Potassium in PDB 5dkp: Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556.

Enzymatic activity of Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556.

All present enzymatic activity of Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556.:
3.4.21.92;

Protein crystallography data

The structure of Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556., PDB code: 5dkp was solved by J.D.Goodreid, J.Janetzko, J.P.Santa Maria Jr., K.Wong, E.Leung, B.T.Eger, S.Bryson, E.F.Pai, S.D.Gray-Owen, S.Walker, W.A.Houry, R.A.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.40 / 2.38
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 117.640, 198.850, 144.040, 90.00, 97.81, 90.00
R / Rfree (%) 19.6 / 23.9

Other elements in 5dkp:

The structure of Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556. also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Potassium atom in the Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556. (pdb code 5dkp). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 28 binding sites of Potassium where determined in the Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556., PDB code: 5dkp:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 28 in 5dkp

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Potassium binding site 1 out of 28 in the Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556.


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 N. Meningitidis Clpp in Complex with Agonist Adep A54556. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K301

b:24.6
occ:1.00
 O A:PRO90 2.7 21.9 1.0
O A:ILE88 2.7 17.5 1.0
O A:MET85 2.7 18.3 1.0
O A:HOH420 2.9 20.5 1.0
O A:HOH416 2.9 22.2 1.0
O A:HOH424 3.0 25.1 1.0
C A:PRO90 3.7 25.7 1.0
C A:ILE88 3.8 24.3 1.0
C A:MET85 4.0 21.7 1.0
CG1 A:ILE88 4.0 20.2 1.0
O A:ASN86 4.1 23.4 1.0
O A:LYS89 4.1 22.9 1.0
CG2 A:VAL92 4.3 15.5 1.0
C A:LYS89 4.3 24.2 1.0
N A:VAL92 4.3 18.8 1.0
CA A:ASP91 4.3 22.3 1.0
N A:ASP91 4.4 21.1 1.0
C A:ASN86 4.4 23.6 1.0
OE1 A:GLU112 4.5 30.1 1.0
N A:ILE88 4.5 20.0 1.0
CA A:ASN86 4.6 21.6 1.0
N A:PRO90 4.6 19.7 1.0
CA A:ILE88 4.6 20.2 1.0
C A:ASP91 4.7 25.2 1.0
N A:LYS89 4.7 20.1 1.0
N A:ASN86 4.8 18.3 1.0
CA A:PRO90 4.8 18.3 1.0
CA A:LYS89 4.8 26.3 1.0
CA A:MET85 4.9 15.8 1.0
CB A:ILE88 4.9 18.6 1.0
CD1 A:ILE88 5.0 15.1 1.0

Potassium binding site 2 out of 28 in 5dkp

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Potassium binding site 2 out of 28 in the Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556.


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 N. Meningitidis Clpp in Complex with Agonist Adep A54556. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K301

b:22.6
occ:1.00
 O B:PRO90 2.7 21.8 1.0
O B:ILE88 2.7 18.4 1.0
O B:MET85 2.8 15.2 1.0
O B:HOH431 2.9 19.7 1.0
O B:HOH410 3.0 34.2 1.0
O B:HOH419 3.0 17.3 1.0
C B:PRO90 3.7 22.0 1.0
CG1 B:ILE88 3.8 20.3 1.0
C B:ILE88 3.8 21.1 1.0
C B:MET85 4.0 21.8 1.0
O B:LYS89 4.1 23.0 1.0
C B:LYS89 4.2 20.1 1.0
CA B:ASP91 4.3 19.4 1.0
O B:ASN86 4.3 20.4 1.0
N B:VAL92 4.4 22.3 1.0
CG2 B:VAL92 4.4 15.7 1.0
N B:ASP91 4.4 21.4 1.0
OE1 B:GLU112 4.5 23.9 1.0
C B:ASN86 4.5 25.7 1.0
N B:ILE88 4.6 20.9 1.0
O B:HOH434 4.6 21.1 1.0
CA B:ILE88 4.6 20.2 1.0
N B:PRO90 4.6 22.2 1.0
CA B:ASN86 4.6 22.5 1.0
CD1 B:ILE88 4.6 19.1 1.0
N B:LYS89 4.7 23.2 1.0
C B:ASP91 4.7 23.6 1.0
CA B:LYS89 4.8 25.0 1.0
CA B:PRO90 4.8 19.4 1.0
N B:ASN86 4.8 15.5 1.0
CB B:ILE88 4.8 24.0 1.0
CA B:MET85 5.0 16.4 1.0

Potassium binding site 3 out of 28 in 5dkp

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Potassium binding site 3 out of 28 in the Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556.


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 N. Meningitidis Clpp in Complex with Agonist Adep A54556. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K301

b:24.0
occ:1.00
 O C:PRO90 2.7 21.6 1.0
O C:MET85 2.8 19.1 1.0
O C:HOH417 2.8 17.2 1.0
O C:ILE88 2.8 15.8 1.0
O C:HOH423 2.9 14.9 1.0
O C:HOH433 2.9 20.4 1.0
C C:PRO90 3.6 21.6 1.0
C C:ILE88 3.9 17.2 1.0
CG1 C:ILE88 4.0 18.6 1.0
C C:MET85 4.1 20.3 1.0
O C:LYS89 4.1 20.4 1.0
CA C:ASP91 4.2 20.2 1.0
C C:LYS89 4.3 17.0 1.0
N C:ASP91 4.3 19.9 1.0
N C:VAL92 4.3 20.6 1.0
OE1 C:GLU112 4.3 20.5 1.0
O C:ASN86 4.4 21.8 1.0
CG2 C:VAL92 4.5 14.4 1.0
N C:PRO90 4.6 18.9 1.0
C C:ASP91 4.6 22.1 1.0
C C:ASN86 4.6 23.3 1.0
CA C:PRO90 4.7 19.7 1.0
N C:ILE88 4.7 23.8 1.0
CA C:ASN86 4.7 22.6 1.0
O C:HOH434 4.7 28.5 1.0
CA C:ILE88 4.8 22.7 1.0
N C:LYS89 4.8 16.2 1.0
CA C:LYS89 4.8 20.3 1.0
N C:ASN86 4.9 19.0 1.0
CD1 C:ILE88 5.0 18.6 1.0

Potassium binding site 4 out of 28 in 5dkp

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Potassium binding site 4 out of 28 in the Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556.


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 N. Meningitidis Clpp in Complex with Agonist Adep A54556. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K301

b:26.4
occ:1.00
 O D:MET85 2.7 17.4 1.0
O D:PRO90 2.8 19.1 1.0
O D:HOH423 2.8 12.7 1.0
O D:ILE88 2.9 16.4 1.0
O D:HOH428 2.9 13.1 1.0
O D:HOH411 3.3 22.9 1.0
C D:PRO90 3.8 19.7 1.0
C D:MET85 3.9 23.1 1.0
C D:ILE88 3.9 20.4 1.0
CG1 D:ILE88 4.1 21.7 1.0
O D:LYS89 4.2 22.8 1.0
N D:VAL92 4.4 20.9 1.0
O D:ASN86 4.4 23.4 1.0
CA D:ASP91 4.4 23.3 1.0
CG2 D:VAL92 4.4 13.9 1.0
C D:LYS89 4.4 20.3 1.0
C D:ASN86 4.5 24.8 1.0
N D:ASP91 4.5 16.7 1.0
OE2 D:GLU112 4.5 28.5 1.0
CA D:ASN86 4.5 20.5 1.0
N D:ILE88 4.6 23.2 1.0
N D:ASN86 4.7 20.9 1.0
CA D:ILE88 4.7 20.2 1.0
C D:ASP91 4.7 22.4 1.0
N D:PRO90 4.7 17.8 1.0
N D:LYS89 4.9 22.2 1.0
CA D:PRO90 4.9 16.1 1.0
CA D:MET85 4.9 19.0 1.0
CA D:LYS89 5.0 26.0 1.0

Potassium binding site 5 out of 28 in 5dkp

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Potassium binding site 5 out of 28 in the Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556.


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 N. Meningitidis Clpp in Complex with Agonist Adep A54556. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K301

b:30.2
occ:1.00
 O E:MET85 2.6 15.5 1.0
O E:PRO90 2.7 19.1 1.0
O E:HOH426 2.8 10.0 1.0
O E:ILE88 2.8 20.6 1.0
O E:HOH414 3.3 25.3 1.0
C E:PRO90 3.8 25.6 1.0
C E:MET85 3.8 22.6 1.0
C E:ILE88 3.9 18.0 1.0
CG1 E:ILE88 3.9 20.1 1.0
O E:LYS89 4.2 18.9 1.0
O E:ASN86 4.3 25.0 1.0
C E:LYS89 4.4 22.1 1.0
CG2 E:VAL92 4.4 15.4 1.0
C E:ASN86 4.4 23.2 1.0
N E:ILE88 4.4 20.5 1.0
CA E:ASP91 4.5 22.4 1.0
N E:ASP91 4.5 18.2 1.0
CA E:ASN86 4.5 22.8 1.0
N E:VAL92 4.5 22.6 1.0
CA E:ILE88 4.6 21.4 1.0
OE2 E:GLU112 4.6 28.5 1.0
N E:ASN86 4.6 21.2 1.0
N E:PRO90 4.7 18.0 1.0
N E:LYS89 4.8 24.4 1.0
CA E:PRO90 4.8 18.6 1.0
C E:ASP91 4.8 26.0 1.0
CA E:MET85 4.9 21.0 1.0
CB E:ILE88 4.9 22.5 1.0
CD1 E:ILE88 4.9 18.4 1.0
CA E:LYS89 4.9 25.0 1.0
C E:PHE87 4.9 22.8 1.0
N E:PHE87 5.0 25.0 1.0

Potassium binding site 6 out of 28 in 5dkp

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Potassium binding site 6 out of 28 in the Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556.


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 N. Meningitidis Clpp in Complex with Agonist Adep A54556. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K301

b:26.0
occ:1.00
 O F:ILE88 2.7 20.7 1.0
O F:PRO90 2.7 19.5 1.0
O F:MET85 2.8 20.0 1.0
O F:HOH423 2.8 21.2 1.0
O F:HOH414 3.0 20.4 1.0
C F:PRO90 3.8 26.0 1.0
C F:ILE88 3.8 21.5 1.0
C F:MET85 4.0 24.1 1.0
CG1 F:ILE88 4.0 17.6 1.0
O F:ASN86 4.0 28.0 1.0
O F:LYS89 4.2 25.6 1.0
C F:ASN86 4.3 20.8 1.0
C F:LYS89 4.3 22.4 1.0
CA F:ASP91 4.4 19.5 1.0
N F:ASP91 4.4 21.6 1.0
CA F:ASN86 4.5 22.4 1.0
CG2 F:VAL92 4.5 13.6 1.0
N F:ILE88 4.5 22.9 1.0
N F:VAL92 4.5 23.1 1.0
OE1 F:GLU112 4.6 30.3 1.0
CA F:ILE88 4.6 22.2 1.0
N F:PRO90 4.7 21.8 1.0
N F:ASN86 4.7 23.6 1.0
N F:LYS89 4.7 23.9 1.0
CA F:PRO90 4.8 20.3 1.0
C F:ASP91 4.8 25.0 1.0
CA F:LYS89 4.8 25.1 1.0
CD1 F:ILE88 4.9 18.6 1.0
C F:PHE87 5.0 23.2 1.0
CB F:ILE88 5.0 21.0 1.0

Potassium binding site 7 out of 28 in 5dkp

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Potassium binding site 7 out of 28 in the Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556.


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 N. Meningitidis Clpp in Complex with Agonist Adep A54556. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K301

b:25.8
occ:1.00
 O G:PRO90 2.7 22.6 1.0
O G:MET85 2.7 19.1 1.0
O G:HOH422 2.7 14.2 1.0
O G:HOH414 2.7 13.7 1.0
O G:ILE88 2.9 14.5 1.0
C G:PRO90 3.7 25.1 1.0
CG1 G:ILE88 3.9 21.0 1.0
C G:MET85 3.9 26.4 1.0
C G:ILE88 4.0 22.8 1.0
O G:ASN86 4.1 22.0 1.0
O G:LYS89 4.2 22.3 1.0
CA G:ASP91 4.3 18.0 1.0
C G:ASN86 4.3 22.9 1.0
N G:ASP91 4.4 18.2 1.0
N G:VAL92 4.4 18.2 1.0
C G:LYS89 4.4 20.2 1.0
OE2 G:GLU112 4.4 26.3 1.0
CA G:ASN86 4.5 16.8 1.0
CG2 G:VAL92 4.5 11.7 1.0
O G:HOH426 4.6 17.5 1.0
N G:ILE88 4.6 22.1 1.0
N G:ASN86 4.7 14.9 1.0
N G:PRO90 4.7 18.9 1.0
C G:ASP91 4.7 27.2 1.0
CA G:ILE88 4.7 18.9 1.0
CD1 G:ILE88 4.7 18.1 1.0
CA G:PRO90 4.8 19.9 1.0
N G:LYS89 4.9 20.3 1.0
CB G:ILE88 5.0 20.4 1.0
CA G:LYS89 5.0 23.9 1.0
CA G:MET85 5.0 16.3 1.0

Potassium binding site 8 out of 28 in 5dkp

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Potassium binding site 8 out of 28 in the Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556.


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 N. Meningitidis Clpp in Complex with Agonist Adep A54556. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K301

b:35.9
occ:1.00
 O H:MET85 2.6 21.3 1.0
O H:PRO90 2.7 24.1 1.0
O H:ILE88 2.8 20.0 1.0
O H:HOH408 3.0 19.0 1.0
O H:HOH410 3.0 21.5 1.0
C H:PRO90 3.7 20.1 1.0
C H:MET85 3.9 27.0 1.0
C H:ILE88 3.9 20.8 1.0
CG1 H:ILE88 4.0 21.6 1.0
O H:ASN86 4.1 26.9 1.0
O H:LYS89 4.2 22.4 1.0
CA H:ASP91 4.2 21.2 1.0
N H:ASP91 4.3 13.2 1.0
C H:ASN86 4.3 23.2 1.0
N H:VAL92 4.4 22.8 1.0
C H:LYS89 4.4 20.5 1.0
CG2 H:VAL92 4.4 11.5 1.0
OE1 H:GLU112 4.4 22.7 1.0
CA H:ASN86 4.5 20.8 1.0
N H:ILE88 4.5 13.0 1.0
N H:ASN86 4.7 21.4 1.0
C H:ASP91 4.7 28.8 1.0
CA H:ILE88 4.7 20.0 1.0
N H:PRO90 4.7 24.7 1.0
CA H:PRO90 4.8 18.4 1.0
N H:LYS89 4.8 21.9 1.0
CA H:MET85 4.9 19.3 1.0
CA H:LYS89 4.9 25.1 1.0
CD1 H:ILE88 5.0 22.5 1.0
C H:PHE87 5.0 25.2 1.0
N H:PHE87 5.0 21.4 1.0

Potassium binding site 9 out of 28 in 5dkp

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Potassium binding site 9 out of 28 in the Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556.


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 N. Meningitidis Clpp in Complex with Agonist Adep A54556. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:K301

b:30.2
occ:1.00
 O I:MET85 2.7 20.8 1.0
O I:ILE88 2.7 22.3 1.0
O I:PRO90 2.7 23.5 1.0
O I:HOH414 2.8 16.4 1.0
O I:HOH425 3.3 27.1 1.0
C I:ILE88 3.8 20.6 1.0
C I:PRO90 3.8 24.5 1.0
C I:MET85 3.9 26.1 1.0
CG1 I:ILE88 3.9 20.4 1.0
O I:LYS89 4.3 26.7 1.0
O I:ASN86 4.3 18.9 1.0
C I:LYS89 4.4 17.7 1.0
CG2 I:VAL92 4.4 15.8 1.0
N I:VAL92 4.4 22.3 1.0
C I:ASN86 4.4 23.3 1.0
CA I:ASP91 4.4 20.3 1.0
OE1 I:GLU112 4.4 33.5 1.0
CA I:ASN86 4.5 24.1 1.0
N I:ASP91 4.5 22.7 1.0
N I:ILE88 4.6 20.8 1.0
CA I:ILE88 4.6 23.1 1.0
N I:PRO90 4.7 21.6 1.0
N I:ASN86 4.7 21.6 1.0
N I:LYS89 4.7 24.5 1.0
C I:ASP91 4.8 25.1 1.0
CA I:LYS89 4.8 25.8 1.0
CD1 I:ILE88 4.9 20.0 1.0
CA I:PRO90 4.9 21.7 1.0
CB I:ILE88 4.9 20.9 1.0
CA I:MET85 5.0 21.4 1.0

Potassium binding site 10 out of 28 in 5dkp

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Potassium binding site 10 out of 28 in the Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556.


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 N. Meningitidis Clpp in Complex with Agonist Adep A54556. within 5.0Å range:
probe atom residue distance (Å) B Occ
J:K301

b:31.3
occ:1.00
 O J:PRO90 2.7 19.8 1.0
O J:MET85 2.7 23.6 1.0
O J:ILE88 2.9 20.1 1.0
O J:HOH422 2.9 24.3 1.0
O J:HOH420 3.0 24.1 1.0
O J:HOH423 3.4 33.9 1.0
C J:PRO90 3.7 23.5 1.0
C J:ILE88 3.9 19.6 1.0
C J:MET85 3.9 24.5 1.0
CG1 J:ILE88 4.0 22.0 1.0
O J:LYS89 4.2 20.6 1.0
CA J:ASP91 4.2 23.8 1.0
N J:ASP91 4.3 19.3 1.0
OE1 J:GLU112 4.3 30.5 1.0
N J:VAL92 4.4 23.6 1.0
C J:LYS89 4.4 20.4 1.0
O J:ASN86 4.4 24.6 1.0
CG2 J:VAL92 4.4 15.8 1.0
C J:ASN86 4.4 25.3 1.0
CA J:ASN86 4.5 21.4 1.0
N J:ILE88 4.6 21.3 1.0
C J:ASP91 4.6 27.9 1.0
N J:PRO90 4.7 14.3 1.0
N J:ASN86 4.7 21.6 1.0
CA J:ILE88 4.7 16.3 1.0
O J:HOH418 4.7 21.7 1.0
CA J:PRO90 4.8 15.5 1.0
N J:LYS89 4.8 24.3 1.0
CD1 J:ILE88 4.9 19.3 1.0
CA J:LYS89 4.9 27.5 1.0
CB J:ILE88 5.0 22.5 1.0

Reference:

J.D.Goodreid, J.Janetzko, J.P.Santa Maria, K.S.Wong, E.Leung, B.T.Eger, S.Bryson, E.F.Pai, S.D.Gray-Owen, S.Walker, W.A.Houry, R.A.Batey. Development and Characterization of Potent Cyclic Acyldepsipeptide Analogues with Increased Antimicrobial Activity. J.Med.Chem. V. 59 624 2016.
ISSN: ISSN 0022-2623
PubMed: 26818454
DOI: 10.1021/ACS.JMEDCHEM.5B01451
Page generated: Sun Dec 13 23:56:23 2020

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