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Potassium in PDB 4izn: Structure of Pcdronpa-A69T Mutant

Protein crystallography data

The structure of Structure of Pcdronpa-A69T Mutant, PDB code: 4izn was solved by E.De Zitter, N.Nguyen Bich, L.Van Meervelt, B.Moeyaert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.80 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.700, 180.930, 113.161, 90.00, 93.37, 90.00
R / Rfree (%) 19.2 / 24.5

Potassium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Potassium atom in the Structure of Pcdronpa-A69T Mutant (pdb code 4izn). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 12 binding sites of Potassium where determined in the Structure of Pcdronpa-A69T Mutant, PDB code: 4izn:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 12 in 4izn

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Potassium binding site 1 out of 12 in the Structure of Pcdronpa-A69T Mutant


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of Pcdronpa-A69T Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K301

b:76.5
occ:1.00
 O A:LYS134 2.9 42.8 1.0
O A:THR136 3.0 30.4 1.0
OE2 A:GLU164 3.3 63.6 1.0
O A:HOH422 3.9 44.6 1.0
C A:LYS134 4.1 40.8 1.0
OH A:TYR204 4.1 66.7 1.0
C A:THR136 4.2 27.9 1.0
N A:THR136 4.3 28.0 1.0
CD A:GLU164 4.3 70.8 1.0
C A:ARG135 4.7 41.5 1.0
CA A:ARG135 4.8 34.2 1.0
N A:ARG135 4.8 37.1 1.0
CA A:THR136 4.9 28.1 1.0
CB A:LYS134 4.9 38.2 1.0
CG A:GLU164 4.9 44.4 1.0

Potassium binding site 2 out of 12 in 4izn

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Potassium binding site 2 out of 12 in the Structure of Pcdronpa-A69T Mutant


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of Pcdronpa-A69T Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K301

b:55.4
occ:1.00
 O B:LYS134 2.6 30.6 1.0
O B:THR136 2.8 28.7 1.0
O B:HOH406 2.9 23.1 1.0
O B:HOH472 2.9 41.7 1.0
O B:HOH452 3.0 39.4 1.0
OE2 B:GLU164 3.1 43.4 1.0
O B:HOH474 3.2 34.7 1.0
C B:LYS134 3.5 23.8 1.0
CD B:GLU164 3.6 41.6 1.0
N B:THR136 3.6 19.8 1.0
C B:THR136 3.9 24.1 1.0
C B:ARG135 3.9 22.6 1.0
O B:HOH497 3.9 29.7 1.0
CA B:ARG135 4.0 28.3 1.0
N B:ARG135 4.1 25.6 1.0
OE1 B:GLU164 4.2 49.4 1.0
CG B:GLU164 4.2 46.3 1.0
CA B:THR136 4.4 23.9 1.0
CA B:LYS134 4.5 22.0 1.0
CB B:LYS134 4.5 25.0 1.0
O B:ARG135 4.6 20.8 1.0
O B:HOH450 4.7 31.7 1.0
OG1 B:THR136 4.8 22.1 1.0
OH B:TYR204 5.0 40.7 1.0
N B:VAL137 5.0 23.4 1.0
O B:HOH453 5.0 42.1 1.0

Potassium binding site 3 out of 12 in 4izn

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Potassium binding site 3 out of 12 in the Structure of Pcdronpa-A69T Mutant


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of Pcdronpa-A69T Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K301

b:67.8
occ:1.00
 O C:THR136 2.9 31.2 1.0
O C:HOH472 3.1 47.7 1.0
O C:LYS134 3.1 39.7 1.0
OE2 C:GLU164 3.3 53.7 1.0
O C:HOH443 3.3 29.0 1.0
O C:HOH457 3.7 41.6 1.0
C C:LYS134 3.8 34.8 1.0
N C:THR136 3.9 24.8 1.0
O C:HOH437 3.9 33.8 1.0
C C:THR136 4.0 24.0 1.0
CA C:ARG135 4.2 30.8 1.0
C C:ARG135 4.2 29.5 1.0
CD C:GLU164 4.3 57.9 1.0
N C:ARG135 4.3 24.5 1.0
O C:HOH468 4.5 41.0 1.0
CA C:THR136 4.6 29.3 1.0
CB C:LYS134 4.7 30.9 1.0
CG C:GLU164 4.7 48.7 1.0
CA C:LYS134 4.8 29.8 1.0
OH C:TYR204 4.8 42.3 1.0
O C:ARG135 4.9 31.9 1.0
OG1 C:THR136 5.0 28.7 1.0

Potassium binding site 4 out of 12 in 4izn

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Potassium binding site 4 out of 12 in the Structure of Pcdronpa-A69T Mutant


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of Pcdronpa-A69T Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K301

b:44.5
occ:1.00
 O D:HOH452 2.6 51.0 1.0
O D:LYS134 2.7 26.6 1.0
OE2 D:GLU164 2.7 56.9 1.0
O D:THR136 2.9 32.0 1.0
O D:HOH484 3.0 20.7 1.0
C D:LYS134 3.6 28.2 1.0
O D:HOH436 3.6 38.3 1.0
CD D:GLU164 3.7 57.2 1.0
N D:THR136 3.7 22.7 1.0
C D:THR136 3.9 26.4 1.0
C D:ARG135 4.0 28.1 1.0
CA D:ARG135 4.1 27.9 1.0
N D:ARG135 4.2 25.4 1.0
OE1 D:GLU164 4.3 59.6 1.0
CA D:THR136 4.5 26.1 1.0
CG D:GLU164 4.5 42.8 1.0
O D:HOH471 4.6 32.6 1.0
CA D:LYS134 4.6 19.8 1.0
CB D:LYS134 4.6 25.5 1.0
O D:ARG135 4.7 27.2 1.0
OH D:TYR204 4.8 36.4 1.0
OG1 D:THR136 4.9 30.5 1.0

Potassium binding site 5 out of 12 in 4izn

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Potassium binding site 5 out of 12 in the Structure of Pcdronpa-A69T Mutant


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Structure of Pcdronpa-A69T Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K301

b:45.9
occ:1.00
 O E:HOH501 2.7 35.1 1.0
O E:LYS134 2.7 25.0 1.0
O E:THR136 2.9 25.9 1.0
OE2 E:GLU164 3.1 60.1 1.0
O E:HOH462 3.1 16.2 1.0
C E:LYS134 3.7 26.9 1.0
O E:HOH426 3.9 24.6 1.0
N E:THR136 3.9 21.0 1.0
O E:HOH503 3.9 38.0 1.0
CD E:GLU164 4.0 50.7 1.0
C E:THR136 4.0 24.0 1.0
O E:HOH515 4.2 37.0 1.0
C E:ARG135 4.2 26.5 1.0
CA E:ARG135 4.3 26.6 1.0
N E:ARG135 4.4 18.7 1.0
O E:HOH478 4.4 24.4 1.0
CG E:GLU164 4.5 39.9 1.0
O E:HOH500 4.5 19.2 1.0
CA E:THR136 4.6 22.8 1.0
CB E:LYS134 4.6 18.9 1.0
OH E:TYR204 4.6 34.1 1.0
CA E:LYS134 4.7 17.8 1.0
O E:ARG135 4.9 22.8 1.0
OE1 E:GLU164 4.9 46.0 1.0
OG1 E:THR136 5.0 19.5 1.0

Potassium binding site 6 out of 12 in 4izn

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Potassium binding site 6 out of 12 in the Structure of Pcdronpa-A69T Mutant


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Structure of Pcdronpa-A69T Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K301

b:43.8
occ:1.00
 O F:LYS134 2.7 39.5 1.0
O F:HOH439 2.7 32.7 1.0
OE2 F:GLU164 2.7 62.6 1.0
O F:HOH477 3.0 34.4 1.0
C F:LYS134 3.1 39.5 1.0
CD F:GLU164 3.4 58.9 1.0
O F:THR136 3.4 28.0 1.0
N F:ARG135 3.5 33.0 1.0
CA F:ARG135 3.5 34.5 1.0
OE1 F:GLU164 3.5 59.0 1.0
N F:THR136 3.7 26.1 1.0
O F:HOH449 3.7 42.7 1.0
C F:ARG135 3.8 29.3 1.0
O F:HOH438 4.0 39.8 1.0
CB F:LYS134 4.1 39.3 1.0
CA F:LYS134 4.1 31.7 1.0
C F:THR136 4.4 27.7 1.0
O F:HOH441 4.5 30.8 1.0
O F:ARG135 4.6 37.2 1.0
CA F:THR136 4.7 28.0 1.0
CG F:GLU164 4.7 42.7 1.0
CB F:ARG135 4.9 38.3 1.0

Potassium binding site 7 out of 12 in 4izn

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Potassium binding site 7 out of 12 in the Structure of Pcdronpa-A69T Mutant


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Structure of Pcdronpa-A69T Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K301

b:47.5
occ:1.00
 O G:HOH538 2.6 33.8 1.0
O G:LYS134 2.7 25.5 1.0
OE2 G:GLU164 2.7 48.6 1.0
O G:THR136 3.0 23.7 1.0
O G:HOH493 3.1 17.0 1.0
O G:HOH497 3.2 35.2 1.0
C G:LYS134 3.6 24.1 1.0
CD G:GLU164 3.6 49.7 1.0
N G:THR136 3.9 21.3 1.0
C G:THR136 4.1 22.0 1.0
C G:ARG135 4.2 22.4 1.0
O G:HOH440 4.2 30.1 1.0
CA G:ARG135 4.2 29.9 1.0
N G:ARG135 4.3 19.1 1.0
OE1 G:GLU164 4.3 38.0 1.0
CB G:LYS134 4.3 14.5 1.0
CG G:GLU164 4.4 31.6 1.0
O G:HOH569 4.5 35.8 1.0
CA G:LYS134 4.5 18.7 1.0
O G:HOH454 4.5 24.8 1.0
CA G:THR136 4.6 24.7 1.0
O G:ARG135 4.9 22.3 1.0
OH G:TYR204 4.9 27.3 1.0
OG1 G:THR136 5.0 16.5 1.0

Potassium binding site 8 out of 12 in 4izn

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Potassium binding site 8 out of 12 in the Structure of Pcdronpa-A69T Mutant


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Structure of Pcdronpa-A69T Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K301

b:48.8
occ:1.00
 O H:LYS134 2.7 39.0 1.0
O H:HOH443 2.7 40.4 1.0
OE2 H:GLU164 3.0 53.5 1.0
O H:THR136 3.1 30.8 1.0
O H:HOH459 3.2 31.5 1.0
O H:HOH483 3.2 31.1 1.0
C H:LYS134 3.4 38.4 1.0
CD H:GLU164 3.5 54.3 1.0
O H:HOH475 3.6 37.7 1.0
OE1 H:GLU164 3.7 43.9 1.0
N H:THR136 3.7 23.2 1.0
C H:ARG135 4.0 31.8 1.0
N H:ARG135 4.0 26.9 1.0
O H:HOH458 4.0 31.4 1.0
CA H:ARG135 4.0 22.7 1.0
C H:THR136 4.1 28.7 1.0
CB H:LYS134 4.4 26.5 1.0
CA H:LYS134 4.4 25.6 1.0
CA H:THR136 4.6 26.3 1.0
CG H:GLU164 4.6 32.9 1.0
O H:ARG135 4.7 25.3 1.0
O H:HOH477 4.9 32.8 1.0
O H:HOH474 5.0 38.4 1.0

Potassium binding site 9 out of 12 in 4izn

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Potassium binding site 9 out of 12 in the Structure of Pcdronpa-A69T Mutant


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Structure of Pcdronpa-A69T Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:K301

b:60.7
occ:1.00
 O I:THR136 2.8 27.8 1.0
O I:HOH495 2.8 49.1 1.0
O I:LYS134 2.9 36.0 1.0
OE2 I:GLU164 3.0 60.6 1.0
O I:HOH465 3.0 26.2 1.0
O I:HOH442 3.6 31.6 1.0
C I:LYS134 3.8 34.4 1.0
N I:THR136 3.8 20.4 1.0
C I:THR136 3.9 26.8 1.0
CD I:GLU164 4.0 58.9 1.0
C I:ARG135 4.2 25.2 1.0
O I:HOH455 4.3 33.9 1.0
CA I:ARG135 4.3 27.0 1.0
N I:ARG135 4.4 32.5 1.0
CA I:THR136 4.5 25.9 1.0
CG I:GLU164 4.6 40.8 1.0
CB I:LYS134 4.6 29.8 1.0
O I:HOH473 4.6 32.8 1.0
CA I:LYS134 4.7 24.9 1.0
OH I:TYR204 4.7 38.4 1.0
OG1 I:THR136 4.8 29.1 1.0
O I:HOH515 4.9 37.8 1.0
OE1 I:GLU164 4.9 50.6 1.0
O I:ARG135 4.9 23.5 1.0
N I:VAL137 5.0 26.1 1.0

Potassium binding site 10 out of 12 in 4izn

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Potassium binding site 10 out of 12 in the Structure of Pcdronpa-A69T Mutant


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Structure of Pcdronpa-A69T Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
J:K301

b:52.0
occ:1.00
 O J:THR136 2.8 27.1 1.0
OE2 J:GLU164 2.9 54.8 1.0
O J:HOH510 3.0 37.2 1.0
O J:LYS134 3.1 21.9 1.0
O J:HOH406 3.7 16.1 1.0
CD J:GLU164 3.8 38.9 1.0
O J:HOH539 3.9 32.5 1.0
C J:THR136 4.0 21.1 1.0
O J:HOH511 4.0 34.5 1.0
C J:LYS134 4.1 22.0 1.0
N J:THR136 4.1 19.6 1.0
CG J:GLU164 4.2 27.3 1.0
C J:ARG135 4.4 25.1 1.0
CA J:ARG135 4.6 24.0 1.0
OH J:TYR204 4.6 35.7 1.0
OE1 J:GLU164 4.7 45.0 1.0
CA J:THR136 4.7 23.6 1.0
O J:HOH507 4.8 40.2 1.0
N J:ARG135 4.8 21.6 1.0
O J:HOH456 4.9 35.0 1.0
N J:VAL137 4.9 21.8 1.0
O J:HOH505 5.0 42.5 1.0

Reference:

B.Moeyaert, N.Nguyen Bich, E.De Zitter, S.Rocha, K.Clays, H.Mizuno, L.Van Meervelt, J.Hofkens, P.Dedecker. Green-to-Red Photoconvertible Dronpa Mutant For Multimodal Super-Resolution Fluorescence Microscopy Acs Nano V. 8 1664 2014.
ISSN: ISSN 1936-0851
PubMed: 24410188
DOI: 10.1021/NN4060144
Page generated: Mon Aug 12 11:02:55 2024

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