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Potassium in PDB 6f3m: Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenosine, K+ and ZN2+ Cations

Enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenosine, K+ and ZN2+ Cations

All present enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenosine, K+ and ZN2+ Cations:
3.3.1.1;

Protein crystallography data

The structure of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenosine, K+ and ZN2+ Cations, PDB code: 6f3m was solved by J.Czyrko, K.Brzezinski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.70 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 175.976, 104.145, 107.634, 90.00, 100.71, 90.00
R / Rfree (%) 15.1 / 17.4

Other elements in 6f3m:

The structure of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenosine, K+ and ZN2+ Cations also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenosine, K+ and ZN2+ Cations (pdb code 6f3m). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenosine, K+ and ZN2+ Cations, PDB code: 6f3m:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6f3m

Go back to Potassium Binding Sites List in 6f3m
Potassium binding site 1 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenosine, K+ and ZN2+ Cations


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 S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenosine, K+ and ZN2+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K505

b:20.8
occ:1.00
 O A:THR380 2.7 21.1 1.0
O A:HOH794 2.8 20.6 1.0
O A:HIS382 2.8 19.5 1.0
O A:HOH824 2.8 23.2 1.0
OG1 A:THR380 2.8 20.9 1.0
O C:HOH771 3.1 20.1 1.0
OE1 A:GLN65 3.2 21.1 1.0
NE2 A:GLN65 3.4 22.3 1.0
CD A:GLN65 3.5 21.2 1.0
CB A:THR380 3.5 21.2 1.0
C A:THR380 3.6 20.7 1.0
C A:HIS382 3.6 18.4 1.0
O A:GLY381 3.8 20.9 1.0
CA A:PRO383 4.0 18.7 1.0
N6 A:ADN502 4.1 19.9 1.0
C A:GLY381 4.1 21.6 1.0
N A:PRO383 4.2 19.4 1.0
CA A:THR380 4.2 20.4 1.0
CB C:ASP216 4.3 21.8 1.0
O A:HOH951 4.4 24.8 1.0
N A:HIS382 4.5 19.9 1.0
N A:GLY381 4.5 20.8 1.0
CG C:ASP216 4.6 22.0 1.0
CG A:GLN65 4.6 20.7 1.0
OD1 C:ASP216 4.7 21.8 1.0
C A:PRO383 4.7 19.3 1.0
CA A:HIS382 4.7 19.9 1.0
CA A:GLY381 4.7 21.1 1.0
N A:SER384 4.7 19.5 1.0
CG2 A:THR380 4.8 21.1 1.0
OE1 A:GLN91 4.8 21.9 1.0
O C:ASP216 5.0 21.9 1.0

Potassium binding site 2 out of 4 in 6f3m

Go back to Potassium Binding Sites List in 6f3m
Potassium binding site 2 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenosine, K+ and ZN2+ Cations


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 S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenosine, K+ and ZN2+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K504

b:21.5
occ:1.00
 O B:THR380 2.7 22.1 1.0
O B:HIS382 2.7 20.0 1.0
O B:HOH769 2.8 21.7 1.0
O B:HOH797 2.8 20.1 1.0
OG1 B:THR380 2.9 21.9 1.0
O D:HOH819 3.0 21.4 1.0
OE1 B:GLN65 3.2 21.9 1.0
NE2 B:GLN65 3.4 22.0 1.0
CD B:GLN65 3.4 21.6 1.0
CB B:THR380 3.6 22.6 1.0
C B:THR380 3.6 20.9 1.0
C B:HIS382 3.6 19.8 1.0
O B:GLY381 3.8 20.4 1.0
N6 B:ADN502 4.0 21.9 1.0
CA B:PRO383 4.0 19.6 1.0
C B:GLY381 4.1 19.9 1.0
CA B:THR380 4.2 21.6 1.0
N B:PRO383 4.2 19.2 1.0
CB D:ASP216 4.3 21.5 1.0
O B:HOH937 4.5 23.7 1.0
N B:HIS382 4.5 20.0 1.0
N B:GLY381 4.5 20.4 1.0
CG B:GLN65 4.6 21.9 1.0
CG D:ASP216 4.6 22.1 1.0
CA B:HIS382 4.7 19.7 1.0
C B:PRO383 4.7 19.5 1.0
OD1 D:ASP216 4.7 22.1 1.0
CA B:GLY381 4.7 20.1 1.0
N B:SER384 4.7 20.6 1.0
OE1 B:GLN91 4.8 24.7 1.0
CG2 B:THR380 4.8 22.5 1.0
O D:ASP216 5.0 20.9 1.0

Potassium binding site 3 out of 4 in 6f3m

Go back to Potassium Binding Sites List in 6f3m
Potassium binding site 3 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenosine, K+ and ZN2+ Cations


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 S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenosine, K+ and ZN2+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K505

b:19.4
occ:1.00
 O C:THR380 2.7 18.9 1.0
O C:HIS382 2.7 18.1 1.0
O C:HOH851 2.8 21.3 1.0
OG1 C:THR380 2.9 21.0 1.0
O C:HOH819 2.9 19.7 1.0
O A:HOH751 3.1 20.5 1.0
OE1 C:GLN65 3.2 19.0 1.0
NE2 C:GLN65 3.4 19.6 1.0
CD C:GLN65 3.5 19.4 1.0
CB C:THR380 3.6 21.0 1.0
C C:THR380 3.6 19.4 1.0
C C:HIS382 3.6 17.2 1.0
O C:GLY381 3.7 18.7 1.0
CA C:PRO383 4.0 16.9 1.0
N6 C:ADN502 4.1 18.9 1.0
C C:GLY381 4.1 18.6 1.0
N C:PRO383 4.2 17.5 1.0
CA C:THR380 4.2 19.9 1.0
CB A:ASP216 4.3 19.6 1.0
N C:HIS382 4.5 17.6 1.0
N C:GLY381 4.5 19.0 1.0
O C:HOH980 4.5 23.5 1.0
CG A:ASP216 4.6 21.7 1.0
OD1 A:ASP216 4.7 21.2 1.0
CG C:GLN65 4.7 18.7 1.0
CA C:HIS382 4.7 17.7 1.0
C C:PRO383 4.7 17.3 1.0
CA C:GLY381 4.7 18.9 1.0
N C:SER384 4.8 17.2 1.0
OE1 C:GLN91 4.8 20.2 1.0
CG2 C:THR380 4.8 21.9 1.0
O A:ASP216 4.9 19.9 1.0

Potassium binding site 4 out of 4 in 6f3m

Go back to Potassium Binding Sites List in 6f3m
Potassium binding site 4 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenosine, K+ and ZN2+ Cations


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 S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Complexed with Adenosine, K+ and ZN2+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K505

b:19.1
occ:1.00
 O D:THR380 2.7 18.8 1.0
O D:HIS382 2.7 17.4 1.0
O D:HOH872 2.8 19.4 1.0
O D:HOH836 2.8 20.1 1.0
OG1 D:THR380 2.8 18.8 1.0
O B:HOH756 3.1 19.5 1.0
OE1 D:GLN65 3.2 17.8 1.0
NE2 D:GLN65 3.4 18.6 1.0
CD D:GLN65 3.5 17.9 1.0
CB D:THR380 3.5 18.9 1.0
C D:THR380 3.6 18.8 1.0
C D:HIS382 3.7 17.4 1.0
O D:GLY381 3.8 17.1 1.0
CA D:PRO383 4.0 17.2 1.0
N6 D:ADN502 4.1 18.7 1.0
C D:GLY381 4.1 17.9 1.0
CA D:THR380 4.2 18.6 1.0
N D:PRO383 4.2 17.6 1.0
CB B:ASP216 4.3 20.4 1.0
O D:HOH1009 4.4 23.5 1.0
N D:HIS382 4.5 17.6 1.0
N D:GLY381 4.5 18.6 1.0
CG B:ASP216 4.5 22.1 1.0
OD1 B:ASP216 4.6 21.1 1.0
CG D:GLN65 4.6 18.0 1.0
C D:PRO383 4.7 18.4 1.0
CA D:HIS382 4.7 17.6 1.0
CA D:GLY381 4.7 18.4 1.0
N D:SER384 4.7 18.3 1.0
CG2 D:THR380 4.8 19.4 1.0
OE1 D:GLN91 4.8 20.8 1.0
O B:ASP216 4.9 20.3 1.0

Reference:

J.Czyrko, J.Sliwiak, B.Imiolczyk, Z.Gdaniec, M.Jaskolski, K.Brzezinski. Metal-Cation Regulation of Enzyme Dynamics Is A Key Factor Influencing the Activity of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa. Sci Rep V. 8 11334 2018.
ISSN: ESSN 2045-2322
PubMed: 30054521
DOI: 10.1038/S41598-018-29535-Y
Page generated: Mon Aug 12 16:04:45 2024

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