Potassium in PDB 8gyr: Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga

Protein crystallography data

The structure of Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga, PDB code: 8gyr was solved by P.Kumar, M.Akif, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 85.92 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 34.219, 63.905, 171.839, 90, 90, 90
R / Rfree (%) 20.8 / 23.4

Other elements in 8gyr:

The structure of Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Chlorine (Cl) 1 atom
Iodine (I) 2 atoms
Sodium (Na) 5 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga (pdb code 8gyr). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga, PDB code: 8gyr:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in 8gyr

Go back to Potassium Binding Sites List in 8gyr
Potassium binding site 1 out of 5 in the Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga


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 A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K201

b:14.8
occ:0.50
 O A:SER172 2.6 15.3 1.0
O A:HOH451 3.0 18.7 1.0
O A:HOH369 3.0 17.3 1.0
N A:ILE97 3.2 14.9 1.0
CB A:SER96 3.5 14.5 1.0
CA A:SER96 3.5 13.9 1.0
C A:SER172 3.6 16.7 1.0
O A:ILE97 3.6 18.0 1.0
O B:HOH345 3.8 19.0 1.0
C A:SER96 3.8 14.0 1.0
O A:HOH435 3.9 30.2 1.0
CA A:SER173 3.9 14.7 1.0
O A:HOH381 3.9 26.6 1.0
O A:HOH397 4.1 12.3 1.0
N A:SER173 4.1 15.7 1.0
CA A:ILE97 4.2 15.6 1.0
CG1 A:VAL171 4.3 12.3 1.0
C A:ILE97 4.3 17.6 1.0
C A:SER173 4.3 15.3 1.0
OG1 B:THR6 4.5 16.4 1.0
CB A:ILE97 4.5 14.9 1.0
N A:ALA174 4.5 16.1 1.0
N A:SER172 4.6 15.2 1.0
O A:THR95 4.7 12.5 1.0
CA A:SER172 4.7 16.0 1.0
OG A:SER96 4.8 19.9 1.0
CB B:THR6 4.8 16.0 1.0
N A:SER96 4.8 13.9 1.0
O A:SER173 4.9 15.0 1.0

Potassium binding site 2 out of 5 in 8gyr

Go back to Potassium Binding Sites List in 8gyr
Potassium binding site 2 out of 5 in the Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga


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 A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K202

b:33.9
occ:1.00
 OG A:SER53 2.8 11.4 1.0
O A:HOH313 2.9 13.3 1.0
O A:HOH318 3.6 11.6 1.0
O A:HOH418 3.7 12.9 1.0
CB A:SER53 3.8 11.7 1.0
CA A:SER53 4.2 11.1 1.0
O A:HOH370 4.3 13.1 1.0
O A:MET54 4.6 11.2 1.0
N A:MET54 4.7 10.3 1.0
C A:SER53 4.9 11.4 1.0

Potassium binding site 3 out of 5 in 8gyr

Go back to Potassium Binding Sites List in 8gyr
Potassium binding site 3 out of 5 in the Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga


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 A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K203

b:42.4
occ:1.00
 O B:HOH394 2.9 22.3 1.0
O B:LEU52 3.0 17.7 1.0
O B:HOH379 3.1 21.6 1.0
O B:SER49 3.1 19.4 1.0
CA B:LYS50 3.7 21.6 1.0
C B:SER49 3.8 20.9 1.0
OG B:SER47 3.9 16.4 1.0
C B:LEU52 3.9 18.6 1.0
N B:LYS50 4.0 21.6 1.0
CA B:SER53 4.1 21.2 1.0
CB B:SER47 4.1 17.3 1.0
O B:HOH420 4.3 21.1 1.0
CG B:LYS50 4.4 24.1 1.0
N B:SER53 4.4 19.2 1.0
C B:LYS50 4.4 20.2 1.0
O B:LYS50 4.6 20.0 1.0
O B:HOH311 4.6 17.2 1.0
O B:SER47 4.6 20.4 1.0
CB B:LYS50 4.6 22.7 1.0
N B:MET54 4.8 24.7 1.0
CB B:SER53 4.9 23.5 1.0
CA B:SER49 4.9 21.1 1.0
N B:SER49 4.9 20.6 1.0
C B:SER53 5.0 20.9 1.0
N B:LEU52 5.0 18.4 1.0

Potassium binding site 4 out of 5 in 8gyr

Go back to Potassium Binding Sites List in 8gyr
Potassium binding site 4 out of 5 in the Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga


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 A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K204

b:35.6
occ:1.00
 O B:SER172 2.7 15.6 1.0
O B:HOH322 2.9 20.9 1.0
N B:ILE97 3.4 19.4 1.0
CB B:SER96 3.4 19.0 1.0
CA B:SER96 3.6 18.1 1.0
OG1 A:THR6 3.7 20.1 1.0
O B:ILE97 3.7 17.4 1.0
C B:SER172 3.7 16.9 1.0
CA B:SER173 3.9 18.8 1.0
CB A:THR6 4.0 20.9 1.0
C B:SER96 4.1 19.4 1.0
C B:SER173 4.1 20.3 1.0
N B:GLN174 4.2 24.0 1.0
N B:SER173 4.2 18.1 1.0
O B:HOH381 4.3 11.3 1.0
CG2 A:THR6 4.3 22.2 1.0
CA B:ILE97 4.4 19.4 1.0
C B:ILE97 4.4 20.8 1.0
CG1 B:VAL171 4.6 13.0 1.0
O B:SER173 4.7 15.6 1.0
O B:THR95 4.7 19.4 1.0
OG B:SER96 4.7 19.7 1.0
CB B:ILE97 4.8 19.6 1.0
N B:SER96 4.9 19.2 1.0
O B:HOH339 4.9 33.1 1.0
N B:SER172 4.9 15.1 1.0
CA B:SER172 5.0 14.4 1.0

Potassium binding site 5 out of 5 in 8gyr

Go back to Potassium Binding Sites List in 8gyr
Potassium binding site 5 out of 5 in the Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga


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 A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K209

b:13.2
occ:1.00
 ND2 B:ASN139 3.6 30.4 1.0
O B:HOH391 4.0 23.0 1.0
O B:HOH421 4.0 25.5 1.0
O B:HOH397 4.1 24.8 1.0
O B:HOH315 4.3 36.0 1.0
O B:HOH350 4.4 16.1 1.0
CG B:ASN139 4.7 26.1 1.0
O B:HOH416 4.8 34.1 1.0
OD1 B:ASN139 4.9 24.7 1.0

Reference:

P.Kumar, P.Vyas, S.M.Faisal, Y.F.Chang, M.Akif. Crystal Structure of A Variable Region Segment of Leptospira Host-Interacting Outer Surface Protein, Liga, Reveals the Orientation of Ig-Like Domains. Int.J.Biol.Macromol. 25445 2023.
ISSN: ISSN 0141-8130
PubMed: 37336372
DOI: 10.1016/J.IJBIOMAC.2023.125445
Page generated: Mon Aug 12 23:52:17 2024

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