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Manganese in PDB 2y42: Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Nadh and Mn

Enzymatic activity of Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Nadh and Mn

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

Protein crystallography data

The structure of Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Nadh and Mn, PDB code: 2y42 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) 19.72 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.380, 161.450, 83.910, 90.00, 91.96, 90.00
R / Rfree (%) 17.637 / 25.422

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Nadh and Mn (pdb code 2y42). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Nadh and Mn, PDB code: 2y42:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 2y42

Go back to Manganese Binding Sites List in 2y42
Manganese binding site 1 out of 4 in the Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Nadh and 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 Nadh and Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn999

b:42.2
occ:1.00
 O22 A:BCN501 1.7 38.0 1.0
OD1 A:ASP241 2.3 36.1 1.0
OD2 A:ASP245 2.4 51.2 1.0
N1 A:BCN501 2.4 29.2 1.0
OD2 B:ASP217 2.5 38.3 1.0
O4 A:BCN501 2.6 19.8 1.0
C2 A:BCN501 2.7 39.0 1.0
C1 A:BCN501 3.1 25.5 1.0
C5 A:BCN501 3.1 29.0 1.0
CG A:ASP241 3.2 37.6 1.0
CG B:ASP217 3.3 38.4 1.0
CG A:ASP245 3.3 43.0 1.0
C3 A:BCN501 3.4 24.1 1.0
OD2 A:ASP241 3.5 43.5 1.0
C4 A:BCN501 3.5 22.6 1.0
CB B:ASP217 3.6 34.2 1.0
OD1 A:ASP245 3.6 46.9 1.0
O21 A:BCN501 3.8 48.2 1.0
OD1 B:ASP217 4.4 49.7 1.0
O A:ASP241 4.5 36.1 1.0
CB A:ASP241 4.6 38.0 1.0
C6 A:BCN501 4.6 35.5 1.0
CB A:ASP245 4.7 39.3 1.0
C A:ASP241 4.8 36.6 1.0
CA A:ASP241 4.9 36.6 1.0

Manganese binding site 2 out of 4 in 2y42

Go back to Manganese Binding Sites List in 2y42
Manganese binding site 2 out of 4 in the Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Nadh and 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 Nadh and Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn999

b:32.7
occ:1.00
 O22 B:BCN501 1.9 33.0 1.0
OD2 B:ASP245 2.0 35.6 1.0
O4 B:BCN501 2.1 28.9 1.0
OD1 B:ASP241 2.1 30.3 1.0
OD2 A:ASP217 2.2 27.5 1.0
N1 B:BCN501 2.4 37.1 1.0
C2 B:BCN501 2.8 34.0 1.0
CG B:ASP245 3.1 35.7 1.0
C5 B:BCN501 3.1 30.8 1.0
CG B:ASP241 3.2 38.4 1.0
C1 B:BCN501 3.2 33.7 1.0
CG A:ASP217 3.2 32.8 1.0
C4 B:BCN501 3.2 27.4 1.0
C3 B:BCN501 3.3 34.4 1.0
OD2 B:ASP241 3.5 41.9 1.0
OD1 B:ASP245 3.5 37.1 1.0
CB A:ASP217 3.6 32.9 1.0
O21 B:BCN501 3.9 47.3 1.0
OD1 A:ASP217 4.3 41.7 1.0
O B:ASP241 4.3 33.7 1.0
CB B:ASP245 4.4 34.8 1.0
O A:HOH2026 4.4 30.9 1.0
CB B:ASP241 4.5 34.9 1.0
C6 B:BCN501 4.6 41.3 1.0
C B:ASP241 4.8 34.4 1.0
NZ A:LYS185 4.8 34.2 1.0
CA B:ASP241 4.8 34.8 1.0
CA A:ASP217 4.9 32.7 1.0

Manganese binding site 3 out of 4 in 2y42

Go back to Manganese Binding Sites List in 2y42
Manganese binding site 3 out of 4 in the Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Nadh and 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 Nadh and Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn999

b:38.1
occ:1.00
 O22 C:BCN501 1.6 52.7 1.0
OD2 D:ASP217 2.2 46.8 1.0
OD2 C:ASP245 2.3 30.2 1.0
O4 C:BCN501 2.3 31.9 1.0
OD1 C:ASP241 2.4 30.7 1.0
N1 C:BCN501 2.5 42.7 1.0
C2 C:BCN501 2.6 49.9 1.0
C1 C:BCN501 3.1 44.5 1.0
C5 C:BCN501 3.2 42.6 1.0
CG D:ASP217 3.2 42.4 1.0
CG C:ASP241 3.2 34.7 1.0
CG C:ASP245 3.4 33.0 1.0
C4 C:BCN501 3.4 37.8 1.0
C3 C:BCN501 3.5 33.0 1.0
OD2 C:ASP241 3.5 40.6 1.0
CB D:ASP217 3.5 37.7 1.0
O21 C:BCN501 3.7 49.6 1.0
OD1 C:ASP245 3.8 27.8 1.0
O C:ASP241 4.2 35.9 1.0
OD1 D:ASP217 4.3 51.2 1.0
C6 C:BCN501 4.5 47.2 1.0
CB C:ASP241 4.6 35.3 1.0
CB C:ASP245 4.7 33.6 1.0
C C:ASP241 4.7 35.4 1.0
NZ D:LYS185 4.8 30.3 1.0
CA C:ASP241 4.8 34.3 1.0
CA D:ASP217 5.0 37.0 1.0

Manganese binding site 4 out of 4 in 2y42

Go back to Manganese Binding Sites List in 2y42
Manganese binding site 4 out of 4 in the Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Nadh and Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Nadh and Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn999

b:40.3
occ:1.00
 O22 D:BCN501 1.7 52.8 1.0
OD2 D:ASP245 2.0 32.6 1.0
OD2 C:ASP217 2.2 47.4 1.0
OD1 D:ASP241 2.2 42.1 1.0
N1 D:BCN501 2.6 40.8 1.0
C2 D:BCN501 2.6 52.7 1.0
O4 D:BCN501 2.7 25.9 1.0
C1 D:BCN501 3.0 41.9 1.0
CG D:ASP241 3.0 38.4 1.0
CG D:ASP245 3.1 37.5 1.0
C5 D:BCN501 3.1 40.1 1.0
CG C:ASP217 3.2 44.8 1.0
OD2 D:ASP241 3.2 32.0 1.0
OD1 D:ASP245 3.4 34.3 1.0
CB C:ASP217 3.6 40.2 1.0
C3 D:BCN501 3.7 35.5 1.0
O21 D:BCN501 3.7 62.4 1.0
C4 D:BCN501 3.8 25.0 1.0
O D:ASP241 4.3 38.3 1.0
OD1 C:ASP217 4.3 52.5 1.0
CB D:ASP241 4.4 39.4 1.0
CB D:ASP245 4.4 36.7 1.0
C6 D:BCN501 4.5 45.6 1.0
C D:ASP241 4.7 38.0 1.0
CA D:ASP241 4.7 38.3 1.0
NZ C:LYS185 4.9 53.5 1.0
CA C:ASP217 5.0 38.6 1.0

Reference:

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
Page generated: Sat Oct 5 15:30:17 2024

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