Potassium in PDB 7q3x: Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions

Enzymatic activity of Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions

All present enzymatic activity of Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions:
1.1.1.37;

Protein crystallography data

The structure of Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions, PDB code: 7q3x was solved by Q.Bertrand, J.Roche, E.Girard, D.Madern, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.42 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 128.274, 115.385, 124.828, 90, 93.02, 90
R / Rfree (%) 21.7 / 24.6

Other elements in 7q3x:

The structure of Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions also contains other interesting chemical elements:

Chlorine (Cl) 28 atoms

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 25;

Binding sites:

The binding sites of Potassium atom in the Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions (pdb code 7q3x). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 25 binding sites of Potassium where determined in the Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions, PDB code: 7q3x:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 25 in 7q3x

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Potassium binding site 1 out of 25 in the Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K507

b:36.6
occ:0.70
 O A:HOH734 2.6 32.7 1.0
O A:HOH725 2.7 42.9 0.5
O A:SER185 2.8 34.5 1.0
O A:HOH752 2.9 42.7 0.5
O A:HOH649 3.0 33.1 1.0
O A:HOH629 3.1 38.0 1.0
O A:HOH659 3.3 34.5 1.0
O A:HOH756 3.5 44.4 1.0
C A:SER185 3.6 34.4 1.0
CA A:SER185 3.9 32.2 1.0
O D:HOH580 4.1 37.6 1.0
O A:PRO194 4.3 36.8 1.0
OE1 A:GLU195 4.5 47.7 1.0
N A:LYS186 4.6 31.5 1.0
CB A:SER185 4.6 35.2 1.0
CB A:ASP193 4.6 34.2 1.0
O A:PHE184 4.7 32.8 1.0
O A:HOH634 4.7 32.4 1.0
OE2 A:GLU195 4.9 47.1 1.0
O A:HOH763 5.0 44.1 1.0
CD A:GLU195 5.0 48.2 1.0

Potassium binding site 2 out of 25 in 7q3x

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Potassium binding site 2 out of 25 in the Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K508

b:33.8
occ:0.60
 K A:K508 0.0 33.8 0.6
K A:K508 2.5 37.8 0.4
O A:ASP240 2.8 33.8 1.0
O C:HOH538 2.9 36.4 1.0
O A:HOH673 2.9 29.6 1.0
O A:HOH666 3.0 31.3 1.0
OD1 C:ASP28 3.1 43.0 1.0
O C:HOH546 3.6 33.3 1.0
O A:HOH746 3.9 41.5 1.0
C A:ASP240 3.9 32.6 1.0
CG C:ASP28 4.1 40.2 1.0
O C:HOH593 4.2 27.1 1.0
K C:K412 4.2 37.7 0.5
O A:HIS239 4.4 35.0 1.0
CA A:THR241 4.4 31.6 1.0
CB C:ASN58 4.5 28.1 1.0
N A:THR241 4.6 31.4 1.0
CB C:ASP28 4.6 35.1 1.0
O A:THR241 4.7 31.9 1.0
CA C:ASP28 4.7 33.0 1.0
O A:HOH757 4.7 58.6 1.0
C A:THR241 4.7 31.1 1.0
OD2 A:ASP240 4.8 39.8 1.0
CB A:ASP240 4.9 34.5 1.0
O C:HOH626 4.9 37.1 1.0
OD1 C:ASP25 5.0 33.6 1.0
OD2 C:ASP28 5.0 40.5 1.0

Potassium binding site 3 out of 25 in 7q3x

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Potassium binding site 3 out of 25 in the Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K508

b:37.8
occ:0.40
 K A:K508 0.0 37.8 0.4
K A:K508 2.5 33.8 0.6
O A:HOH757 2.8 58.6 1.0
OD2 A:ASP240 2.9 39.8 1.0
O A:HOH746 3.0 41.5 1.0
O A:ASP240 3.2 33.8 1.0
OD1 C:ASP28 3.3 43.0 1.0
CG C:ASP28 3.6 40.2 1.0
CG A:ASP240 3.7 35.5 1.0
O A:HOH673 4.0 29.6 1.0
O C:HOH546 4.1 33.3 1.0
CB C:ASP28 4.1 35.1 1.0
OD2 C:ASP28 4.1 40.5 1.0
CB A:ASP240 4.2 34.5 1.0
C A:ASP240 4.3 32.6 1.0
OD1 A:ASP240 4.5 34.7 1.0
O A:HOH713 4.8 34.9 1.0
O C:HOH538 4.8 36.4 1.0
CA A:ASP240 4.9 32.6 1.0
CA C:ASP28 4.9 33.0 1.0

Potassium binding site 4 out of 25 in 7q3x

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Potassium binding site 4 out of 25 in the Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K509

b:42.2
occ:0.75
 O D:ASP193 2.8 38.2 1.0
O A:HOH741 2.9 36.3 1.0
OD2 A:ASP280 3.1 52.5 1.0
CL A:CL501 3.3 31.8 1.0
O D:HOH619 3.7 49.5 1.0
CG A:ASP280 3.8 47.7 1.0
C D:ASP193 3.8 36.9 1.0
CB A:ASP280 3.9 44.2 1.0
O D:HOH510 4.0 36.0 1.0
CB D:ASP193 4.4 36.4 1.0
CA D:ASP193 4.4 35.8 1.0
N D:ASP193 4.5 35.2 1.0
N D:PRO194 4.7 36.6 1.0
OD1 A:ASP280 4.7 52.0 1.0
CA D:PRO194 4.8 37.8 1.0

Potassium binding site 5 out of 25 in 7q3x

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Potassium binding site 5 out of 25 in the Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K510

b:48.0
occ:0.70
 O A:GLY86 2.7 52.1 1.0
C A:GLY86 3.4 51.0 1.0
O A:HOH740 3.4 60.0 1.0
CA A:GLY86 3.8 53.0 1.0
N A:GLN87 4.3 48.4 1.0
CA A:GLN87 4.7 47.8 1.0
O A:PRO85 4.9 52.9 1.0

Potassium binding site 6 out of 25 in 7q3x

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Potassium binding site 6 out of 25 in the Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K511

b:36.1
occ:0.50
 O A:HOH692 2.8 51.3 1.0
O A:HOH648 2.9 33.8 1.0
O C:HOH574 2.9 34.9 1.0
OD1 A:ASP25 3.0 29.7 1.0
OD1 A:ASP28 3.1 42.3 1.0
O A:ALA27 3.3 28.3 1.0
O A:HOH676 3.3 44.6 1.0
O A:ASP25 3.5 30.0 1.0
C A:ALA27 3.5 29.5 1.0
O A:HOH613 3.7 37.1 0.5
N A:ASP28 3.9 28.9 1.0
K C:K410 4.0 32.6 0.6
N A:ALA27 4.0 26.5 1.0
C A:ASP25 4.1 29.2 1.0
CG A:ASP25 4.1 31.7 1.0
CG A:ASP28 4.1 41.9 1.0
C A:ILE26 4.2 29.4 1.0
CA A:ASP28 4.2 31.5 1.0
CA A:ALA27 4.2 30.7 1.0
O C:HOH619 4.3 46.6 1.0
O C:HIS239 4.4 32.9 1.0
O A:ILE26 4.4 31.9 1.0
N A:ILE26 4.7 27.2 1.0
CA A:ILE26 4.7 29.5 1.0
CB A:ASP28 4.8 33.5 1.0
CA A:ASP25 4.8 26.8 1.0
O A:HOH716 4.8 29.9 1.0
OG1 A:THR59 4.8 28.9 1.0
OD2 A:ASP25 4.9 32.1 1.0
CB A:ASP25 4.9 28.7 1.0
OD2 A:ASP28 5.0 44.3 1.0

Potassium binding site 7 out of 25 in 7q3x

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Potassium binding site 7 out of 25 in the Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K512

b:50.0
occ:0.55
 O A:HOH628 2.6 40.4 1.0
O A:HOH641 2.9 42.9 1.0
O A:TYR131 3.0 37.4 1.0
O A:GLY134 3.1 40.4 1.0
O A:GLU132 3.4 41.1 1.0
C A:GLU132 3.8 39.5 1.0
CA A:GLU132 3.9 38.5 1.0
C A:TYR131 4.0 37.4 1.0
C A:GLY134 4.2 41.4 1.0
O A:HOH680 4.2 55.0 1.0
O A:HOH731 4.3 57.6 1.0
CZ A:TYR131 4.4 38.0 1.0
N A:GLU132 4.5 37.5 1.0
CE1 A:TYR131 4.5 36.1 1.0
CE2 A:TYR131 4.5 37.1 1.0
N A:GLY134 4.7 40.5 1.0
OE1 A:GLU132 4.7 40.7 1.0
OH A:TYR131 4.8 42.3 1.0
N A:ALA133 4.8 38.7 1.0
CD1 A:TYR131 4.8 34.8 1.0
CD2 A:TYR131 4.8 35.7 1.0
CG A:TYR131 4.9 35.6 1.0

Potassium binding site 8 out of 25 in 7q3x

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Potassium binding site 8 out of 25 in the Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K513

b:45.5
occ:0.70
 O A:ASP113 2.6 54.5 0.5
O A:ASP113 2.6 54.6 0.5
O A:HOH732 2.7 39.2 0.5
O A:HOH723 2.7 55.8 0.5
O A:SER72 2.8 35.6 1.0
O A:HOH610 3.0 46.1 0.5
O A:HOH669 3.7 34.2 1.0
C A:ASP113 3.8 53.1 0.5
C A:SER72 3.8 35.1 1.0
C A:ASP113 3.8 53.2 0.5
CA A:ASP73 4.2 31.6 1.0
OD1 A:ASP73 4.3 37.9 1.0
N A:ASP73 4.4 32.0 1.0
CA A:TYR114 4.4 40.1 1.0
N A:TYR114 4.6 44.4 1.0
CB A:TYR114 4.6 35.6 1.0
C A:GLY71 4.6 38.1 1.0
O A:GLY71 4.7 36.5 1.0
N A:SER72 4.7 35.5 1.0
CA A:ASP113 4.8 54.2 0.5
CA A:ASP113 4.9 54.2 0.5
CA A:SER72 4.9 34.6 1.0
O A:ASP73 4.9 30.8 1.0
N A:ASP113 4.9 55.4 0.5
N A:ASP113 5.0 55.4 0.5
CG A:ASP73 5.0 36.9 1.0
C A:ASP73 5.0 29.4 1.0
CB A:ASP113 5.0 56.8 0.5

Potassium binding site 9 out of 25 in 7q3x

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Potassium binding site 9 out of 25 in the Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K514

b:33.4
occ:0.40
 O B:HOH760 2.7 34.1 1.0
OE2 A:GLU223 2.7 30.4 1.0
O A:HOH758 2.8 27.1 1.0
OE2 B:GLU223 2.9 34.6 1.0
O A:HOH607 3.4 43.0 1.0
O A:HOH728 3.5 35.1 1.0
CD A:GLU223 3.6 29.9 1.0
O A:HOH709 3.6 31.2 1.0
OE1 A:GLU223 3.7 32.4 1.0
O A:HOH612 3.7 25.9 1.0
O B:HOH620 3.7 44.6 1.0
O B:HOH604 3.8 25.9 1.0
CD B:GLU223 3.8 32.5 1.0
O B:HOH732 3.9 39.6 1.0
OE1 B:GLU223 3.9 30.9 1.0
O B:HOH670 4.0 29.1 1.0
CG A:GLU223 5.0 28.1 1.0

Potassium binding site 10 out of 25 in 7q3x

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Potassium binding site 10 out of 25 in the Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Crystal Structure of Malate Dehydrogenase From Haloarcula Marismortui with Potassium and Chloride Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K506

b:33.0
occ:0.80
 O B:HOH701 2.5 36.2 1.0
O B:HOH735 2.6 30.1 1.0
O B:SER185 2.8 34.2 1.0
O B:HOH658 2.8 29.3 1.0
O B:HOH649 3.2 29.6 1.0
C B:SER185 3.6 33.5 1.0
O B:HOH757 4.0 44.8 1.0
CA B:SER185 4.0 34.3 1.0
O B:PRO194 4.2 34.7 1.0
O B:HOH611 4.5 26.1 1.0
CB B:ASP193 4.6 34.4 1.0
N B:LYS186 4.7 32.3 1.0
O B:PHE184 4.7 32.8 1.0
OE2 B:GLU195 4.7 54.4 1.0
CB B:SER185 4.8 35.4 1.0
O B:ASP193 4.9 35.5 1.0

Reference:

E.Girard, R.Talon, Q.Bertrand, J.Roche, S.Engilberge, S.Sacquin-Mora, S.Blanquart, G.Zaccai, M.Gouy, B.Franzetti, D.Madern. Resurrection of Ancestral Malate Dehydrogenases Reveals the Evolutionary History of Haloarchaeal Proteins. To Be Published.
Page generated: Wed Apr 5 09:49:33 2023

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