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Potassium 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:

Manganese (Mn) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 7 binding sites of Potassium where determined in the Structure of Isopropylmalate Dehydrogenase From Thermus Thermophilus in Complex with Ipm, Mn and Nadh, PDB code: 4f7i:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in 4f7i

Go back to Potassium Binding Sites List in 4f7i
Potassium binding site 1 out of 7 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 Potassium with other atoms in the K 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:K1001

b:29.8
occ:1.00
 O A:PRO271 2.6 22.6 1.0
O A:GLY70 2.6 22.7 1.0
OE1 A:GLU270 2.7 26.2 1.0
N7N A:NAD900 2.7 25.8 1.0
O A:HIS273 2.9 22.7 1.0
OG A:SER71 2.9 29.9 1.0
C7N A:NAD900 3.5 24.3 1.0
C A:PRO271 3.6 19.3 1.0
O A:HOH2022 3.6 24.9 1.0
CD A:GLU270 3.7 26.4 1.0
C A:GLY70 3.7 23.7 1.0
CA A:SER71 3.9 23.9 1.0
CB A:SER71 3.9 26.8 1.0
N A:PRO271 4.0 21.0 1.0
CB A:GLU270 4.0 22.7 1.0
O7N A:NAD900 4.0 22.3 1.0
CD A:PRO271 4.1 21.0 1.0
CB A:PRO271 4.1 21.9 1.0
C A:HIS273 4.1 21.3 1.0
CG A:GLU270 4.1 23.1 1.0
CA A:PRO271 4.2 20.8 1.0
N A:SER71 4.2 23.7 1.0
CG A:PRO271 4.2 22.4 1.0
C3N A:NAD900 4.3 22.7 1.0
O A:VAL272 4.4 19.6 1.0
C A:VAL272 4.5 18.3 1.0
C A:GLU270 4.5 20.4 1.0
OE2 A:GLU270 4.7 26.4 1.0
N A:HIS273 4.7 18.1 1.0
N A:VAL272 4.7 17.4 1.0
C4N A:NAD900 4.7 22.0 1.0
CA A:GLU270 4.8 20.3 1.0
CA A:GLY70 4.9 22.6 1.0
CA A:GLY274 4.9 21.4 1.0
N A:GLY274 5.0 21.0 1.0
CA A:HIS273 5.0 19.7 1.0
CA A:VAL272 5.0 17.4 1.0

Potassium binding site 2 out of 7 in 4f7i

Go back to Potassium Binding Sites List in 4f7i
Potassium binding site 2 out of 7 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 Potassium with other atoms in the K 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
A:K1002

b:39.7
occ:1.00
 O A:ALA64 2.6 32.4 1.0
OG1 A:THR266 2.8 25.7 1.0
O A:GLU62 2.9 40.0 1.0
C A:ALA64 3.9 32.1 1.0
CB A:THR266 3.9 25.7 1.0
C A:GLU62 4.0 39.2 1.0
O A:VAL61 4.2 30.8 1.0
CG2 A:THR266 4.3 24.1 1.0
CA A:THR266 4.3 26.0 1.0
N A:ALA64 4.4 35.1 1.0
N A:THR266 4.5 27.3 1.0
C A:GLU63 4.5 38.0 1.0
O A:HOH2104 4.6 51.2 1.0
N A:GLU65 4.7 32.5 1.0
CA A:GLU65 4.7 32.5 1.0
CA A:ALA64 4.8 33.3 1.0
N A:GLU63 4.8 36.8 1.0
CA A:GLU63 4.8 38.3 1.0
CA A:GLU62 4.9 37.6 1.0
O A:GLU63 4.9 40.6 1.0

Potassium binding site 3 out of 7 in 4f7i

Go back to Potassium Binding Sites List in 4f7i
Potassium binding site 3 out of 7 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 Potassium with other atoms in the K 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
B:K1001

b:22.2
occ:0.80
 OE1 B:GLU270 2.7 28.1 1.0
O B:PRO271 2.7 19.7 1.0
O B:GLY70 2.7 25.5 1.0
O B:HIS273 2.8 23.6 1.0
N7N B:NAD900 2.8 24.3 1.0
OG B:SER71 2.8 29.1 1.0
C7N B:NAD900 3.5 27.1 1.0
C B:PRO271 3.7 19.4 1.0
CD B:GLU270 3.8 27.5 1.0
C B:GLY70 3.8 24.0 1.0
O B:HOH2021 3.8 27.4 1.0
O7N B:NAD900 3.8 24.0 1.0
CA B:SER71 3.8 23.6 1.0
CB B:SER71 3.8 24.9 1.0
N B:PRO271 4.0 21.1 1.0
C B:HIS273 4.0 22.3 1.0
CB B:GLU270 4.0 22.8 1.0
CD B:PRO271 4.0 21.5 1.0
CB B:PRO271 4.1 21.1 1.0
CA B:PRO271 4.2 20.9 1.0
N B:SER71 4.2 21.4 1.0
CG B:GLU270 4.3 23.6 1.0
CG B:PRO271 4.4 23.0 1.0
C3N B:NAD900 4.4 22.2 1.0
O B:VAL272 4.4 21.1 1.0
C B:VAL272 4.5 21.9 1.0
C B:GLU270 4.6 21.3 1.0
C4N B:NAD900 4.6 23.6 1.0
N B:HIS273 4.7 21.3 1.0
N B:VAL272 4.7 20.6 1.0
OE2 B:GLU270 4.7 27.9 1.0
CA B:GLY274 4.9 21.3 1.0
N B:GLY274 4.9 20.6 1.0
CA B:GLU270 4.9 22.1 1.0
ND1 B:HIS273 4.9 20.4 1.0
CA B:HIS273 4.9 21.5 1.0

Potassium binding site 4 out of 7 in 4f7i

Go back to Potassium Binding Sites List in 4f7i
Potassium binding site 4 out of 7 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 Potassium with other atoms in the K 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
B:K1002

b:43.3
occ:1.00
 O B:HOH2050 2.6 45.7 1.0
O B:ALA64 2.7 34.7 1.0
OG1 B:THR266 2.7 27.3 1.0
O B:HOH2051 2.7 49.6 1.0
O B:GLU62 2.8 40.1 1.0
C B:GLU62 3.8 39.0 1.0
C B:ALA64 3.9 35.5 1.0
CB B:THR266 3.9 26.9 1.0
O B:VAL61 4.0 29.4 1.0
CG2 B:THR266 4.4 25.8 1.0
CA B:THR266 4.4 27.2 1.0
N B:ALA64 4.4 36.4 1.0
CA B:GLU62 4.5 38.3 1.0
N B:THR266 4.6 28.6 1.0
C B:GLU63 4.6 39.4 1.0
N B:GLU63 4.7 38.3 1.0
CA B:ALA64 4.8 34.7 1.0
CA B:GLU65 4.8 31.3 1.0
N B:GLU65 4.8 33.1 1.0
CA B:GLU63 5.0 41.2 1.0

Potassium binding site 5 out of 7 in 4f7i

Go back to Potassium Binding Sites List in 4f7i
Potassium binding site 5 out of 7 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 Potassium with other atoms in the K binding site number 5 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:K1001

b:25.9
occ:1.00
 O C:GLY70 2.6 23.8 1.0
OE1 C:GLU270 2.7 25.8 1.0
O C:PRO271 2.7 20.5 1.0
O C:HIS273 2.8 20.8 1.0
N7N C:NAD900 2.8 31.2 1.0
OG C:SER71 2.9 27.4 1.0
C7N C:NAD900 3.5 27.3 1.0
C C:GLY70 3.7 23.9 1.0
C C:PRO271 3.7 20.3 1.0
O C:HOH2014 3.8 27.2 1.0
CA C:SER71 3.8 24.5 1.0
CB C:SER71 3.8 25.1 1.0
CD C:GLU270 3.8 26.1 1.0
CD C:PRO271 3.9 21.4 1.0
CB C:PRO271 4.0 22.2 1.0
O7N C:NAD900 4.0 26.3 1.0
N C:PRO271 4.0 20.3 1.0
C C:HIS273 4.0 23.0 1.0
CB C:GLU270 4.1 19.9 1.0
CA C:PRO271 4.2 20.7 1.0
N C:SER71 4.2 22.6 1.0
CG C:GLU270 4.3 22.6 1.0
CG C:PRO271 4.3 22.6 1.0
C3N C:NAD900 4.3 24.3 1.0
O C:VAL272 4.4 21.8 1.0
C C:VAL272 4.5 20.5 1.0
C4N C:NAD900 4.5 22.9 1.0
C C:GLU270 4.6 21.2 1.0
N C:HIS273 4.7 19.4 1.0
N C:VAL272 4.8 19.0 1.0
CA C:GLY274 4.8 21.2 1.0
OE2 C:GLU270 4.8 23.9 1.0
CA C:GLU270 4.9 20.7 1.0
N C:GLY274 4.9 21.8 1.0
CA C:GLY70 4.9 21.3 1.0
CA C:HIS273 5.0 19.8 1.0

Potassium binding site 6 out of 7 in 4f7i

Go back to Potassium Binding Sites List in 4f7i
Potassium binding site 6 out of 7 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 Potassium with other atoms in the K binding site number 6 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:K1002

b:49.3
occ:1.00
 O C:ALA64 2.7 30.9 1.0
OG1 C:THR266 2.8 29.1 1.0
O C:HOH2098 2.9 55.8 1.0
O C:GLU62 3.0 42.8 1.0
C C:GLU62 3.9 42.0 1.0
C C:ALA64 4.0 32.1 1.0
CB C:THR266 4.0 27.9 1.0
O C:VAL61 4.1 31.5 1.0
CA C:THR266 4.4 28.2 1.0
CG2 C:THR266 4.4 27.3 1.0
N C:ALA64 4.4 32.9 1.0
N C:THR266 4.5 29.4 1.0
CA C:GLU62 4.6 39.3 1.0
C C:GLU63 4.7 39.0 1.0
N C:GLU63 4.8 39.9 1.0
CA C:GLU65 4.8 33.4 1.0
N C:GLU65 4.8 32.6 1.0
CA C:ALA64 4.9 32.5 1.0
CA C:GLU63 4.9 39.9 1.0

Potassium binding site 7 out of 7 in 4f7i

Go back to Potassium Binding Sites List in 4f7i
Potassium binding site 7 out of 7 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 Potassium with other atoms in the K binding site number 7 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:K1001

b:25.6
occ:0.80
 O D:PRO271 2.7 21.9 1.0
O D:GLY70 2.7 26.9 1.0
N7N D:NAD900 2.7 29.2 1.0
OE1 D:GLU270 2.8 28.7 1.0
O D:HIS273 2.8 20.3 1.0
OG D:SER71 2.9 34.9 1.0
C7N D:NAD900 3.4 27.4 1.0
C D:PRO271 3.6 21.3 1.0
C D:GLY70 3.8 26.9 1.0
O D:HOH2016 3.8 23.7 1.0
CD D:GLU270 3.8 27.8 1.0
CA D:SER71 3.8 27.4 1.0
O7N D:NAD900 3.8 32.2 1.0
CB D:SER71 3.9 27.5 1.0
CB D:PRO271 4.0 21.5 1.0
N D:PRO271 4.0 22.7 1.0
CB D:GLU270 4.0 25.3 1.0
C D:HIS273 4.1 21.9 1.0
CD D:PRO271 4.1 23.0 1.0
CA D:PRO271 4.1 21.9 1.0
CG D:GLU270 4.2 26.9 1.0
N D:SER71 4.2 28.0 1.0
CG D:PRO271 4.4 22.8 1.0
C3N D:NAD900 4.4 23.7 1.0
C D:VAL272 4.4 20.6 1.0
O D:VAL272 4.4 20.7 1.0
C D:GLU270 4.6 23.4 1.0
N D:HIS273 4.6 21.2 1.0
C4N D:NAD900 4.7 24.4 1.0
N D:VAL272 4.7 20.2 1.0
OE2 D:GLU270 4.8 28.4 1.0
CA D:GLU270 4.9 25.4 1.0
CA D:GLY274 5.0 19.6 1.0
CA D:HIS273 5.0 21.0 1.0
N D:GLY274 5.0 20.0 1.0
CA D:VAL272 5.0 20.6 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: Mon Aug 12 10:41:11 2024

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