Manganese in PDB 3ufx: Thermus Aquaticus Succinyl-Coa Synthetase in Complex with Gdp-MN2+

The structure of Thermus Aquaticus Succinyl-Coa Synthetase in Complex with Gdp-MN2+, PDB code: 3ufx was solved by M.E.Fraser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.99 / 2.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	261.700, 126.800, 110.600, 90.00, 112.76, 90.00
R / Rfree (%)	20.4 / 24.5

The binding sites of Manganese atom in the Thermus Aquaticus Succinyl-Coa Synthetase in Complex with Gdp-MN2+ (pdb code 3ufx). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Thermus Aquaticus Succinyl-Coa Synthetase in Complex with Gdp-MN2+, PDB code: 3ufx:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Thermus Aquaticus Succinyl-Coa Synthetase in Complex with Gdp-MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Thermus Aquaticus Succinyl-Coa Synthetase in Complex with Gdp-MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn399 b:55.9 occ:0.80 O2A B:GDP398 2.2 60.2 0.8 O B:ASN190 2.5 42.6 1.0 O3B B:GDP398 2.6 49.9 0.8 OD2 B:ASP204 2.6 44.9 1.0 PA B:GDP398 3.4 52.7 0.8 PB B:GDP398 3.5 52.0 0.8 CG B:ASP204 3.6 48.2 1.0 C B:ASN190 3.7 32.5 1.0 O3A B:GDP398 3.7 56.7 0.8 CB B:ASP204 3.9 37.3 1.0 O1B B:GDP398 4.2 46.0 0.8 O1A B:GDP398 4.2 44.0 0.8 CD B:PRO191 4.3 35.5 1.0 N B:PRO191 4.4 35.7 1.0 CB B:ASN190 4.5 29.8 1.0 C5' B:GDP398 4.5 43.8 0.8 O5' B:GDP398 4.6 51.1 0.8 CG B:ASN190 4.6 37.2 1.0 ND2 B:ASN190 4.6 35.4 1.0 CA B:ASN190 4.7 37.1 1.0 OD1 B:ASP204 4.7 42.8 1.0 O2B B:GDP398 4.8 49.7 0.8

Manganese binding site 2 out of 4 in the Thermus Aquaticus Succinyl-Coa Synthetase in Complex with Gdp-MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Thermus Aquaticus Succinyl-Coa Synthetase in Complex with Gdp-MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn399 b:55.3 occ:0.85 O3B E:GDP398 2.2 58.9 0.8 O E:ASN190 2.3 40.1 1.0 O2A E:GDP398 2.4 46.9 0.8 OD2 E:ASP204 2.8 46.0 1.0 C E:ASN190 3.4 34.3 1.0 PB E:GDP398 3.5 54.6 0.8 PA E:GDP398 3.6 63.5 0.8 CG E:ASP204 3.8 45.2 1.0 O3A E:GDP398 3.9 56.8 0.8 CB E:ASP204 4.0 32.8 1.0 CB E:ASN190 4.2 30.0 1.0 CD E:PRO191 4.2 37.4 1.0 N E:PRO191 4.2 31.4 1.0 ND2 E:ASN190 4.3 36.9 1.0 O E:HOH712 4.3 37.6 1.0 CG E:ASN190 4.3 35.8 1.0 O1A E:GDP398 4.3 39.0 0.8 O1B E:GDP398 4.4 45.3 0.8 CA E:ASN190 4.4 36.8 1.0 O2B E:GDP398 4.6 43.4 0.8 O3' E:GDP398 4.8 58.1 0.8 O5' E:GDP398 4.8 49.4 0.8 OD1 E:ASN190 4.9 36.1 1.0 OD1 E:ASP204 5.0 41.8 1.0

Manganese binding site 3 out of 4 in the Thermus Aquaticus Succinyl-Coa Synthetase in Complex with Gdp-MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Thermus Aquaticus Succinyl-Coa Synthetase in Complex with Gdp-MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn399 b:55.4 occ:0.77 O3B G:GDP398 2.2 59.3 0.8 O G:ASN190 2.3 42.2 1.0 O2A G:GDP398 2.5 52.1 0.8 OD2 G:ASP204 2.6 40.8 1.0 C G:ASN190 3.5 32.3 1.0 CG G:ASP204 3.6 46.6 1.0 PB G:GDP398 3.7 51.7 0.8 PA G:GDP398 3.8 59.5 0.8 CB G:ASP204 3.8 35.2 1.0 CB G:ASN190 4.1 29.4 1.0 O3A G:GDP398 4.2 55.1 0.8 N G:PRO191 4.3 33.5 1.0 CG G:ASN190 4.4 37.7 1.0 ND2 G:ASN190 4.4 35.5 1.0 CD G:PRO191 4.4 39.2 1.0 CA G:ASN190 4.4 36.7 1.0 O2B G:GDP398 4.4 46.1 0.8 O1A G:GDP398 4.5 43.2 0.8 O1B G:GDP398 4.6 48.4 0.8 OD1 G:ASP204 4.7 38.5 1.0 O5' G:GDP398 4.9 52.3 0.8

Manganese binding site 4 out of 4 in the Thermus Aquaticus Succinyl-Coa Synthetase in Complex with Gdp-MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Thermus Aquaticus Succinyl-Coa Synthetase in Complex with Gdp-MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn399 b:51.2 occ:0.80 O3B I:GDP398 2.3 46.1 0.8 O I:ASN190 2.4 38.3 1.0 O2A I:GDP398 2.4 58.4 0.8 OD2 I:ASP204 2.9 46.6 1.0 C I:ASN190 3.5 31.6 1.0 PB I:GDP398 3.5 50.4 0.8 PA I:GDP398 3.6 56.2 0.8 CG I:ASP204 3.8 48.5 1.0 O3A I:GDP398 3.9 50.3 0.8 CB I:ASP204 4.0 36.3 1.0 CD I:PRO191 4.2 34.1 1.0 O2B I:GDP398 4.2 41.6 0.8 N I:PRO191 4.2 28.8 1.0 CB I:ASN190 4.3 31.4 1.0 ND2 I:ASN190 4.3 35.1 1.0 CG I:ASN190 4.3 38.4 1.0 O1A I:GDP398 4.3 41.6 0.8 O I:HOH420 4.5 38.5 1.0 CA I:ASN190 4.5 35.9 1.0 O1B I:GDP398 4.6 39.9 0.8 O3' I:GDP398 4.7 42.9 0.8 O5' I:GDP398 4.8 41.0 0.8 OD1 I:ASN190 4.9 38.8 1.0 C5' I:GDP398 5.0 46.8 0.8

M.A.Joyce, K.Hayakawa, W.T.Wolodko, M.E.Fraser. Biochemical and Structural Characterization of the Gtp-Preferring Succinyl-Coa Synthetase From Thermus Aquaticus. Acta Crystallogr.,Sect.D V. 68 751 2012.
ISSN: ISSN 0907-4449
PubMed: 22751660
DOI: 10.1107/S0907444912010852