Potassium in PDB 5w53: Crystal Structure of the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2B (PVRBP2B)

Protein crystallography data

The structure of Crystal Structure of the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2B (PVRBP2B), PDB code: 5w53 was solved by J.Gruszczyk, W.H.Tham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.17 / 1.71
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.500, 124.200, 65.310, 90.00, 97.75, 90.00
R / Rfree (%) 16.8 / 18.8

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2B (PVRBP2B) (pdb code 5w53). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Crystal Structure of the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2B (PVRBP2B), PDB code: 5w53:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 5w53

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Potassium binding site 1 out of 8 in the Crystal Structure of the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2B (PVRBP2B)


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 the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2B (PVRBP2B) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K504

b:60.4
occ:1.00
 O A:ASN231 4.0 29.1 1.0
O A:HOH890 4.1 40.6 1.0
CB A:ASN231 4.2 30.3 1.0
CB A:ARG235 4.2 29.4 1.0
O A:HOH624 4.2 46.6 1.0
CD A:ARG235 4.3 44.5 1.0
C A:ASN231 4.4 28.0 1.0
CG A:ARG235 4.7 32.5 1.0
OE2 A:GLU232 4.7 62.2 1.0
CA A:ASN231 4.9 25.6 1.0
N A:GLU232 4.9 28.1 1.0
CG A:ASN231 4.9 36.7 1.0
OD1 A:ASN231 4.9 35.8 1.0
CD A:GLU232 5.0 53.3 1.0

Potassium binding site 2 out of 8 in 5w53

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Potassium binding site 2 out of 8 in the Crystal Structure of the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2B (PVRBP2B)


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 the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2B (PVRBP2B) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K505

b:53.5
occ:1.00
 O A:HOH959 2.3 56.2 1.0
CE A:LYS410 3.6 48.0 1.0
CG2 A:ILE325 3.7 30.1 1.0
CG A:LYS326 3.7 44.1 1.0
CD1 A:PHE322 3.8 29.9 1.0
CB A:SER406 3.8 41.5 1.0
O A:PHE322 3.9 31.3 1.0
CA A:SER406 3.9 34.6 1.0
CE A:LYS326 3.9 42.0 1.0
CB A:ILE325 4.2 27.4 1.0
NZ A:LYS410 4.3 50.9 1.0
CB A:PHE322 4.4 31.6 1.0
N A:LYS326 4.4 31.8 1.0
O A:SER406 4.4 40.0 1.0
CD A:LYS326 4.5 42.7 1.0
CG A:PHE322 4.5 31.1 1.0
CA A:PHE322 4.6 29.9 1.0
CE1 A:PHE322 4.6 30.0 1.0
C A:PHE322 4.6 31.6 1.0
C A:SER406 4.7 38.7 1.0
CD A:LYS410 4.7 43.0 1.0
C A:ILE325 4.9 32.6 1.0
CA A:LYS326 4.9 30.9 1.0
CB A:LYS326 4.9 33.3 1.0
N A:SER406 5.0 33.1 1.0

Potassium binding site 3 out of 8 in 5w53

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Potassium binding site 3 out of 8 in the Crystal Structure of the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2B (PVRBP2B)


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 the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2B (PVRBP2B) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K506

b:59.9
occ:1.00
 O A:HOH714 2.4 59.1 1.0
CG A:GLU302 3.6 54.1 1.0
CB A:GLU302 3.6 40.4 1.0
CG A:LYS225 4.0 40.6 1.0
CG1 A:ILE299 4.1 30.3 1.0
OE1 A:GLU302 4.1 72.3 1.0
CD A:GLU302 4.1 66.9 1.0
CA A:ILE299 4.2 36.3 1.0
O A:LYS298 4.4 38.2 1.0
CG2 A:ILE221 4.4 39.4 1.0
CB A:LYS225 4.5 38.9 1.0
N A:ILE299 4.5 36.0 1.0
CD A:LYS225 4.5 42.2 1.0
CE A:LYS225 4.5 55.5 1.0
C A:LYS298 4.6 36.1 1.0
CB A:ILE299 4.7 32.2 1.0
O A:HOH685 4.8 50.4 1.0
NE2 A:GLN295 5.0 52.6 1.0

Potassium binding site 4 out of 8 in 5w53

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Potassium binding site 4 out of 8 in the Crystal Structure of the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2B (PVRBP2B)


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 the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2B (PVRBP2B) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K507

b:80.6
occ:1.00
 O A:HOH815 4.3 33.9 1.0
O A:HOH895 4.8 35.7 1.0

Potassium binding site 5 out of 8 in 5w53

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Potassium binding site 5 out of 8 in the Crystal Structure of the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2B (PVRBP2B)


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 the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2B (PVRBP2B) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K501

b:74.6
occ:1.00
 O B:HOH955 2.9 68.6 1.0
NE B:ARG193 3.8 49.0 1.0
NH2 B:ARG193 3.9 54.4 1.0
CZ B:ARG193 3.9 50.6 1.0
O B:HOH896 4.1 62.4 1.0
N B:SCN503 4.1 45.0 1.0
CD B:ARG193 4.5 49.5 1.0
NH1 B:ARG193 4.5 54.5 1.0
O B:HOH1004 4.7 54.4 1.0

Potassium binding site 6 out of 8 in 5w53

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Potassium binding site 6 out of 8 in the Crystal Structure of the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2B (PVRBP2B)


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 the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2B (PVRBP2B) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K504

b:54.0
occ:1.00
 CB B:GLU302 3.7 37.8 1.0
CG B:GLU302 3.7 39.6 1.0
CG1 B:ILE299 4.0 31.7 1.0
CG B:LYS298 4.1 40.4 1.0
CA B:ILE299 4.2 31.7 1.0
CG B:LYS225 4.2 41.5 1.0
CD B:GLU302 4.3 60.9 1.0
OE2 B:GLU302 4.3 70.5 1.0
CE B:LYS298 4.4 60.0 1.0
O B:LYS298 4.4 35.8 1.0
CG2 B:ILE221 4.5 38.6 1.0
N B:ILE299 4.5 34.0 1.0
CD B:LYS225 4.6 47.5 1.0
C B:LYS298 4.6 34.9 1.0
CD B:LYS298 4.6 48.1 1.0
CB B:LYS225 4.7 35.5 1.0
CB B:ILE299 4.7 30.3 1.0
CE B:LYS225 4.7 63.4 1.0
O B:HOH732 4.7 46.1 1.0

Potassium binding site 7 out of 8 in 5w53

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Potassium binding site 7 out of 8 in the Crystal Structure of the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2B (PVRBP2B)


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 the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2B (PVRBP2B) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K505

b:79.4
occ:1.00
 O B:HOH997 2.9 42.0 1.0
N B:SCN502 3.0 26.1 1.0
O B:HOH703 3.1 41.7 1.0
C B:SCN502 3.7 30.0 1.0
ND1 B:HIS449 4.0 30.6 1.0
CE1 B:HIS449 4.2 32.6 1.0
CB B:ASN174 4.2 30.9 1.0
CG B:HIS449 4.3 25.8 1.0
CB B:ASP173 4.4 33.1 1.0
O B:HOH923 4.4 60.6 1.0
NE2 B:HIS449 4.7 39.6 1.0
CD2 B:HIS449 4.7 31.1 1.0
CB B:HIS449 4.8 25.1 1.0
N B:ASN174 4.8 22.1 1.0
OD2 B:ASP173 4.8 39.1 1.0

Potassium binding site 8 out of 8 in 5w53

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Potassium binding site 8 out of 8 in the Crystal Structure of the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2B (PVRBP2B)


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 the Erythrocyte-Binding Domain From Plasmodium Vivax Reticulocyte-Binding Protein 2B (PVRBP2B) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K506

b:98.7
occ:1.00
 O B:HOH802 2.3 43.4 1.0
CB B:ARG217 3.2 62.7 1.0
N B:ARG217 3.2 57.6 1.0
CA B:ILE215 3.3 59.7 1.0
C B:ILE215 3.3 65.8 1.0
O B:GLU214 3.4 58.1 1.0
N B:LYS216 3.5 61.8 1.0
CG B:ARG217 3.8 74.5 1.0
CA B:ARG217 3.8 59.8 1.0
O B:ILE215 3.9 67.9 1.0
CD2 B:LEU306 4.0 49.3 1.0
C B:GLU214 4.2 49.5 1.0
N B:ILE215 4.2 60.7 1.0
C B:LYS216 4.3 64.2 1.0
CB B:ILE215 4.3 61.8 1.0
NE B:ARG217 4.4 82.1 1.0
CA B:LYS216 4.4 77.6 1.0
CG2 B:ILE215 4.6 63.9 1.0
CD B:ARG217 4.7 78.6 1.0
NZ B:LYS309 4.8 67.3 1.0
C B:ARG217 4.9 52.5 1.0
N B:TYR218 4.9 47.2 1.0

Reference:

J.Gruszczyk, U.Kanjee, L.J.Chan, S.Menant, B.Malleret, N.T.Y.Lim, C.Q.Schmidt, Y.F.Mok, K.M.Lin, R.D.Pearson, G.Rangel, B.J.Smith, M.J.Call, M.P.Weekes, M.D.W.Griffin, J.M.Murphy, J.Abraham, K.Sriprawat, M.J.Menezes, M.U.Ferreira, B.Russell, L.Renia, M.T.Duraisingh, W.H.Tham. Transferrin Receptor 1 Is A Reticulocyte-Specific Receptor For Plasmodium Vivax. Science V. 359 48 2018.
ISSN: ESSN 1095-9203
PubMed: 29302006
DOI: 10.1126/SCIENCE.AAN1078
Page generated: Mon Dec 14 00:10:47 2020

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