Manganese in PDB 2y40: Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Mn

All present enzymatic activity of Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Mn:
1.1.1.85;

The structure of Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Mn, PDB code: 2y40 was solved by E.Graczer, A.Merlin, R.K.Singh, K.Manikandan, P.Zavodsky, M.S.Weiss, M.Vas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.12 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.490, 112.010, 82.260, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 29.8

The binding sites of Manganese atom in the Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Mn (pdb code 2y40). 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 Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Mn, PDB code: 2y40:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:51.5 occ:1.00 OD2 B:ASP217 1.9 48.8 1.0 OD2 A:ASP245 2.1 41.0 1.0 OD1 A:ASP241 2.3 41.5 1.0 O A:HOH2045 2.4 18.8 1.0 O A:HOH2036 2.6 4.6 1.0 CG B:ASP217 3.0 48.5 1.0 CG A:ASP241 3.2 47.7 1.0 CG A:ASP245 3.3 46.4 1.0 OD2 A:ASP241 3.4 52.6 1.0 CB B:ASP217 3.7 48.4 1.0 OD1 A:ASP245 3.7 51.7 1.0 OD1 B:ASP217 3.9 47.9 1.0 O A:HOH2021 4.4 22.9 1.0 O A:ASP241 4.5 43.6 1.0 CB A:ASP245 4.6 41.8 1.0 CB A:ASP241 4.6 45.0 1.0 NZ B:LYS185 4.7 62.5 1.0 NH1 A:ARG132 4.7 58.8 1.0 CA A:ASP241 5.0 43.8 1.0 C A:ASP241 5.0 43.8 1.0

Manganese binding site 2 out of 3 in the Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Mn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:49.8 occ:1.00 OD2 B:ASP245 2.1 46.9 1.0 OD2 A:ASP217 2.1 37.9 1.0 OD1 B:ASP241 2.2 44.5 1.0 O B:HOH2025 2.2 13.6 1.0 O B:HOH2026 2.8 2.8 1.0 CG B:ASP245 3.1 41.9 1.0 CG A:ASP217 3.2 46.4 1.0 CG B:ASP241 3.3 46.5 1.0 OD1 B:ASP245 3.5 43.2 1.0 OD2 B:ASP241 3.7 46.8 1.0 CB A:ASP217 3.8 42.0 1.0 OD1 A:ASP217 4.3 48.0 1.0 O B:ASP241 4.4 47.2 1.0 CB B:ASP245 4.5 41.7 1.0 CB B:ASP241 4.6 47.6 1.0 NZ A:LYS185 4.7 68.4 1.0 C B:ASP241 4.8 46.3 1.0 CA B:ASP241 4.9 46.8 1.0

Manganese binding site 3 out of 3 in the Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Mn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:87.0 occ:1.00 O B:HOH2003 2.9 27.8 1.0 OE1 B:GLU37 4.0 84.8 1.0 O B:HOH2007 4.5 54.9 1.0 OE2 B:GLU37 4.8 80.2 1.0 CD B:GLU37 4.8 82.2 1.0

E.Graczer, A.Merli, R.K.Singh, M.Karuppasamy, P.Zavodszky, M.S.Weiss, M.Vas. Atomic Level Description of the Domain Closure in A Dimeric Enzyme: Thermus Thermophilus 3-Isopropylmalate Dehydrogenase. Mol.Biosyst. V. 7 1646 2011.
ISSN: ISSN 1742-206X
PubMed: 21387033
DOI: 10.1039/C0MB00346H