Manganese in PDB 7yz9: Structure of Catalytic Domain of RV1625C Bound to Nanobody NB4

All present enzymatic activity of Structure of Catalytic Domain of RV1625C Bound to Nanobody NB4:
4.6.1.1;

The structure of Structure of Catalytic Domain of RV1625C Bound to Nanobody NB4, PDB code: 7yz9 was solved by B.Khanppnavar, V.J.Mehta, T.Iype, V.M.Korkhov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.07 / 1.97
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	94.793, 94.793, 119.655, 90, 90, 120
R / Rfree (%)	20.6 / 24.4

The binding sites of Manganese atom in the Structure of Catalytic Domain of RV1625C Bound to Nanobody NB4 (pdb code 7yz9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Structure of Catalytic Domain of RV1625C Bound to Nanobody NB4, PDB code: 7yz9:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Structure of Catalytic Domain of RV1625C Bound to Nanobody NB4


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Catalytic Domain of RV1625C Bound to Nanobody NB4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:48.6 occ:1.00 OD1 A:ASP60 1.8 38.9 1.0 O3G A:ONM306 2.0 41.9 1.0 O A:ILE61 2.1 42.2 1.0 O2B A:ONM306 2.3 47.4 1.0 O2A A:ONM306 2.8 40.0 1.0 CG A:ASP60 2.9 39.0 1.0 OD2 A:ASP104 3.1 51.7 1.0 C A:ILE61 3.2 42.1 1.0 O A:HOH440 3.3 42.0 1.0 PG A:ONM306 3.4 44.8 1.0 OD2 A:ASP60 3.4 40.9 1.0 PB A:ONM306 3.5 42.7 1.0 N A:ILE61 3.6 37.7 1.0 O1B A:ONM306 3.8 44.3 1.0 MN A:MN303 3.8 44.2 1.0 O2G A:ONM306 3.9 42.7 1.0 PA A:ONM306 3.9 43.0 1.0 CA A:ILE61 3.9 39.1 1.0 O1A A:ONM306 4.0 42.5 1.0 CG A:ASP104 4.0 49.2 1.0 C A:ASP60 4.0 34.9 1.0 OD1 A:ASP104 4.1 46.4 1.0 N A:VAL62 4.1 41.2 1.0 CB A:ASP60 4.1 33.4 1.0 CA A:VAL62 4.4 39.7 1.0 O1G A:ONM306 4.4 44.1 1.0 O A:ASP60 4.5 35.5 1.0 CA A:ASP60 4.5 33.2 1.0 CB A:ILE61 4.6 39.6 1.0 N A:GLY63 4.6 40.4 1.0 O3A A:ONM306 4.7 43.5 1.0 O3B A:ONM306 4.8 44.3 1.0 C A:VAL62 4.8 40.9 1.0 NH1 A:ARG148 4.9 36.2 1.0 CB A:PHE64 5.0 43.9 1.0

Manganese binding site 2 out of 3 in the Structure of Catalytic Domain of RV1625C Bound to Nanobody NB4


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Catalytic Domain of RV1625C Bound to Nanobody NB4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:109.7 occ:1.00 OD1 A:ASP81 3.2 65.0 1.0 O A:HOH465 4.4 65.5 1.0 CG A:ASP81 4.4 64.5 1.0 OG A:SER85 4.4 47.0 1.0

Manganese binding site 3 out of 3 in the Structure of Catalytic Domain of RV1625C Bound to Nanobody NB4


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Catalytic Domain of RV1625C Bound to Nanobody NB4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:44.2 occ:1.00 OD2 A:ASP60 2.2 40.9 1.0 O2A A:ONM306 2.5 40.0 1.0 OD1 A:ASP104 2.7 46.4 1.0 CG A:ASP60 3.2 39.0 1.0 PA A:ONM306 3.5 43.0 1.0 OD1 A:ASP60 3.6 38.9 1.0 CG A:ASP104 3.7 49.2 1.0 MN A:MN301 3.8 48.6 1.0 O3A A:ONM306 3.8 43.5 1.0 OD2 A:ASP104 4.0 51.7 1.0 O5' A:ONM306 4.1 45.7 1.0 CB A:SER105 4.4 48.5 1.0 CB A:ASP60 4.4 33.4 1.0 C A:ASP104 4.6 42.1 1.0 N A:SER105 4.6 43.8 1.0 O A:ASP104 4.7 36.3 1.0 O2B A:ONM306 4.8 47.4 1.0 O1A A:ONM306 4.8 42.5 1.0 CA A:SER105 4.9 44.4 1.0 C5' A:ONM306 4.9 49.0 1.0 O3G A:ONM306 4.9 41.9 1.0 CB A:ASP104 5.0 46.4 1.0 OG A:SER105 5.0 56.1 1.0

V.Mehta, B.Khanppnavar, D.Schuster, I.Kantarci, I.Vercellino, A.Kosturanova, T.Iype, S.Stefanic, P.Picotti, V.M.Korkhov. Structure of Mycobacterium Tuberculosis Cya, An Evolutionary Ancestor of the Mammalian Membrane Adenylyl Cyclases. Elife V. 11 2022.
ISSN: ESSN 2050-084X
PubMed: 35980026
DOI: 10.7554/ELIFE.77032