Manganese in PDB 8c4o: Cdaa-Atp Complex

All present enzymatic activity of Cdaa-Atp Complex:
2.7.7.85;

The structure of Cdaa-Atp Complex, PDB code: 8c4o was solved by P.Neumann, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.73 / 1.97
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.5, 64.65, 129.39, 90, 90, 90
R / Rfree (%)	23.5 / 25.4

The structure of Cdaa-Atp Complex also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Magnesium	(Mg)	1 atom

The binding sites of Manganese atom in the Cdaa-Atp Complex (pdb code 8c4o). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Cdaa-Atp Complex, PDB code: 8c4o:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Cdaa-Atp Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Cdaa-Atp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:94.9 occ:1.00 ND1 A:HIS11 2.5 71.9 1.0 HB2 A:HIS11 3.2 81.8 1.0 CE1 A:HIS11 3.4 75.6 1.0 OE1 A:GLU14 3.4 83.2 1.0 HA A:HIS11 3.5 79.8 1.0 CG A:HIS11 3.5 71.8 1.0 HE1 A:HIS11 3.5 90.7 1.0 CB A:HIS11 3.7 68.2 1.0 CA A:HIS11 4.1 66.5 1.0 NE2 A:HIS11 4.6 73.7 1.0 CD2 A:HIS11 4.6 71.3 1.0 HB3 A:HIS11 4.6 81.8 1.0 CD A:GLU14 4.7 86.2 1.0 HB2 A:GLU14 4.7 83.1 1.0 N A:HIS11 5.0 65.5 1.0

Manganese binding site 2 out of 3 in the Cdaa-Atp Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Cdaa-Atp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:93.1 occ:1.00 O A:HOH309 1.9 75.3 1.0 O A:HOH305 2.0 83.6 1.0 NE2 A:HIS70 2.2 79.3 1.0 CE1 A:HIS70 3.0 78.7 1.0 HE1 A:HIS70 3.0 94.5 1.0 CD2 A:HIS70 3.4 76.3 1.0 HD2 A:HIS70 3.7 91.6 1.0 H A:ASN66 3.7 94.8 1.0 OD1 A:ASP71 4.1 103.0 1.0 HO3' A:ATP203 4.2 92.8 1.0 ND1 A:HIS70 4.2 74.2 1.0 HB2 A:ASP71 4.2 102.6 1.0 OD1 A:ASN66 4.3 88.6 1.0 CG A:HIS70 4.4 74.3 1.0 HA A:ASN66 4.5 97.0 1.0 N A:ASN66 4.5 79.0 1.0 HB3 A:PRO65 4.6 93.5 1.0 O A:HOH310 4.7 86.5 1.0 HA A:PRO65 4.8 88.7 1.0 HH22 A:ARG103 4.8 89.5 1.0 H3' A:ATP203 4.9 98.4 1.0 HD1 A:HIS70 4.9 89.0 1.0 HA A:ASP71 5.0 96.8 1.0 CB A:ASP71 5.0 85.5 1.0 CG A:ASP71 5.0 99.3 1.0

Manganese binding site 3 out of 3 in the Cdaa-Atp Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Cdaa-Atp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn204 b:89.5 occ:1.00 NE2 B:HIS70 2.2 76.5 1.0 O B:HOH317 2.2 75.1 1.0 O B:HOH303 2.2 77.6 1.0 CE1 B:HIS70 3.1 72.8 1.0 CD2 B:HIS70 3.1 69.7 1.0 HE1 B:HIS70 3.3 87.4 1.0 HD2 B:HIS70 3.3 83.6 1.0 H B:ASN66 3.6 91.7 1.0 OD1 B:ASN66 4.0 94.3 1.0 ND1 B:HIS70 4.2 68.1 1.0 HA B:ASN66 4.3 94.9 1.0 CG B:HIS70 4.3 67.5 1.0 N B:ASN66 4.4 76.4 1.0 HA B:PRO65 4.6 81.6 1.0 HB3 B:PRO65 4.7 83.5 1.0 O3' B:ATP201 4.7 82.9 1.0 HO3' B:ATP201 4.8 99.5 1.0 CA B:ASN66 4.9 79.1 1.0

P.Neumann, P.Kloskowski, R.Ficner. Computer-Aided Design of A Cyclic Di-Amp Synthesizing Enzyme Cdaa Inhibitor. Microlife V. 4 AD021 2023.
ISSN: ISSN 2633-6693
PubMed: 37223749
DOI: 10.1093/FEMSML/UQAD021