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Potassium in PDB 7kd9: Crystal Structure of Gallic Acid Decarboxylase From Arxula Adeninivorans

Protein crystallography data

The structure of Crystal Structure of Gallic Acid Decarboxylase From Arxula Adeninivorans, PDB code: 7kd9 was solved by M.Zeug, N.Markovic, C.V.Iancu, J.Tripp, M.Oreb, J.Choe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.61 / 1.94
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 91.632, 265.301, 93.728, 90, 90, 90
R / Rfree (%) 19.1 / 23.8

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Gallic Acid Decarboxylase From Arxula Adeninivorans (pdb code 7kd9). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Crystal Structure of Gallic Acid Decarboxylase From Arxula Adeninivorans, PDB code: 7kd9:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 7kd9

Go back to Potassium Binding Sites List in 7kd9
Potassium binding site 1 out of 3 in the Crystal Structure of Gallic Acid Decarboxylase From Arxula Adeninivorans


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Gallic Acid Decarboxylase From Arxula Adeninivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K301

b:26.8
occ:1.00
 OE1 B:GLU88 2.8 28.2 1.0
OE1 A:GLU88 2.8 27.8 1.0
O D:GLU88 2.8 20.1 1.0
O B:GLU88 2.9 26.0 1.0
OE2 D:GLU88 2.9 29.8 1.0
O A:GLU88 2.9 24.8 1.0
CD A:GLU88 3.7 29.4 1.0
CD B:GLU88 3.7 29.7 1.0
CD D:GLU88 3.7 27.5 1.0
C D:GLU88 3.7 24.6 1.0
C A:GLU88 3.7 23.9 1.0
C B:GLU88 3.8 26.4 1.0
CA A:CYS89 3.8 27.9 1.0
CA D:CYS89 3.8 27.3 1.0
CA B:CYS89 3.9 24.4 1.0
OE2 B:GLU88 4.0 27.3 1.0
OE1 D:GLU88 4.1 25.7 1.0
OE2 A:GLU88 4.1 25.1 1.0
O B:HOH320 4.1 30.7 1.0
O A:HOH407 4.1 28.8 1.0
N A:CYS89 4.1 22.7 1.0
N D:CYS89 4.2 23.1 1.0
N B:CYS89 4.2 25.5 1.0
O D:HOH319 4.3 25.4 1.0
N B:GLY90 4.4 21.2 1.0
N A:GLY90 4.4 22.7 1.0
C A:CYS89 4.5 27.7 1.0
C B:CYS89 4.5 24.4 1.0
N D:GLY90 4.5 25.5 1.0
C D:CYS89 4.5 20.5 1.0
CB A:GLU88 4.8 20.2 1.0
CB D:CYS89 4.8 32.6 1.0
CB D:GLU88 4.8 24.0 1.0
CG A:GLU88 4.8 21.7 1.0
CB B:GLU88 4.8 21.1 1.0
O B:HOH354 4.8 44.8 1.0
CA D:GLU88 4.8 26.6 1.0
CG D:GLU88 4.8 24.0 1.0
CB B:CYS89 4.8 33.5 1.0
CG B:GLU88 4.9 25.9 1.0
CB A:CYS89 4.9 35.1 1.0
CA A:GLU88 4.9 24.1 1.0
CA B:GLU88 4.9 23.4 1.0

Potassium binding site 2 out of 3 in 7kd9

Go back to Potassium Binding Sites List in 7kd9
Potassium binding site 2 out of 3 in the Crystal Structure of Gallic Acid Decarboxylase From Arxula Adeninivorans


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 Gallic Acid Decarboxylase From Arxula Adeninivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K301

b:29.3
occ:1.00
 OE2 F:GLU88 2.8 37.1 1.0
OE2 E:GLU88 2.9 30.4 1.0
OE1 C:GLU88 2.9 33.9 1.0
O C:GLU88 2.9 24.6 1.0
O F:GLU88 2.9 31.6 1.0
O E:GLU88 3.0 29.8 1.0
CD F:GLU88 3.6 39.7 1.0
CD E:GLU88 3.7 35.0 1.0
C F:GLU88 3.7 33.7 1.0
CD C:GLU88 3.7 36.1 1.0
C C:GLU88 3.7 29.6 1.0
C E:GLU88 3.8 34.2 1.0
CA E:CYS89 3.9 30.4 1.0
OE1 F:GLU88 4.0 31.1 1.0
OE1 E:GLU88 4.1 29.9 1.0
OE2 C:GLU88 4.1 32.0 1.0
N E:CYS89 4.1 29.4 1.0
O E:HOH309 4.2 32.9 1.0
N F:CYS89 4.2 32.2 1.0
O F:HOH315 4.2 31.6 1.0
N C:CYS89 4.2 27.4 1.0
CA F:CYS89 4.3 34.4 1.0
O C:HOH426 4.3 30.1 1.0
CA C:CYS89 4.3 34.6 1.0
N F:GLY90 4.3 29.0 1.0
N C:GLY90 4.4 34.0 1.0
C E:CYS89 4.5 26.8 1.0
C F:CYS89 4.5 33.5 1.0
C C:CYS89 4.6 29.3 1.0
N E:GLY90 4.6 27.1 1.0
CB C:GLU88 4.7 32.1 1.0
CB F:GLU88 4.7 31.2 1.0
CG F:GLU88 4.8 38.3 1.0
CB E:GLU88 4.8 25.2 1.0
CA F:GLU88 4.8 34.5 1.0
CA C:GLU88 4.8 27.9 1.0
CG E:GLU88 4.8 29.5 1.0
CB E:CYS89 4.8 34.0 1.0
CG C:GLU88 4.8 34.9 1.0
CA E:GLU88 4.9 25.2 1.0

Potassium binding site 3 out of 3 in 7kd9

Go back to Potassium Binding Sites List in 7kd9
Potassium binding site 3 out of 3 in the Crystal Structure of Gallic Acid Decarboxylase From Arxula Adeninivorans


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 Gallic Acid Decarboxylase From Arxula Adeninivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K301

b:25.1
occ:1.00
 OE2 H:GLU88 2.8 27.4 1.0
OE2 I:GLU88 2.8 25.2 1.0
O G:GLU88 2.8 23.1 1.0
O H:GLU88 2.9 22.1 1.0
O I:GLU88 2.9 22.3 1.0
OE1 G:GLU88 2.9 28.1 1.0
CD I:GLU88 3.6 30.5 1.0
CD H:GLU88 3.7 21.8 1.0
C I:GLU88 3.7 21.3 1.0
C G:GLU88 3.7 22.9 1.0
C H:GLU88 3.8 22.9 1.0
CD G:GLU88 3.8 30.5 1.0
CA H:CYS89 3.8 28.5 1.0
CA I:CYS89 3.9 20.8 1.0
OE1 I:GLU88 4.0 26.4 1.0
O G:HOH415 4.1 27.0 1.0
OE1 H:GLU88 4.1 25.5 1.0
CA G:CYS89 4.1 25.6 1.0
OE2 G:GLU88 4.2 25.2 1.0
O I:HOH308 4.2 26.8 1.0
N I:CYS89 4.2 19.9 1.0
O I:HOH322 4.2 24.3 1.0
N H:CYS89 4.2 23.9 1.0
N G:CYS89 4.3 23.7 1.0
N I:GLY90 4.3 19.8 1.0
C I:CYS89 4.4 21.9 1.0
N G:GLY90 4.4 22.7 1.0
C G:CYS89 4.5 22.9 1.0
N H:GLY90 4.5 20.2 1.0
C H:CYS89 4.5 28.4 1.0
O H:HOH371 4.6 46.2 1.0
CB H:CYS89 4.7 28.4 1.0
CB G:GLU88 4.8 26.1 1.0
CB I:GLU88 4.8 18.3 1.0
CG I:GLU88 4.8 22.8 1.0
CB H:GLU88 4.8 21.5 1.0
CG H:GLU88 4.8 19.1 1.0
CA G:GLU88 4.9 20.2 1.0
CA I:GLU88 4.9 18.5 1.0
CA H:GLU88 4.9 22.9 1.0
CG G:GLU88 4.9 27.2 1.0
CB I:CYS89 4.9 27.9 1.0

Reference:

M.Zeug, N.Markovic, C.V.Iancu, J.Tripp, M.Oreb, J.Y.Choe. Crystal Structures of Non-Oxidative Decarboxylases Reveal A New Mechanism of Action with A Catalytic Dyad and Structural Twists. Sci Rep V. 11 3056 2021.
ISSN: ESSN 2045-2322
PubMed: 33542397
DOI: 10.1038/S41598-021-82660-Z
Page generated: Mon Aug 12 19:15:33 2024

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