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Potassium in PDB 4bgu: 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii

Enzymatic activity of 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii

All present enzymatic activity of 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii:
1.1.1.37;

Protein crystallography data

The structure of 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii, PDB code: 4bgu was solved by R.Talon, D.Madern, E.Girard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.479 / 1.49
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 143.760, 82.319, 112.750, 90.00, 101.72, 90.00
R / Rfree (%) 15.58 / 17.88

Other elements in 4bgu:

The structure of 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii also contains other interesting chemical elements:

Chlorine (Cl) 71 atoms

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Potassium atom in the 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii (pdb code 4bgu). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 23 binding sites of Potassium where determined in the 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii, PDB code: 4bgu:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 23 in 4bgu

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Potassium binding site 1 out of 23 in the 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1305

b:15.9
occ:0.68
 O A:HOH2052 2.4 23.9 1.0
OD1 A:ASP28 2.7 15.6 1.0
O A:HOH2108 2.8 12.0 1.0
O A:HOH2042 2.8 15.5 1.0
O C:HOH2358 2.9 17.8 1.0
O C:ASP240 3.1 13.8 1.0
O A:HOH2048 3.2 18.6 1.0
CG A:ASP28 3.8 15.6 1.0
O A:HOH2051 4.1 41.1 1.0
C C:ASP240 4.1 13.7 1.0
O C:HOH2360 4.1 26.9 1.0
O A:HOH2040 4.3 27.5 1.0
O A:HOH2106 4.4 18.6 1.0
CB A:ASN58 4.4 9.0 1.0
CB A:ASP28 4.4 15.6 1.0
O A:HOH2041 4.4 13.2 1.0
O C:HIS239 4.4 17.5 1.0
CA A:ASP28 4.5 15.4 1.0
CA C:THR241 4.6 9.8 1.0
O A:HOH2046 4.7 33.2 1.0
OD2 C:ASP240 4.7 14.4 1.0
OD2 A:ASP28 4.8 15.7 1.0
CB C:ASP240 4.8 13.9 1.0
O A:ASN58 4.8 8.6 1.0
N C:THR241 4.8 10.0 1.0
O C:THR241 4.9 9.9 1.0
C C:THR241 4.9 10.1 1.0
OD1 A:ASP25 4.9 13.1 1.0
CG C:ASP240 5.0 14.3 1.0

Potassium binding site 2 out of 23 in 4bgu

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Potassium binding site 2 out of 23 in the 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1306

b:15.6
occ:0.74
 O A:HOH2224 2.4 27.1 1.0
OD1 A:ASP101 2.8 16.5 1.0
O A:HOH2249 2.9 17.7 1.0
O A:ASP101 2.9 15.4 1.0
O A:THR133 2.9 14.1 1.0
O A:HOH2220 3.0 26.0 1.0
OG A:SER105 3.0 14.3 1.0
OG1 A:THR133 3.3 12.7 1.0
O A:HOH2209 3.4 38.4 1.0
N A:SER105 3.4 13.0 1.0
C A:THR133 3.7 13.6 1.0
CB A:THR133 3.7 13.7 1.0
C A:ASP101 3.8 15.6 1.0
C A:GLY104 3.9 12.2 1.0
CG A:ASP101 3.9 16.8 1.0
CA A:ASP101 4.0 15.3 1.0
CA A:SER105 4.0 13.5 1.0
CB A:SER105 4.0 14.3 1.0
CA A:GLY104 4.1 11.7 1.0
O A:HOH2208 4.1 19.9 1.0
CA A:THR133 4.4 13.7 1.0
O A:HOH2223 4.4 32.8 1.0
N A:GLY134 4.4 13.1 1.0
CA A:GLY134 4.5 13.3 1.0
CB A:ASP101 4.6 16.3 1.0
N A:GLY104 4.7 11.7 1.0
O A:GLY104 4.7 12.9 1.0
O A:HOH2261 4.8 34.9 1.0
O A:HOH2219 4.8 37.2 1.0
OD2 A:ASP101 4.9 17.7 1.0

Potassium binding site 3 out of 23 in 4bgu

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Potassium binding site 3 out of 23 in the 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1307

b:29.6
occ:0.32
 O A:GLU109 2.7 20.6 1.0
OH4 A:1PE1342 2.9 42.2 0.7
OH3 A:1PE1342 2.9 24.6 0.3
OH2 A:1PE1342 2.9 41.3 0.7
OH5 A:1PE1342 2.9 31.6 0.3
OH6 A:1PE1342 2.9 38.8 0.7
OH4 A:1PE1342 3.0 26.9 0.3
OH5 A:1PE1342 3.1 43.8 0.7
OH2 A:1PE1342 3.1 23.8 0.3
OH6 A:1PE1342 3.3 28.6 0.3
OH3 A:1PE1342 3.3 31.8 0.7
C16 A:1PE1342 3.6 39.2 0.7
C23 A:1PE1342 3.6 28.5 0.7
C13 A:1PE1342 3.7 26.3 0.3
C26 A:1PE1342 3.7 37.0 0.7
C22 A:1PE1342 3.7 21.5 0.3
C23 A:1PE1342 3.7 21.3 0.3
C12 A:1PE1342 3.7 26.5 0.3
C13 A:1PE1342 3.7 33.9 0.7
C24 A:1PE1342 3.7 26.9 0.3
C12 A:1PE1342 3.7 35.2 0.7
C14 A:1PE1342 3.8 27.9 0.3
C15 A:1PE1342 3.8 30.2 0.3
C22 A:1PE1342 3.8 30.5 0.7
C24 A:1PE1342 3.8 38.1 0.7
C25 A:1PE1342 3.8 32.3 0.3
C26 A:1PE1342 3.8 28.4 0.3
C14 A:1PE1342 3.8 37.3 0.7
C15 A:1PE1342 3.8 39.7 0.7
C25 A:1PE1342 3.9 42.2 0.7
C A:GLU109 3.9 19.5 1.0
C16 A:1PE1342 4.0 29.5 0.3
CA A:TYR110 4.4 16.8 1.0
N A:TYR110 4.6 16.1 1.0
CD1 A:TYR110 4.7 17.7 1.0
OH7 A:1PE1342 4.8 41.4 0.7
O A:HOH2513 4.9 36.4 1.0
OH7 A:1PE1342 4.9 29.3 0.3

Potassium binding site 4 out of 23 in 4bgu

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Potassium binding site 4 out of 23 in the 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1308

b:32.5
occ:0.35
 O2 A:PGE1341 2.9 26.3 0.3
O1 A:PGE1341 2.9 36.2 0.7
O2 A:PGE1341 3.0 32.7 0.7
O3 A:PGE1341 3.1 36.2 0.3
O3 A:PGE1341 3.2 42.3 0.7
O A:HOH2262 3.2 28.5 1.0
C4 A:PGE1341 3.4 33.9 0.7
O1 A:PGE1341 3.4 32.7 0.3
O A:HOH2253 3.4 39.5 1.0
C4 A:PGE1341 3.4 29.0 0.3
C3 A:PGE1341 3.6 27.6 0.3
C3 A:PGE1341 3.7 31.6 0.7
C1 A:PGE1341 3.8 31.0 0.7
C2 A:PGE1341 3.9 30.2 0.7
C2 A:PGE1341 3.9 27.4 0.3
C1 A:PGE1341 4.0 29.8 0.3

Potassium binding site 5 out of 23 in 4bgu

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Potassium binding site 5 out of 23 in the 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1309

b:17.5
occ:0.40
 O A:HOH2352 2.7 15.6 1.0
O A:HOH2141 2.8 40.3 1.0
O A:SER185 2.8 10.9 1.0
O A:HOH2364 2.9 25.8 1.0
O A:HOH2216 2.9 49.0 1.0
O A:HOH2345 3.1 15.7 1.0
O A:HOH2346 3.3 26.8 1.0
C A:SER185 3.6 10.6 1.0
CA A:SER185 4.0 10.5 1.0
O A:HOH2349 4.1 13.2 1.0
O A:PRO194 4.3 12.5 1.0
O A:HOH2347 4.3 38.4 1.0
CB A:ASP193 4.4 12.4 1.0
O A:PHE184 4.5 10.9 1.0
N A:LYS186 4.6 10.4 1.0
O A:ASP193 4.7 12.3 1.0
CB A:SER185 4.8 10.6 1.0
C A:ASP193 4.9 12.2 1.0

Potassium binding site 6 out of 23 in 4bgu

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Potassium binding site 6 out of 23 in the 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1310

b:30.1
occ:0.34
 O A:HOH2146 2.5 21.1 1.0
O A:HOH2145 2.5 34.6 1.0
O A:HOH2150 2.7 44.9 1.0
O A:ASP113 2.7 24.6 1.0
O A:SER72 3.3 12.2 1.0
O A:HOH2233 3.5 34.9 1.0
C A:ASP113 3.9 24.1 1.0
OD1 A:ASP73 4.0 12.2 0.5
C A:SER72 4.1 11.9 1.0
C A:GLY71 4.4 17.9 1.0
CA A:ASP73 4.5 11.9 0.5
CA A:ASP73 4.5 12.0 0.5
O A:GLY71 4.6 17.8 1.0
N A:ASP73 4.6 12.2 1.0
CA A:GLY71 4.6 18.2 1.0
N A:SER72 4.7 12.2 1.0
CA A:PHE114 4.7 13.4 1.0
O A:HOH2149 4.7 16.1 1.0
N A:PHE114 4.8 13.4 1.0
CB A:PHE114 4.8 13.7 1.0
CA A:ASP113 4.8 24.1 1.0
N A:ASP113 4.9 24.4 1.0
CL A:CL1330 4.9 23.9 0.2
CB A:ASP113 4.9 24.5 1.0

Potassium binding site 7 out of 23 in 4bgu

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Potassium binding site 7 out of 23 in the 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1312

b:25.4
occ:1.00
 O A:HOH2514 2.8 47.9 1.0
C17 A:P331343 2.9 26.8 1.0
C11 A:P331343 2.9 25.3 1.0
O4 A:P331343 2.9 33.6 1.0
C14 A:P331343 3.0 26.7 1.0
O22 A:P331343 3.0 29.4 1.0
O1 A:P331343 3.0 36.4 1.0
O7 A:P331343 3.2 42.4 1.0
O19 A:P331343 3.2 36.5 1.0
C18 A:P331343 3.5 29.1 1.0
O10 A:P331343 3.6 42.6 1.0
C5 A:P331343 3.6 31.7 1.0
C3 A:P331343 3.6 30.5 1.0
O13 A:P331343 3.8 38.1 1.0
C2 A:P331343 3.8 32.6 1.0
C21 A:P331343 3.8 30.5 1.0
C15 A:P331343 3.8 29.9 1.0
O16 A:P331343 3.8 31.1 1.0
C12 A:P331343 3.8 27.9 1.0
C6 A:P331343 3.9 38.0 1.0
C20 A:P331343 4.0 32.0 1.0
C8 A:P331343 4.2 45.2 1.0
C9 A:P331343 4.4 47.4 1.0

Potassium binding site 8 out of 23 in 4bgu

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Potassium binding site 8 out of 23 in the 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1305

b:15.2
occ:0.80
 O B:HOH2044 2.4 16.6 1.0
OD1 B:ASP28 2.7 16.0 1.0
O B:HOH2035 2.8 14.5 1.0
O B:HOH2088 2.9 11.1 1.0
O D:HOH2346 2.9 14.0 1.0
O D:ASP240 3.0 11.3 1.0
O B:HOH2042 3.0 18.3 1.0
CG B:ASP28 3.8 16.0 1.0
C D:ASP240 4.1 10.9 1.0
O D:HOH2347 4.1 19.6 1.0
O B:HOH2038 4.2 36.3 1.0
O B:HOH2087 4.3 16.2 1.0
CB B:ASP28 4.4 16.1 1.0
O B:HOH2034 4.4 22.1 1.0
O D:HIS239 4.4 16.4 1.0
CB B:ASN58 4.4 7.8 1.0
O B:HOH2036 4.5 10.2 1.0
CA D:THR241 4.5 9.0 1.0
CA B:ASP28 4.5 15.9 1.0
OD2 B:ASP28 4.8 16.0 1.0
OD2 D:ASP240 4.8 11.2 1.0
N D:THR241 4.8 8.7 1.0
O D:THR241 4.8 9.3 1.0
CB D:ASP240 4.8 10.8 1.0
C D:THR241 4.9 9.2 1.0
O B:ASN58 4.9 8.1 1.0
O B:HOH2022 4.9 49.7 1.0
CG D:ASP240 5.0 10.8 1.0

Potassium binding site 9 out of 23 in 4bgu

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Potassium binding site 9 out of 23 in the 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1306

b:21.8
occ:0.73
 O B:HOH2179 2.7 51.5 1.0
O B:HOH2208 2.8 24.0 1.0
OD1 B:ASP101 2.8 22.1 1.0
O B:ASP101 2.8 18.9 1.0
O B:THR133 2.9 17.6 1.0
OG B:SER105 3.0 22.7 1.0
O B:HOH2072 3.1 26.6 1.0
O B:HOH2166 3.3 35.1 1.0
OG1 B:THR133 3.4 16.7 1.0
N B:SER105 3.4 18.9 1.0
C B:THR133 3.6 17.2 1.0
C B:ASP101 3.8 18.8 1.0
CB B:THR133 3.8 17.4 1.0
C B:GLY104 3.9 17.8 1.0
CG B:ASP101 3.9 22.2 1.0
CA B:SER105 4.0 20.7 1.0
CA B:ASP101 4.0 18.4 1.0
CB B:SER105 4.0 22.3 1.0
CA B:GLY104 4.1 16.3 1.0
N B:GLY134 4.3 18.0 1.0
CA B:GLY134 4.4 17.9 1.0
CA B:THR133 4.4 17.4 1.0
O B:HOH2165 4.5 28.8 1.0
O B:HOH2178 4.5 37.6 1.0
CB B:ASP101 4.6 20.3 1.0
O B:GLY104 4.6 18.4 1.0
N B:GLY104 4.7 15.8 1.0
OD2 B:ASP101 4.9 24.1 1.0
O B:HOH2219 4.9 46.4 1.0
N B:ASP102 5.0 19.2 1.0

Potassium binding site 10 out of 23 in 4bgu

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Potassium binding site 10 out of 23 in the 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of 1.50 A Resolution Structure of the Malate Dehydrogenase From Haloferax Volcanii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1307

b:30.7
occ:0.65
 O B:GLU109 2.7 31.0 1.0
OH3 B:1PE1342 2.8 33.2 0.7
OH5 B:1PE1342 2.9 25.5 0.7
OH6 B:1PE1342 3.0 27.3 0.7
OH2 B:1PE1342 3.2 40.1 0.7
OH4 B:1PE1342 3.2 35.7 0.7
C13 B:1PE1342 3.2 35.5 0.7
OH7 B:1PE1342 3.4 30.1 0.7
C23 B:1PE1342 3.4 33.7 0.7
C14 B:1PE1342 3.6 23.0 0.7
C22 B:1PE1342 3.7 33.6 0.7
C15 B:1PE1342 3.7 23.1 0.7
C25 B:1PE1342 3.7 22.9 0.7
C26 B:1PE1342 3.7 27.1 0.7
C16 B:1PE1342 3.8 27.3 0.7
C24 B:1PE1342 3.9 23.8 0.7
C12 B:1PE1342 3.9 37.1 0.7
C B:GLU109 3.9 29.7 1.0
CA B:TYR110 4.4 22.0 1.0
N B:TYR110 4.7 21.8 1.0
CD1 B:TYR110 4.7 23.5 1.0
O B:HOH2449 4.8 39.0 1.0

Reference:

R.Talon, E.Girard, B.Franzetti, G.Zaccai, D.Madern. Insight Into Structural Evolution of Extremophilic Proteins To Be Published.
Page generated: Mon Aug 12 10:11:55 2024

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