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Potassium in PDB 3q9b: Crystal Structure of Apah Complexed with M344

Protein crystallography data

The structure of Crystal Structure of Apah Complexed with M344, PDB code: 3q9b was solved by P.M.Lombardi, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.25
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 118.657, 119.734, 119.526, 98.09, 95.15, 115.33
R / Rfree (%) 17.1 / 20.2

Other elements in 3q9b:

The structure of Crystal Structure of Apah Complexed with M344 also contains other interesting chemical elements:

Zinc (Zn) 12 atoms
Sodium (Na) 12 atoms

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Potassium atom in the Crystal Structure of Apah Complexed with M344 (pdb code 3q9b). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 23 binding sites of Potassium where determined in the Crystal Structure of Apah Complexed with M344, PDB code: 3q9b:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 23 in 3q9b

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Potassium binding site 1 out of 23 in the Crystal Structure of Apah Complexed with M344


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 Apah Complexed with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K343

b:11.3
occ:1.00
OG A:SER216 2.6 9.4 1.0
O A:HIS197 2.6 13.1 1.0
O A:LEU217 2.7 14.6 1.0
O A:ASP195 2.7 14.3 1.0
OD1 A:ASP193 2.7 17.8 1.0
O A:ASP193 3.0 13.0 1.0
CG A:ASP193 3.3 16.4 1.0
C A:HIS197 3.6 13.4 1.0
C A:ASP193 3.6 13.0 1.0
C A:LEU217 3.6 14.6 1.0
CB A:ASP193 3.6 13.2 1.0
C A:ASP195 3.8 14.1 1.0
CB A:HIS218 3.8 10.6 1.0
N A:LEU217 3.8 14.1 1.0
N A:ASP195 3.8 13.8 1.0
CB A:SER216 3.9 11.8 1.0
CA A:HIS198 4.0 12.9 1.0
ND1 A:HIS218 4.1 9.4 1.0
OD2 A:ASP193 4.2 16.9 1.0
N A:HIS198 4.2 13.0 1.0
CA A:ASP193 4.2 13.2 1.0
CA A:ASP195 4.2 13.1 1.0
N A:GLY199 4.3 12.8 1.0
N A:VAL194 4.3 12.3 1.0
C A:VAL194 4.3 13.8 1.0
CA A:SER216 4.3 13.1 1.0
C A:SER216 4.4 14.3 1.0
N A:HIS218 4.4 12.4 1.0
CB A:ASP195 4.4 12.7 1.0
CA A:HIS218 4.4 13.2 1.0
CG A:HIS218 4.4 10.5 1.0
CA A:LEU217 4.4 14.2 1.0
C A:HIS198 4.5 12.6 1.0
N A:HIS197 4.5 13.1 1.0
CA A:VAL194 4.5 12.7 1.0
C A:PHE196 4.6 13.8 1.0
CA A:HIS197 4.6 12.5 1.0
O A:PHE196 4.7 13.4 1.0
O A:HOH552 4.8 8.0 1.0
N A:PHE196 4.9 13.7 1.0

Potassium binding site 2 out of 23 in 3q9b

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Potassium binding site 2 out of 23 in the Crystal Structure of Apah Complexed with M344


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 Apah Complexed with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K346

b:39.1
occ:0.60
O A:HOH1861 2.6 45.6 1.0
O A:ASP289 2.8 26.6 1.0
OG A:SER292 2.8 28.0 1.0
O A:SER292 2.8 21.9 1.0
O A:PHE286 3.0 20.9 1.0
O A:PHE294 3.2 26.1 1.0
O A:GLU287 3.3 30.2 1.0
C A:SER292 3.4 21.4 1.0
C A:GLU287 3.7 29.3 1.0
CA A:GLU287 3.8 28.8 1.0
C A:ASP289 3.9 26.6 1.0
CB A:SER292 3.9 25.4 1.0
C A:PHE286 3.9 21.7 1.0
N A:PHE293 4.0 20.3 1.0
N A:PHE294 4.0 21.5 1.0
N A:ASP289 4.0 29.5 1.0
CA A:SER292 4.1 22.8 1.0
CA A:PHE293 4.2 20.4 1.0
N A:SER292 4.3 23.1 1.0
N A:GLU287 4.3 24.6 1.0
C A:PHE294 4.4 25.4 1.0
CA A:ASP289 4.4 27.3 1.0
C A:PHE293 4.4 20.7 1.0
CB A:ASP289 4.5 27.1 1.0
N A:GLN288 4.5 30.3 1.0
O A:ASP284 4.8 20.2 1.0
C A:GLN288 4.8 31.6 1.0
O A:THR285 4.8 19.8 1.0
CA A:PHE294 4.9 23.2 1.0
N A:PRO290 5.0 26.7 1.0

Potassium binding site 3 out of 23 in 3q9b

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Potassium binding site 3 out of 23 in the Crystal Structure of Apah Complexed with M344


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 Apah Complexed with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K343

b:19.5
occ:1.00
O B:ASP195 2.6 17.6 1.0
O B:LEU217 2.7 13.9 1.0
OG B:SER216 2.7 11.8 1.0
OD1 B:ASP193 2.8 21.9 1.0
O B:ASP193 2.8 16.0 1.0
O B:HIS197 2.9 17.6 1.0
CG B:ASP193 3.3 21.7 1.0
C B:ASP193 3.4 16.4 1.0
CB B:ASP193 3.6 18.3 1.0
C B:ASP195 3.6 17.4 1.0
N B:ASP195 3.7 18.0 1.0
C B:LEU217 3.7 14.4 1.0
C B:HIS197 3.8 16.8 1.0
N B:LEU217 3.8 12.7 1.0
CB B:HIS218 3.9 13.1 1.0
CB B:SER216 4.0 12.2 1.0
CA B:ASP195 4.1 17.1 1.0
OD2 B:ASP193 4.1 21.5 1.0
CA B:ASP193 4.1 16.9 1.0
C B:VAL194 4.2 18.8 1.0
N B:VAL194 4.2 17.1 1.0
CA B:HIS198 4.2 15.2 1.0
CB B:ASP195 4.2 16.0 1.0
ND1 B:HIS218 4.3 11.0 1.0
CA B:SER216 4.4 12.8 1.0
N B:HIS198 4.4 16.0 1.0
N B:GLY199 4.4 14.2 1.0
C B:SER216 4.4 13.3 1.0
CA B:VAL194 4.4 17.4 1.0
CA B:LEU217 4.5 14.3 1.0
N B:HIS218 4.5 14.1 1.0
CA B:HIS218 4.5 13.8 1.0
O B:HOH571 4.5 12.6 1.0
N B:HIS197 4.6 16.4 1.0
CG B:HIS218 4.6 11.2 1.0
C B:HIS198 4.6 14.6 1.0
C B:PHE196 4.6 17.1 1.0
N B:PHE196 4.7 17.1 1.0
CA B:HIS197 4.8 15.6 1.0
O B:PHE196 4.8 18.3 1.0
O B:VAL194 4.9 19.9 1.0

Potassium binding site 4 out of 23 in 3q9b

Go back to Potassium Binding Sites List in 3q9b
Potassium binding site 4 out of 23 in the Crystal Structure of Apah Complexed with M344


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 Apah Complexed with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K346

b:42.0
occ:0.50
O B:HOH1756 2.6 47.1 1.0
O B:SER292 2.7 30.9 1.0
O B:ASP289 2.8 37.1 1.0
O B:GLU287 3.1 34.6 1.0
OG B:SER292 3.2 38.7 1.0
O B:PHE294 3.3 27.8 1.0
O B:PHE286 3.4 27.4 1.0
C B:SER292 3.4 32.0 1.0
C B:GLU287 3.7 35.0 1.0
CA B:PHE293 3.9 28.8 1.0
N B:PHE293 3.9 29.6 1.0
N B:PHE294 3.9 29.8 1.0
C B:ASP289 4.0 36.8 1.0
CA B:GLU287 4.0 34.5 1.0
N B:ASP289 4.2 36.9 1.0
C B:PHE293 4.2 28.5 1.0
CA B:SER292 4.3 33.5 1.0
C B:PHE286 4.3 28.0 1.0
CB B:SER292 4.4 36.8 1.0
C B:PHE294 4.4 29.8 1.0
CA B:ASP289 4.5 37.5 1.0
N B:SER292 4.6 34.2 1.0
N B:GLN288 4.6 35.8 1.0
N B:GLU287 4.6 30.9 1.0
CB B:ASP289 4.7 36.7 1.0
C B:GLN288 4.8 37.3 1.0
CA B:PHE294 4.8 29.2 1.0

Potassium binding site 5 out of 23 in 3q9b

Go back to Potassium Binding Sites List in 3q9b
Potassium binding site 5 out of 23 in the Crystal Structure of Apah Complexed with M344


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Apah Complexed with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K342

b:15.0
occ:1.00
OD1 C:ASP193 2.5 15.9 1.0
O C:LEU217 2.6 12.1 1.0
O C:ASP195 2.6 13.7 1.0
O C:HIS197 2.9 16.4 1.0
O C:ASP193 2.9 13.7 1.0
OG C:SER216 2.9 9.9 1.0
CG C:ASP193 3.1 17.5 1.0
C C:ASP193 3.5 14.3 1.0
CB C:ASP193 3.5 13.7 1.0
C C:ASP195 3.6 14.6 1.0
C C:LEU217 3.6 14.1 1.0
N C:ASP195 3.7 14.8 1.0
C C:HIS197 3.8 16.6 1.0
N C:LEU217 3.8 12.5 1.0
CB C:HIS218 3.8 11.0 1.0
OD2 C:ASP193 4.0 19.7 1.0
CB C:SER216 4.0 11.4 1.0
CA C:ASP195 4.1 13.5 1.0
CA C:ASP193 4.1 13.8 1.0
CA C:HIS198 4.1 14.5 1.0
N C:VAL194 4.1 13.7 1.0
C C:VAL194 4.2 15.3 1.0
CB C:ASP195 4.3 15.9 1.0
N C:GLY199 4.3 14.3 1.0
CA C:SER216 4.3 12.5 1.0
N C:HIS198 4.3 14.9 1.0
ND1 C:HIS218 4.4 11.6 1.0
C C:SER216 4.4 13.3 1.0
CA C:VAL194 4.4 14.3 1.0
CA C:LEU217 4.5 13.5 1.0
CA C:HIS218 4.5 12.6 1.0
N C:HIS218 4.5 11.3 1.0
CG C:HIS218 4.5 13.2 1.0
C C:HIS198 4.6 14.4 1.0
C C:PHE196 4.6 14.8 1.0
N C:HIS197 4.6 14.3 1.0
O C:PHE196 4.7 14.4 1.0
O C:HOH376 4.8 17.6 1.0
N C:PHE196 4.8 13.0 1.0
CA C:HIS197 4.8 14.7 1.0
O C:VAL194 4.9 15.6 1.0
CE1 C:HIS158 5.0 17.8 1.0

Potassium binding site 6 out of 23 in 3q9b

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Potassium binding site 6 out of 23 in the Crystal Structure of Apah Complexed with M344


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of Apah Complexed with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K345

b:35.9
occ:0.60
O C:ASP289 2.6 26.4 1.0
O C:SER292 2.7 19.1 1.0
OG C:SER292 2.9 27.3 1.0
O C:PHE286 3.0 22.8 1.0
O C:GLU287 3.2 30.0 1.0
O C:PHE294 3.3 27.6 1.0
C C:SER292 3.4 20.4 1.0
C C:GLU287 3.5 29.0 1.0
CA C:GLU287 3.7 28.5 1.0
C C:ASP289 3.7 25.8 1.0
N C:ASP289 3.8 27.7 1.0
C C:PHE286 4.0 23.6 1.0
CB C:SER292 4.1 24.9 1.0
N C:PHE293 4.1 18.8 1.0
N C:PHE294 4.2 20.9 1.0
CA C:SER292 4.2 22.5 1.0
CA C:ASP289 4.2 26.4 1.0
N C:GLU287 4.3 25.7 1.0
CA C:PHE293 4.3 18.9 1.0
N C:SER292 4.3 23.1 1.0
N C:GLN288 4.4 28.3 1.0
CB C:ASP289 4.4 26.2 1.0
C C:PHE294 4.4 25.9 1.0
C C:PHE293 4.5 18.6 1.0
C C:GLN288 4.7 28.8 1.0
N C:PRO290 4.8 25.3 1.0
CA C:GLN288 4.9 29.8 1.0
CB C:GLU287 4.9 31.6 1.0
O C:ASP284 4.9 19.1 1.0
CA C:PHE294 5.0 23.5 1.0

Potassium binding site 7 out of 23 in 3q9b

Go back to Potassium Binding Sites List in 3q9b
Potassium binding site 7 out of 23 in the Crystal Structure of Apah Complexed with M344


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of Apah Complexed with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K344

b:16.8
occ:1.00
O D:LEU217 2.6 14.8 1.0
OD1 D:ASP193 2.6 17.8 1.0
O D:ASP195 2.6 14.6 1.0
O D:HIS197 2.7 12.6 1.0
OG D:SER216 2.7 12.9 1.0
O D:ASP193 2.9 13.3 1.0
CG D:ASP193 3.2 19.2 1.0
C D:ASP193 3.5 13.3 1.0
CB D:ASP193 3.6 15.3 1.0
C D:LEU217 3.6 15.1 1.0
C D:HIS197 3.6 13.1 1.0
C D:ASP195 3.7 14.9 1.0
N D:ASP195 3.8 15.6 1.0
CB D:HIS218 3.8 12.6 1.0
N D:LEU217 3.8 13.2 1.0
CB D:SER216 3.9 13.4 1.0
OD2 D:ASP193 4.0 19.5 1.0
CA D:HIS198 4.1 13.7 1.0
CA D:ASP195 4.1 14.3 1.0
CA D:ASP193 4.2 15.2 1.0
C D:VAL194 4.2 17.4 1.0
N D:VAL194 4.2 14.3 1.0
N D:HIS198 4.3 14.4 1.0
N D:GLY199 4.3 13.0 1.0
ND1 D:HIS218 4.3 13.5 1.0
CB D:ASP195 4.3 15.2 1.0
CA D:SER216 4.3 13.8 1.0
C D:SER216 4.4 13.8 1.0
CA D:HIS218 4.4 13.7 1.0
N D:HIS218 4.5 14.1 1.0
CA D:LEU217 4.5 14.8 1.0
CA D:VAL194 4.5 16.6 1.0
CG D:HIS218 4.5 14.0 1.0
N D:HIS197 4.5 14.2 1.0
C D:HIS198 4.5 13.3 1.0
C D:PHE196 4.6 13.4 1.0
O D:HOH523 4.7 14.1 1.0
CA D:HIS197 4.7 12.2 1.0
N D:PHE196 4.8 13.8 1.0
O D:PHE196 4.8 12.8 1.0
O D:VAL194 4.9 18.7 1.0

Potassium binding site 8 out of 23 in 3q9b

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Potassium binding site 8 out of 23 in the Crystal Structure of Apah Complexed with M344


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of Apah Complexed with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K347

b:35.4
occ:0.60
OG D:SER292 2.7 28.8 1.0
O D:ASP289 2.7 26.7 1.0
O D:HOH1860 2.8 47.8 1.0
O D:PHE286 2.9 23.1 1.0
O D:SER292 2.9 22.7 1.0
O D:HOH1732 3.1 36.8 1.0
O D:PHE294 3.3 25.3 1.0
O D:GLU287 3.3 31.8 1.0
C D:SER292 3.4 24.0 1.0
C D:GLU287 3.6 30.5 1.0
CA D:GLU287 3.7 29.1 1.0
C D:ASP289 3.8 26.6 1.0
C D:PHE286 3.9 22.5 1.0
CB D:SER292 3.9 26.1 1.0
N D:PHE293 4.0 23.0 1.0
N D:PHE294 4.0 22.4 1.0
CA D:SER292 4.0 24.1 1.0
N D:ASP289 4.1 30.0 1.0
CA D:PHE293 4.2 21.9 1.0
N D:GLU287 4.2 25.5 1.0
N D:SER292 4.3 22.5 1.0
C D:PHE294 4.4 25.9 1.0
C D:PHE293 4.4 22.2 1.0
N D:GLN288 4.4 31.1 1.0
CA D:ASP289 4.4 28.4 1.0
CB D:ASP289 4.5 26.6 1.0
C D:GLN288 4.7 32.0 1.0
O D:ASP284 4.7 20.7 1.0
CA D:PHE294 4.8 24.2 1.0
O D:THR285 4.8 18.9 1.0
N D:PRO290 5.0 26.3 1.0

Potassium binding site 9 out of 23 in 3q9b

Go back to Potassium Binding Sites List in 3q9b
Potassium binding site 9 out of 23 in the Crystal Structure of Apah Complexed with M344


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Crystal Structure of Apah Complexed with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K343

b:16.6
occ:1.00
O E:ASP195 2.6 16.7 1.0
OD1 E:ASP193 2.6 18.0 1.0
O E:LEU217 2.7 16.0 1.0
O E:HIS197 2.7 17.1 1.0
OG E:SER216 2.9 10.1 1.0
O E:ASP193 2.9 15.6 1.0
CG E:ASP193 3.2 19.0 1.0
C E:ASP193 3.5 16.4 1.0
CB E:ASP193 3.6 16.8 1.0
C E:ASP195 3.6 16.7 1.0
N E:ASP195 3.7 16.6 1.0
C E:HIS197 3.7 15.8 1.0
C E:LEU217 3.7 15.0 1.0
N E:LEU217 3.9 14.6 1.0
CB E:HIS218 3.9 12.0 1.0
OD2 E:ASP193 4.0 20.1 1.0
CA E:ASP195 4.1 15.8 1.0
CB E:SER216 4.1 12.9 1.0
N E:VAL194 4.1 17.1 1.0
CA E:HIS198 4.1 14.3 1.0
C E:VAL194 4.1 17.1 1.0
CA E:ASP193 4.2 16.8 1.0
ND1 E:HIS218 4.2 11.8 1.0
CB E:ASP195 4.3 15.2 1.0
N E:GLY199 4.3 15.9 1.0
N E:HIS198 4.3 14.7 1.0
CA E:VAL194 4.4 16.8 1.0
CA E:SER216 4.5 13.1 1.0
C E:SER216 4.5 14.6 1.0
CA E:LEU217 4.5 13.9 1.0
CA E:HIS218 4.5 14.3 1.0
CG E:HIS218 4.5 13.1 1.0
N E:HIS218 4.5 13.1 1.0
C E:PHE196 4.6 16.0 1.0
C E:HIS198 4.6 14.9 1.0
N E:HIS197 4.6 15.6 1.0
O E:HOH504 4.6 18.1 1.0
O E:PHE196 4.7 15.9 1.0
CA E:HIS197 4.7 15.5 1.0
N E:PHE196 4.7 15.9 1.0
O E:VAL194 4.9 18.6 1.0
OD1 E:ASP195 5.0 16.5 1.0

Potassium binding site 10 out of 23 in 3q9b

Go back to Potassium Binding Sites List in 3q9b
Potassium binding site 10 out of 23 in the Crystal Structure of Apah Complexed with M344


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Crystal Structure of Apah Complexed with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K346

b:45.7
occ:0.50
O E:SER292 2.7 31.7 1.0
O E:ASP289 2.8 33.5 1.0
O E:HOH1766 2.8 52.2 1.0
OG E:SER292 3.0 38.8 1.0
O E:GLU287 3.0 34.4 1.0
O E:PHE286 3.1 25.8 1.0
O E:PHE294 3.3 31.1 1.0
C E:SER292 3.3 31.9 1.0
C E:GLU287 3.5 33.8 1.0
CA E:GLU287 3.8 33.8 1.0
C E:ASP289 3.9 33.6 1.0
N E:PHE293 3.9 29.2 1.0
N E:PHE294 4.0 28.6 1.0
N E:ASP289 4.1 34.5 1.0
CA E:PHE293 4.1 27.4 1.0
C E:PHE286 4.1 27.3 1.0
CB E:SER292 4.1 35.8 1.0
CA E:SER292 4.2 32.9 1.0
C E:PHE293 4.3 27.3 1.0
C E:PHE294 4.4 30.9 1.0
N E:GLU287 4.4 29.9 1.0
CA E:ASP289 4.4 33.8 1.0
N E:SER292 4.4 33.9 1.0
N E:GLN288 4.5 34.6 1.0
CB E:ASP289 4.6 33.0 1.0
C E:GLN288 4.7 35.5 1.0
CA E:PHE294 4.9 29.2 1.0
CA E:GLN288 5.0 35.7 1.0

Reference:

P.M.Lombardi, H.D.Angell, D.A.Whittington, E.F.Flynn, K.R.Rajashankar, D.W.Christianson. Structure of Prokaryotic Polyamine Deacetylase Reveals Evolutionary Functional Relationships with Eukaryotic Histone Deacetylases . Biochemistry V. 50 1808 2011.
ISSN: ISSN 0006-2960
PubMed: 21268586
DOI: 10.1021/BI101859K
Page generated: Sun Dec 13 23:21:51 2020

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