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Potassium in PDB 4igl: Structure of the Rhs-Repeat Containing Bc Component of the Secreted Abc Toxin Complex From Yersinia Entomophaga

Protein crystallography data

The structure of Structure of the Rhs-Repeat Containing Bc Component of the Secreted Abc Toxin Complex From Yersinia Entomophaga, PDB code: 4igl was solved by J.N.Busby, S.Panjikar, M.J.Landsberg, M.R.H.Hurst, J.S.Lott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.55 / 2.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 133.719, 147.596, 274.354, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 25.1

Potassium Binding Sites:

The binding sites of Potassium atom in the Structure of the Rhs-Repeat Containing Bc Component of the Secreted Abc Toxin Complex From Yersinia Entomophaga (pdb code 4igl). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Structure of the Rhs-Repeat Containing Bc Component of the Secreted Abc Toxin Complex From Yersinia Entomophaga, PDB code: 4igl:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 4igl

Go back to Potassium Binding Sites List in 4igl
Potassium binding site 1 out of 6 in the Structure of the Rhs-Repeat Containing Bc Component of the Secreted Abc Toxin Complex From Yersinia Entomophaga


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of the Rhs-Repeat Containing Bc Component of the Secreted Abc Toxin Complex From Yersinia Entomophaga within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1503

b:45.3
occ:1.00
 OD1 A:ASP625 2.5 50.1 1.0
O A:THR629 2.6 43.3 1.0
OG1 A:THR629 2.7 41.2 1.0
OD1 A:ASP631 2.7 44.8 1.0
OD1 A:ASP623 2.8 47.6 1.0
OD2 A:ASP631 2.8 44.9 1.0
OG A:SER627 2.8 46.7 1.0
CG A:ASP631 3.1 45.0 1.0
C A:THR629 3.4 42.4 1.0
CG A:ASP625 3.5 52.4 1.0
CG A:ASP623 3.6 46.6 1.0
CB A:SER627 3.6 47.9 1.0
N A:THR629 3.8 43.6 1.0
CB A:THR629 3.8 42.2 1.0
CA A:THR629 3.9 43.9 1.0
OD2 A:ASP625 4.0 49.1 1.0
N A:SER627 4.0 51.4 1.0
CA A:ASP623 4.1 42.4 1.0
N A:ILE624 4.3 45.6 1.0
N A:ASP625 4.3 50.4 1.0
OD2 A:ASP623 4.3 51.0 1.0
CA A:SER627 4.3 48.9 1.0
CB A:ASP623 4.4 45.1 1.0
O A:ASN645 4.4 47.2 1.0
N A:GLY628 4.5 45.9 1.0
N A:ASP631 4.5 42.6 1.0
CB A:ASP631 4.5 44.5 1.0
N A:ASN630 4.5 42.2 1.0
C A:ASP623 4.6 44.9 1.0
N A:ASN645 4.6 44.5 1.0
CB A:ASN645 4.6 42.7 1.0
C A:ASN630 4.7 43.8 1.0
CB A:ASP625 4.7 52.1 1.0
C A:SER627 4.8 43.9 1.0
N A:GLY626 4.8 50.4 1.0
CA A:ASN630 4.8 44.1 1.0
C A:GLY628 4.9 46.8 1.0
CA A:ASP625 4.9 50.8 1.0
CA A:ASP631 4.9 45.9 1.0
CG2 A:THR629 5.0 39.3 1.0

Potassium binding site 2 out of 6 in 4igl

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Potassium binding site 2 out of 6 in the Structure of the Rhs-Repeat Containing Bc Component of the Secreted Abc Toxin Complex From Yersinia Entomophaga


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of the Rhs-Repeat Containing Bc Component of the Secreted Abc Toxin Complex From Yersinia Entomophaga within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1504

b:49.4
occ:1.00
 O A:ASN1201 2.7 50.2 1.0
OD1 B:ASN166 2.7 49.0 1.0
O B:LYS163 2.7 50.4 1.0
OG1 A:THR1223 2.8 53.4 1.0
OD1 A:ASN1203 2.8 47.9 1.0
O B:HOH959 3.2 50.3 1.0
CG A:ASN1203 3.6 49.4 1.0
O A:THR1223 3.6 55.6 1.0
O A:HOH2391 3.6 49.9 1.0
C B:LYS163 3.7 50.7 1.0
ND2 A:ASN1203 3.7 49.5 1.0
N A:THR1223 3.8 51.8 1.0
CG B:ASN166 3.8 48.1 1.0
C A:ASN1201 3.9 48.8 1.0
CB A:THR1223 4.0 53.3 1.0
CB A:ASN1201 4.1 48.9 1.0
CA B:ASN164 4.1 52.3 1.0
CA A:THR1223 4.2 52.4 1.0
C A:THR1223 4.2 52.2 1.0
N B:ASN164 4.3 49.7 1.0
ND2 B:ASN166 4.4 51.1 1.0
C B:ASN164 4.4 52.7 1.0
O B:ASN164 4.5 53.5 1.0
CA A:ASN1201 4.6 49.8 1.0
O A:ASP1202 4.6 46.2 1.0
C A:ASP1202 4.6 46.9 1.0
N B:ASN166 4.7 48.3 1.0
CA B:LYS163 4.7 51.0 1.0
N A:ASN1203 4.8 45.5 1.0
OD1 B:ASN164 4.8 51.9 1.0
CA B:ASN166 4.8 47.9 1.0
C A:GLY1222 4.9 49.3 1.0
CB B:LYS163 4.9 50.9 1.0
CG2 A:THR1223 4.9 50.0 1.0
N A:ASP1202 4.9 50.0 1.0
CB A:ASN1203 4.9 45.1 1.0
CB B:ASN166 4.9 47.2 1.0

Potassium binding site 3 out of 6 in 4igl

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Potassium binding site 3 out of 6 in the Structure of the Rhs-Repeat Containing Bc Component of the Secreted Abc Toxin Complex From Yersinia Entomophaga


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of the Rhs-Repeat Containing Bc Component of the Secreted Abc Toxin Complex From Yersinia Entomophaga within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1505

b:57.2
occ:1.00
 O B:THR9 2.6 53.6 1.0
OD1 A:ASP1480 2.6 55.0 1.0
OG1 B:THR9 2.6 56.4 1.0
O B:SER370 3.1 44.8 1.0
OD2 A:ASP1480 3.3 50.9 1.0
CG A:ASP1480 3.3 53.4 1.0
CB B:THR9 3.6 50.8 1.0
OH B:TYR372 3.7 47.1 1.0
C B:THR9 3.7 53.0 1.0
O B:HOH931 4.0 47.0 1.0
C B:SER370 4.2 46.2 1.0
CZ B:TYR372 4.2 44.9 1.0
OD2 A:ASP1477 4.3 48.3 1.0
CA B:THR9 4.4 51.6 1.0
CB B:SER370 4.5 47.1 1.0
OD1 A:ASP1477 4.6 46.9 1.0
CE2 B:TYR372 4.6 38.4 1.0
CA B:SER370 4.7 49.0 1.0
CG A:ASP1477 4.8 47.4 1.0
N B:PRO10 4.8 50.7 1.0
CB A:ASP1480 4.8 50.6 1.0
CE1 B:TYR372 4.8 44.7 1.0
CG2 B:THR9 4.9 54.9 1.0
CD1 B:PHE6 4.9 49.8 1.0
CA B:PRO10 4.9 48.0 1.0

Potassium binding site 4 out of 6 in 4igl

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Potassium binding site 4 out of 6 in the Structure of the Rhs-Repeat Containing Bc Component of the Secreted Abc Toxin Complex From Yersinia Entomophaga


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of the Rhs-Repeat Containing Bc Component of the Secreted Abc Toxin Complex From Yersinia Entomophaga within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1506

b:39.2
occ:1.00
 OD1 C:ASP625 2.6 49.8 1.0
O C:THR629 2.7 40.9 1.0
OD1 C:ASP623 2.7 47.0 1.0
OG C:SER627 2.7 43.9 1.0
OD1 C:ASP631 2.8 44.4 1.0
OD2 C:ASP631 2.8 43.3 1.0
OG1 C:THR629 2.8 40.1 1.0
O C:HOH1618 2.9 44.0 1.0
CG C:ASP631 3.1 43.2 1.0
CB C:SER627 3.4 44.3 1.0
CG C:ASP623 3.5 45.2 1.0
C C:THR629 3.6 42.3 1.0
CG C:ASP625 3.7 49.8 1.0
N C:THR629 3.9 43.2 1.0
N C:SER627 4.0 49.7 1.0
CB C:THR629 4.0 40.7 1.0
CA C:THR629 4.0 43.0 1.0
CA C:ASP623 4.1 44.5 1.0
OD2 C:ASP625 4.1 55.4 1.0
CA C:SER627 4.2 47.6 1.0
OD2 C:ASP623 4.2 42.3 1.0
N C:ILE624 4.3 46.4 1.0
CB C:ASP623 4.3 43.1 1.0
N C:ASP625 4.4 46.7 1.0
O C:ASN645 4.5 43.4 1.0
N C:GLY628 4.5 42.9 1.0
CB C:ASP631 4.5 42.1 1.0
C C:ASP623 4.6 45.9 1.0
N C:ASP631 4.6 44.2 1.0
N C:ASN630 4.7 40.3 1.0
C C:SER627 4.7 44.3 1.0
N C:GLY626 4.8 47.0 1.0
N C:ASN645 4.8 43.1 1.0
CB C:ASP625 4.9 47.4 1.0
C C:ASN630 4.9 40.4 1.0
CB C:ASN645 4.9 39.3 1.0
CA C:ASN630 5.0 39.5 1.0

Potassium binding site 5 out of 6 in 4igl

Go back to Potassium Binding Sites List in 4igl
Potassium binding site 5 out of 6 in the Structure of the Rhs-Repeat Containing Bc Component of the Secreted Abc Toxin Complex From Yersinia Entomophaga


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Structure of the Rhs-Repeat Containing Bc Component of the Secreted Abc Toxin Complex From Yersinia Entomophaga within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1507

b:50.3
occ:1.00
 OD1 D:ASN166 2.6 52.4 1.0
OG1 C:THR1223 2.6 56.2 1.0
O D:LYS163 2.7 51.9 1.0
OD1 C:ASN1203 2.8 49.0 1.0
O C:ASN1201 2.9 51.7 1.0
O D:HOH969 3.4 55.2 1.0
O C:THR1223 3.5 55.6 1.0
CG C:ASN1203 3.5 47.4 1.0
CG D:ASN166 3.6 50.0 1.0
ND2 C:ASN1203 3.7 42.1 1.0
C D:LYS163 3.7 51.9 1.0
N C:THR1223 3.7 52.8 1.0
CB C:THR1223 3.9 59.0 1.0
C C:ASN1201 4.0 48.6 1.0
CA D:ASN164 4.0 54.1 1.0
CA C:THR1223 4.1 57.1 1.0
ND2 D:ASN166 4.1 47.8 1.0
C C:THR1223 4.1 55.1 1.0
CB C:ASN1201 4.2 48.1 1.0
C D:ASN164 4.3 55.6 1.0
N D:ASN164 4.3 52.5 1.0
O D:ASN164 4.3 56.8 1.0
N D:ASN166 4.5 50.3 1.0
CA D:ASN166 4.7 47.9 1.0
CA C:ASN1201 4.7 48.8 1.0
CB D:ASN166 4.7 50.0 1.0
OD1 D:ASN164 4.8 61.1 1.0
CG2 C:THR1223 4.8 55.2 1.0
C C:ASP1202 4.8 49.9 1.0
O C:ASP1202 4.8 53.3 1.0
CA D:LYS163 4.8 51.5 1.0
C C:GLY1222 4.9 53.3 1.0
N C:ASN1203 4.9 49.5 1.0
CB C:ASN1203 4.9 47.6 1.0

Potassium binding site 6 out of 6 in 4igl

Go back to Potassium Binding Sites List in 4igl
Potassium binding site 6 out of 6 in the Structure of the Rhs-Repeat Containing Bc Component of the Secreted Abc Toxin Complex From Yersinia Entomophaga


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Structure of the Rhs-Repeat Containing Bc Component of the Secreted Abc Toxin Complex From Yersinia Entomophaga within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1508

b:56.4
occ:1.00
 O D:THR9 2.5 51.2 1.0
OD1 C:ASP1480 2.7 53.7 1.0
OG1 D:THR9 2.7 47.0 1.0
OD2 C:ASP1480 3.2 51.1 1.0
O D:SER370 3.2 41.2 1.0
CG C:ASP1480 3.3 52.8 1.0
C D:THR9 3.7 49.1 1.0
CB D:THR9 3.7 47.2 1.0
OH D:TYR372 3.8 43.4 1.0
OD2 C:ASP1477 3.9 49.9 1.0
O D:HOH1043 4.0 41.3 1.0
O C:HOH2446 4.0 52.1 1.0
CZ D:TYR372 4.3 42.8 1.0
CA D:THR9 4.4 47.8 1.0
C D:SER370 4.4 41.0 1.0
OD1 C:ASP1477 4.5 45.2 1.0
CG C:ASP1477 4.6 47.1 1.0
CE2 D:TYR372 4.6 42.9 1.0
N D:PRO10 4.7 48.2 1.0
CA D:PRO10 4.8 46.9 1.0
CB D:SER370 4.8 44.9 1.0
CB C:ASP1480 4.9 49.6 1.0
C D:PRO10 4.9 46.8 1.0
CE1 D:TYR372 4.9 45.0 1.0
CG2 D:THR9 5.0 49.2 1.0
CA D:SER370 5.0 43.4 1.0
O D:PRO10 5.0 45.5 1.0

Reference:

J.N.Busby, S.Panjikar, M.J.Landsberg, M.R.H.Hurst, J.S.Lott. The Bc Component of Abc Toxins Is An Rhs-Repeat-Containing Protein Encapsulation Device Nature V. 501 547 2013.
ISSN: ISSN 0028-0836
PubMed: 23913273
DOI: 10.1038/NATURE12465
Page generated: Sun Dec 13 23:31:32 2020

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