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Sodium in PDB 3q9f: Crystal Structure of Apah Complexed with Caps

Protein crystallography data

The structure of Crystal Structure of Apah Complexed with Caps, PDB code: 3q9f 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 / 2.35
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 118.252, 119.651, 119.571, 98.34, 94.94, 114.95
R / Rfree (%) 18.9 / 22.5

Other elements in 3q9f:

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

Potassium (K) 20 atoms
Zinc (Zn) 12 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Apah Complexed with Caps (pdb code 3q9f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the Crystal Structure of Apah Complexed with Caps, PDB code: 3q9f:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 3q9f

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Sodium binding site 1 out of 12 in the Crystal Structure of Apah Complexed with Caps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Apah Complexed with Caps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na343

b:14.7
occ:1.00
O A:PHE206 2.5 28.6 1.0
OG1 A:THR243 2.6 34.7 1.0
O A:VAL212 2.6 30.4 1.0
O A:HOH376 2.7 26.2 1.0
O A:THR243 2.9 33.3 1.0
O A:ARG209 2.9 36.7 1.0
O A:HOH712 3.2 28.5 1.0
CB A:THR243 3.4 34.4 1.0
C A:PHE206 3.5 28.6 1.0
C A:THR243 3.7 33.1 1.0
OG1 A:THR244 3.7 34.1 1.0
CB A:PHE206 3.8 27.1 1.0
C A:VAL212 3.8 30.5 1.0
C A:ARG209 4.1 34.2 1.0
CA A:THR243 4.2 33.1 1.0
CA A:PHE206 4.3 27.8 1.0
N A:PHE214 4.4 31.0 1.0
CA A:PHE213 4.4 29.2 1.0
N A:TYR207 4.4 27.2 1.0
O A:GLY240 4.5 30.8 1.0
CA A:TYR207 4.5 27.6 1.0
N A:ARG209 4.6 29.5 1.0
N A:PHE213 4.6 29.5 1.0
C A:TYR207 4.6 30.1 1.0
CG2 A:THR243 4.6 34.8 1.0
N A:THR244 4.7 33.9 1.0
O A:TYR207 4.8 32.5 1.0
C A:PHE213 4.8 30.4 1.0
CA A:ARG209 4.8 31.8 1.0
CB A:PHE214 4.8 28.4 1.0
CB A:ARG209 4.8 31.6 1.0
CA A:VAL212 4.9 30.5 1.0
CA A:GLY240 4.9 28.4 1.0
CB A:THR244 5.0 34.7 1.0

Sodium binding site 2 out of 12 in 3q9f

Go back to Sodium Binding Sites List in 3q9f
Sodium binding site 2 out of 12 in the Crystal Structure of Apah Complexed with Caps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Apah Complexed with Caps within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na343

b:13.2
occ:1.00
O B:HOH347 2.6 24.6 1.0
O B:PHE206 2.7 30.3 1.0
OG1 B:THR243 2.7 34.7 1.0
O B:VAL212 2.7 34.6 1.0
O B:ARG209 2.8 35.8 1.0
O B:THR243 2.8 33.0 1.0
O B:HOH794 3.1 40.4 1.0
CB B:THR243 3.4 34.8 1.0
C B:PHE206 3.6 28.7 1.0
C B:THR243 3.6 33.4 1.0
OG1 B:THR244 3.8 37.0 1.0
CB B:PHE206 4.0 26.9 1.0
C B:VAL212 4.0 34.0 1.0
C B:ARG209 4.0 34.7 1.0
CA B:THR243 4.1 34.1 1.0
N B:TYR207 4.4 29.6 1.0
CA B:PHE206 4.4 28.0 1.0
O B:GLY240 4.4 30.5 1.0
CA B:TYR207 4.5 28.3 1.0
N B:PHE214 4.5 30.1 1.0
N B:THR244 4.5 32.2 1.0
CA B:PHE213 4.6 32.1 1.0
O B:TYR207 4.6 26.1 1.0
C B:TYR207 4.6 29.7 1.0
N B:ARG209 4.6 32.1 1.0
N B:PHE213 4.7 32.5 1.0
CG2 B:THR243 4.8 35.2 1.0
CA B:ARG209 4.8 33.4 1.0
CA B:GLY240 4.8 30.1 1.0
CB B:PHE214 4.9 26.2 1.0
CB B:THR244 4.9 34.2 1.0
C B:PHE213 4.9 31.1 1.0
N B:THR243 4.9 35.1 1.0
CA B:THR244 5.0 32.5 1.0
N B:GLY210 5.0 36.5 1.0

Sodium binding site 3 out of 12 in 3q9f

Go back to Sodium Binding Sites List in 3q9f
Sodium binding site 3 out of 12 in the Crystal Structure of Apah Complexed with Caps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Apah Complexed with Caps within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na343

b:14.8
occ:1.00
O C:VAL212 2.6 32.7 1.0
O C:PHE206 2.6 26.9 1.0
O C:HOH366 2.6 26.8 1.0
OG1 C:THR243 2.6 31.4 1.0
O C:ARG209 2.8 32.5 1.0
O C:THR243 2.9 27.6 1.0
CB C:THR243 3.3 31.0 1.0
O C:HOH576 3.4 22.6 1.0
C C:THR243 3.6 28.5 1.0
C C:PHE206 3.6 27.5 1.0
C C:VAL212 3.8 31.2 1.0
CB C:PHE206 3.8 28.2 1.0
OG1 C:THR244 4.0 32.3 1.0
C C:ARG209 4.1 34.2 1.0
CA C:THR243 4.1 29.1 1.0
CA C:PHE206 4.4 28.4 1.0
CA C:PHE213 4.4 28.6 1.0
N C:PHE214 4.4 28.8 1.0
O C:GLY240 4.5 32.7 1.0
CG2 C:THR243 4.5 31.7 1.0
N C:PHE213 4.6 29.0 1.0
N C:TYR207 4.6 24.6 1.0
N C:THR244 4.6 28.9 1.0
N C:ARG209 4.6 32.2 1.0
CA C:TYR207 4.6 27.0 1.0
C C:PHE213 4.7 27.8 1.0
C C:TYR207 4.8 29.7 1.0
CA C:ARG209 4.8 34.1 1.0
CA C:GLY240 4.8 30.9 1.0
CA C:VAL212 4.8 30.6 1.0
CB C:PHE214 4.9 27.4 1.0
O C:TYR207 4.9 29.6 1.0
N C:THR243 5.0 28.8 1.0
N C:VAL212 5.0 31.8 1.0

Sodium binding site 4 out of 12 in 3q9f

Go back to Sodium Binding Sites List in 3q9f
Sodium binding site 4 out of 12 in the Crystal Structure of Apah Complexed with Caps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Apah Complexed with Caps within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na343

b:14.8
occ:1.00
O D:PHE206 2.5 29.4 1.0
O D:HOH366 2.6 19.9 1.0
O D:VAL212 2.7 34.7 1.0
OG1 D:THR243 2.7 30.1 1.0
O D:THR243 2.8 31.7 1.0
O D:ARG209 2.8 34.9 1.0
O D:HOH690 3.2 31.9 1.0
CB D:THR243 3.5 28.7 1.0
C D:PHE206 3.5 27.4 1.0
C D:THR243 3.6 31.9 1.0
OG1 D:THR244 3.7 35.8 1.0
CB D:PHE206 4.0 22.6 1.0
C D:VAL212 4.0 32.2 1.0
C D:ARG209 4.0 34.2 1.0
CA D:THR243 4.1 29.9 1.0
O D:GLY240 4.3 30.5 1.0
CA D:PHE206 4.4 25.6 1.0
N D:TYR207 4.4 27.2 1.0
CA D:TYR207 4.5 27.7 1.0
N D:ARG209 4.5 34.3 1.0
O D:TYR207 4.5 30.8 1.0
C D:TYR207 4.5 30.4 1.0
N D:PHE214 4.5 27.3 1.0
CA D:PHE213 4.6 30.6 1.0
N D:THR244 4.6 31.4 1.0
CA D:ARG209 4.7 34.1 1.0
CA D:GLY240 4.7 29.1 1.0
N D:PHE213 4.7 29.9 1.0
CG2 D:THR243 4.8 29.4 1.0
N D:THR243 4.9 30.4 1.0
CB D:THR244 4.9 35.0 1.0
C D:PHE213 5.0 29.7 1.0
CB D:ARG209 5.0 32.7 1.0
CA D:THR244 5.0 32.3 1.0

Sodium binding site 5 out of 12 in 3q9f

Go back to Sodium Binding Sites List in 3q9f
Sodium binding site 5 out of 12 in the Crystal Structure of Apah Complexed with Caps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Apah Complexed with Caps within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na343

b:16.1
occ:1.00
O E:PHE206 2.4 26.0 1.0
OG1 E:THR243 2.5 32.1 1.0
O E:VAL212 2.6 33.0 1.0
O E:HOH359 2.7 27.1 1.0
O E:ARG209 2.9 33.4 1.0
O E:THR243 3.0 31.1 1.0
O E:HOH558 3.0 30.2 1.0
CB E:THR243 3.3 31.8 1.0
C E:PHE206 3.5 25.8 1.0
C E:THR243 3.7 31.0 1.0
C E:VAL212 3.9 31.7 1.0
CB E:PHE206 3.9 24.1 1.0
OG1 E:THR244 4.0 26.5 1.0
C E:ARG209 4.1 34.0 1.0
CA E:THR243 4.1 30.9 1.0
CA E:PHE206 4.3 25.2 1.0
N E:TYR207 4.4 26.4 1.0
O E:GLY240 4.5 32.3 1.0
CA E:TYR207 4.5 27.9 1.0
CG2 E:THR243 4.5 32.5 1.0
N E:PHE214 4.5 29.0 1.0
CA E:PHE213 4.5 29.4 1.0
O E:TYR207 4.5 29.6 1.0
C E:TYR207 4.6 29.6 1.0
N E:ARG209 4.6 33.3 1.0
N E:THR244 4.6 30.5 1.0
N E:PHE213 4.7 29.9 1.0
CA E:ARG209 4.8 33.5 1.0
C E:PHE213 4.9 29.2 1.0
CA E:GLY240 4.9 29.8 1.0
CA E:VAL212 4.9 30.5 1.0
N E:THR243 4.9 31.3 1.0
CB E:PHE214 5.0 27.9 1.0

Sodium binding site 6 out of 12 in 3q9f

Go back to Sodium Binding Sites List in 3q9f
Sodium binding site 6 out of 12 in the Crystal Structure of Apah Complexed with Caps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Apah Complexed with Caps within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na343

b:27.5
occ:1.00
O F:PHE206 2.5 37.1 1.0
OG1 F:THR243 2.5 48.4 1.0
O F:THR243 2.7 45.1 1.0
O F:VAL212 2.7 44.4 1.0
O F:HOH367 2.9 29.2 1.0
O F:ARG209 3.0 44.7 1.0
CB F:THR243 3.2 46.1 1.0
O F:HOH507 3.3 48.2 1.0
C F:THR243 3.5 45.1 1.0
C F:PHE206 3.5 36.6 1.0
OG1 F:THR244 3.7 39.4 1.0
CB F:PHE206 3.8 33.9 1.0
C F:VAL212 3.9 42.9 1.0
CA F:THR243 4.0 45.6 1.0
C F:ARG209 4.2 43.5 1.0
CA F:PHE206 4.3 35.5 1.0
N F:TYR207 4.4 37.3 1.0
N F:PHE214 4.4 41.2 1.0
CA F:PHE213 4.4 42.0 1.0
CA F:TYR207 4.4 36.6 1.0
N F:THR244 4.5 43.5 1.0
CG2 F:THR243 4.5 45.5 1.0
O F:GLY240 4.6 46.7 1.0
N F:PHE213 4.6 42.3 1.0
O F:TYR207 4.6 34.5 1.0
C F:TYR207 4.6 35.6 1.0
N F:ARG209 4.7 42.7 1.0
C F:PHE213 4.8 43.0 1.0
N F:THR243 4.8 45.9 1.0
CB F:THR244 4.9 40.4 1.0
CA F:THR244 4.9 40.7 1.0
CA F:ARG209 4.9 42.9 1.0
CB F:PHE214 5.0 39.3 1.0
CA F:VAL212 5.0 42.6 1.0

Sodium binding site 7 out of 12 in 3q9f

Go back to Sodium Binding Sites List in 3q9f
Sodium binding site 7 out of 12 in the Crystal Structure of Apah Complexed with Caps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Apah Complexed with Caps within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na343

b:16.1
occ:1.00
OG1 G:THR243 2.5 35.0 1.0
O G:HOH361 2.6 23.7 1.0
O G:PHE206 2.7 27.6 1.0
O G:VAL212 2.7 32.1 1.0
O G:THR243 3.1 31.6 1.0
O G:ARG209 3.1 33.9 1.0
CB G:THR243 3.3 33.8 1.0
O G:HOH1147 3.3 39.2 1.0
C G:PHE206 3.6 28.1 1.0
C G:THR243 3.7 31.7 1.0
C G:VAL212 3.9 31.1 1.0
CB G:PHE206 4.0 24.6 1.0
OG1 G:THR244 4.0 24.8 1.0
CA G:THR243 4.1 32.4 1.0
C G:ARG209 4.2 33.7 1.0
O G:GLY240 4.4 31.8 1.0
O G:TYR207 4.4 31.8 1.0
CA G:PHE206 4.4 26.5 1.0
N G:TYR207 4.5 27.6 1.0
CG2 G:THR243 4.5 33.5 1.0
N G:PHE214 4.5 27.9 1.0
CA G:PHE213 4.5 30.3 1.0
CA G:TYR207 4.6 28.9 1.0
C G:TYR207 4.6 30.3 1.0
N G:THR244 4.6 30.2 1.0
N G:ARG209 4.6 34.1 1.0
N G:PHE213 4.7 29.8 1.0
CA G:GLY240 4.8 29.0 1.0
CA G:ARG209 4.8 33.9 1.0
CB G:ARG209 4.9 34.6 1.0
N G:THR243 4.9 31.8 1.0
CA G:VAL212 4.9 29.9 1.0
C G:PHE213 5.0 30.6 1.0

Sodium binding site 8 out of 12 in 3q9f

Go back to Sodium Binding Sites List in 3q9f
Sodium binding site 8 out of 12 in the Crystal Structure of Apah Complexed with Caps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Apah Complexed with Caps within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na343

b:24.1
occ:1.00
O H:PHE206 2.5 32.2 1.0
OG1 H:THR243 2.7 34.0 1.0
O H:VAL212 2.7 40.7 1.0
O H:HOH362 2.8 19.7 1.0
O H:THR243 2.9 37.7 1.0
O H:ARG209 2.9 42.3 1.0
CB H:THR243 3.4 36.4 1.0
O H:HOH642 3.5 32.5 1.0
C H:PHE206 3.5 34.7 1.0
C H:THR243 3.7 37.0 1.0
CB H:PHE206 3.8 33.8 1.0
OG1 H:THR244 3.9 35.3 1.0
C H:VAL212 3.9 37.5 1.0
C H:ARG209 4.1 41.1 1.0
CA H:THR243 4.2 37.0 1.0
CA H:PHE206 4.3 34.4 1.0
N H:TYR207 4.3 35.4 1.0
O H:GLY240 4.3 39.9 1.0
CA H:TYR207 4.4 36.1 1.0
O H:TYR207 4.4 37.2 1.0
C H:TYR207 4.5 37.8 1.0
N H:ARG209 4.5 41.8 1.0
N H:PHE214 4.5 35.7 1.0
CA H:PHE213 4.6 35.5 1.0
CG2 H:THR243 4.7 36.3 1.0
N H:THR244 4.7 34.8 1.0
N H:PHE213 4.7 36.1 1.0
CA H:ARG209 4.8 40.9 1.0
CA H:GLY240 4.8 40.3 1.0
CA H:VAL212 4.9 37.6 1.0
C H:PHE213 5.0 35.5 1.0
N H:THR243 5.0 38.5 1.0
CB H:ARG209 5.0 39.4 1.0

Sodium binding site 9 out of 12 in 3q9f

Go back to Sodium Binding Sites List in 3q9f
Sodium binding site 9 out of 12 in the Crystal Structure of Apah Complexed with Caps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Apah Complexed with Caps within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na343

b:20.4
occ:1.00
OG1 I:THR243 2.3 37.4 1.0
O I:PHE206 2.6 29.8 1.0
O I:VAL212 2.7 34.3 1.0
O I:HOH369 2.8 28.0 1.0
O I:ARG209 2.9 40.7 1.0
O I:THR243 3.0 34.3 1.0
CB I:THR243 3.2 35.5 1.0
O I:HOH935 3.4 31.9 1.0
C I:PHE206 3.6 30.5 1.0
C I:THR243 3.6 34.4 1.0
C I:VAL212 4.0 33.2 1.0
CA I:THR243 4.0 35.4 1.0
CB I:PHE206 4.0 27.1 1.0
OG1 I:THR244 4.1 30.6 1.0
C I:ARG209 4.1 38.8 1.0
N I:TYR207 4.4 30.6 1.0
O I:GLY240 4.4 32.1 1.0
CG2 I:THR243 4.4 35.9 1.0
CA I:TYR207 4.4 30.4 1.0
CA I:PHE206 4.4 29.3 1.0
N I:PHE214 4.5 29.1 1.0
C I:TYR207 4.5 33.0 1.0
N I:ARG209 4.5 38.9 1.0
O I:TYR207 4.6 33.6 1.0
CA I:PHE213 4.6 31.2 1.0
N I:THR244 4.6 33.0 1.0
CA I:GLY240 4.7 32.9 1.0
N I:PHE213 4.8 30.9 1.0
N I:THR243 4.8 36.8 1.0
CA I:ARG209 4.8 39.1 1.0
CA I:VAL212 5.0 34.0 1.0
C I:PHE213 5.0 30.6 1.0

Sodium binding site 10 out of 12 in 3q9f

Go back to Sodium Binding Sites List in 3q9f
Sodium binding site 10 out of 12 in the Crystal Structure of Apah Complexed with Caps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Apah Complexed with Caps within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na343

b:22.7
occ:1.00
O J:PHE206 2.6 35.3 1.0
OG1 J:THR243 2.6 42.8 1.0
O J:VAL212 2.6 40.1 1.0
O J:HOH379 2.7 32.6 1.0
O J:ARG209 2.9 42.5 1.0
O J:THR243 3.0 42.6 1.0
CB J:THR243 3.3 42.2 1.0
C J:PHE206 3.6 35.2 1.0
C J:THR243 3.7 41.6 1.0
CB J:PHE206 3.8 33.1 1.0
C J:VAL212 3.8 38.5 1.0
OG1 J:THR244 3.9 38.9 1.0
C J:ARG209 4.1 41.3 1.0
CA J:THR243 4.1 41.8 1.0
CA J:PHE206 4.3 34.0 1.0
N J:TYR207 4.4 35.9 1.0
CA J:PHE213 4.4 38.3 1.0
N J:PHE214 4.5 36.7 1.0
O J:GLY240 4.5 37.5 1.0
CG2 J:THR243 4.5 43.7 1.0
CA J:TYR207 4.5 36.1 1.0
N J:PHE213 4.6 38.5 1.0
N J:ARG209 4.6 40.5 1.0
C J:TYR207 4.7 36.1 1.0
N J:THR244 4.7 40.6 1.0
O J:TYR207 4.7 35.2 1.0
CA J:ARG209 4.8 41.2 1.0
C J:PHE213 4.8 38.2 1.0
CA J:VAL212 4.9 39.1 1.0
CA J:GLY240 4.9 37.0 1.0
N J:THR243 5.0 41.2 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: Tue Dec 15 06:22:35 2020

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