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Manganese in PDB 4f7i: Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus in Complex with Ipm, Mn and Nadh

Enzymatic activity of Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus in Complex with Ipm, Mn and Nadh

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

Protein crystallography data

The structure of Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus in Complex with Ipm, Mn and Nadh, PDB code: 4f7i was solved by A.Pallo, E.Graczer, P.Zavodszky, M.S.Weiss, M.Vas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 148.380, 50.720, 178.240, 90.00, 93.09, 90.00
R / Rfree (%) 15.2 / 19.6

Other elements in 4f7i:

The structure of Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus in Complex with Ipm, Mn and Nadh also contains other interesting chemical elements:

Potassium (K) 7 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus in Complex with Ipm, Mn and Nadh (pdb code 4f7i). 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 in Complex with Ipm, Mn and Nadh, PDB code: 4f7i:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4f7i

Go back to Manganese Binding Sites List in 4f7i
Manganese binding site 1 out of 4 in the Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus in Complex with Ipm, Mn and Nadh


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 in Complex with Ipm, Mn and Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn999

b:20.4
occ:1.00
 OD2 B:ASP217 2.0 20.9 1.0
O1 A:IPM800 2.1 24.1 1.0
OD1 A:ASP241 2.1 18.9 1.0
O A:HOH2002 2.2 21.5 1.0
O A:HOH2001 2.3 17.5 1.0
O2 A:IPM800 2.4 22.6 1.0
CG B:ASP217 3.1 21.5 1.0
CG A:ASP241 3.2 20.1 1.0
C2 A:IPM800 3.5 30.2 1.0
C1 A:IPM800 3.5 34.3 1.0
OD2 A:ASP241 3.7 24.1 1.0
CB B:ASP217 3.7 19.6 1.0
NZ B:LYS185 3.8 21.7 1.0
OD1 A:ASP245 3.9 19.5 1.0
NH1 A:ARG104 4.0 18.3 1.0
O A:ASP241 4.1 17.3 1.0
OD1 B:ASP217 4.2 21.7 1.0
O A:HOH2006 4.2 19.0 1.0
O B:HOH2013 4.2 26.1 1.0
CG A:ASP245 4.3 19.0 1.0
O5 A:IPM800 4.3 27.6 1.0
CB A:ASP241 4.4 18.3 1.0
C5N A:NAD900 4.4 20.8 1.0
OD2 A:ASP245 4.5 19.8 1.0
O A:VAL272 4.6 19.6 1.0
O A:HOH2004 4.6 20.7 1.0
CA A:ASP241 4.6 18.8 1.0
C4 A:IPM800 4.6 29.7 1.0
C A:ASP241 4.7 16.7 1.0
C3 A:IPM800 4.7 28.6 1.0
C4N A:NAD900 4.8 22.0 1.0
O3 A:IPM800 4.8 28.3 1.0
CG1 A:VAL272 5.0 15.8 1.0

Manganese binding site 2 out of 4 in 4f7i

Go back to Manganese Binding Sites List in 4f7i
Manganese binding site 2 out of 4 in the Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus in Complex with Ipm, Mn and Nadh


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 in Complex with Ipm, Mn and Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn999

b:22.1
occ:1.00
 OD1 B:ASP241 2.0 22.3 1.0
OD2 A:ASP217 2.0 18.0 1.0
O1 B:IPM800 2.1 25.3 1.0
O B:HOH2002 2.2 18.5 1.0
O B:HOH2001 2.3 20.4 1.0
O2 B:IPM800 2.5 25.0 1.0
CG A:ASP217 3.0 18.9 1.0
CG B:ASP241 3.2 22.2 1.0
C2 B:IPM800 3.4 36.2 1.0
C1 B:IPM800 3.5 34.4 1.0
CB A:ASP217 3.6 18.0 1.0
OD2 B:ASP241 3.7 25.1 1.0
OD1 B:ASP245 3.8 20.4 1.0
NZ A:LYS185 4.0 20.0 1.0
NH1 B:ARG104 4.0 18.7 1.0
O A:HOH2013 4.1 22.1 1.0
OD1 A:ASP217 4.1 21.3 1.0
O B:ASP241 4.1 16.4 1.0
O B:HOH2016 4.2 22.1 1.0
C5N B:NAD900 4.3 22.4 1.0
CG B:ASP245 4.3 20.8 1.0
O5 B:IPM800 4.4 25.8 1.0
CB B:ASP241 4.4 20.3 1.0
OD2 B:ASP245 4.5 20.6 1.0
O B:HOH2009 4.6 21.0 1.0
C B:ASP241 4.6 18.5 1.0
O B:VAL272 4.6 21.1 1.0
CA B:ASP241 4.6 20.6 1.0
C4 B:IPM800 4.6 29.3 1.0
C3 B:IPM800 4.6 29.6 1.0
C4N B:NAD900 4.7 23.6 1.0
O3 B:IPM800 4.8 25.6 1.0
NH2 B:ARG104 5.0 19.4 1.0
CG1 B:VAL272 5.0 17.7 1.0

Manganese binding site 3 out of 4 in 4f7i

Go back to Manganese Binding Sites List in 4f7i
Manganese binding site 3 out of 4 in the Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus in Complex with Ipm, Mn and Nadh


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 in Complex with Ipm, Mn and Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn999

b:21.6
occ:1.00
 OD1 C:ASP241 2.1 21.2 1.0
OD2 D:ASP217 2.1 18.6 1.0
O C:HOH2001 2.2 16.0 1.0
O1 C:IPM800 2.2 27.7 1.0
O C:HOH2002 2.3 18.7 1.0
O2 C:IPM800 2.4 24.3 1.0
CG D:ASP217 3.2 18.9 1.0
CG C:ASP241 3.2 22.2 1.0
C1 C:IPM800 3.5 35.2 1.0
C2 C:IPM800 3.6 34.9 1.0
CB D:ASP217 3.7 17.5 1.0
OD2 C:ASP241 3.7 25.4 1.0
OD1 C:ASP245 3.8 19.2 1.0
NZ D:LYS185 3.9 21.9 1.0
NH1 C:ARG104 4.0 18.4 1.0
O C:ASP241 4.1 20.4 1.0
O D:HOH2007 4.2 23.1 1.0
CG C:ASP245 4.2 20.8 1.0
O C:HOH2004 4.3 21.8 1.0
OD1 D:ASP217 4.3 18.1 1.0
O5 C:IPM800 4.4 28.1 1.0
C5N C:NAD900 4.4 25.9 1.0
CB C:ASP241 4.4 20.7 1.0
OD2 C:ASP245 4.5 20.3 1.0
O C:HOH2011 4.5 23.6 1.0
O C:VAL272 4.6 21.8 1.0
CA C:ASP241 4.6 20.1 1.0
C C:ASP241 4.6 18.4 1.0
C4 C:IPM800 4.7 32.6 1.0
O3 C:IPM800 4.8 30.4 1.0
C3 C:IPM800 4.8 31.6 1.0
C4N C:NAD900 4.8 22.9 1.0
CZ C:ARG104 5.0 20.8 1.0
NH2 C:ARG104 5.0 20.2 1.0

Manganese binding site 4 out of 4 in 4f7i

Go back to Manganese Binding Sites List in 4f7i
Manganese binding site 4 out of 4 in the Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus in Complex with Ipm, Mn and Nadh


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 in Complex with Ipm, Mn and Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn999

b:22.2
occ:1.00
 OD2 C:ASP217 2.0 20.7 1.0
OD1 D:ASP241 2.1 22.3 1.0
O D:HOH2001 2.2 18.9 1.0
O D:HOH2002 2.3 19.7 1.0
O1 D:IPM800 2.3 27.5 1.0
O2 D:IPM800 2.4 23.2 1.0
CG C:ASP217 3.1 21.2 1.0
CG D:ASP241 3.2 22.4 1.0
C1 D:IPM800 3.5 35.0 1.0
C2 D:IPM800 3.6 33.3 1.0
CB C:ASP217 3.6 19.8 1.0
OD2 D:ASP241 3.7 26.1 1.0
OD1 D:ASP245 3.8 18.8 1.0
NZ C:LYS185 4.0 25.3 1.0
NH1 D:ARG104 4.0 20.6 1.0
O D:ASP241 4.0 18.6 1.0
OD1 C:ASP217 4.1 20.8 1.0
O D:HOH2006 4.2 23.4 1.0
CG D:ASP245 4.2 19.0 1.0
O C:HOH2017 4.3 23.0 1.0
C5N D:NAD900 4.4 25.6 1.0
CB D:ASP241 4.4 20.4 1.0
O5 D:IPM800 4.4 23.6 1.0
OD2 D:ASP245 4.5 19.2 1.0
O D:VAL272 4.5 20.7 1.0
O D:HOH2003 4.6 19.1 1.0
C D:ASP241 4.6 18.4 1.0
CA D:ASP241 4.7 20.6 1.0
C4 D:IPM800 4.8 30.5 1.0
O3 D:IPM800 4.8 25.6 1.0
C3 D:IPM800 4.8 29.2 1.0
C4N D:NAD900 4.8 24.4 1.0
NH2 D:ARG104 4.9 22.2 1.0
CG1 D:VAL272 4.9 18.7 1.0
CZ D:ARG104 4.9 21.1 1.0

Reference:

A.Pallo, J.Olah, E.Graczer, A.Merli, P.Zavodszky, M.S.Weiss, M.Vas. Structural and Energetic Basis of Isopropylmalate Dehydrogenase Enzyme Catalysis. Febs J. V. 281 5063 2014.
ISSN: ISSN 1742-464X
PubMed: 25211160
DOI: 10.1111/FEBS.13044
Page generated: Sat Oct 5 19:22:14 2024

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