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Potassium in PDB 6naq: Crystal Structure of Neisseria Meningitidis Clpp Protease in Apo Form

Enzymatic activity of Crystal Structure of Neisseria Meningitidis Clpp Protease in Apo Form

All present enzymatic activity of Crystal Structure of Neisseria Meningitidis Clpp Protease in Apo Form:
3.4.21.92;

Protein crystallography data

The structure of Crystal Structure of Neisseria Meningitidis Clpp Protease in Apo Form, PDB code: 6naq was solved by W.A.Houry, M.F.Mabanglo, E.F.Pai, B.T.Eger, S.Bryson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.39 / 2.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 98.584, 127.945, 120.195, 90.00, 90.19, 90.00
R / Rfree (%) 20.7 / 24.6

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Potassium atom in the Crystal Structure of Neisseria Meningitidis Clpp Protease in Apo Form (pdb code 6naq). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 14 binding sites of Potassium where determined in the Crystal Structure of Neisseria Meningitidis Clpp Protease in Apo Form, PDB code: 6naq:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 14 in 6naq

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Potassium binding site 1 out of 14 in the Crystal Structure of Neisseria Meningitidis Clpp Protease in Apo Form


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 Neisseria Meningitidis Clpp Protease in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K301

b:15.5
occ:1.00
O A:MET85 2.7 16.8 1.0
O A:HOH435 2.8 16.6 1.0
O A:PRO90 2.8 17.7 1.0
O A:ILE88 2.8 16.0 1.0
O A:HOH437 2.9 14.7 1.0
C A:PRO90 3.7 19.9 1.0
C A:ILE88 3.9 21.3 1.0
C A:MET85 3.9 21.9 1.0
O A:LYS89 3.9 19.4 1.0
O A:HOH454 4.0 12.9 1.0
CG1 A:ILE88 4.1 18.2 1.0
O A:ASN86 4.1 22.2 1.0
C A:LYS89 4.2 13.9 1.0
C A:ASN86 4.3 21.9 1.0
CA A:ASN86 4.3 22.7 1.0
CA A:ASP91 4.4 20.7 1.0
N A:ASP91 4.4 17.7 1.0
N A:VAL92 4.5 16.5 1.0
OE1 A:GLU112 4.5 21.2 1.0
N A:ILE88 4.6 17.6 1.0
N A:ASN86 4.6 17.5 1.0
CG2 A:VAL92 4.7 16.1 1.0
N A:PRO90 4.7 16.5 1.0
O A:HOH433 4.7 18.6 1.0
CA A:ILE88 4.7 17.9 1.0
CA A:PRO90 4.8 17.4 1.0
N A:LYS89 4.8 21.4 1.0
CA A:LYS89 4.8 14.3 1.0
C A:ASP91 4.8 20.5 1.0
N A:PHE87 5.0 18.4 1.0

Potassium binding site 2 out of 14 in 6naq

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Potassium binding site 2 out of 14 in the Crystal Structure of Neisseria Meningitidis Clpp Protease in Apo Form


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 Neisseria Meningitidis Clpp Protease in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K301

b:20.7
occ:1.00
O B:MET85 2.7 19.5 1.0
O B:PRO90 2.7 18.7 1.0
O B:HOH422 2.8 14.2 1.0
O B:HOH445 2.8 16.4 1.0
O B:ILE88 2.8 19.0 1.0
O B:HOH409 2.9 21.9 1.0
C B:PRO90 3.8 25.3 1.0
C B:MET85 3.9 21.0 1.0
C B:ILE88 3.9 21.4 1.0
O B:LYS89 4.1 19.7 1.0
CG1 B:ILE88 4.1 15.0 1.0
O B:HOH453 4.2 20.4 1.0
O B:ASN86 4.2 22.1 1.0
CA B:ASN86 4.3 18.9 1.0
CA B:ASP91 4.3 19.8 1.0
C B:LYS89 4.4 17.1 1.0
C B:ASN86 4.4 22.1 1.0
N B:VAL92 4.4 20.6 1.0
N B:ASP91 4.4 19.4 1.0
OE1 B:GLU112 4.4 24.2 1.0
O B:HOH447 4.4 29.9 1.0
N B:ASN86 4.6 16.9 1.0
O B:HOH441 4.6 18.1 1.0
CG2 B:VAL92 4.6 16.7 1.0
N B:ILE88 4.7 17.6 1.0
N B:PRO90 4.7 17.8 1.0
C B:ASP91 4.7 19.3 1.0
CA B:ILE88 4.8 21.2 1.0
N B:LYS89 4.8 21.3 1.0
CA B:PRO90 4.8 18.4 1.0
CA B:LYS89 4.9 21.9 1.0
CA B:MET85 5.0 20.8 1.0

Potassium binding site 3 out of 14 in 6naq

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Potassium binding site 3 out of 14 in the Crystal Structure of Neisseria Meningitidis Clpp Protease in Apo Form


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 Neisseria Meningitidis Clpp Protease in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K301

b:18.8
occ:1.00
O C:MET85 2.7 16.4 1.0
O C:PRO90 2.7 17.0 1.0
O C:ILE88 2.8 16.8 1.0
O C:HOH421 2.8 17.5 1.0
O C:HOH407 2.9 15.4 1.0
C C:PRO90 3.7 23.5 1.0
C C:MET85 3.9 21.5 1.0
C C:ILE88 3.9 18.1 1.0
CG1 C:ILE88 4.0 17.2 1.0
O C:LYS89 4.1 18.0 1.0
CA C:ASP91 4.3 18.1 1.0
C C:LYS89 4.3 18.3 1.0
O C:HOH445 4.3 11.6 1.0
O C:ASN86 4.3 23.6 1.0
N C:ASP91 4.3 16.3 1.0
N C:VAL92 4.3 17.5 1.0
CA C:ASN86 4.4 17.5 1.0
C C:ASN86 4.4 14.5 1.0
OE1 C:GLU112 4.5 22.5 1.0
O C:HOH434 4.6 15.6 1.0
CG2 C:VAL92 4.6 15.0 1.0
N C:ASN86 4.6 17.9 1.0
N C:PRO90 4.6 16.8 1.0
C C:ASP91 4.7 21.1 1.0
N C:ILE88 4.7 19.8 1.0
CA C:PRO90 4.7 16.4 1.0
CA C:ILE88 4.7 16.9 1.0
N C:LYS89 4.8 18.4 1.0
CA C:LYS89 4.9 18.9 1.0
CA C:MET85 5.0 16.9 1.0

Potassium binding site 4 out of 14 in 6naq

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Potassium binding site 4 out of 14 in the Crystal Structure of Neisseria Meningitidis Clpp Protease in Apo Form


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 Neisseria Meningitidis Clpp Protease in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K301

b:22.4
occ:1.00
O D:PRO90 2.7 24.0 1.0
O D:MET85 2.7 19.5 1.0
O D:HOH439 2.7 25.9 1.0
O D:HOH427 2.8 26.0 1.0
O D:ILE88 3.0 21.9 1.0
O D:HOH411 3.0 15.6 1.0
C D:PRO90 3.7 23.3 1.0
O D:HOH428 3.9 24.2 1.0
C D:MET85 3.9 24.8 1.0
C D:ILE88 4.0 21.6 1.0
O D:LYS89 4.1 22.9 1.0
CG1 D:ILE88 4.1 17.3 1.0
O D:ASN86 4.1 22.0 1.0
O D:HOH441 4.1 19.0 1.0
CA D:ASP91 4.3 21.8 1.0
C D:ASN86 4.3 26.5 1.0
CG2 D:VAL92 4.3 14.9 1.0
N D:VAL92 4.3 19.8 1.0
CA D:ASN86 4.3 21.0 1.0
N D:ASP91 4.4 18.6 1.0
C D:LYS89 4.4 18.0 1.0
OE1 D:GLU112 4.4 26.0 1.0
N D:ASN86 4.6 20.9 1.0
C D:ASP91 4.7 23.4 1.0
O D:HOH413 4.7 22.9 1.0
N D:ILE88 4.7 23.5 1.0
N D:PRO90 4.7 16.6 1.0
CA D:PRO90 4.8 17.2 1.0
CA D:ILE88 4.8 22.9 1.0
N D:LYS89 4.9 20.5 1.0
CA D:LYS89 5.0 20.6 1.0

Potassium binding site 5 out of 14 in 6naq

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Potassium binding site 5 out of 14 in the Crystal Structure of Neisseria Meningitidis Clpp Protease in Apo Form


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 Neisseria Meningitidis Clpp Protease in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K301

b:33.1
occ:1.00
O E:MET85 2.6 22.5 1.0
O E:ILE88 2.7 22.9 1.0
O E:PRO90 2.8 27.0 1.0
O E:HOH424 2.8 41.4 1.0
O E:HOH404 3.0 14.7 1.0
O E:HOH402 3.2 25.4 1.0
C E:ILE88 3.8 22.6 1.0
C E:PRO90 3.8 25.8 1.0
C E:MET85 3.8 25.1 1.0
CG1 E:ILE88 3.9 22.0 1.0
O E:LYS89 4.1 27.5 1.0
C E:LYS89 4.3 22.0 1.0
O E:ASN86 4.3 26.3 1.0
CA E:ASN86 4.3 22.9 1.0
C E:ASN86 4.3 23.0 1.0
CA E:ASP91 4.3 23.8 1.0
N E:VAL92 4.4 20.2 1.0
OE1 E:GLU112 4.4 25.2 1.0
N E:ASP91 4.4 21.9 1.0
N E:ASN86 4.5 23.6 1.0
CG2 E:VAL92 4.5 16.4 1.0
N E:ILE88 4.5 24.3 1.0
CA E:ILE88 4.6 23.9 1.0
N E:LYS89 4.6 26.3 1.0
N E:PRO90 4.7 22.7 1.0
CA E:LYS89 4.7 21.0 1.0
C E:ASP91 4.7 26.1 1.0
CD1 E:ILE88 4.9 19.3 1.0
CA E:PRO90 4.9 21.4 1.0
CB E:ILE88 4.9 21.6 1.0
N E:PHE87 5.0 20.4 1.0
CA E:MET85 5.0 21.1 1.0

Potassium binding site 6 out of 14 in 6naq

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Potassium binding site 6 out of 14 in the Crystal Structure of Neisseria Meningitidis Clpp Protease in Apo Form


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 Neisseria Meningitidis Clpp Protease in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K301

b:29.0
occ:1.00
O F:PRO90 2.7 22.4 1.0
O F:HOH417 2.7 27.0 1.0
O F:MET85 2.7 24.6 1.0
O F:ILE88 2.7 20.0 1.0
O F:HOH432 2.9 26.8 1.0
O F:HOH420 3.0 26.8 1.0
C F:PRO90 3.7 25.8 1.0
C F:ILE88 3.8 21.4 1.0
C F:MET85 3.9 23.3 1.0
O F:LYS89 4.0 23.0 1.0
CG1 F:ILE88 4.1 19.4 1.0
O F:HOH437 4.1 21.8 1.0
O F:ASN86 4.1 25.2 1.0
C F:LYS89 4.2 15.4 1.0
C F:ASN86 4.3 23.1 1.0
CA F:ASN86 4.3 23.0 1.0
CA F:ASP91 4.3 21.6 1.0
N F:ASP91 4.4 19.6 1.0
N F:VAL92 4.5 22.8 1.0
N F:ASN86 4.6 21.4 1.0
N F:PRO90 4.6 20.2 1.0
OE1 F:GLU112 4.6 29.2 1.0
N F:ILE88 4.6 17.9 1.0
CA F:ILE88 4.7 18.0 1.0
N F:LYS89 4.7 25.6 1.0
O F:HOH422 4.7 23.7 1.0
CA F:PRO90 4.8 15.4 1.0
C F:ASP91 4.8 24.9 1.0
CA F:LYS89 4.8 22.8 1.0
CG2 F:VAL92 4.9 19.5 1.0
OD1 F:ASP91 5.0 21.1 1.0

Potassium binding site 7 out of 14 in 6naq

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Potassium binding site 7 out of 14 in the Crystal Structure of Neisseria Meningitidis Clpp Protease in Apo Form


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 Neisseria Meningitidis Clpp Protease in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K301

b:18.7
occ:1.00
O G:MET85 2.7 18.2 1.0
O G:PRO90 2.7 20.7 1.0
O G:HOH443 2.8 15.8 1.0
O G:ILE88 2.8 16.5 1.0
O G:HOH427 2.9 15.3 1.0
O G:HOH415 3.5 27.1 1.0
C G:PRO90 3.8 23.9 1.0
C G:MET85 3.9 22.1 1.0
C G:ILE88 3.9 21.4 1.0
O G:HOH449 4.0 8.9 1.0
O G:ASN86 4.1 21.6 1.0
CG1 G:ILE88 4.1 16.9 1.0
O G:LYS89 4.2 14.1 1.0
C G:ASN86 4.2 24.3 1.0
CA G:ASN86 4.3 21.7 1.0
C G:LYS89 4.4 16.2 1.0
CA G:ASP91 4.4 20.5 1.0
OE1 G:GLU112 4.4 18.6 1.0
N G:ASP91 4.4 20.2 1.0
N G:VAL92 4.5 16.1 1.0
CG2 G:VAL92 4.5 13.2 1.0
N G:ILE88 4.5 20.9 1.0
N G:ASN86 4.6 17.9 1.0
N G:PRO90 4.7 15.3 1.0
CA G:ILE88 4.7 20.9 1.0
C G:ASP91 4.8 21.6 1.0
CA G:PRO90 4.8 13.8 1.0
N G:LYS89 4.9 18.5 1.0
N G:PHE87 4.9 21.7 1.0
CA G:LYS89 4.9 19.9 1.0

Potassium binding site 8 out of 14 in 6naq

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Potassium binding site 8 out of 14 in the Crystal Structure of Neisseria Meningitidis Clpp Protease in Apo Form


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 Neisseria Meningitidis Clpp Protease in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K301

b:28.2
occ:1.00
O H:MET85 2.7 23.2 1.0
O H:HOH418 2.8 19.3 1.0
O H:PRO90 2.8 21.9 1.0
O H:ILE88 2.9 19.1 1.0
O H:HOH402 2.9 24.1 1.0
C H:PRO90 3.8 21.4 1.0
C H:MET85 3.9 25.9 1.0
C H:ILE88 4.0 20.7 1.0
O H:LYS89 4.0 20.1 1.0
CG1 H:ILE88 4.1 21.0 1.0
O H:ASN86 4.2 26.3 1.0
CA H:ASP91 4.3 22.1 1.0
C H:ASN86 4.3 23.5 1.0
N H:VAL92 4.3 23.4 1.0
C H:LYS89 4.3 20.0 1.0
CA H:ASN86 4.4 25.0 1.0
N H:ASP91 4.4 18.6 1.0
OE1 H:GLU112 4.5 26.4 1.0
CG2 H:VAL92 4.5 18.0 1.0
N H:ASN86 4.6 23.4 1.0
N H:ILE88 4.7 22.4 1.0
C H:ASP91 4.7 22.2 1.0
N H:PRO90 4.8 18.5 1.0
CA H:ILE88 4.8 20.3 1.0
N H:LYS89 4.9 23.9 1.0
CA H:LYS89 4.9 22.7 1.0
CA H:PRO90 4.9 21.0 1.0
CA H:MET85 5.0 23.0 1.0

Potassium binding site 9 out of 14 in 6naq

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Potassium binding site 9 out of 14 in the Crystal Structure of Neisseria Meningitidis Clpp Protease in Apo Form


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 Neisseria Meningitidis Clpp Protease in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
I:K301

b:33.5
occ:1.00
O I:PRO90 2.6 27.2 1.0
O I:MET85 2.6 26.1 1.0
O I:ILE88 2.7 22.1 1.0
O I:HOH416 2.8 25.7 1.0
O I:HOH426 3.1 41.3 1.0
C I:PRO90 3.7 26.0 1.0
C I:MET85 3.8 26.5 1.0
C I:ILE88 3.9 23.9 1.0
CG1 I:ILE88 4.0 20.8 1.0
O I:HOH424 4.0 30.8 1.0
O I:LYS89 4.1 26.8 1.0
O I:HOH428 4.2 37.5 1.0
CA I:ASP91 4.2 23.1 1.0
O I:ASN86 4.3 26.0 1.0
C I:LYS89 4.3 20.9 1.0
N I:ASP91 4.3 18.9 1.0
CA I:ASN86 4.4 24.6 1.0
C I:ASN86 4.4 24.4 1.0
N I:VAL92 4.4 25.4 1.0
OE1 I:GLU112 4.5 29.2 1.0
CG2 I:VAL92 4.6 15.7 1.0
N I:ASN86 4.6 23.6 1.0
N I:ILE88 4.6 26.8 1.0
N I:PRO90 4.6 21.7 1.0
C I:ASP91 4.7 25.1 1.0
CA I:ILE88 4.7 24.5 1.0
N I:LYS89 4.8 24.1 1.0
CA I:PRO90 4.8 20.8 1.0
O I:HOH418 4.8 27.0 1.0
CA I:LYS89 4.8 19.1 1.0
CD1 I:ILE88 4.9 19.0 1.0
CA I:MET85 4.9 20.5 1.0
CB I:ILE88 5.0 19.9 1.0
OD1 I:ASP91 5.0 22.2 1.0

Potassium binding site 10 out of 14 in 6naq

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Potassium binding site 10 out of 14 in the Crystal Structure of Neisseria Meningitidis Clpp Protease in Apo Form


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 Neisseria Meningitidis Clpp Protease in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
J:K301

b:17.1
occ:1.00
O J:MET85 2.6 16.2 1.0
O J:PRO90 2.7 21.2 1.0
O J:HOH430 2.8 21.0 1.0
O J:HOH410 2.8 17.9 1.0
O J:ILE88 3.0 16.0 1.0
C J:PRO90 3.8 22.5 1.0
O J:HOH412 3.8 29.7 1.0
C J:MET85 3.8 24.4 1.0
C J:ILE88 4.0 20.5 1.0
CG1 J:ILE88 4.1 19.0 1.0
O J:LYS89 4.1 20.3 1.0
O J:HOH444 4.1 14.2 1.0
O J:ASN86 4.3 21.8 1.0
C J:ASN86 4.3 25.4 1.0
OE1 J:GLU112 4.3 18.2 1.0
CA J:ASN86 4.3 23.0 1.0
CA J:ASP91 4.3 19.3 1.0
C J:LYS89 4.4 20.6 1.0
N J:VAL92 4.4 17.1 1.0
N J:ASP91 4.4 17.4 1.0
CG2 J:VAL92 4.5 12.2 1.0
O J:HOH428 4.6 19.3 1.0
N J:ASN86 4.6 18.6 1.0
N J:ILE88 4.7 19.4 1.0
N J:PRO90 4.7 15.4 1.0
C J:ASP91 4.8 20.6 1.0
CA J:ILE88 4.8 23.0 1.0
CA J:PRO90 4.8 17.4 1.0
CA J:MET85 4.9 18.4 1.0
N J:LYS89 4.9 21.6 1.0
N J:PHE87 5.0 21.3 1.0

Reference:

M.F.Mabanglo, W.A.Houry. Molecular Basis of Clpp Activation By Small Molecules To Be Published.
Page generated: Mon Aug 12 16:57:52 2024

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