Manganese in PDB 7ody: Cyanophage S-2L Mazg-Like Pyrophosphohydrolase Bound to Dgdp and Three Catalytic MN2+ Ions Per Active Site

The structure of Cyanophage S-2L Mazg-Like Pyrophosphohydrolase Bound to Dgdp and Three Catalytic MN2+ Ions Per Active Site, PDB code: 7ody was solved by D.Czernecki, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.45 / 1.43
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.59, 91.37, 114.28, 90, 90, 90
R / Rfree (%)	16.4 / 16.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Manganese atom in the Cyanophage S-2L Mazg-Like Pyrophosphohydrolase Bound to Dgdp and Three Catalytic MN2+ Ions Per Active Site (pdb code 7ody). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 12 binding sites of Manganese where determined in the Cyanophage S-2L Mazg-Like Pyrophosphohydrolase Bound to Dgdp and Three Catalytic MN2+ Ions Per Active Site, PDB code: 7ody:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in the Cyanophage S-2L Mazg-Like Pyrophosphohydrolase Bound to Dgdp and Three Catalytic MN2+ Ions Per Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Cyanophage S-2L Mazg-Like Pyrophosphohydrolase Bound to Dgdp and Three Catalytic MN2+ Ions Per Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:18.8 occ:1.00 OE1 A:GLU35 2.0 19.0 1.0 OE2 A:GLU50 2.1 25.4 1.0 OD2 A:ASP53 2.2 20.7 1.0 OE1 A:GLU38 2.2 21.4 1.0 O1B A:DGI201 2.2 19.5 1.0 O A:HOH311 2.3 26.1 1.0 CD A:GLU50 3.1 30.6 1.0 CD A:GLU35 3.1 18.5 1.0 CD A:GLU38 3.1 18.4 1.0 CG A:ASP53 3.3 18.1 1.0 PB A:DGI201 3.3 20.8 1.0 OE1 A:GLU50 3.3 35.0 1.0 MN A:MN203 3.5 18.8 1.0 OE2 A:GLU38 3.5 17.6 1.0 H5' A:DGI201 3.6 25.1 1.0 HB2 A:ASP53 3.6 21.5 1.0 OE2 A:GLU35 3.6 19.0 1.0 HOB3 A:DGI201 3.6 30.2 1.0 O2B A:DGI201 3.7 22.6 1.0 MN A:MN204 3.7 34.8 0.4 HB3 A:ASP53 3.7 21.5 1.0 CB A:ASP53 3.8 17.9 1.0 HZ1 B:LYS76 3.9 26.9 1.0 O3B A:DGI201 3.9 25.2 1.0 HOB2 A:DGI201 4.0 27.1 1.0 HB2 A:GLU38 4.0 23.3 1.0 O B:HOH378 4.1 36.5 1.0 HA A:GLU50 4.1 34.9 1.0 O D:HOH310 4.2 33.7 1.0 HA A:GLU35 4.2 18.7 1.0 HZ2 B:LYS76 4.2 26.9 1.0 HB3 A:GLU35 4.2 20.1 1.0 HB3 A:GLU38 4.2 23.3 1.0 HZ3 B:LYS76 4.3 26.9 1.0 OD1 A:ASP53 4.3 19.8 1.0 NZ B:LYS76 4.3 22.4 1.0 CG A:GLU38 4.4 17.5 1.0 CG A:GLU35 4.4 16.6 1.0 CB A:GLU38 4.4 19.4 1.0 CG A:GLU50 4.4 34.2 1.0 HG3 A:GLU50 4.5 41.0 1.0 HG3 A:GLU35 4.6 19.9 1.0 O3A A:DGI201 4.6 21.3 1.0 C5' A:DGI201 4.6 20.9 1.0 CB A:GLU35 4.7 16.7 1.0 H3' A:DGI201 4.7 21.9 1.0 HG3 A:GLU38 4.9 20.9 1.0 CA A:GLU35 4.9 15.6 1.0 O1A A:DGI201 4.9 20.3 1.0 O A:HOH341 5.0 20.9 1.0 H5'' A:DGI201 5.0 25.1 1.0 HG2 A:GLU38 5.0 20.9 1.0

Manganese binding site 2 out of 12 in the Cyanophage S-2L Mazg-Like Pyrophosphohydrolase Bound to Dgdp and Three Catalytic MN2+ Ions Per Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Cyanophage S-2L Mazg-Like Pyrophosphohydrolase Bound to Dgdp and Three Catalytic MN2+ Ions Per Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn203 b:18.8 occ:1.00 OE2 A:GLU35 2.1 19.0 1.0 OE2 A:GLU38 2.1 17.6 1.0 O1A A:DGI201 2.2 20.3 1.0 O1B A:DGI201 2.2 19.5 1.0 OE2 A:GLU34 2.3 19.0 1.0 O A:HOH341 2.3 20.9 1.0 CD A:GLU35 3.0 18.5 1.0 CD A:GLU38 3.1 18.4 1.0 OE1 A:GLU35 3.2 19.0 1.0 PB A:DGI201 3.3 20.8 1.0 CD A:GLU34 3.4 17.6 1.0 O3A A:DGI201 3.4 21.3 1.0 OE1 A:GLU38 3.4 21.4 1.0 PA A:DGI201 3.4 21.1 1.0 HG2 A:GLU34 3.5 21.5 1.0 HH12 B:ARG94 3.5 28.4 1.0 HZ1 A:LYS31 3.5 24.3 1.0 MN A:MN202 3.5 18.8 1.0 H5' A:DGI201 3.6 25.1 1.0 HE3 A:LYS31 3.7 23.9 1.0 H5'' A:DGI201 3.8 25.1 1.0 CG A:GLU34 4.0 17.9 1.0 HZ2 A:LYS31 4.0 24.3 1.0 O3B A:DGI201 4.0 25.2 1.0 C5' A:DGI201 4.1 20.9 1.0 NZ A:LYS31 4.1 20.2 1.0 O5' A:DGI201 4.1 23.1 1.0 HOB3 A:DGI201 4.2 30.2 1.0 O A:HOH350 4.2 25.9 1.0 NH1 B:ARG94 4.2 23.6 1.0 O D:HOH310 4.3 33.7 1.0 OE1 A:GLU34 4.3 19.5 1.0 CE A:LYS31 4.4 19.9 1.0 HH11 B:ARG94 4.4 28.4 1.0 CG A:GLU35 4.4 16.6 1.0 CG A:GLU38 4.4 17.5 1.0 HG3 A:GLU34 4.5 21.5 1.0 HG2 A:GLU35 4.5 19.9 1.0 HA A:GLU35 4.5 18.7 1.0 HG3 A:GLU38 4.5 20.9 1.0 O2B A:DGI201 4.5 22.6 1.0 O2A A:DGI201 4.6 21.8 1.0 O B:HOH346 4.8 29.7 1.0 HE2 A:LYS31 4.8 23.9 1.0 HOA2 A:DGI201 4.8 26.1 1.0 HG2 A:GLU38 4.8 20.9 1.0 HG3 A:GLU35 4.9 19.9 1.0 HZ3 A:LYS31 4.9 24.3 1.0 O A:HOH311 5.0 26.1 1.0

Manganese binding site 3 out of 12 in the Cyanophage S-2L Mazg-Like Pyrophosphohydrolase Bound to Dgdp and Three Catalytic MN2+ Ions Per Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Cyanophage S-2L Mazg-Like Pyrophosphohydrolase Bound to Dgdp and Three Catalytic MN2+ Ions Per Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn204 b:34.8 occ:0.39 O D:HOH310 2.2 33.7 1.0 O D:HOH396 2.3 34.9 1.0 OE1 A:GLU38 2.4 21.4 1.0 OE1 A:GLU50 2.5 35.0 1.0 O D:HOH311 2.7 45.8 1.0 O A:HOH311 2.8 26.1 1.0 HB3 A:GLU38 3.0 23.3 1.0 HOB3 A:DGI201 3.1 30.2 1.0 CD A:GLU38 3.2 18.4 1.0 CD A:GLU50 3.5 30.6 1.0 MN A:MN202 3.7 18.8 1.0 HB2 D:ASP89 3.7 33.5 1.0 HG2 A:GLU38 3.7 20.9 1.0 CG A:GLU38 3.8 17.5 1.0 CB A:GLU38 3.8 19.4 1.0 OE2 A:GLU50 3.8 25.4 1.0 HB3 D:ASP89 4.1 33.5 1.0 O3B A:DGI201 4.1 25.2 1.0 O A:HOH321 4.2 52.1 1.0 OE2 A:GLU38 4.2 17.6 1.0 O A:HOH352 4.2 31.4 1.0 O D:HOH308 4.2 25.2 1.0 HB2 A:GLU38 4.2 23.3 1.0 CB D:ASP89 4.3 27.9 1.0 O4 D:SO4205 4.3 37.1 0.8 O1B A:DGI201 4.4 19.5 1.0 OD2 D:ASP89 4.5 46.4 1.0 O A:HOH353 4.5 45.1 1.0 O B:HOH378 4.6 36.5 1.0 HG2 A:GLU50 4.6 41.0 1.0 O D:HOH408 4.7 50.0 1.0 CG A:GLU50 4.7 34.2 1.0 HG3 A:GLU38 4.7 20.9 1.0 PB A:DGI201 4.8 20.8 1.0 O A:HOH330 4.8 51.1 1.0 CG D:ASP89 4.9 42.9 1.0

Manganese binding site 4 out of 12 in the Cyanophage S-2L Mazg-Like Pyrophosphohydrolase Bound to Dgdp and Three Catalytic MN2+ Ions Per Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Cyanophage S-2L Mazg-Like Pyrophosphohydrolase Bound to Dgdp and Three Catalytic MN2+ Ions Per Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn202 b:16.7 occ:1.00 OE1 B:GLU35 2.1 17.1 1.0 OD2 B:ASP53 2.1 19.0 1.0 O B:HOH321 2.2 21.2 1.0 O1B B:DGI201 2.2 18.1 1.0 OE1 B:GLU38 2.3 19.0 1.0 OE1 B:GLU50 2.4 22.2 1.0 CD B:GLU38 3.2 16.9 1.0 CD B:GLU35 3.2 17.1 1.0 CG B:ASP53 3.2 17.9 1.0 CD B:GLU50 3.3 28.3 1.0 PB B:DGI201 3.3 19.7 1.0 OE2 B:GLU50 3.4 30.9 1.0 OE2 B:GLU38 3.5 16.8 1.0 O2B B:DGI201 3.6 21.5 1.0 MN B:MN204 3.6 25.1 0.3 MN B:MN203 3.6 16.2 1.0 HB2 B:ASP53 3.6 20.4 1.0 H5' B:DGI201 3.6 23.1 1.0 HOB3 B:DGI201 3.6 30.3 1.0 OE2 B:GLU35 3.7 16.4 1.0 HB3 B:ASP53 3.7 20.4 1.0 CB B:ASP53 3.8 17.0 1.0 O3B B:DGI201 3.9 25.3 1.0 HB2 B:GLU38 4.0 18.7 1.0 HZ1 A:LYS76 4.0 29.3 1.0 HA B:GLU50 4.1 29.3 1.0 HOB2 B:DGI201 4.1 25.8 1.0 O C:HOH303 4.2 32.8 1.0 HA B:GLU35 4.2 16.4 1.0 HB3 B:GLU38 4.3 18.7 1.0 O A:HOH376 4.3 34.2 1.0 OD1 B:ASP53 4.3 18.2 1.0 HZ2 A:LYS76 4.3 29.3 1.0 HZ3 A:LYS76 4.4 29.3 1.0 CG B:GLU38 4.4 15.8 1.0 CG B:GLU35 4.4 16.0 1.0 CB B:GLU38 4.4 15.6 1.0 NZ A:LYS76 4.5 24.4 1.0 HB3 B:GLU35 4.5 18.9 1.0 HG3 B:GLU35 4.6 19.2 1.0 O3A B:DGI201 4.6 19.5 1.0 CG B:GLU50 4.7 39.7 1.0 H3' B:DGI201 4.7 19.2 1.0 C5' B:DGI201 4.7 19.3 1.0 O B:HOH328 4.8 18.3 1.0 O1A B:DGI201 4.8 17.2 1.0 CB B:GLU35 4.8 15.8 1.0 HG3 B:GLU38 4.9 18.9 1.0 CA B:GLU50 5.0 24.4 1.0 HG2 B:GLU50 5.0 47.6 1.0

Manganese binding site 5 out of 12 in the Cyanophage S-2L Mazg-Like Pyrophosphohydrolase Bound to Dgdp and Three Catalytic MN2+ Ions Per Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Cyanophage S-2L Mazg-Like Pyrophosphohydrolase Bound to Dgdp and Three Catalytic MN2+ Ions Per Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn203 b:16.2 occ:1.00 O1A B:DGI201 2.0 17.2 1.0 OE2 B:GLU38 2.1 16.8 1.0 O B:HOH328 2.2 18.3 1.0 OE2 B:GLU35 2.2 16.4 1.0 O1B B:DGI201 2.2 18.1 1.0 OE2 B:GLU34 2.2 17.2 1.0 CD B:GLU35 3.1 17.1 1.0 CD B:GLU38 3.1 16.9 1.0 PA B:DGI201 3.3 18.9 1.0 OE1 B:GLU35 3.3 17.1 1.0 CD B:GLU34 3.3 16.4 1.0 PB B:DGI201 3.3 19.7 1.0 O3A B:DGI201 3.4 19.5 1.0 OE1 B:GLU38 3.4 19.0 1.0 H5' B:DGI201 3.4 23.1 1.0 HG2 B:GLU34 3.4 18.7 1.0 HH12 A:ARG94 3.5 21.7 1.0 HE3 B:LYS31 3.5 21.0 1.0 HZ1 B:LYS31 3.6 20.3 1.0 MN B:MN202 3.6 16.7 1.0 H5'' B:DGI201 3.8 23.1 1.0 CG B:GLU34 3.9 15.6 1.0 C5' B:DGI201 4.0 19.3 1.0 HZ2 B:LYS31 4.0 20.3 1.0 O B:HOH350 4.0 22.7 1.0 O5' B:DGI201 4.1 20.1 1.0 NZ B:LYS31 4.1 16.9 1.0 O3B B:DGI201 4.1 25.3 1.0 O C:HOH303 4.1 32.8 1.0 NH1 A:ARG94 4.2 18.1 1.0 HOB3 B:DGI201 4.2 30.3 1.0 HH11 A:ARG94 4.3 21.7 1.0 CE B:LYS31 4.3 17.5 1.0 OE1 B:GLU34 4.3 18.1 1.0 HG3 B:GLU34 4.4 18.7 1.0 CG B:GLU35 4.5 16.0 1.0 CG B:GLU38 4.5 15.8 1.0 HG3 B:GLU38 4.5 18.9 1.0 HG2 B:GLU35 4.5 19.2 1.0 O2A B:DGI201 4.6 17.9 1.0 O C:HOH365 4.6 24.0 1.0 O2B B:DGI201 4.6 21.5 1.0 HA B:GLU35 4.6 16.4 1.0 HE2 B:LYS31 4.7 21.0 1.0 HOA2 B:DGI201 4.8 21.4 1.0 O B:HOH321 4.9 21.2 1.0 HG2 B:GLU38 4.9 18.9 1.0 HZ3 B:LYS31 4.9 20.3 1.0 HG3 B:GLU35 4.9 19.2 1.0

Manganese binding site 6 out of 12 in the Cyanophage S-2L Mazg-Like Pyrophosphohydrolase Bound to Dgdp and Three Catalytic MN2+ Ions Per Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Cyanophage S-2L Mazg-Like Pyrophosphohydrolase Bound to Dgdp and Three Catalytic MN2+ Ions Per Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn204 b:25.1 occ:0.30 O B:HOH374 2.0 28.4 1.0 OE2 B:GLU50 2.1 30.9 1.0 O C:HOH348 2.3 37.2 1.0 OE1 B:GLU38 2.3 19.0 1.0 O C:HOH303 2.3 32.8 1.0 O B:HOH321 2.6 21.2 1.0 HOB3 B:DGI201 3.0 30.3 1.0 HB3 B:GLU38 3.2 18.7 1.0 CD B:GLU50 3.2 28.3 1.0 CD B:GLU38 3.2 16.9 1.0 HB2 C:ASP89 3.5 27.6 1.0 MN B:MN202 3.6 16.7 1.0 OE1 B:GLU50 3.7 22.2 1.0 HG2 B:GLU38 3.8 18.9 1.0 CG B:GLU38 3.9 15.8 1.0 CB B:GLU38 3.9 15.6 1.0 HB3 C:ASP89 3.9 27.6 1.0 O3B B:DGI201 4.0 25.3 1.0 O B:HOH315 4.0 39.8 1.0 OE2 B:GLU38 4.2 16.8 1.0 O C:HOH324 4.2 20.4 1.0 CB C:ASP89 4.2 23.0 1.0 O B:HOH337 4.2 23.5 1.0 O1B B:DGI201 4.2 18.1 1.0 O1 C:SO4205 4.3 32.6 0.8 HB2 B:GLU38 4.3 18.7 1.0 OD2 C:ASP89 4.4 40.6 1.0 CG B:GLU50 4.5 39.7 1.0 HG3 B:GLU50 4.6 47.6 1.0 HG2 B:GLU50 4.6 47.6 1.0 PB B:DGI201 4.7 19.7 1.0 O A:HOH376 4.7 34.2 1.0 HG3 B:GLU38 4.8 18.9 1.0 O B:HOH328 4.8 18.3 1.0 CG C:ASP89 4.8 33.8 1.0 O C:HOH408 4.9 45.6 1.0

Manganese binding site 7 out of 12 in the Cyanophage S-2L Mazg-Like Pyrophosphohydrolase Bound to Dgdp and Three Catalytic MN2+ Ions Per Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Cyanophage S-2L Mazg-Like Pyrophosphohydrolase Bound to Dgdp and Three Catalytic MN2+ Ions Per Active Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn202 b:17.4 occ:1.00 OE2 C:GLU50 2.1 22.4 1.0 O1B C:DGI201 2.1 17.8 1.0 OE1 C:GLU35 2.1 17.7 1.0 OE1 C:GLU38 2.1 19.4 1.0 OD2 C:ASP53 2.2 19.9 1.0 O C:HOH340 2.4 23.3 1.0 CD C:GLU38 3.1 17.9 1.0 CD C:GLU50 3.1 26.0 1.0 CD C:GLU35 3.2 17.4 1.0 CG C:ASP53 3.3 20.8 1.0 PB C:DGI201 3.3 20.6 1.0 MN C:MN204 3.4 26.2 0.3 OE2 C:GLU38 3.5 18.8 1.0 OE1 C:GLU50 3.5 31.3 1.0 H5'' C:DGI201 3.5 24.9 1.0 OE2 C:GLU35 3.6 17.8 1.0 HOB3 C:DGI201 3.6 29.6 1.0 MN C:MN203 3.6 17.6 1.0 HB2 C:ASP53 3.7 21.1 1.0 O2B C:DGI201 3.7 22.7 1.0 HB3 C:ASP53 3.8 21.1 1.0 CB C:ASP53 3.9 17.5 1.0 O3B C:DGI201 3.9 24.7 1.0 HZ1 D:LYS76 3.9 26.5 1.0 HB2 C:GLU38 4.0 20.1 1.0 HOB2 C:DGI201 4.0 27.3 1.0 HA C:GLU50 4.2 30.5 1.0 HB3 C:GLU38 4.2 20.1 1.0 O B:HOH302 4.2 33.3 1.0 O D:HOH348 4.2 36.5 1.0 HA C:GLU35 4.3 18.3 1.0 CG C:GLU38 4.3 16.9 1.0 OD1 C:ASP53 4.3 18.3 1.0 CB C:GLU38 4.3 16.7 1.0 HZ2 D:LYS76 4.4 26.5 1.0 HZ3 D:LYS76 4.4 26.5 1.0 HG3 C:GLU50 4.4 41.0 1.0 NZ D:LYS76 4.4 22.1 1.0 CG C:GLU50 4.4 34.1 1.0 CG C:GLU35 4.5 15.8 1.0 HB3 C:GLU35 4.5 18.5 1.0 C5' C:DGI201 4.6 20.8 1.0 O3A C:DGI201 4.6 22.7 1.0 H3' C:DGI201 4.6 20.7 1.0 HG3 C:GLU35 4.7 18.9 1.0 HG3 C:GLU38 4.8 20.2 1.0 O C:HOH378 4.8 29.8 1.0 O C:HOH345 4.8 20.9 1.0 O1A C:DGI201 4.8 18.4 1.0 CB C:GLU35 4.9 15.4 1.0 H5' C:DGI201 4.9 24.9 1.0 HG2 C:GLU38 4.9 20.2 1.0

Manganese binding site 8 out of 12 in the Cyanophage S-2L Mazg-Like Pyrophosphohydrolase Bound to Dgdp and Three Catalytic MN2+ Ions Per Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Cyanophage S-2L Mazg-Like Pyrophosphohydrolase Bound to Dgdp and Three Catalytic MN2+ Ions Per Active Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn203 b:17.6 occ:1.00 O1A C:DGI201 2.0 18.4 1.0 OE2 C:GLU38 2.1 18.8 1.0 OE2 C:GLU35 2.1 17.8 1.0 O C:HOH345 2.2 20.9 1.0 OE2 C:GLU34 2.3 18.0 1.0 O1B C:DGI201 2.3 17.8 1.0 CD C:GLU35 3.1 17.4 1.0 CD C:GLU38 3.1 17.9 1.0 CD C:GLU34 3.3 17.1 1.0 HG2 C:GLU34 3.3 21.5 1.0 PB C:DGI201 3.3 20.6 1.0 PA C:DGI201 3.4 21.3 1.0 O3A C:DGI201 3.4 22.7 1.0 OE1 C:GLU35 3.4 17.7 1.0 OE1 C:GLU38 3.4 19.4 1.0 HE3 C:LYS31 3.5 24.4 1.0 H5'' C:DGI201 3.5 24.9 1.0 HH12 D:ARG94 3.5 27.8 1.0 MN C:MN202 3.6 17.4 1.0 HZ1 C:LYS31 3.6 23.2 1.0 H5' C:DGI201 3.7 24.9 1.0 CG C:GLU34 3.8 17.9 1.0 HZ2 C:LYS31 4.0 23.2 1.0 C5' C:DGI201 4.0 20.8 1.0 O C:HOH361 4.0 26.0 1.0 O3B C:DGI201 4.0 24.7 1.0 NZ C:LYS31 4.1 19.3 1.0 O5' C:DGI201 4.1 21.9 1.0 HOB3 C:DGI201 4.2 29.6 1.0 NH1 D:ARG94 4.2 23.2 1.0 HG3 C:GLU34 4.2 21.5 1.0 CE C:LYS31 4.2 20.4 1.0 HH11 D:ARG94 4.2 27.8 1.0 O B:HOH302 4.3 33.3 1.0 OE1 C:GLU34 4.3 19.3 1.0 CG C:GLU38 4.4 16.9 1.0 CG C:GLU35 4.5 15.8 1.0 HG3 C:GLU38 4.5 20.2 1.0 HG2 C:GLU35 4.5 18.9 1.0 O2A C:DGI201 4.6 22.9 1.0 O D:HOH376 4.6 28.3 1.0 HA C:GLU35 4.6 18.3 1.0 O2B C:DGI201 4.6 22.7 1.0 HE2 C:LYS31 4.7 24.4 1.0 HOA2 C:DGI201 4.8 27.5 1.0 O3 B:SO4205 4.8 37.8 0.6 HG2 C:GLU38 4.8 20.2 1.0 HZ3 C:LYS31 4.9 23.2 1.0 HG3 C:GLU35 4.9 18.9 1.0

Manganese binding site 9 out of 12 in the Cyanophage S-2L Mazg-Like Pyrophosphohydrolase Bound to Dgdp and Three Catalytic MN2+ Ions Per Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Cyanophage S-2L Mazg-Like Pyrophosphohydrolase Bound to Dgdp and Three Catalytic MN2+ Ions Per Active Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn204 b:26.2 occ:0.29 O C:HOH378 1.9 29.8 1.0 OE1 C:GLU38 2.3 19.4 1.0 O B:HOH302 2.3 33.3 1.0 O B:HOH347 2.4 43.8 1.0 O C:HOH340 2.4 23.3 1.0 OE1 C:GLU50 2.5 31.3 1.0 HOB3 C:DGI201 3.0 29.6 1.0 HB3 C:GLU38 3.1 20.1 1.0 CD C:GLU38 3.2 17.9 1.0 CD C:GLU50 3.3 26.0 1.0 MN C:MN202 3.4 17.4 1.0 HB2 B:ASP89 3.5 29.6 1.0 OE2 C:GLU50 3.5 22.4 1.0 HG2 C:GLU38 3.9 20.2 1.0 CB C:GLU38 3.9 16.7 1.0 CG C:GLU38 3.9 16.9 1.0 O3B C:DGI201 3.9 24.7 1.0 O1B C:DGI201 4.1 17.8 1.0 OE2 C:GLU38 4.1 18.8 1.0 HB3 B:ASP89 4.1 29.6 1.0 O B:HOH334 4.2 22.6 1.0 HB2 C:GLU38 4.2 20.1 1.0 CB B:ASP89 4.2 24.7 1.0 O C:HOH338 4.3 25.6 1.0 O3 B:SO4205 4.3 37.8 0.6 OD2 B:ASP89 4.3 42.2 1.0 O D:HOH348 4.6 36.5 1.0 HG2 C:GLU50 4.6 41.0 1.0 PB C:DGI201 4.6 20.6 1.0 O D:HOH359 4.6 40.6 1.0 CG C:GLU50 4.6 34.1 1.0 CG B:ASP89 4.8 38.7 1.0 HG3 C:GLU38 4.8 20.2 1.0 O C:HOH332 4.9 32.3 1.0 O C:HOH345 4.9 20.9 1.0

Manganese binding site 10 out of 12 in the Cyanophage S-2L Mazg-Like Pyrophosphohydrolase Bound to Dgdp and Three Catalytic MN2+ Ions Per Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Cyanophage S-2L Mazg-Like Pyrophosphohydrolase Bound to Dgdp and Three Catalytic MN2+ Ions Per Active Site within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn202 b:17.1 occ:1.00 OE1 D:GLU35 2.0 18.7 1.0 OE2 D:GLU50 2.1 22.8 1.0 OD2 D:ASP53 2.1 18.5 1.0 OE1 D:GLU38 2.2 20.0 1.0 O D:HOH316 2.2 22.7 1.0 O1B D:DGI201 2.3 17.5 1.0 CD D:GLU38 3.1 18.1 1.0 CD D:GLU50 3.1 31.4 1.0 CD D:GLU35 3.2 17.9 1.0 CG D:ASP53 3.2 18.1 1.0 MN D:MN204 3.3 21.6 0.2 PB D:DGI201 3.4 20.0 1.0 OE1 D:GLU50 3.5 32.2 1.0 OE2 D:GLU38 3.5 18.6 1.0 HB2 D:ASP53 3.6 18.9 1.0 H5'' D:DGI201 3.6 22.1 1.0 HB3 D:ASP53 3.6 18.9 1.0 MN D:MN203 3.6 16.6 1.0 OE2 D:GLU35 3.7 17.7 1.0 CB D:ASP53 3.7 15.8 1.0 O2B D:DGI201 3.7 22.3 1.0 HZ1 C:LYS76 3.9 22.9 1.0 O C:HOH350 3.9 37.0 1.0 O3B D:DGI201 4.0 23.0 1.0 HB2 D:GLU38 4.0 20.6 1.0 HA D:GLU50 4.1 28.2 1.0 O D:HOH305 4.1 35.4 1.0 HOB2 D:DGI201 4.1 26.8 1.0 HB3 D:GLU38 4.2 20.6 1.0 HB3 D:GLU35 4.2 18.0 1.0 HA D:GLU35 4.2 17.3 1.0 OD1 D:ASP53 4.3 17.1 1.0 HZ2 C:LYS76 4.3 22.9 1.0 CG D:GLU38 4.3 17.4 1.0 HOB3 D:DGI201 4.4 27.6 1.0 HZ3 C:LYS76 4.4 22.9 1.0 CB D:GLU38 4.4 17.1 1.0 CG D:GLU35 4.4 14.9 1.0 NZ C:LYS76 4.4 19.1 1.0 CG D:GLU50 4.5 33.3 1.0 HG3 D:GLU50 4.5 40.0 1.0 HG3 D:GLU35 4.6 17.8 1.0 C5' D:DGI201 4.6 18.4 1.0 H3' D:DGI201 4.7 18.4 1.0 CB D:GLU35 4.7 15.0 1.0 O3A D:DGI201 4.7 21.4 1.0 HG3 D:GLU38 4.8 20.9 1.0 H5' D:DGI201 4.8 22.1 1.0 O1A D:DGI201 4.9 18.4 1.0 CA D:GLU35 4.9 14.4 1.0 HG2 D:GLU38 5.0 20.9 1.0 O A:HOH346 5.0 19.1 1.0 CA D:GLU50 5.0 23.5 1.0

D.Czernecki, F.Bonhomme, P.A.Kaminski, M.Delarue. Characterization of A Triad of Genes in Cyanophage S-2L Sufficient to Replace Adenine By 2-Aminoadenine in Bacterial Dna. Nat Commun V. 12 4710 2021.
ISSN: ESSN 2041-1723
PubMed: 34354070
DOI: 10.1038/S41467-021-25064-X