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Potassium in PDB 3men: Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak

Protein crystallography data

The structure of Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak, PDB code: 3men 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 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.700, 162.120, 173.070, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 23.7

Other elements in 3men:

The structure of Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak also contains other interesting chemical elements:

Iodine (I) 35 atoms
Zinc (Zn) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak (pdb code 3men). 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 Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak, PDB code: 3men:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 3men

Go back to Potassium Binding Sites List in 3men
Potassium binding site 1 out of 4 in the Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak


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 Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K402

b:29.8
occ:1.00
 OD1 A:ASP190 2.8 8.6 1.0
O A:ASP192 2.8 9.4 1.0
O A:ILE214 2.8 8.6 1.0
OG A:SER213 2.9 10.1 1.0
O A:HIS194 2.9 9.4 1.0
O A:ASP190 2.9 7.4 1.0
CG A:ASP190 3.1 8.7 1.0
C A:ASP190 3.5 9.4 1.0
OD2 A:ASP190 3.7 13.5 1.0
C A:HIS194 3.7 9.4 1.0
N A:ASP192 3.7 10.1 1.0
C A:ASP192 3.8 10.2 1.0
CB A:ASP190 3.8 7.9 1.0
C A:ILE214 3.8 10.2 1.0
CB A:HIS215 3.9 9.6 1.0
CB A:SER213 4.0 9.4 1.0
N A:ILE214 4.1 10.0 1.0
CA A:ASP192 4.1 10.5 1.0
CA A:HIS195 4.1 8.5 1.0
N A:THR191 4.1 10.3 1.0
C A:THR191 4.2 10.8 1.0
CB A:ASP192 4.2 11.1 1.0
N A:HIS195 4.3 8.0 1.0
ND1 A:HIS215 4.3 11.7 1.0
CA A:ASP190 4.3 8.8 1.0
N A:GLY196 4.3 8.9 1.0
CA A:THR191 4.3 11.2 1.0
CA A:SER213 4.4 8.7 1.0
C A:SER213 4.5 9.3 1.0
N A:HIS194 4.5 10.0 1.0
CA A:HIS215 4.5 11.2 1.0
C A:HIS195 4.6 8.3 1.0
N A:HIS215 4.6 10.5 1.0
CG A:HIS215 4.6 11.9 1.0
CA A:ILE214 4.7 10.8 1.0
OH A:TYR211 4.7 7.2 1.0
CA A:HIS194 4.7 10.5 1.0
CE1 A:HIS156 4.7 11.0 1.0
ND1 A:HIS156 4.8 6.9 1.0
N A:MET193 4.9 10.4 1.0
O A:HOH386 4.9 9.0 1.0
C A:MET193 5.0 11.0 1.0
O A:THR191 5.0 10.6 1.0

Potassium binding site 2 out of 4 in 3men

Go back to Potassium Binding Sites List in 3men
Potassium binding site 2 out of 4 in the Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak


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 Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K402

b:39.2
occ:1.00
 O B:ILE214 2.7 15.4 1.0
O B:ASP192 2.7 16.2 1.0
OD1 B:ASP190 2.7 20.0 1.0
OG B:SER213 2.8 18.6 1.0
O B:HIS194 2.9 14.3 1.0
O B:ASP190 3.0 17.0 1.0
CG B:ASP190 3.2 19.6 1.0
C B:ASP190 3.6 17.7 1.0
C B:ASP192 3.6 15.9 1.0
N B:ASP192 3.6 17.6 1.0
C B:ILE214 3.6 16.8 1.0
OD2 B:ASP190 3.7 18.0 1.0
C B:HIS194 3.7 17.2 1.0
CB B:ASP190 3.8 18.9 1.0
CB B:HIS215 3.8 16.9 1.0
N B:ILE214 4.0 17.7 1.0
CA B:ASP192 4.0 16.9 1.0
CB B:SER213 4.0 19.3 1.0
C B:THR191 4.1 18.1 1.0
ND1 B:HIS215 4.1 20.8 1.0
N B:THR191 4.2 18.2 1.0
CB B:ASP192 4.2 17.3 1.0
CA B:HIS195 4.3 18.1 1.0
CA B:ASP190 4.3 18.7 1.0
CA B:THR191 4.3 18.3 1.0
N B:HIS195 4.3 17.7 1.0
N B:GLY196 4.4 19.2 1.0
N B:HIS194 4.4 16.8 1.0
CA B:SER213 4.4 19.5 1.0
CG B:HIS215 4.4 18.4 1.0
CA B:HIS215 4.5 17.5 1.0
N B:HIS215 4.5 17.9 1.0
CA B:ILE214 4.5 17.3 1.0
C B:SER213 4.5 19.0 1.0
C B:MET193 4.7 15.5 1.0
C B:HIS195 4.7 18.4 1.0
CA B:HIS194 4.7 17.2 1.0
CE1 B:HIS156 4.7 15.3 1.0
N B:MET193 4.7 15.6 1.0
O B:THR191 4.8 18.3 1.0
O B:HOH425 4.8 20.0 1.0
OH B:TYR211 4.9 17.3 1.0
ND1 B:HIS156 4.9 12.1 1.0

Potassium binding site 3 out of 4 in 3men

Go back to Potassium Binding Sites List in 3men
Potassium binding site 3 out of 4 in the Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak


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 Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K402

b:57.9
occ:1.00
 O C:HIS194 2.8 25.8 1.0
OD1 C:ASP190 2.8 27.6 1.0
O C:ASP192 2.8 28.3 1.0
O C:ASP190 2.9 30.3 1.0
O C:ILE214 3.1 29.2 1.0
OG C:SER213 3.1 27.2 1.0
CG C:ASP190 3.2 29.0 1.0
C C:ASP190 3.5 30.0 1.0
N C:ASP192 3.5 30.5 1.0
C C:HIS194 3.7 26.7 1.0
OD2 C:ASP190 3.7 28.3 1.0
C C:ASP192 3.7 29.6 1.0
CB C:ASP190 3.8 28.8 1.0
C C:ILE214 4.0 28.7 1.0
CA C:ASP192 4.0 30.5 1.0
C C:THR191 4.1 31.6 1.0
CB C:HIS215 4.1 28.0 1.0
N C:THR191 4.1 30.0 1.0
N C:ILE214 4.1 28.1 1.0
CB C:ASP192 4.2 29.8 1.0
CA C:HIS195 4.2 25.1 1.0
CB C:SER213 4.3 26.7 1.0
N C:HIS195 4.3 25.5 1.0
ND1 C:HIS215 4.3 27.1 1.0
CA C:ASP190 4.3 29.5 1.0
CA C:THR191 4.3 31.1 1.0
N C:GLY196 4.4 24.8 1.0
N C:HIS194 4.4 27.7 1.0
CE1 C:HIS156 4.6 26.4 1.0
CA C:SER213 4.6 27.2 1.0
CG C:HIS215 4.6 28.4 1.0
ND1 C:HIS156 4.6 26.1 1.0
C C:SER213 4.7 27.6 1.0
C C:HIS195 4.7 25.0 1.0
CA C:HIS194 4.7 27.2 1.0
OH C:TYR211 4.7 24.0 1.0
CA C:ILE214 4.7 28.9 1.0
CA C:HIS215 4.7 29.5 1.0
N C:HIS215 4.8 29.3 1.0
O C:THR191 4.9 32.7 1.0
OD2 C:ASP192 4.9 33.0 1.0
N C:MET193 4.9 29.5 1.0
C C:MET193 4.9 28.7 1.0
O C:HOH386 4.9 29.5 1.0

Potassium binding site 4 out of 4 in 3men

Go back to Potassium Binding Sites List in 3men
Potassium binding site 4 out of 4 in the Crystal Structure of Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak


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 Acetylpolyamine Aminohydrolase From Burkholderia Pseudomallei, Iodide Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K402

b:37.9
occ:1.00
 OD1 D:ASP190 2.7 17.9 1.0
OG D:SER213 2.7 15.5 1.0
O D:ASP190 2.8 17.4 1.0
O D:ILE214 2.9 18.9 1.0
O D:ASP192 2.9 20.4 1.0
O D:HIS194 3.0 16.1 1.0
CG D:ASP190 3.1 17.0 1.0
C D:ASP190 3.4 18.3 1.0
OD2 D:ASP190 3.6 15.6 1.0
CB D:ASP190 3.7 16.8 1.0
N D:ASP192 3.8 20.6 1.0
C D:ILE214 3.8 19.7 1.0
C D:HIS194 3.8 17.3 1.0
C D:ASP192 3.9 20.9 1.0
N D:ILE214 3.9 18.9 1.0
CB D:SER213 4.0 16.4 1.0
CB D:HIS215 4.1 20.5 1.0
N D:THR191 4.1 19.6 1.0
CA D:ASP192 4.2 20.7 1.0
CA D:ASP190 4.2 17.3 1.0
CA D:HIS195 4.2 15.9 1.0
C D:THR191 4.2 21.3 1.0
CB D:ASP192 4.3 20.4 1.0
ND1 D:HIS215 4.3 17.0 1.0
N D:GLY196 4.4 14.5 1.0
CA D:SER213 4.4 16.9 1.0
N D:HIS195 4.4 16.4 1.0
CA D:THR191 4.4 20.7 1.0
C D:SER213 4.5 18.2 1.0
CA D:ILE214 4.5 19.8 1.0
OH D:TYR211 4.6 11.8 1.0
N D:HIS215 4.6 20.2 1.0
N D:HIS194 4.7 19.8 1.0
CG D:HIS215 4.7 17.4 1.0
CA D:HIS215 4.7 21.0 1.0
C D:HIS195 4.7 15.7 1.0
CE1 D:HIS156 4.8 17.5 1.0
ND1 D:HIS156 4.9 14.3 1.0
CA D:HIS194 4.9 19.1 1.0
C D:MET193 5.0 21.6 1.0
N D:MET193 5.0 22.1 1.0

Reference:

J.Abendroth, A.S.Gardberg, J.I.Robinson, J.S.Christensen, B.L.Staker, P.J.Myler, L.J.Stewart, T.E.Edwards. Sad Phasing Using Iodide Ions in A High-Throughput Structural Genomics Environment. J Struct Funct Genomics V. 12 83 2011.
PubMed: 21359836
DOI: 10.1007/S10969-011-9101-7
Page generated: Mon Aug 12 08:46:48 2024

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