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Potassium in PDB 6eej: Streptomyces Bingchenggensis Aldolase-Dehydratase in Covalent Complex with Dienone Product.

Protein crystallography data

The structure of Streptomyces Bingchenggensis Aldolase-Dehydratase in Covalent Complex with Dienone Product., PDB code: 6eej was solved by L.S.Mydy, N.R.Silvaggi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.79 / 1.89
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 157.050, 123.746, 53.097, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 18.1

Potassium Binding Sites:

The binding sites of Potassium atom in the Streptomyces Bingchenggensis Aldolase-Dehydratase in Covalent Complex with Dienone Product. (pdb code 6eej). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Streptomyces Bingchenggensis Aldolase-Dehydratase in Covalent Complex with Dienone Product., PDB code: 6eej:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6eej

Go back to Potassium Binding Sites List in 6eej
Potassium binding site 1 out of 4 in the Streptomyces Bingchenggensis Aldolase-Dehydratase in Covalent Complex with Dienone Product.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Streptomyces Bingchenggensis Aldolase-Dehydratase in Covalent Complex with Dienone Product. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K303

b:28.1
occ:1.00
 O A:GLY137 2.6 17.1 1.0
O A:THR140 2.6 14.2 1.0
O A:HOH630 2.8 22.4 1.0
O A:HOH604 2.8 30.3 1.0
O C:HOH432 3.4 17.6 1.0
O A:HOH550 3.5 41.5 1.0
C A:GLY137 3.5 16.3 1.0
HA A:PRO138 3.6 17.5 1.0
H A:GLY137 3.7 21.0 1.0
HG23 A:VAL142 3.8 28.1 1.0
HA A:PRO141 3.9 19.0 1.0
C A:THR140 3.9 15.0 1.0
H A:THR140 3.9 14.4 1.0
HG23 A:THR140 4.0 19.1 1.0
HH C:TYR74 4.2 20.2 1.0
N A:GLY137 4.2 17.5 1.0
CA A:PRO138 4.3 14.6 1.0
N A:PRO138 4.3 15.8 1.0
CA A:GLY137 4.4 16.5 1.0
CA A:PRO141 4.5 15.8 1.0
HG22 A:VAL142 4.5 28.1 1.0
CG2 A:VAL142 4.6 23.4 1.0
HA2 A:GLY137 4.6 19.8 1.0
C A:PRO141 4.6 17.2 1.0
HE2 C:TYR74 4.6 18.3 1.0
HG22 A:THR140 4.6 19.1 1.0
O A:HOH526 4.7 15.7 1.0
N A:PRO141 4.7 14.5 1.0
N A:THR140 4.7 12.0 1.0
CG2 A:THR140 4.7 15.9 1.0
H A:VAL142 4.7 21.9 1.0
N A:VAL142 4.8 18.2 1.0
OH C:TYR74 4.8 16.9 1.0
C A:PRO138 4.8 15.6 1.0
CA A:THR140 4.9 15.2 1.0
O C:HOH656 4.9 39.6 1.0
HA2 A:GLY136 5.0 19.8 1.0
HG21 A:VAL142 5.0 28.1 1.0

Potassium binding site 2 out of 4 in 6eej

Go back to Potassium Binding Sites List in 6eej
Potassium binding site 2 out of 4 in the Streptomyces Bingchenggensis Aldolase-Dehydratase in Covalent Complex with Dienone Product.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Streptomyces Bingchenggensis Aldolase-Dehydratase in Covalent Complex with Dienone Product. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K303

b:22.1
occ:1.00
 O B:THR140 2.7 13.7 1.0
O B:GLY137 2.7 15.6 1.0
O B:HOH634 2.8 29.4 1.0
O B:HOH605 2.8 28.2 1.0
O D:HOH485 3.1 17.0 1.0
O B:HOH575 3.3 36.1 1.0
HG23 B:VAL142 3.4 26.8 1.0
HA B:PRO138 3.5 19.0 1.0
C B:GLY137 3.5 15.9 1.0
H B:GLY137 3.8 21.1 1.0
H B:THR140 3.9 17.5 1.0
C B:THR140 3.9 15.0 1.0
HA B:PRO141 3.9 17.5 1.0
HG23 B:THR140 4.0 18.9 1.0
HH D:TYR74 4.1 19.3 1.0
CA B:PRO138 4.2 15.8 1.0
N B:PRO138 4.2 14.7 1.0
CG2 B:VAL142 4.3 22.3 1.0
N B:GLY137 4.3 17.6 1.0
CA B:GLY137 4.4 16.4 1.0
HG21 B:VAL142 4.5 26.8 1.0
HE2 D:TYR74 4.5 17.4 1.0
HG22 B:VAL142 4.5 26.8 1.0
CA B:PRO141 4.6 14.6 1.0
HG22 B:THR140 4.6 18.9 1.0
O B:HOH654 4.6 39.1 1.0
HA2 B:GLY137 4.6 19.7 1.0
N B:THR140 4.7 14.6 1.0
O B:HOH563 4.7 16.7 1.0
N B:PRO141 4.7 14.7 1.0
C B:PRO141 4.7 15.0 1.0
C B:PRO138 4.7 17.1 1.0
CG2 B:THR140 4.7 15.7 1.0
H B:VAL142 4.8 18.0 1.0
OH D:TYR74 4.8 16.1 1.0
N B:VAL142 4.9 15.0 1.0
CA B:THR140 4.9 14.8 1.0

Potassium binding site 3 out of 4 in 6eej

Go back to Potassium Binding Sites List in 6eej
Potassium binding site 3 out of 4 in the Streptomyces Bingchenggensis Aldolase-Dehydratase in Covalent Complex with Dienone Product.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Streptomyces Bingchenggensis Aldolase-Dehydratase in Covalent Complex with Dienone Product. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K303

b:26.9
occ:1.00
 O C:THR140 2.6 15.2 1.0
O C:GLY137 2.7 15.8 1.0
O C:HOH661 2.8 28.1 1.0
O C:HOH624 2.9 32.2 1.0
O A:HOH418 3.5 19.4 1.0
C C:GLY137 3.5 16.4 1.0
HA C:PRO138 3.7 19.4 1.0
H C:GLY137 3.7 20.7 1.0
HG23 C:VAL142 3.8 27.9 1.0
C C:THR140 3.9 15.4 1.0
HG23 C:THR140 3.9 19.7 1.0
H C:THR140 3.9 17.0 1.0
HA C:PRO141 3.9 17.2 1.0
N C:GLY137 4.2 17.3 1.0
HH A:TYR74 4.3 19.6 1.0
N C:PRO138 4.3 15.3 1.0
CA C:GLY137 4.3 17.7 1.0
CA C:PRO138 4.3 16.2 1.0
HG22 C:VAL142 4.5 27.9 1.0
HA2 C:GLY137 4.5 21.2 1.0
HG22 C:THR140 4.6 19.7 1.0
CA C:PRO141 4.6 14.3 1.0
CG2 C:VAL142 4.6 23.2 1.0
N C:THR140 4.6 14.2 1.0
CG2 C:THR140 4.7 16.4 1.0
C C:PRO141 4.7 15.4 1.0
N C:PRO141 4.7 14.8 1.0
O C:HOH644 4.7 45.5 1.0
HE2 A:TYR74 4.7 19.7 1.0
H C:VAL142 4.8 20.5 1.0
O C:HOH572 4.8 14.1 1.0
C C:PRO138 4.8 16.7 1.0
CA C:THR140 4.8 14.3 1.0
N C:VAL142 4.8 17.1 1.0
HA2 C:GLY136 4.9 20.4 1.0
OH A:TYR74 4.9 16.3 1.0
HG21 C:VAL142 5.0 27.9 1.0

Potassium binding site 4 out of 4 in 6eej

Go back to Potassium Binding Sites List in 6eej
Potassium binding site 4 out of 4 in the Streptomyces Bingchenggensis Aldolase-Dehydratase in Covalent Complex with Dienone Product.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Streptomyces Bingchenggensis Aldolase-Dehydratase in Covalent Complex with Dienone Product. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K304

b:27.6
occ:1.00
 O D:THR140 2.6 14.5 1.0
O D:GLY137 2.7 14.9 1.0
O D:HOH644 2.7 24.5 1.0
O D:HOH619 2.9 34.4 1.0
O D:HOH588 3.0 35.7 1.0
O B:HOH458 3.4 20.5 1.0
C D:GLY137 3.6 14.7 1.0
HA D:PRO138 3.6 17.2 1.0
HG23 D:VAL142 3.7 27.9 1.0
H D:GLY137 3.7 21.5 1.0
C D:THR140 3.9 14.5 1.0
HA D:PRO141 3.9 14.4 1.0
H D:THR140 3.9 16.4 1.0
HG23 D:THR140 3.9 14.9 1.0
HH B:TYR74 4.2 18.4 1.0
N D:GLY137 4.2 17.9 1.0
CA D:PRO138 4.3 14.3 1.0
N D:PRO138 4.3 14.2 1.0
CA D:GLY137 4.4 17.1 1.0
HG22 D:VAL142 4.5 27.9 1.0
CG2 D:VAL142 4.5 23.3 1.0
CA D:PRO141 4.5 12.0 1.0
H D:VAL142 4.6 19.9 1.0
HG22 D:THR140 4.6 14.9 1.0
HA2 D:GLY137 4.6 20.5 1.0
C D:PRO141 4.6 14.6 1.0
N D:THR140 4.7 13.6 1.0
O D:HOH539 4.7 15.9 1.0
N D:PRO141 4.7 11.6 1.0
HE2 B:TYR74 4.7 17.0 1.0
CG2 D:THR140 4.7 12.4 1.0
N D:VAL142 4.7 16.6 1.0
C D:PRO138 4.8 14.2 1.0
CA D:THR140 4.8 13.5 1.0
OH B:TYR74 4.9 15.3 1.0
HA2 D:GLY136 4.9 20.7 1.0
HG21 D:VAL142 4.9 27.9 1.0

Reference:

L.S.Mydy, R.W.Hoppe, T.M.Hagemann, A.W.Schwabacher, N.R.Silvaggi. Mechanistic Studies of Thestreptomyces Bingchenggensisaldolase-Dehydratase: Implications For Substrate and Reaction Specificity in the Acetoacetate Decarboxylase-Like Superfamily. Biochemistry V. 58 4136 2019.
ISSN: ISSN 0006-2960
PubMed: 31524380
DOI: 10.1021/ACS.BIOCHEM.9B00652
Page generated: Mon Aug 12 16:00:05 2024

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