46.8 1.0 ND1 A:HIS376 4.2 29.3 1.0 CG A:HIS376 4.6 32.2 1.0 ND1 A:HIS326 4.6 31.1 1.0 CB A:ASP328 4.7 38.4 1.0 C4 A:OGA1002 4.9 13.8 1.0 N A:ASP328 4.9 36.2 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of the Dioxygenase Cctet From Coprinopsis Cinereain in Complex with Mn(II) and N-Oxalylglycine


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 in Complex with Mn(II) and N-Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1001 b:89.3 occ:1.00 NE2 B:HIS326 2.5 46.5 1.0 O B:HOH1172 2.8 42.3 1.0 CE1 B:HIS326 3.5 44.5 1.0 CD2 B:HIS326 3.5 42.5 1.0 NE2 B:HIS376 3.6 40.9 1.0 CE1 B:HIS376 3.9 40.9 1.0 O B:HOH1186 4.0 48.7 1.0 CB B:ASP328 4.2 49.0 1.0 CA B:ASP328 4.6 44.9 1.0 ND1 B:HIS326 4.6 47.4 1.0 N B:ASP328 4.6 46.4 1.0 CG B:HIS326 4.7 43.5 1.0 CD2 B:HIS376 4.9 33.2 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of the Dioxygenase Cctet From Coprinopsis Cinereain in Complex with Mn(II) and N-Oxalylglycine


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 in Complex with Mn(II) and N-Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1001 b:114.2 occ:1.00 NE2 C:HIS326 2.5 64.4 1.0 NE2 C:HIS376 2.7 60.3 1.0 CE1 C:HIS326 3.0 63.2 1.0 CE1 C:HIS376 3.1 62.6 1.0 CD2 C:HIS326 3.8 64.8 1.0 CD2 C:HIS376 3.9 57.0 1.0 ND1 C:HIS326 4.3 61.5 1.0 ND1 C:HIS376 4.3 57.7 1.0 CG C:HIS326 4.7 64.7 1.0 CG C:HIS376 4.7 49.6 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of the Dioxygenase Cctet From Coprinopsis Cinereain in Complex with Mn(II) and N-Oxalylglycine


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 in Complex with Mn(II) and N-Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1001 b:111.6 occ:1.00 NE2 D:HIS326 2.8 66.0 1.0 CE1 D:HIS326 3.6 66.9 1.0 NE2 D:HIS376 3.6 66.8 1.0 CE1 D:HIS376 3.9 69.6 1.0 CD2 D:HIS326 3.9 60.6 1.0 CA D:ASP328 4.6 77.6 1.0 N D:ASP328 4.7 67.1 1.0 CB D:ASP328 4.7 84.3 1.0 ND1 D:HIS326 4.7 66.9 1.0 CG D:ASP328 4.8 89.3 1.0 OD2 D:ASP328 4.9 91.1 1.0 CD2 D:HIS376 4.9 62.4 1.0 CG D:HIS326 4.9 64.2 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