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Potassium in PDB 6w9t: Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06

Enzymatic activity of Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06

All present enzymatic activity of Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06:
3.4.21.92;

Protein crystallography data

The structure of Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06, PDB code: 6w9t was solved by M.F.Mabanglo, W.A.Houry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 97.33 / 1.64
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.328, 119.150, 127.763, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 28.2

Other elements in 6w9t:

The structure of Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06 also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Chlorine (Cl) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06 (pdb code 6w9t). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 7 binding sites of Potassium where determined in the Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06, PDB code: 6w9t:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in 6w9t

Go back to Potassium Binding Sites List in 6w9t
Potassium binding site 1 out of 7 in the Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06


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 Complex with Small Molecule Activator ACP1-06 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K301

b:22.9
occ:1.00
 O A:MET85 2.6 19.1 1.0
O A:PRO90 2.7 24.4 1.0
O A:HOH431 2.8 29.4 1.0
O A:HOH451 2.9 20.0 1.0
O A:ILE88 2.9 27.7 1.0
O A:HOH481 3.1 36.8 1.0
HG13 A:ILE88 3.4 25.0 1.0
HG23 A:VAL92 3.5 15.4 1.0
HA A:ASP91 3.6 21.7 1.0
HA A:ASN86 3.6 26.1 1.0
C A:PRO90 3.7 24.1 1.0
C A:MET85 3.8 20.4 1.0
HG12 A:ILE88 3.8 25.0 1.0
C A:ILE88 3.9 19.0 1.0
H A:VAL92 4.0 24.3 1.0
O A:ASN86 4.1 24.5 1.0
CG1 A:ILE88 4.1 20.9 1.0
O A:LYS89 4.1 22.7 1.0
CA A:ASN86 4.2 21.7 1.0
C A:ASN86 4.3 18.2 1.0
CA A:ASP91 4.3 18.1 1.0
N A:ASP91 4.3 21.0 1.0
C A:LYS89 4.3 26.7 1.0
H A:ILE88 4.4 19.6 1.0
CG2 A:VAL92 4.5 12.8 1.0
N A:VAL92 4.5 20.2 1.0
N A:ASN86 4.5 18.4 1.0
OE1 A:GLU112 4.6 26.4 1.0
N A:ILE88 4.6 16.3 1.0
N A:PRO90 4.7 19.1 1.0
HD11 A:ILE88 4.7 22.1 1.0
O A:HOH435 4.7 22.6 1.0
CA A:ILE88 4.7 23.0 1.0
CA A:PRO90 4.8 20.0 1.0
HA A:MET85 4.8 24.9 1.0
C A:ASP91 4.8 20.7 1.0
HA A:LYS89 4.8 28.4 1.0
HG21 A:VAL92 4.8 15.4 1.0
N A:LYS89 4.9 22.6 1.0
HG22 A:VAL92 4.9 15.4 1.0
CA A:MET85 4.9 20.8 1.0
HD2 A:PRO90 4.9 25.7 1.0
CA A:LYS89 4.9 23.7 1.0

Potassium binding site 2 out of 7 in 6w9t

Go back to Potassium Binding Sites List in 6w9t
Potassium binding site 2 out of 7 in the Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06


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 Complex with Small Molecule Activator ACP1-06 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K301

b:29.2
occ:1.00
 O B:MET85 2.5 27.8 1.0
O B:HOH473 2.6 41.6 1.0
O B:PRO90 2.6 28.7 1.0
O B:HOH445 2.7 22.1 1.0
O B:HOH405 3.1 31.2 1.0
O B:ILE88 3.1 29.2 1.0
HA B:ASN86 3.5 45.8 1.0
HG13 B:ILE88 3.6 34.7 1.0
HA B:ASP91 3.6 35.3 1.0
C B:PRO90 3.7 35.9 1.0
C B:MET85 3.8 30.5 1.0
HG23 B:VAL92 3.9 32.2 1.0
HG12 B:ILE88 3.9 34.7 1.0
H B:VAL92 3.9 25.6 1.0
C B:ILE88 4.1 25.3 1.0
O B:LYS89 4.1 35.2 1.0
O B:ASN86 4.2 30.1 1.0
CG1 B:ILE88 4.2 28.9 1.0
CA B:ASN86 4.2 38.1 1.0
O B:HOH489 4.2 43.8 1.0
C B:ASN86 4.3 27.6 1.0
CA B:ASP91 4.3 29.4 1.0
N B:ASP91 4.3 23.1 1.0
C B:LYS89 4.3 24.8 1.0
OE1 B:GLU112 4.5 30.2 1.0
N B:ASN86 4.5 29.9 1.0
N B:VAL92 4.5 21.3 1.0
H B:ILE88 4.6 36.0 1.0
N B:PRO90 4.6 27.3 1.0
N B:ILE88 4.7 30.0 1.0
CG2 B:VAL92 4.7 26.8 1.0
O B:HOH475 4.7 37.9 1.0
CA B:PRO90 4.7 24.1 1.0
HA B:MET85 4.8 34.1 1.0
C B:ASP91 4.8 25.2 1.0
HA B:LYS89 4.8 40.0 1.0
HD11 B:ILE88 4.9 26.8 1.0
CA B:MET85 4.9 28.4 1.0
HG21 B:VAL92 4.9 32.2 1.0
CA B:ILE88 4.9 25.7 1.0
HB B:VAL92 4.9 25.5 1.0
HB3 B:MET85 4.9 25.6 1.0
N B:LYS89 4.9 26.1 1.0
CA B:LYS89 5.0 33.3 1.0

Potassium binding site 3 out of 7 in 6w9t

Go back to Potassium Binding Sites List in 6w9t
Potassium binding site 3 out of 7 in the Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06


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 Complex with Small Molecule Activator ACP1-06 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K301

b:35.4
occ:1.00
 O C:MET85 2.6 33.7 1.0
O C:PRO90 2.7 31.3 1.0
O C:ILE88 2.8 27.8 1.0
O C:HOH467 2.9 43.6 1.0
O C:HOH416 2.9 35.9 1.0
HG13 C:ILE88 3.5 31.8 1.0
HA C:ASP91 3.6 40.9 1.0
C C:PRO90 3.7 29.9 1.0
HA C:ASN86 3.7 34.8 1.0
HG23 C:VAL92 3.8 32.7 1.0
C C:MET85 3.8 29.8 1.0
C C:ILE88 3.9 28.6 1.0
HG12 C:ILE88 3.9 31.8 1.0
H C:VAL92 4.0 50.2 1.0
O C:LYS89 4.0 44.5 1.0
CG1 C:ILE88 4.2 26.4 1.0
C C:LYS89 4.2 28.8 1.0
OE1 C:GLU112 4.2 44.4 1.0
O C:ASN86 4.2 38.2 1.0
CA C:ASP91 4.3 34.0 1.0
CA C:ASN86 4.3 29.0 1.0
C C:ASN86 4.3 26.7 1.0
N C:ASP91 4.3 32.9 1.0
H C:ILE88 4.5 52.7 1.0
N C:VAL92 4.5 41.9 1.0
N C:ASN86 4.5 28.5 1.0
N C:PRO90 4.6 28.1 1.0
N C:ILE88 4.6 43.9 1.0
HA C:LYS89 4.6 34.8 1.0
CG2 C:VAL92 4.7 27.2 1.0
HA C:MET85 4.7 48.6 1.0
C C:ASP91 4.7 53.8 1.0
CA C:ILE88 4.7 35.6 1.0
O C:HOH414 4.7 32.5 1.0
CA C:PRO90 4.8 31.8 1.0
N C:LYS89 4.8 35.2 1.0
CA C:LYS89 4.8 29.1 1.0
HD11 C:ILE88 4.8 41.9 1.0
CA C:MET85 4.9 40.5 1.0
HG21 C:VAL92 4.9 32.7 1.0

Potassium binding site 4 out of 7 in 6w9t

Go back to Potassium Binding Sites List in 6w9t
Potassium binding site 4 out of 7 in the Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06


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 Complex with Small Molecule Activator ACP1-06 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K301

b:30.1
occ:1.00
 O D:PRO90 2.6 30.3 1.0
O D:HOH449 2.7 28.5 1.0
O D:MET85 2.7 22.4 1.0
O D:ILE88 2.7 28.9 1.0
HG13 D:ILE88 3.3 31.3 1.0
HA D:ASP91 3.4 60.7 1.0
HG23 D:VAL92 3.6 42.9 1.0
C D:PRO90 3.6 33.6 1.0
O D:HOH469 3.7 39.6 1.0
HG12 D:ILE88 3.8 31.3 1.0
H D:VAL92 3.8 35.6 1.0
HA D:ASN86 3.8 34.6 1.0
C D:ILE88 3.9 35.5 1.0
C D:MET85 3.9 39.4 1.0
O D:LYS89 4.0 34.0 1.0
CG1 D:ILE88 4.0 26.1 1.0
CA D:ASP91 4.1 50.6 1.0
O D:ASN86 4.2 30.7 1.0
N D:ASP91 4.2 40.4 1.0
C D:LYS89 4.3 35.0 1.0
N D:VAL92 4.4 29.7 1.0
C D:ASN86 4.4 27.4 1.0
CA D:ASN86 4.4 28.8 1.0
H D:ILE88 4.5 39.1 1.0
CG2 D:VAL92 4.6 35.7 1.0
N D:ILE88 4.6 32.5 1.0
OE1 D:GLU112 4.6 36.0 1.0
C D:ASP91 4.6 38.6 1.0
HD11 D:ILE88 4.6 38.5 1.0
O D:HOH464 4.6 26.1 1.0
N D:PRO90 4.7 35.1 1.0
HA D:LYS89 4.7 53.9 1.0
N D:ASN86 4.7 22.7 1.0
CA D:ILE88 4.7 28.5 1.0
CA D:PRO90 4.8 33.9 1.0
N D:LYS89 4.8 33.2 1.0
HA D:MET85 4.8 36.6 1.0
OD1 D:ASP91 4.9 30.0 1.0
HG21 D:VAL92 4.9 42.9 1.0
CA D:LYS89 4.9 44.9 1.0
CD1 D:ILE88 5.0 32.1 1.0
H D:ASP91 5.0 48.5 1.0

Potassium binding site 5 out of 7 in 6w9t

Go back to Potassium Binding Sites List in 6w9t
Potassium binding site 5 out of 7 in the Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06


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 Complex with Small Molecule Activator ACP1-06 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K301

b:26.6
occ:1.00
 O E:MET85 2.7 25.7 1.0
O E:PRO90 2.7 23.2 1.0
O E:ILE88 2.8 22.9 1.0
O E:HOH415 2.8 25.2 1.0
O E:HOH474 2.8 42.2 1.0
O E:HOH473 2.9 35.9 1.0
HG23 E:VAL92 3.5 25.4 1.0
HG13 E:ILE88 3.5 27.0 1.0
HA E:ASP91 3.6 30.7 1.0
HA E:ASN86 3.6 28.9 1.0
C E:PRO90 3.7 24.8 1.0
HG12 E:ILE88 3.9 27.0 1.0
C E:MET85 3.9 27.7 1.0
C E:ILE88 3.9 34.4 1.0
H E:VAL92 3.9 27.2 1.0
O E:LYS89 4.0 32.2 1.0
CG1 E:ILE88 4.1 22.5 1.0
O E:ASN86 4.2 28.9 1.0
C E:LYS89 4.2 23.7 1.0
CA E:ASN86 4.3 24.1 1.0
CA E:ASP91 4.3 25.6 1.0
C E:ASN86 4.3 28.1 1.0
N E:ASP91 4.3 25.3 1.0
OE1 E:GLU112 4.4 37.4 1.0
N E:VAL92 4.4 22.6 1.0
CG2 E:VAL92 4.4 21.2 1.0
H E:ILE88 4.5 32.0 1.0
N E:ASN86 4.6 27.5 1.0
N E:PRO90 4.6 30.6 1.0
N E:ILE88 4.6 26.6 1.0
O E:HOH439 4.7 26.0 1.0
HA E:LYS89 4.7 33.6 1.0
C E:ASP91 4.7 24.2 1.0
CA E:ILE88 4.7 31.3 1.0
CA E:PRO90 4.8 31.6 1.0
N E:LYS89 4.8 25.1 1.0
HG21 E:VAL92 4.8 25.4 1.0
HD11 E:ILE88 4.8 26.1 1.0
CA E:LYS89 4.8 27.9 1.0
HA E:MET85 4.9 24.1 1.0
HG22 E:VAL92 4.9 25.4 1.0
HB E:VAL92 4.9 39.7 1.0
CA E:MET85 5.0 20.0 1.0

Potassium binding site 6 out of 7 in 6w9t

Go back to Potassium Binding Sites List in 6w9t
Potassium binding site 6 out of 7 in the Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06


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 Complex with Small Molecule Activator ACP1-06 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K302

b:27.7
occ:1.00
 O F:MET85 2.6 19.8 1.0
O F:ILE88 2.7 25.3 1.0
O F:PRO90 2.8 27.2 1.0
O F:HOH411 2.8 39.1 1.0
O F:HOH447 2.8 31.6 1.0
O F:HOH484 3.1 64.8 1.0
HG13 F:ILE88 3.4 30.1 1.0
HA F:ASN86 3.5 28.5 1.0
HG23 F:VAL92 3.5 37.8 1.0
HA F:ASP91 3.8 38.0 1.0
C F:MET85 3.8 24.8 1.0
C F:PRO90 3.8 26.4 1.0
C F:ILE88 3.9 28.4 1.0
HG12 F:ILE88 3.9 30.1 1.0
H F:VAL92 4.0 31.8 1.0
O F:ASN86 4.1 31.1 1.0
CG1 F:ILE88 4.1 25.1 1.0
O F:LYS89 4.1 23.9 1.0
CA F:ASN86 4.1 23.8 1.0
C F:ASN86 4.2 35.8 1.0
C F:LYS89 4.4 22.9 1.0
CG2 F:VAL92 4.4 31.5 1.0
N F:ASN86 4.4 16.9 1.0
H F:ILE88 4.5 25.8 1.0
CA F:ASP91 4.5 31.6 1.0
OE1 F:GLU112 4.5 28.4 1.0
N F:VAL92 4.5 26.5 1.0
N F:ASP91 4.5 28.7 1.0
N F:ILE88 4.6 21.5 1.0
HG21 F:VAL92 4.6 37.8 1.0
HD11 F:ILE88 4.7 23.4 1.0
N F:PRO90 4.7 24.4 1.0
HA F:LYS89 4.7 25.0 1.0
CA F:ILE88 4.7 28.4 1.0
N F:LYS89 4.8 20.4 1.0
HB F:VAL92 4.8 20.8 1.0
C F:ASP91 4.8 22.3 1.0
HA F:MET85 4.9 17.3 1.0
CA F:PRO90 4.9 20.6 1.0
CA F:LYS89 4.9 20.8 1.0
HG22 F:VAL92 5.0 37.8 1.0
CA F:MET85 5.0 14.4 1.0
N F:PHE87 5.0 28.2 1.0

Potassium binding site 7 out of 7 in 6w9t

Go back to Potassium Binding Sites List in 6w9t
Potassium binding site 7 out of 7 in the Crystal Structure of Neisseria Meningitidis Clpp Protease Complex with Small Molecule Activator ACP1-06


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 Complex with Small Molecule Activator ACP1-06 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K301

b:21.9
occ:1.00
 O G:PRO90 2.6 19.5 1.0
O G:HOH466 2.7 28.5 1.0
O G:MET85 2.7 15.7 1.0
O G:HOH495 2.8 29.3 1.0
O G:ILE88 2.8 19.3 1.0
O G:HOH428 2.9 23.4 1.0
HA G:ASP91 3.5 22.6 1.0
HG23 G:VAL92 3.5 22.5 1.0
HG12 G:ILE88 3.6 17.2 1.0
HG13 G:ILE88 3.6 17.2 1.0
C G:PRO90 3.7 15.9 1.0
HA G:ASN86 3.7 19.4 1.0
H G:VAL92 3.9 28.8 1.0
C G:ILE88 3.9 15.4 1.0
C G:MET85 3.9 14.1 1.0
O G:HOH436 3.9 37.9 1.0
CG1 G:ILE88 4.1 14.3 1.0
O G:LYS89 4.1 21.1 1.0
O G:HOH498 4.2 52.7 1.0
CA G:ASP91 4.3 18.8 1.0
C G:LYS89 4.3 18.1 1.0
N G:ASP91 4.3 22.4 1.0
O G:ASN86 4.4 23.3 1.0
CA G:ASN86 4.4 16.2 1.0
N G:VAL92 4.4 24.0 1.0
OE1 G:GLU112 4.4 21.8 1.0
C G:ASN86 4.4 24.4 1.0
H G:ILE88 4.5 20.3 1.0
CG2 G:VAL92 4.5 18.7 1.0
O G:HOH494 4.5 49.7 1.0
N G:ILE88 4.6 16.9 1.0
N G:PRO90 4.6 16.8 1.0
O G:HOH469 4.6 19.3 1.0
N G:ASN86 4.6 14.8 1.0
C G:ASP91 4.7 22.4 1.0
HA G:LYS89 4.7 20.2 1.0
CA G:ILE88 4.7 14.5 1.0
CA G:PRO90 4.7 27.3 1.0
HD11 G:ILE88 4.7 28.3 1.0
HA G:MET85 4.8 18.5 1.0
N G:LYS89 4.8 18.6 1.0
HG22 G:VAL92 4.9 22.5 1.0
HG21 G:VAL92 4.9 22.5 1.0
O G:HOH515 4.9 60.4 1.0
CA G:LYS89 4.9 16.9 1.0
HB G:VAL92 5.0 15.1 1.0

Reference:

G.Binepal, M.F.Mabanglo, J.D.Goodreid, E.Leung, M.M.Barghash, K.S.Wong, F.Lin, M.Cossette, J.Bansagi, B.Song, V.H.Balasco Serrao, E.F.Pai, R.A.Batey, S.D.Gray-Owen, W.A.Houry. Development of Antibiotics That Dysregulate the Neisserial Clpp Protease. Acs Infect Dis. 2020.
ISSN: ESSN 2373-8227
PubMed: 33237740
DOI: 10.1021/ACSINFECDIS.0C00599
Page generated: Mon Aug 12 18:12:42 2024

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