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Potassium in PDB 6w4n: Co-Crystal Structure of PD_DINASE with Probe Glycine-Propargylglycine- Aomk

Protein crystallography data

The structure of Co-Crystal Structure of PD_DINASE with Probe Glycine-Propargylglycine- Aomk, PDB code: 6w4n was solved by J.H.Xu, A.Solania, D.W.Wolan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.14 / 2.62
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.113, 138.613, 220.13, 90, 90, 90
R / Rfree (%) 20.8 / 22.9

Potassium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Potassium atom in the Co-Crystal Structure of PD_DINASE with Probe Glycine-Propargylglycine- Aomk (pdb code 6w4n). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 12 binding sites of Potassium where determined in the Co-Crystal Structure of PD_DINASE with Probe Glycine-Propargylglycine- Aomk, PDB code: 6w4n:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 12 in 6w4n

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Potassium binding site 1 out of 12 in the Co-Crystal Structure of PD_DINASE with Probe Glycine-Propargylglycine- Aomk


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Co-Crystal Structure of PD_DINASE with Probe Glycine-Propargylglycine- Aomk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K602

b:71.2
occ:1.00
 O A:GLU335 2.5 49.4 1.0
O A:HOH715 2.5 42.9 1.0
OG A:SER273 2.6 58.8 1.0
OE2 A:GLU274 2.7 60.1 1.0
OD2 A:ASP271 2.9 54.4 1.0
O A:SER273 3.2 74.1 1.0
OD1 A:ASP271 3.3 57.6 1.0
C A:GLU335 3.4 42.2 1.0
CG A:ASP271 3.4 53.3 1.0
CB A:SER273 3.8 56.9 1.0
CD A:GLU274 3.8 63.5 1.0
C A:SER273 4.0 66.5 1.0
CA A:GLU335 4.0 39.3 1.0
O A:TYR334 4.3 36.5 1.0
N A:THR336 4.3 40.4 1.0
O A:HOH734 4.3 43.3 1.0
CA A:SER273 4.3 60.2 1.0
OG1 A:THR337 4.4 41.6 1.0
CA A:THR336 4.5 39.0 1.0
OE1 A:GLU274 4.6 60.2 1.0
OD2 A:ASP339 4.6 56.6 1.0
NZ A:LYS383 4.7 42.3 1.0
CG A:GLU274 4.7 62.3 1.0
N A:SER273 4.7 59.0 1.0
N A:THR337 4.7 41.6 1.0
CB A:ASP271 4.9 48.7 1.0
CB A:GLU335 4.9 41.6 1.0

Potassium binding site 2 out of 12 in 6w4n

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Potassium binding site 2 out of 12 in the Co-Crystal Structure of PD_DINASE with Probe Glycine-Propargylglycine- Aomk


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Co-Crystal Structure of PD_DINASE with Probe Glycine-Propargylglycine- Aomk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K603

b:80.2
occ:1.00
 OE1 A:GLU126 2.5 63.6 1.0
OD1 A:ASP78 2.6 69.1 1.0
OE1 A:GLU81 2.7 57.0 1.0
O A:LEU79 3.1 61.7 1.0
OE2 A:GLU81 3.1 52.2 1.0
CD A:GLU81 3.3 57.8 1.0
CD A:GLU126 3.4 70.9 1.0
CG A:ASP78 3.8 57.9 1.0
OE2 A:GLU126 4.0 66.4 1.0
CD A:LYS48 4.0 59.3 1.0
CE A:LYS48 4.1 68.3 1.0
NZ A:LYS48 4.2 68.0 1.0
C A:LEU79 4.3 57.0 1.0
OD2 A:ASP78 4.3 61.3 1.0
CG A:LYS48 4.3 60.8 1.0
CG A:GLU126 4.4 62.1 1.0
OE2 A:GLU66 4.5 59.3 1.0
CB A:GLU126 4.6 59.0 1.0
N A:LEU79 4.7 61.1 1.0
C A:ASP78 4.7 64.1 1.0
CE2 A:TYR59 4.7 59.6 1.0
CG A:GLU81 4.8 58.0 1.0
N A:GLU81 4.9 52.9 1.0
CA A:ASP78 5.0 63.1 1.0
CD2 A:TYR59 5.0 61.8 1.0
CB A:LYS48 5.0 58.5 1.0
CB A:ASP78 5.0 58.9 1.0

Potassium binding site 3 out of 12 in 6w4n

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Potassium binding site 3 out of 12 in the Co-Crystal Structure of PD_DINASE with Probe Glycine-Propargylglycine- Aomk


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Co-Crystal Structure of PD_DINASE with Probe Glycine-Propargylglycine- Aomk within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K602

b:63.0
occ:1.00
 OD1 B:ASP78 2.6 39.6 1.0
O B:LEU79 2.6 42.7 1.0
OE2 B:GLU81 2.8 48.2 1.0
OE1 B:GLU126 2.9 55.1 1.0
OE1 B:GLU81 3.0 43.7 1.0
CD B:GLU81 3.3 43.3 1.0
OE2 B:GLU66 3.7 42.1 1.0
C B:LEU79 3.7 38.5 1.0
N B:LEU79 3.8 40.6 1.0
CG B:ASP78 3.8 47.3 1.0
O B:HOH713 3.9 44.5 1.0
CE B:LYS48 3.9 46.6 1.0
CD B:GLU126 4.0 57.6 1.0
C B:ASP78 4.1 41.3 1.0
CD B:LYS48 4.2 50.2 1.0
CA B:ASP78 4.3 41.5 1.0
CA B:LEU79 4.3 42.8 1.0
O B:HOH735 4.5 40.9 1.0
CG B:LYS48 4.5 46.2 1.0
OD2 B:ASP78 4.6 53.9 1.0
O B:ASP78 4.7 42.3 1.0
OE2 B:GLU126 4.7 54.9 1.0
CB B:ASP78 4.7 44.4 1.0
CD B:GLU66 4.7 42.0 1.0
CG B:GLU81 4.8 43.3 1.0
NZ B:LYS48 4.8 48.0 1.0
CB B:GLU126 4.8 46.0 1.0
N B:SER80 4.8 38.5 1.0
CG B:GLU126 4.9 46.5 1.0
OE1 B:GLU66 4.9 41.6 1.0
N B:GLU81 4.9 42.2 1.0

Potassium binding site 4 out of 12 in 6w4n

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Potassium binding site 4 out of 12 in the Co-Crystal Structure of PD_DINASE with Probe Glycine-Propargylglycine- Aomk


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Co-Crystal Structure of PD_DINASE with Probe Glycine-Propargylglycine- Aomk within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K603

b:71.4
occ:1.00
 OE2 B:GLU274 2.5 63.0 1.0
O B:GLU335 2.5 50.7 1.0
OG B:SER273 2.7 58.1 1.0
O B:SER273 2.8 56.1 1.0
OD2 B:ASP271 2.8 57.9 1.0
OD1 B:ASP271 2.9 54.2 1.0
CG B:ASP271 3.2 54.1 1.0
CD B:GLU274 3.5 61.6 1.0
C B:SER273 3.5 55.2 1.0
O B:HOH749 3.6 47.9 1.0
C B:GLU335 3.6 51.3 1.0
CB B:SER273 3.7 52.3 1.0
CA B:SER273 4.1 52.4 1.0
CG B:GLU274 4.2 49.6 1.0
O B:HOH737 4.2 48.8 1.0
CA B:GLU335 4.3 46.8 1.0
OE1 B:GLU274 4.3 63.2 1.0
N B:SER273 4.4 52.9 1.0
NZ B:LYS383 4.4 44.1 1.0
N B:THR336 4.5 48.5 1.0
N B:GLU274 4.5 54.2 1.0
CB B:ASP271 4.6 47.7 1.0
OD2 B:ASP339 4.6 57.5 1.0
CA B:THR336 4.6 47.7 1.0
OG1 B:THR337 4.9 52.2 1.0
CA B:GLU274 4.9 55.6 1.0
O B:TYR334 4.9 45.2 1.0
CB B:GLU335 5.0 45.6 1.0

Potassium binding site 5 out of 12 in 6w4n

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Potassium binding site 5 out of 12 in the Co-Crystal Structure of PD_DINASE with Probe Glycine-Propargylglycine- Aomk


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Co-Crystal Structure of PD_DINASE with Probe Glycine-Propargylglycine- Aomk within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K602

b:91.4
occ:1.00
 O C:GLU335 2.1 58.7 1.0
OE2 C:GLU274 2.4 71.2 1.0
OD2 C:ASP271 2.7 63.8 1.0
OG C:SER273 3.0 64.9 1.0
C C:GLU335 3.0 51.9 1.0
OD1 C:ASP271 3.3 70.0 1.0
CG C:ASP271 3.3 64.8 1.0
O C:SER273 3.4 77.8 1.0
CD C:GLU274 3.6 69.7 1.0
CA C:GLU335 3.7 55.0 1.0
N C:THR336 3.9 49.5 1.0
CB C:SER273 4.1 65.4 1.0
O C:TYR334 4.2 45.8 1.0
CA C:THR336 4.2 54.3 1.0
C C:SER273 4.2 75.6 1.0
OE1 C:GLU274 4.3 71.3 1.0
OG1 C:THR337 4.4 51.1 1.0
N C:THR337 4.5 53.5 1.0
CG C:GLU274 4.6 66.3 1.0
CB C:GLU335 4.6 48.5 1.0
CA C:SER273 4.6 71.3 1.0
OD2 C:ASP339 4.7 64.5 1.0
CB C:ASP271 4.7 60.9 1.0
NZ C:LYS383 4.7 57.3 1.0
N C:GLU335 4.8 52.8 1.0
C C:THR336 4.8 54.6 1.0
N C:SER273 4.9 73.6 1.0
C C:TYR334 4.9 49.5 1.0

Potassium binding site 6 out of 12 in 6w4n

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Potassium binding site 6 out of 12 in the Co-Crystal Structure of PD_DINASE with Probe Glycine-Propargylglycine- Aomk


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Co-Crystal Structure of PD_DINASE with Probe Glycine-Propargylglycine- Aomk within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K603

b:90.1
occ:1.00
 OE1 C:GLU126 2.1 67.3 1.0
OE2 C:GLU81 2.5 62.1 1.0
OD1 C:ASP78 2.7 68.7 1.0
O C:LEU79 2.7 56.7 1.0
OE1 C:GLU81 2.8 64.3 1.0
CD C:GLU81 3.0 62.0 1.0
CD C:GLU126 3.2 75.2 1.0
OE2 C:GLU126 3.5 74.7 1.0
OE2 C:GLU66 3.6 69.2 1.0
C C:LEU79 3.8 56.5 1.0
CG C:ASP78 3.9 68.0 1.0
N C:LEU79 3.9 64.1 1.0
CE C:LYS48 4.0 64.1 1.0
C C:ASP78 4.3 62.9 1.0
CD C:LYS48 4.3 71.5 1.0
CG C:LYS48 4.3 70.7 1.0
CA C:LEU79 4.5 63.6 1.0
CA C:ASP78 4.5 67.9 1.0
CG C:GLU81 4.5 59.3 1.0
CG C:GLU126 4.6 63.9 1.0
CD C:GLU66 4.7 71.9 1.0
OD2 C:ASP78 4.7 69.2 1.0
NZ C:LYS48 4.7 69.1 1.0
N C:GLU81 4.8 52.9 1.0
CB C:TYR62 4.8 56.2 1.0
CB C:ASP78 4.8 65.0 1.0
CD2 C:TYR62 4.9 51.5 1.0
OE1 C:GLU66 4.9 74.7 1.0
O C:ASP78 4.9 55.0 1.0
N C:SER80 4.9 58.4 1.0
CB C:GLU126 4.9 66.7 1.0

Potassium binding site 7 out of 12 in 6w4n

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Potassium binding site 7 out of 12 in the Co-Crystal Structure of PD_DINASE with Probe Glycine-Propargylglycine- Aomk


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Co-Crystal Structure of PD_DINASE with Probe Glycine-Propargylglycine- Aomk within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K602

b:73.8
occ:1.00
 OD1 D:ASP78 2.7 69.4 1.0
OE2 D:GLU81 2.8 58.7 1.0
OE1 D:GLU81 2.8 51.4 1.0
O D:LEU79 2.8 51.7 1.0
OE1 D:GLU126 2.9 64.4 1.0
CD D:GLU81 3.2 53.3 1.0
CE D:LYS48 3.8 63.0 1.0
OE2 D:GLU66 3.9 55.8 1.0
CG D:ASP78 4.0 69.8 1.0
C D:LEU79 4.0 51.6 1.0
CD D:GLU126 4.0 68.4 1.0
CD D:LYS48 4.0 55.0 1.0
N D:LEU79 4.1 62.4 1.0
O D:HOH732 4.2 55.1 1.0
CG D:LYS48 4.3 50.8 1.0
C D:ASP78 4.4 64.1 1.0
CA D:ASP78 4.6 58.9 1.0
OE2 D:GLU126 4.6 65.0 1.0
CA D:LEU79 4.7 57.5 1.0
CG D:GLU81 4.7 49.6 1.0
NZ D:LYS48 4.7 61.0 1.0
OD2 D:ASP78 4.7 83.2 1.0
CD D:GLU66 4.9 53.9 1.0
CB D:ASP78 4.9 67.6 1.0
N D:GLU81 4.9 48.1 1.0
CE2 D:TYR59 4.9 54.6 1.0
O D:ASP78 5.0 55.7 1.0
CB D:GLU126 5.0 54.9 1.0
CG D:GLU126 5.0 67.5 1.0
OE1 D:GLU66 5.0 50.7 1.0

Potassium binding site 8 out of 12 in 6w4n

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Potassium binding site 8 out of 12 in the Co-Crystal Structure of PD_DINASE with Probe Glycine-Propargylglycine- Aomk


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Co-Crystal Structure of PD_DINASE with Probe Glycine-Propargylglycine- Aomk within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K603

b:61.0
occ:1.00
 OD2 D:ASP271 2.2 52.1 1.0
OE2 D:GLU274 2.4 50.9 1.0
OG D:SER273 2.5 54.3 1.0
O D:GLU335 2.7 41.4 1.0
O D:SER273 2.8 53.8 1.0
CG D:ASP271 3.0 50.2 1.0
OD1 D:ASP271 3.2 51.7 1.0
CD D:GLU274 3.4 61.0 1.0
C D:SER273 3.4 54.6 1.0
CB D:SER273 3.6 57.7 1.0
C D:GLU335 3.8 36.5 1.0
CA D:SER273 3.9 57.2 1.0
CG D:GLU274 4.1 58.8 1.0
N D:SER273 4.1 58.6 1.0
OD2 D:ASP339 4.3 46.2 1.0
OE1 D:GLU274 4.3 57.6 1.0
CB D:ASP271 4.3 45.6 1.0
N D:GLU274 4.4 53.6 1.0
O E:HOH817 4.4 49.1 1.0
CA D:GLU335 4.5 33.9 1.0
NZ D:LYS383 4.6 38.2 1.0
N D:THR336 4.6 34.0 1.0
OG1 D:THR337 4.6 40.9 1.0
CA D:THR336 4.7 33.3 1.0
CA D:GLU274 4.8 57.4 1.0
N D:THR337 4.9 41.2 1.0

Potassium binding site 9 out of 12 in 6w4n

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Potassium binding site 9 out of 12 in the Co-Crystal Structure of PD_DINASE with Probe Glycine-Propargylglycine- Aomk


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Co-Crystal Structure of PD_DINASE with Probe Glycine-Propargylglycine- Aomk within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K602

b:47.5
occ:1.00
 OD1 E:ASP78 2.6 30.7 1.0
O E:LEU79 2.7 32.2 1.0
OE1 E:GLU81 2.7 30.6 1.0
OE1 E:GLU126 2.8 38.3 1.0
O E:HOH827 2.8 34.4 1.0
OE2 E:GLU81 2.8 36.6 1.0
CD E:GLU81 3.1 27.5 1.0
CD E:GLU126 3.8 33.0 1.0
NZ E:LYS48 3.8 42.4 1.0
C E:LEU79 3.8 29.1 1.0
CG E:ASP78 3.9 30.3 1.0
N E:LEU79 4.0 25.5 1.0
OE2 E:GLU66 4.1 34.1 1.0
CE E:LYS48 4.2 27.1 1.0
CD E:LYS48 4.3 27.3 1.0
C E:ASP78 4.3 29.9 1.0
OE2 E:GLU126 4.5 33.0 1.0
CG E:LYS48 4.5 33.6 1.0
O E:HOH716 4.5 28.9 1.0
CA E:LEU79 4.5 26.7 1.0
CA E:ASP78 4.6 26.1 1.0
OD2 E:ASP78 4.6 39.6 1.0
CG E:GLU81 4.6 32.0 1.0
CG E:GLU126 4.8 29.3 1.0
N E:GLU81 4.8 27.7 1.0
CB E:GLU126 4.8 26.9 1.0
O E:ASP78 4.8 32.3 1.0
CB E:ASP78 4.9 27.5 1.0
N E:SER80 4.9 24.2 1.0
CE2 E:TYR59 4.9 29.9 1.0

Potassium binding site 10 out of 12 in 6w4n

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Potassium binding site 10 out of 12 in the Co-Crystal Structure of PD_DINASE with Probe Glycine-Propargylglycine- Aomk


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Co-Crystal Structure of PD_DINASE with Probe Glycine-Propargylglycine- Aomk within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K603

b:48.2
occ:1.00
 OG E:SER273 2.6 43.5 1.0
O E:GLU335 2.7 38.8 1.0
OE2 E:GLU274 2.7 48.4 1.0
O E:SER273 2.8 46.8 1.0
OD2 E:ASP271 2.9 48.4 1.0
OD1 E:ASP271 3.0 44.0 1.0
CG E:ASP271 3.3 42.4 1.0
C E:SER273 3.6 39.4 1.0
C E:GLU335 3.6 37.8 1.0
CB E:SER273 3.7 37.7 1.0
CD E:GLU274 3.7 51.9 1.0
CA E:SER273 4.1 40.3 1.0
CA E:GLU335 4.3 41.1 1.0
CG E:GLU274 4.4 42.9 1.0
N E:SER273 4.4 39.6 1.0
N E:THR336 4.5 39.1 1.0
OE1 E:GLU274 4.5 62.6 1.0
N E:GLU274 4.6 47.0 1.0
OD2 E:ASP339 4.6 37.8 1.0
OG1 E:THR337 4.6 39.3 1.0
NZ E:LYS383 4.6 40.6 1.0
O E:TYR334 4.7 39.3 1.0
CA E:THR336 4.7 39.3 1.0
CB E:ASP271 4.7 34.3 1.0
N E:THR337 4.9 39.2 1.0

Reference:

J.H.Xu, A.Solania, D.W.Wolan. Co-Crystal Structure of PD_DINASE with Probe Glycine-Propargylglycine-Aomk To Be Published.
Page generated: Sat Apr 3 16:10:15 2021

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