Manganese in PDB 5xd2: Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with AP5A, Atp and Manganese

The structure of Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with AP5A, Atp and Manganese, PDB code: 5xd2 was solved by S.M.Arif, U.Varshney, M.Vijayan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.55 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.160, 83.930, 43.640, 90.00, 93.63, 90.00
R / Rfree (%)	17.8 / 22.8

The binding sites of Manganese atom in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with AP5A, Atp and Manganese (pdb code 5xd2). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with AP5A, Atp and Manganese, PDB code: 5xd2:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with AP5A, Atp and Manganese


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 Mycobacterium Smegmatis MUTT1 in Complex with AP5A, Atp and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn404 b:26.0 occ:1.00 OE2 A:GLU85 2.1 21.9 1.0 O1G A:5FA401 2.1 25.5 1.0 O1D A:5FA401 2.1 31.3 1.0 O A:LYS65 2.2 20.3 1.0 O A:HOH555 2.2 20.9 1.0 O A:HOH516 2.2 24.7 1.0 CD A:GLU85 3.1 18.8 1.0 MN A:MN405 3.2 44.5 1.0 PG A:5FA401 3.3 26.6 1.0 PD A:5FA401 3.3 45.3 1.0 C A:LYS65 3.4 24.3 1.0 OE1 A:GLU85 3.4 19.5 1.0 O3G A:5FA401 3.6 31.8 1.0 NH2 A:ARG55 3.8 22.8 1.0 OE1 A:GLU127 3.9 30.8 1.0 CA A:GLY66 4.0 20.5 1.0 O3B A:5FA401 4.0 29.6 1.0 N A:GLY66 4.1 20.0 1.0 O3D A:5FA401 4.2 45.5 1.0 OE1 A:GLU81 4.2 24.8 1.0 N A:LYS65 4.3 25.4 1.0 OE2 A:GLU127 4.4 46.7 1.0 CA A:LYS65 4.4 24.4 1.0 CG A:GLU85 4.5 19.1 1.0 NZ A:LYS65 4.5 32.1 1.0 CD A:GLU127 4.6 47.1 1.0 O A:HOH559 4.6 44.4 1.0 O2G A:5FA401 4.6 30.6 1.0 O2D A:5FA401 4.6 33.5 1.0 CG A:LYS65 4.6 26.6 1.0 O A:HOH558 4.7 19.8 1.0 CD A:LYS65 4.9 30.1 1.0 CZ A:ARG55 4.9 24.7 1.0 CD A:ARG55 4.9 22.5 1.0 O2E A:5FA401 5.0 63.1 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with AP5A, Atp and Manganese


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 Mycobacterium Smegmatis MUTT1 in Complex with AP5A, Atp and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn405 b:44.5 occ:1.00 O1D A:5FA401 2.1 31.3 1.0 OE2 A:GLU85 2.2 21.9 1.0 OE1 A:GLU81 2.2 24.8 1.0 O A:HOH553 2.3 35.6 1.0 OE1 A:GLU127 2.6 30.8 1.0 O2E A:5FA401 2.8 63.1 1.0 CD A:GLU85 3.2 18.8 1.0 MN A:MN404 3.2 26.0 1.0 CD A:GLU81 3.3 25.6 1.0 PD A:5FA401 3.3 45.3 1.0 CG A:GLU85 3.5 19.1 1.0 MN A:MN406 3.6 36.8 0.5 OE2 A:GLU81 3.7 29.1 1.0 O A:HOH516 3.7 24.7 1.0 PE A:5FA401 3.8 66.7 1.0 O A:HOH614 3.8 52.1 1.0 CD A:GLU127 3.8 47.1 1.0 O3D A:5FA401 3.9 45.5 1.0 O A:LYS65 4.0 20.3 1.0 O1E A:5FA401 4.0 66.6 1.0 O2D A:5FA401 4.1 33.5 1.0 OE1 A:GLU85 4.3 19.5 1.0 OE2 A:GLU127 4.5 46.7 1.0 CG A:GLU81 4.6 24.0 1.0 OE2 A:GLU84 4.6 30.0 1.0 CA A:GLY66 4.7 20.5 1.0 O3G A:5FA401 4.7 31.8 1.0 CB A:GLU81 4.8 22.3 1.0 O A:HOH555 4.8 20.9 1.0 O1G A:5FA401 4.9 25.5 1.0 C A:LYS65 4.9 24.3 1.0 CG A:GLU127 4.9 46.4 1.0 CB A:GLU85 5.0 17.9 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with AP5A, Atp and Manganese


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 Mycobacterium Smegmatis MUTT1 in Complex with AP5A, Atp and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn406 b:36.8 occ:0.50 O A:HOH573 2.1 38.6 1.0 OE2 A:GLU81 2.3 29.1 1.0 O2D A:5FA401 2.3 33.5 1.0 O2E A:5FA401 2.4 63.1 1.0 O A:HOH661 2.7 51.3 1.0 PD A:5FA401 3.2 45.3 1.0 CD A:GLU81 3.2 25.6 1.0 PE A:5FA401 3.5 66.7 1.0 OE1 A:GLU81 3.5 24.8 1.0 O1D A:5FA401 3.6 31.3 1.0 MN A:MN405 3.6 44.5 1.0 O3D A:5FA401 3.7 45.5 1.0 O3E A:5FA401 3.9 71.1 1.0 O A:HOH553 4.1 35.6 1.0 NH1 A:ARG80 4.2 27.5 1.0 N A:LYS67 4.3 21.2 1.0 O A:LYS67 4.4 22.7 1.0 OE2 A:GLU84 4.5 30.0 1.0 CG A:GLU81 4.6 24.0 1.0 O3G A:5FA401 4.6 31.8 1.0 CA A:GLY66 4.7 20.5 1.0 NH2 A:ARG80 4.7 26.2 1.0 O1E A:5FA401 4.9 66.6 1.0 CZ A:ARG80 5.0 24.8 1.0 C A:GLY66 5.0 22.3 1.0

S.M.Arif, U.Varshney, M.Vijayan. Hydrolysis of Diadenosine Polyphosphates. Exploration of An Additional Role of Mycobacterium Smegmatis MUTT1 J. Struct. Biol. V. 199 165 2017.
ISSN: ESSN 1095-8657
PubMed: 28705712
DOI: 10.1016/J.JSB.2017.07.002