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Manganese in PDB 1dah: Dethiobiotin Synthetase Complexed with 7,8-Diamino-Nonanoic Acid, 5'-Adenosyl-Methylene-Triphosphate, and Manganese

Enzymatic activity of Dethiobiotin Synthetase Complexed with 7,8-Diamino-Nonanoic Acid, 5'-Adenosyl-Methylene-Triphosphate, and Manganese

All present enzymatic activity of Dethiobiotin Synthetase Complexed with 7,8-Diamino-Nonanoic Acid, 5'-Adenosyl-Methylene-Triphosphate, and Manganese:
6.3.3.3;

Protein crystallography data

The structure of Dethiobiotin Synthetase Complexed with 7,8-Diamino-Nonanoic Acid, 5'-Adenosyl-Methylene-Triphosphate, and Manganese, PDB code: 1dah was solved by W.Huang, J.Jia, G.Schneider, Y.Lindqvist, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 1.64
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 73.200, 49.200, 61.800, 90.00, 107.10, 90.00
R / Rfree (%) 17.4 / n/a

Manganese Binding Sites:

The binding sites of Manganese atom in the Dethiobiotin Synthetase Complexed with 7,8-Diamino-Nonanoic Acid, 5'-Adenosyl-Methylene-Triphosphate, and Manganese (pdb code 1dah). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Dethiobiotin Synthetase Complexed with 7,8-Diamino-Nonanoic Acid, 5'-Adenosyl-Methylene-Triphosphate, and Manganese, PDB code: 1dah:

Manganese binding site 1 out of 1 in 1dah

Go back to Manganese Binding Sites List in 1dah
Manganese binding site 1 out of 1 in the Dethiobiotin Synthetase Complexed with 7,8-Diamino-Nonanoic Acid, 5'-Adenosyl-Methylene-Triphosphate, and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dethiobiotin Synthetase Complexed with 7,8-Diamino-Nonanoic Acid, 5'-Adenosyl-Methylene-Triphosphate, and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn369

b:28.4
occ:1.00
 O2G A:ACP226 2.2 36.5 1.0
O1B A:ACP226 2.2 37.8 1.0
OD2 A:ASP54 2.3 30.3 1.0
OG1 A:THR16 2.4 16.6 1.0
OE2 A:GLU115 2.5 27.9 1.0
CG A:ASP54 2.9 26.9 1.0
OD1 A:ASP54 3.3 29.5 1.0
PG A:ACP226 3.4 39.1 1.0
PB A:ACP226 3.4 38.6 1.0
C3B A:ACP226 3.4 36.9 1.0
CD A:GLU115 3.6 23.8 1.0
CB A:THR16 3.7 16.4 1.0
NZ A:LYS37 3.7 18.8 1.0
N A:THR16 3.9 15.7 1.0
CB A:ASP54 4.0 22.9 1.0
O3G A:ACP226 4.0 38.7 1.0
O1A A:ACP226 4.1 39.8 1.0
OE1 A:GLU115 4.1 25.7 1.0
CE A:LYS15 4.1 26.8 1.0
CA A:THR16 4.3 16.5 1.0
O3A A:ACP226 4.4 39.3 1.0
O A:HOH368 4.4 25.1 1.0
O2B A:ACP226 4.4 36.0 1.0
NZ A:LYS15 4.5 30.1 1.0
O A:HOH279 4.5 34.0 1.0
CB A:LYS15 4.5 20.5 1.0
O1G A:ACP226 4.6 37.2 1.0
PA A:ACP226 4.7 39.1 1.0
C A:LYS15 4.7 18.8 1.0
CG2 A:THR16 4.7 16.4 1.0
CG A:GLU115 4.8 19.6 1.0
CE A:LYS37 4.8 17.4 1.0
O2A A:ACP226 5.0 37.6 1.0

Reference:

W.Huang, J.Jia, K.J.Gibson, W.S.Taylor, A.R.Rendina, G.Schneider, Y.Lindqvist. Mechanism of An Atp-Dependent Carboxylase, Dethiobiotin Synthetase, Based on Crystallographic Studies of Complexes with Substrates and A Reaction Intermediate. Biochemistry V. 34 10985 1995.
ISSN: ISSN 0006-2960
PubMed: 7669756
DOI: 10.1021/BI00035A004
Page generated: Tue Dec 15 03:47:05 2020

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