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Manganese in PDB 2y41: Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Ipm and Mn

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

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

Protein crystallography data

The structure of Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Ipm and Mn, PDB code: 2y41 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) 28.20 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 50.240, 146.330, 175.210, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22.4

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Ipm and Mn (pdb code 2y41). 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 Ipm and Mn, PDB code: 2y41:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 2y41

Go back to Manganese Binding Sites List in 2y41
Manganese binding site 1 out of 4 in the Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Ipm 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 Ipm and Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn999

b:32.8
occ:1.00
 OD1 A:ASP241 2.1 31.5 1.0
O1 A:IPM800 2.1 33.3 1.0
OD2 B:ASP217 2.2 32.6 1.0
O2 A:IPM800 2.2 32.5 1.0
O A:HOH2119 2.4 15.3 1.0
O A:HOH2118 2.5 21.7 1.0
C1 A:IPM800 3.0 31.2 1.0
C2 A:IPM800 3.1 32.9 1.0
CG A:ASP241 3.2 31.6 1.0
CG B:ASP217 3.3 30.9 1.0
NZ B:LYS185 3.7 26.8 1.0
OD2 A:ASP241 3.7 30.5 1.0
CB B:ASP217 3.8 29.1 1.0
OD1 A:ASP245 3.8 33.2 1.0
O A:HOH2116 3.9 22.6 1.0
O5 A:IPM800 4.0 31.7 1.0
O A:ASP241 4.1 29.4 1.0
NH1 A:ARG104 4.1 29.0 1.0
C4 A:IPM800 4.1 34.3 1.0
C3 A:IPM800 4.1 32.6 1.0
O3 A:IPM800 4.2 32.0 1.0
CG A:ASP245 4.2 35.8 1.0
CB A:ASP241 4.3 27.2 1.0
OD1 B:ASP217 4.4 33.1 1.0
OD2 A:ASP245 4.5 37.5 1.0
CA A:ASP241 4.5 28.3 1.0
C A:ASP241 4.6 28.9 1.0
O B:HOH2047 4.7 23.0 1.0
O4 A:IPM800 4.7 30.8 1.0
O A:HOH2094 4.7 27.1 1.0
NH1 A:ARG132 4.8 27.8 1.0

Manganese binding site 2 out of 4 in 2y41

Go back to Manganese Binding Sites List in 2y41
Manganese binding site 2 out of 4 in the Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Ipm 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 Ipm and Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn999

b:35.3
occ:1.00
 OD1 B:ASP241 2.1 30.1 1.0
O3 B:IPM800 2.1 35.5 1.0
OD2 A:ASP217 2.2 35.2 1.0
O B:HOH2081 2.2 21.5 1.0
O B:HOH2080 2.2 19.4 1.0
O1 B:IPM800 2.3 34.3 1.0
C1 B:IPM800 3.0 34.2 1.0
CG B:ASP241 3.2 31.8 1.0
C2 B:IPM800 3.2 33.4 1.0
CG A:ASP217 3.2 33.5 1.0
OD1 B:ASP245 3.7 36.8 1.0
OD2 B:ASP241 3.7 30.7 1.0
CB A:ASP217 3.8 33.2 1.0
O B:HOH2078 3.8 42.3 1.0
NZ A:LYS185 3.9 36.9 1.0
O B:ASP241 4.0 29.9 1.0
NH1 B:ARG104 4.0 40.1 1.0
O5 B:IPM800 4.1 34.6 1.0
C4 B:IPM800 4.1 33.9 1.0
O2 B:IPM800 4.1 35.8 1.0
CG B:ASP245 4.2 38.4 1.0
OD1 A:ASP217 4.3 32.9 1.0
C3 B:IPM800 4.3 31.1 1.0
CB B:ASP241 4.3 30.3 1.0
OD2 B:ASP245 4.5 36.7 1.0
CA B:ASP241 4.5 31.2 1.0
NH1 B:ARG132 4.6 44.2 1.0
C B:ASP241 4.6 30.3 1.0
O4 B:IPM800 4.7 34.6 1.0

Manganese binding site 3 out of 4 in 2y41

Go back to Manganese Binding Sites List in 2y41
Manganese binding site 3 out of 4 in the Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Ipm 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 Ipm and Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1000

b:41.0
occ:0.50
 O B:HOH2082 1.9 38.0 1.0
O B:HOH2084 2.1 21.4 1.0
O B:HOH2083 2.3 23.7 1.0
O B:HOH2085 2.4 20.3 1.0
O B:HOH2068 3.9 40.6 1.0
O B:HOH2069 4.0 30.4 1.0
O B:HOH2020 4.1 40.5 1.0
CA B:GLY265 4.8 42.9 1.0
OE2 B:GLU62 4.9 48.5 1.0
O B:HOH2072 5.0 24.6 1.0

Manganese binding site 4 out of 4 in 2y41

Go back to Manganese Binding Sites List in 2y41
Manganese binding site 4 out of 4 in the Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus - Complex with Ipm 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 Ipm and Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1001

b:41.8
occ:0.50
 O B:HOH2088 2.0 17.4 1.0
O B:HOH2087 2.0 8.5 1.0
O B:HOH2090 2.4 46.2 1.0
O B:HOH2086 2.8 2.0 1.0
O B:HOH2089 2.9 16.9 1.0
OE1 B:GLU30 4.2 87.4 1.0
OE2 B:GLU30 4.7 84.3 1.0
CD B:GLU30 4.9 86.1 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: Tue Dec 15 04:06:43 2020

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