Manganese in PDB 5o5k: X-Ray Structure of A Bacterial Adenylyl Cyclase Soluble Domain

All present enzymatic activity of X-Ray Structure of A Bacterial Adenylyl Cyclase Soluble Domain:
4.6.1.1;

The structure of X-Ray Structure of A Bacterial Adenylyl Cyclase Soluble Domain, PDB code: 5o5k was solved by I.Vercellino, V.M.Korkhov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.30 / 3.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	145.420, 85.690, 318.010, 90.00, 103.77, 90.00
R / Rfree (%)	24.5 / 26.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Manganese atom in the X-Ray Structure of A Bacterial Adenylyl Cyclase Soluble Domain (pdb code 5o5k). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 22 binding sites of Manganese where determined in the X-Ray Structure of A Bacterial Adenylyl Cyclase Soluble Domain, PDB code: 5o5k:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 22 in the X-Ray Structure of A Bacterial Adenylyl Cyclase Soluble Domain


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Structure of A Bacterial Adenylyl Cyclase Soluble Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:67.8 occ:1.00 O3B A:ONM501 1.8 86.5 1.0 OD1 A:ASP256 2.0 70.6 1.0 OD2 A:ASP300 2.0 70.1 1.0 O3G A:ONM501 2.3 91.8 1.0 O A:ILE257 2.4 48.5 1.0 O2A A:ONM501 2.5 83.9 1.0 PB A:ONM501 3.1 82.5 1.0 CG A:ASP256 3.1 68.0 1.0 PG A:ONM501 3.2 94.0 1.0 CG A:ASP300 3.3 75.0 1.0 O2G A:ONM501 3.3 97.8 1.0 O1B A:ONM501 3.6 87.2 1.0 C A:ILE257 3.6 49.4 1.0 PA A:ONM501 3.6 80.2 1.0 OD2 A:ASP256 3.7 72.3 1.0 O1A A:ONM501 3.7 79.2 1.0 MN A:MN503 3.8 0.6 1.0 CB A:ASP300 4.0 64.9 1.0 N A:ILE257 4.2 44.0 1.0 CB A:PHE260 4.2 61.7 1.0 OD1 A:ASP300 4.2 80.1 1.0 O2B A:ONM501 4.3 78.5 1.0 CB A:ASP256 4.4 65.0 1.0 C5' A:ONM501 4.4 75.0 1.0 N A:PHE260 4.4 67.9 1.0 CA A:ILE257 4.5 47.1 1.0 N A:GLY259 4.5 98.2 1.0 O1G A:ONM501 4.6 96.3 1.0 N A:VAL258 4.6 81.9 1.0 C A:ASP256 4.6 72.7 1.0 CA A:VAL258 4.6 83.8 1.0 O5' A:ONM501 4.7 76.9 1.0 O3A A:ONM501 4.7 74.4 1.0 C A:VAL258 4.8 88.4 1.0 CA A:ASP256 4.9 65.8 1.0 CB A:ILE257 4.9 46.9 1.0 CA A:PHE260 5.0 66.0 1.0

Manganese binding site 2 out of 22 in the X-Ray Structure of A Bacterial Adenylyl Cyclase Soluble Domain


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Structure of A Bacterial Adenylyl Cyclase Soluble Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:0.6 occ:1.00 O2A A:ONM501 2.3 83.9 1.0 OD2 A:ASP256 2.5 72.3 1.0 PA A:ONM501 3.4 80.2 1.0 CB A:ASP300 3.4 64.9 1.0 CG A:ASP256 3.4 68.0 1.0 O3A A:ONM501 3.5 74.4 1.0 OD1 A:ASP256 3.6 70.6 1.0 MN A:MN502 3.8 67.8 1.0 OD2 A:ASP300 3.9 70.1 1.0 O5' A:ONM501 3.9 76.9 1.0 CG A:ASP300 4.1 75.0 1.0 OG A:SER301 4.1 71.7 1.0 N A:SER301 4.2 65.7 1.0 CA A:ASP300 4.2 62.5 1.0 C A:ASP300 4.2 61.2 1.0 O3G A:ONM501 4.3 91.8 1.0 C5' A:ONM501 4.3 75.0 1.0 N A:ASP300 4.4 63.1 1.0 O A:SER298 4.4 53.6 1.0 O4' A:ONM501 4.4 66.9 1.0 C8 A:ONM501 4.6 67.5 1.0 CB A:ASP256 4.7 65.0 1.0 CB A:SER301 4.8 65.0 1.0 O1A A:ONM501 4.8 79.2 1.0 O3B A:ONM501 4.8 86.5 1.0 CA A:SER301 4.9 64.0 1.0 O A:ASP300 4.9 59.4 1.0

Manganese binding site 3 out of 22 in the X-Ray Structure of A Bacterial Adenylyl Cyclase Soluble Domain


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Structure of A Bacterial Adenylyl Cyclase Soluble Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn503 b:88.4 occ:1.00 OD2 B:ASP300 1.7 83.6 1.0 O3B B:ONM501 1.9 86.5 1.0 OD1 B:ASP256 2.1 65.9 1.0 O2A B:ONM501 2.2 83.2 1.0 O2G B:ONM501 2.4 80.7 1.0 O B:ILE257 2.5 46.6 1.0 CG B:ASP300 2.9 83.1 1.0 PB B:ONM501 3.1 87.1 1.0 CG B:ASP256 3.3 63.6 1.0 PA B:ONM501 3.3 80.9 1.0 O1A B:ONM501 3.6 84.1 1.0 PG B:ONM501 3.6 83.0 1.0 CB B:ASP300 3.7 69.2 1.0 C B:ILE257 3.7 48.9 1.0 O1B B:ONM501 3.8 87.0 1.0 OD2 B:ASP256 3.9 61.8 1.0 OD1 B:ASP300 3.9 88.8 1.0 N B:ILE257 4.1 45.6 1.0 O5' B:ONM501 4.1 76.2 1.0 MN B:MN504 4.2 0.9 1.0 NH2 B:ARG344 4.3 85.9 1.0 O2B B:ONM501 4.3 89.5 1.0 CA B:ILE257 4.4 48.5 1.0 CB B:ASP256 4.4 60.7 1.0 C B:ASP256 4.5 66.7 1.0 O1G B:ONM501 4.6 79.0 1.0 O3G B:ONM501 4.6 84.3 1.0 CB B:PHE260 4.6 63.4 1.0 O3A B:ONM501 4.6 82.1 1.0 N B:VAL258 4.7 85.3 1.0 CB B:ILE257 4.8 48.8 1.0 CA B:ASP256 4.9 62.2 1.0 C5' B:ONM501 4.9 74.7 1.0 NH1 B:ARG344 4.9 69.7 1.0 N B:PHE260 5.0 65.0 1.0 CA B:VAL258 5.0 86.3 1.0

Manganese binding site 4 out of 22 in the X-Ray Structure of A Bacterial Adenylyl Cyclase Soluble Domain


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of X-Ray Structure of A Bacterial Adenylyl Cyclase Soluble Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn504 b:0.9 occ:1.00 O2A B:ONM501 2.8 83.2 1.0 OD2 B:ASP256 2.8 61.8 1.0 CB B:ASP300 3.6 69.2 1.0 CG B:ASP256 3.7 63.6 1.0 PA B:ONM501 3.7 80.9 1.0 OD1 B:ASP256 3.8 65.9 1.0 C5' B:ONM501 3.9 74.7 1.0 O3A B:ONM501 3.9 82.1 1.0 MN B:MN503 4.2 88.4 1.0 O5' B:ONM501 4.2 76.2 1.0 OD2 B:ASP300 4.2 83.6 1.0 CG B:ASP300 4.4 83.1 1.0 CA B:ASP300 4.6 68.3 1.0 N B:ASP300 4.6 65.8 1.0 N3 B:ONM501 4.6 78.4 1.0 N B:SER301 4.7 57.7 1.0 N2 B:ONM501 4.8 70.5 1.0 C2 B:ONM501 4.8 75.1 1.0 C B:ASP300 4.8 69.8 1.0 CB B:SER301 4.8 57.1 1.0

Manganese binding site 5 out of 22 in the X-Ray Structure of A Bacterial Adenylyl Cyclase Soluble Domain


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of X-Ray Structure of A Bacterial Adenylyl Cyclase Soluble Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn502 b:79.7 occ:1.00 O3B D:ONM501 1.7 80.5 1.0 OD1 D:ASP256 2.0 74.8 1.0 O D:ILE257 2.0 63.6 1.0 OD2 D:ASP300 2.1 52.2 1.0 O3G D:ONM501 2.6 86.2 1.0 O2G D:ONM501 2.8 92.6 1.0 O2A D:ONM501 3.0 78.2 1.0 PB D:ONM501 3.1 75.6 1.0 PG D:ONM501 3.1 88.2 1.0 CG D:ASP256 3.1 74.8 1.0 C D:ILE257 3.2 65.7 1.0 CG D:ASP300 3.3 58.5 1.0 O1A D:ONM501 3.7 72.0 1.0 OD2 D:ASP256 3.7 80.5 1.0 O1B D:ONM501 3.8 80.4 1.0 PA D:ONM501 3.9 73.5 1.0 N D:ILE257 3.9 61.9 1.0 MN D:MN503 3.9 0.7 1.0 CB D:ASP300 4.0 48.8 1.0 CA D:ILE257 4.1 63.2 1.0 N D:VAL258 4.2 77.0 1.0 O2B D:ONM501 4.2 70.9 1.0 CB D:ASP256 4.3 72.8 1.0 C D:ASP256 4.3 77.4 1.0 CA D:VAL258 4.3 76.8 1.0 CB D:PHE260 4.3 49.6 1.0 OD1 D:ASP300 4.4 64.5 1.0 N D:GLY259 4.4 60.2 1.0 N D:PHE260 4.5 51.4 1.0 O1G D:ONM501 4.5 90.5 1.0 CB D:ILE257 4.6 63.3 1.0 C D:VAL258 4.6 79.0 1.0 O5' D:ONM501 4.7 69.7 1.0 CA D:ASP256 4.8 73.5 1.0 O D:ASP256 4.8 79.7 1.0 C5' D:ONM501 4.9 67.4 1.0

Manganese binding site 6 out of 22 in the X-Ray Structure of A Bacterial Adenylyl Cyclase Soluble Domain


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of X-Ray Structure of A Bacterial Adenylyl Cyclase Soluble Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn503 b:0.7 occ:1.00 O2A D:ONM501 2.0 78.2 1.0 OD2 D:ASP256 2.3 80.5 1.0 CB D:ASP300 3.1 48.8 1.0 CG D:ASP256 3.1 74.8 1.0 PA D:ONM501 3.3 73.5 1.0 OD1 D:ASP256 3.4 74.8 1.0 O5' D:ONM501 3.6 69.7 1.0 O3A D:ONM501 3.8 67.5 1.0 MN D:MN502 3.9 79.7 1.0 OD2 D:ASP300 3.9 52.2 1.0 CG D:ASP300 4.0 58.5 1.0 CA D:ASP300 4.0 49.9 1.0 N D:ASP300 4.1 49.1 1.0 N D:SER301 4.1 65.9 1.0 O3G D:ONM501 4.2 86.2 1.0 C D:ASP300 4.2 53.3 1.0 O D:SER298 4.3 64.1 1.0 O4' D:ONM501 4.4 59.8 1.0 CB D:SER301 4.4 69.0 1.0 CB D:ASP256 4.5 72.8 1.0 C5' D:ONM501 4.6 67.4 1.0 O1A D:ONM501 4.6 72.0 1.0 CA D:SER301 4.8 68.2 1.0 C8 D:ONM501 4.8 60.5 1.0 O3B D:ONM501 4.9 80.5 1.0 OG D:SER301 5.0 77.2 1.0

Manganese binding site 7 out of 22 in the X-Ray Structure of A Bacterial Adenylyl Cyclase Soluble Domain


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of X-Ray Structure of A Bacterial Adenylyl Cyclase Soluble Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn504 b:68.9 occ:1.00 OD2 C:ASP300 1.6 67.4 1.0 OD1 C:ASP256 1.9 79.6 1.0 O3B C:ONM501 2.0 82.7 1.0 O C:ILE257 2.1 51.8 1.0 O2G C:ONM501 2.2 76.8 1.0 O2A C:ONM501 2.4 79.9 1.0 CG C:ASP300 2.8 67.1 1.0 CG C:ASP256 3.0 76.3 1.0 C C:ILE257 3.3 54.1 1.0 PB C:ONM501 3.3 83.2 1.0 OD2 C:ASP256 3.5 74.3 1.0 PA C:ONM501 3.6 77.6 1.0 PG C:ONM501 3.6 78.9 1.0 OD1 C:ASP300 3.6 72.7 1.0 N C:ILE257 3.8 49.5 1.0 CB C:ASP300 3.9 53.7 1.0 O5' C:ONM501 3.9 73.2 1.0 O1B C:ONM501 3.9 83.0 1.0 O1A C:ONM501 3.9 80.5 1.0 CA C:ILE257 4.0 53.4 1.0 CB C:ASP256 4.3 72.9 1.0 N C:VAL258 4.3 78.7 1.0 C C:ASP256 4.4 80.0 1.0 O3G C:ONM501 4.5 79.9 1.0 CB C:ILE257 4.5 54.4 1.0 CA C:VAL258 4.5 78.8 1.0 O1G C:ONM501 4.5 74.8 1.0 CB C:PHE260 4.5 51.7 1.0 O2B C:ONM501 4.5 85.6 1.0 MN C:MN505 4.6 0.1 1.0 NH2 C:ARG344 4.6 73.1 1.0 N C:GLY259 4.6 88.6 1.0 CA C:ASP256 4.8 74.2 1.0 N C:PHE260 4.8 54.0 1.0 C C:VAL258 4.8 83.5 1.0 O3A C:ONM501 4.9 78.9 1.0

Manganese binding site 8 out of 22 in the X-Ray Structure of A Bacterial Adenylyl Cyclase Soluble Domain


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of X-Ray Structure of A Bacterial Adenylyl Cyclase Soluble Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn505 b:0.1 occ:1.00 OD2 C:ASP256 2.9 74.3 1.0 O2A C:ONM501 3.0 79.9 1.0 O3A C:ONM501 3.6 78.9 1.0 PA C:ONM501 3.7 77.6 1.0 C5' C:ONM501 3.8 71.8 1.0 CB C:ASP300 3.9 53.7 1.0 O5' C:ONM501 3.9 73.2 1.0 CG C:ASP256 4.0 76.3 1.0 OD2 C:ASP300 4.1 67.4 1.0 OD1 C:ASP256 4.3 79.6 1.0 CG C:ASP300 4.5 67.1 1.0 MN C:MN504 4.6 68.9 1.0 CB C:SER301 4.6 58.8 1.0 N C:ASP300 4.7 51.4 1.0 N C:SER301 4.7 60.7 1.0 N3 C:ONM501 4.7 75.8 1.0 CA C:ASP300 4.7 52.6 1.0 C2 C:ONM501 4.9 72.4 1.0 C C:ASP300 4.9 51.5 1.0 N2 C:ONM501 5.0 67.7 1.0 O C:SER298 5.0 50.0 1.0 C4' C:ONM501 5.0 71.7 1.0

Manganese binding site 9 out of 22 in the X-Ray Structure of A Bacterial Adenylyl Cyclase Soluble Domain


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of X-Ray Structure of A Bacterial Adenylyl Cyclase Soluble Domain within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn502 b:0.6 occ:1.00 O3B E:ONM501 2.1 1.0 1.0 OD1 E:ASP256 2.2 0.3 1.0 OD2 E:ASP300 2.2 0.5 1.0 O E:ILE257 2.2 0.8 1.0 PB E:ONM501 3.0 0.6 1.0 O3G E:ONM501 3.0 0.8 1.0 O1B E:ONM501 3.1 1.0 1.0 O2G E:ONM501 3.2 0.5 1.0 CG E:ASP256 3.2 0.6 1.0 CG E:ASP300 3.3 0.4 1.0 PG E:ONM501 3.3 0.3 1.0 O2A E:ONM501 3.4 0.5 1.0 C E:ILE257 3.4 0.5 1.0 MN E:MN503 3.6 1.0 1.0 OD2 E:ASP256 3.7 0.9 1.0 O1A E:ONM501 3.7 0.2 1.0 CB E:ASP300 3.9 0.4 1.0 N E:ILE257 4.0 99.9 1.0 PA E:ONM501 4.0 0.7 1.0 CA E:ILE257 4.2 0.0 1.0 O2B E:ONM501 4.3 0.4 1.0 OD1 E:ASP300 4.3 0.1 1.0 N E:VAL258 4.4 0.1 1.0 C E:ASP256 4.4 0.5 1.0 CB E:ASP256 4.5 0.6 1.0 C5' E:ONM501 4.5 0.1 1.0 CB E:PHE260 4.5 0.3 1.0 CA E:VAL258 4.6 0.9 1.0 N E:PHE260 4.6 0.6 1.0 N E:GLY259 4.6 0.6 1.0 O5' E:ONM501 4.7 0.6 1.0 CB E:ILE257 4.7 1.0 1.0 O1G E:ONM501 4.8 0.0 1.0 CA E:ASP256 4.9 0.6 1.0 C E:VAL258 4.9 0.3 1.0 O E:ASP256 4.9 0.1 1.0

Manganese binding site 10 out of 22 in the X-Ray Structure of A Bacterial Adenylyl Cyclase Soluble Domain


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of X-Ray Structure of A Bacterial Adenylyl Cyclase Soluble Domain within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn503 b:1.0 occ:1.00 O2A E:ONM501 2.2 0.5 1.0 CB E:ASP300 2.4 0.4 1.0 OD2 E:ASP256 3.1 0.9 1.0 CA E:ASP300 3.3 0.8 1.0 O4' E:ONM501 3.4 0.2 1.0 PA E:ONM501 3.4 0.7 1.0 CG E:ASP300 3.5 0.4 1.0 O5' E:ONM501 3.5 0.6 1.0 C E:ASP300 3.6 0.4 1.0 OD2 E:ASP300 3.6 0.5 1.0 MN E:MN502 3.6 0.6 1.0 N E:ASP300 3.6 0.7 1.0 N E:SER301 3.7 0.6 1.0 CG E:ASP256 3.8 0.6 1.0 OD1 E:ASP256 3.9 0.3 1.0 C5' E:ONM501 4.1 0.1 1.0 O E:ASP300 4.2 0.3 1.0 C4' E:ONM501 4.3 1.0 1.0 O3B E:ONM501 4.3 1.0 1.0 O3A E:ONM501 4.4 1.0 1.0 O3G E:ONM501 4.4 0.8 1.0 O E:SER298 4.5 0.5 1.0 CB E:SER301 4.5 0.1 1.0 CA E:SER301 4.5 0.3 1.0 C8 E:ONM501 4.6 0.4 1.0 O1A E:ONM501 4.6 0.2 1.0 OD1 E:ASP300 4.6 0.1 1.0 C1' E:ONM501 4.7 0.5 1.0 C E:GLY299 5.0 0.1 1.0

I.Vercellino, L.Rezabkova, V.Olieric, Y.Polyhach, T.Weinert, R.A.Kammerer, G.Jeschke, V.M.Korkhov. Role of the Nucleotidyl Cyclase Helical Domain in Catalytically Active Dimer Formation. Proc. Natl. Acad. Sci. V. 114 E9821 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29087332
DOI: 10.1073/PNAS.1712621114