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Potassium in PDB 6uk3: Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Acanthamoeba Castellanii with Bound Nad and Adenosine

Enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Acanthamoeba Castellanii with Bound Nad and Adenosine

All present enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Acanthamoeba Castellanii with Bound Nad and Adenosine:
3.3.1.1;

Protein crystallography data

The structure of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Acanthamoeba Castellanii with Bound Nad and Adenosine, PDB code: 6uk3 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 96.030, 112.730, 105.920, 90.00, 114.73, 90.00
R / Rfree (%) 13 / 16.1

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Acanthamoeba Castellanii with Bound Nad and Adenosine (pdb code 6uk3). 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 Acanthamoeba Castellanii with Bound Nad and Adenosine, PDB code: 6uk3:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6uk3

Go back to Potassium Binding Sites List in 6uk3
Potassium binding site 1 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Acanthamoeba Castellanii with Bound Nad and Adenosine


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 Acanthamoeba Castellanii with Bound Nad and Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K504

b:13.3
occ:0.72
 O A:THR398 2.7 13.1 1.0
O A:HIS400 2.8 12.3 1.0
O A:HOH934 2.9 15.1 1.0
OG1 A:THR398 2.9 14.6 1.0
O A:HOH879 2.9 13.7 1.0
O D:HOH702 2.9 13.4 1.0
OE1 A:GLN68 3.1 13.4 1.0
CD A:GLN68 3.5 12.4 1.0
NE2 A:GLN68 3.5 13.1 1.0
CB A:THR398 3.5 13.6 1.0
C A:THR398 3.6 12.1 1.0
O A:GLY399 3.6 11.2 1.0
C A:HIS400 3.7 11.9 1.0
N6 A:ADN502 3.9 12.7 1.0
C A:GLY399 4.0 11.4 1.0
CA A:PRO401 4.1 11.3 1.0
CA A:THR398 4.2 12.9 1.0
N A:PRO401 4.2 11.7 1.0
CB D:ASP254 4.3 13.3 1.0
N A:GLY399 4.5 12.5 1.0
O A:HOH1000 4.5 14.1 1.0
N A:HIS400 4.5 11.9 1.0
CG D:ASP254 4.6 14.1 1.0
NE2 A:GLN94 4.6 18.5 1.0
CG A:GLN68 4.6 12.1 1.0
CA A:GLY399 4.6 12.4 1.0
OD1 D:ASP254 4.7 14.8 1.0
CA A:HIS400 4.7 11.5 1.0
C A:PRO401 4.7 11.2 1.0
N A:SER402 4.8 11.2 1.0
CG2 A:THR398 4.8 15.8 1.0
O D:HOH710 4.9 16.4 1.0
O D:ASP254 4.9 13.9 1.0

Potassium binding site 2 out of 4 in 6uk3

Go back to Potassium Binding Sites List in 6uk3
Potassium binding site 2 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Acanthamoeba Castellanii with Bound Nad and Adenosine


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 Acanthamoeba Castellanii with Bound Nad and Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K507

b:13.2
occ:0.76
 O B:THR398 2.8 12.6 1.0
O B:HIS400 2.8 11.7 1.0
O B:HOH897 2.9 14.4 1.0
O B:HOH844 2.9 15.0 1.0
OG1 B:THR398 2.9 13.8 1.0
O C:HOH728 2.9 13.1 1.0
OE1 B:GLN68 3.1 13.5 1.0
NE2 B:GLN68 3.4 13.5 1.0
CD B:GLN68 3.4 12.7 1.0
CB B:THR398 3.5 12.9 1.0
C B:THR398 3.6 11.1 1.0
O B:GLY399 3.6 11.7 1.0
C B:HIS400 3.7 11.1 1.0
N6 B:ADN502 3.9 12.3 1.0
C B:GLY399 4.0 11.9 1.0
CA B:PRO401 4.1 11.4 1.0
CA B:THR398 4.2 11.6 1.0
N B:PRO401 4.2 11.6 1.0
CB C:ASP254 4.3 12.6 1.0
N B:GLY399 4.5 11.2 1.0
O B:HOH957 4.5 14.2 1.0
N B:HIS400 4.5 11.5 1.0
CG C:ASP254 4.6 12.9 1.0
NE2 B:GLN94 4.6 16.7 1.0
CG B:GLN68 4.6 12.8 1.0
CA B:GLY399 4.6 12.0 1.0
OD1 C:ASP254 4.7 13.8 1.0
CA B:HIS400 4.7 11.4 1.0
C B:PRO401 4.7 11.3 1.0
N B:SER402 4.8 11.1 1.0
CG2 B:THR398 4.9 13.9 1.0
O C:HOH737 4.9 16.8 1.0
O C:ASP254 5.0 12.7 1.0

Potassium binding site 3 out of 4 in 6uk3

Go back to Potassium Binding Sites List in 6uk3
Potassium binding site 3 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Acanthamoeba Castellanii with Bound Nad and Adenosine


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 Acanthamoeba Castellanii with Bound Nad and Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K506

b:13.8
occ:0.77
 O C:THR398 2.8 12.3 1.0
O C:HIS400 2.8 12.8 1.0
O C:HOH853 2.9 13.5 1.0
O B:HOH710 2.9 13.3 1.0
OG1 C:THR398 2.9 13.0 1.0
O C:HOH906 2.9 15.3 1.0
OE1 C:GLN68 3.2 13.6 1.0
NE2 C:GLN68 3.4 13.5 1.0
CD C:GLN68 3.5 12.8 1.0
CB C:THR398 3.5 13.1 1.0
O C:GLY399 3.6 12.2 1.0
C C:THR398 3.6 11.2 1.0
C C:HIS400 3.7 12.3 1.0
N6 C:ADN502 4.0 12.9 1.0
C C:GLY399 4.0 11.4 1.0
CA C:PRO401 4.0 12.5 1.0
N C:PRO401 4.2 12.7 1.0
CA C:THR398 4.2 12.0 1.0
CB B:ASP254 4.3 12.5 1.0
O C:HOH974 4.4 13.7 1.0
N C:GLY399 4.5 11.1 1.0
N C:HIS400 4.5 11.9 1.0
CG B:ASP254 4.5 13.0 1.0
NE2 C:GLN94 4.6 17.0 1.0
CG C:GLN68 4.6 13.5 1.0
OD1 B:ASP254 4.6 13.0 1.0
CA C:GLY399 4.6 11.9 1.0
C C:PRO401 4.7 12.6 1.0
CA C:HIS400 4.7 11.8 1.0
N C:SER402 4.8 11.6 1.0
CG2 C:THR398 4.9 14.5 1.0
O B:HOH718 4.9 16.2 1.0
O B:ASP254 4.9 13.0 1.0

Potassium binding site 4 out of 4 in 6uk3

Go back to Potassium Binding Sites List in 6uk3
Potassium binding site 4 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Acanthamoeba Castellanii with Bound Nad and Adenosine


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 Acanthamoeba Castellanii with Bound Nad and Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K508

b:15.5
occ:0.78
 O D:THR398 2.8 15.0 1.0
O D:HIS400 2.8 14.4 1.0
O D:HOH915 2.9 16.0 1.0
O D:HOH857 2.9 16.6 1.0
OG1 D:THR398 2.9 15.3 1.0
O A:HOH698 2.9 15.1 1.0
OE1 D:GLN68 3.2 14.8 1.0
NE2 D:GLN68 3.4 14.9 1.0
CD D:GLN68 3.5 14.5 1.0
CB D:THR398 3.5 14.4 1.0
O D:GLY399 3.6 13.2 1.0
C D:THR398 3.6 13.3 1.0
C D:HIS400 3.7 13.9 1.0
N6 D:ADN502 4.0 14.0 1.0
C D:GLY399 4.0 12.9 1.0
CA D:PRO401 4.0 13.1 1.0
CA D:THR398 4.2 13.6 1.0
N D:PRO401 4.2 14.0 1.0
CB A:ASP254 4.3 14.6 1.0
O D:HOH959 4.4 16.4 1.0
N D:GLY399 4.5 13.0 1.0
N D:HIS400 4.5 13.5 1.0
CG A:ASP254 4.5 14.4 1.0
NE2 D:GLN94 4.6 19.9 1.0
CG D:GLN68 4.6 14.5 1.0
CA D:GLY399 4.6 13.6 1.0
OD1 A:ASP254 4.7 15.6 1.0
CA D:HIS400 4.7 13.2 1.0
C D:PRO401 4.7 12.9 1.0
N D:SER402 4.8 13.2 1.0
CG2 D:THR398 4.8 16.1 1.0
O A:HOH713 4.9 18.4 1.0
O A:ASP254 5.0 14.7 1.0

Reference:

C.T.Romanaggi, D.M.Dranow, J.Abendroth, D.D.Lorimer, P.S.Horanyi, T.E.Edwards. Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Acanthamoeba Castellanii with Bound Nad and Adenosine To Be Published.
Page generated: Mon Aug 12 17:50:11 2024

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