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Potassium in PDB 2vgb: Human Erythrocyte Pyruvate Kinase

Enzymatic activity of Human Erythrocyte Pyruvate Kinase

All present enzymatic activity of Human Erythrocyte Pyruvate Kinase:
2.7.1.40;

Protein crystallography data

The structure of Human Erythrocyte Pyruvate Kinase, PDB code: 2vgb was solved by G.Valentini, L.Chiarelli, R.Fortin, M.Dolzan, A.Galizzi, D.J.Abraham, C.Wang, P.Bianchi, A.Zanella, A.Mattevi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.73
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.413, 172.058, 85.512, 90.00, 92.46, 90.00
R / Rfree (%) 22.7 / 27.1

Other elements in 2vgb:

The structure of Human Erythrocyte Pyruvate Kinase also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Human Erythrocyte Pyruvate Kinase (pdb code 2vgb). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Human Erythrocyte Pyruvate Kinase, PDB code: 2vgb:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 2vgb

Go back to Potassium Binding Sites List in 2vgb
Potassium binding site 1 out of 4 in the Human Erythrocyte Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Human Erythrocyte Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K582

b:78.1
occ:1.00
OD1 A:ASP156 2.9 35.9 1.0
O A:THR157 3.0 37.9 1.0
O2P A:PGA581 3.1 0.3 1.0
OD1 A:ASN118 3.1 43.3 1.0
OG A:SER120 3.4 41.8 1.0
CB A:SER120 3.7 41.2 1.0
NZ A:LYS313 3.7 34.1 1.0
OG A:SER286 3.8 40.4 1.0
CG A:ASP156 3.9 36.3 1.0
OE2 A:GLU161 4.0 37.5 1.0
C A:THR157 4.0 37.3 1.0
CG A:ASN118 4.1 39.9 1.0
CA A:LYS158 4.2 38.1 1.0
O A:LYS158 4.3 39.4 1.0
NH2 A:ARG116 4.3 34.4 1.0
N A:SER120 4.4 41.1 1.0
OD2 A:ASP156 4.4 34.9 1.0
O A:ASP156 4.5 36.5 1.0
P A:PGA581 4.5 0.9 1.0
ND2 A:ASN118 4.5 37.8 1.0
N A:LYS158 4.6 37.8 1.0
CA A:SER120 4.6 41.3 1.0
C A:LYS158 4.7 38.5 1.0
C A:ASP156 4.8 36.4 1.0
O4P A:PGA581 4.9 0.5 1.0
CB A:SER286 4.9 40.4 1.0
CB A:ASP156 4.9 36.2 1.0
N A:THR157 5.0 36.2 1.0

Potassium binding site 2 out of 4 in 2vgb

Go back to Potassium Binding Sites List in 2vgb
Potassium binding site 2 out of 4 in the Human Erythrocyte Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Human Erythrocyte Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K586

b:81.5
occ:1.00
OD1 B:ASP156 2.6 36.2 1.0
O B:THR157 2.9 37.7 1.0
O2P B:PGA581 2.9 0.5 1.0
OD1 B:ASN118 3.2 43.2 1.0
NZ B:LYS313 3.5 34.3 1.0
CG B:ASP156 3.5 36.2 1.0
OG B:SER286 3.5 40.1 1.0
C B:THR157 3.9 37.2 1.0
CB B:SER120 3.9 41.3 1.0
OD2 B:ASP156 3.9 34.6 1.0
OG B:SER120 3.9 41.9 1.0
NH2 B:ARG116 4.0 34.6 1.0
CG B:ASN118 4.1 39.7 1.0
P B:PGA581 4.2 0.9 1.0
O B:ASP156 4.2 36.8 1.0
CA B:LYS158 4.3 38.3 1.0
O B:LYS158 4.3 39.2 1.0
OE2 B:GLU161 4.4 37.3 1.0
N B:LYS158 4.5 38.1 1.0
O4P B:PGA581 4.5 0.6 1.0
C B:ASP156 4.5 36.5 1.0
N B:SER120 4.5 41.1 1.0
ND2 B:ASN118 4.6 37.7 1.0
CB B:ASP156 4.6 36.2 1.0
N B:THR157 4.7 36.3 1.0
CB B:SER286 4.7 40.3 1.0
C B:LYS158 4.8 38.6 1.0
CA B:SER120 4.8 41.3 1.0
O1P B:PGA581 4.9 0.6 1.0
CE B:LYS313 4.9 36.7 1.0
CA B:THR157 4.9 36.6 1.0

Potassium binding site 3 out of 4 in 2vgb

Go back to Potassium Binding Sites List in 2vgb
Potassium binding site 3 out of 4 in the Human Erythrocyte Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Human Erythrocyte Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K590

b:67.5
occ:1.00
OD1 C:ASP156 2.7 36.0 1.0
O C:THR157 2.9 37.9 1.0
OD1 C:ASN118 2.9 43.2 1.0
O2P C:PGA581 3.0 0.8 1.0
CG C:ASP156 3.5 36.5 1.0
NZ C:LYS313 3.7 33.9 1.0
CB C:SER120 3.7 41.2 1.0
OG C:SER120 3.8 41.9 1.0
OG C:SER286 3.8 40.2 1.0
C C:THR157 3.9 37.2 1.0
CG C:ASN118 3.9 39.5 1.0
NH2 C:ARG116 4.0 34.3 1.0
OD2 C:ASP156 4.1 34.2 1.0
O C:ASP156 4.2 36.6 1.0
CA C:LYS158 4.3 38.3 1.0
N C:SER120 4.3 40.9 1.0
ND2 C:ASN118 4.4 37.7 1.0
OE2 C:GLU161 4.4 37.3 1.0
O C:LYS158 4.4 39.5 1.0
P C:PGA581 4.4 0.9 1.0
N C:LYS158 4.5 38.1 1.0
C C:ASP156 4.5 36.2 1.0
CB C:ASP156 4.5 36.4 1.0
CA C:SER120 4.6 41.3 1.0
N C:THR157 4.7 36.1 1.0
C C:LYS158 4.8 38.6 1.0
CA C:THR157 4.9 36.6 1.0
O1P C:PGA581 4.9 0.7 1.0
N C:PHE119 5.0 39.8 1.0
CB C:SER286 5.0 40.1 1.0
CB C:ASN118 5.0 38.8 1.0

Potassium binding site 4 out of 4 in 2vgb

Go back to Potassium Binding Sites List in 2vgb
Potassium binding site 4 out of 4 in the Human Erythrocyte Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Human Erythrocyte Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K594

b:60.4
occ:1.00
OD1 D:ASP156 2.6 36.2 1.0
O2P D:PGA581 2.9 0.6 1.0
OD1 D:ASN118 3.0 43.3 1.0
O D:THR157 3.0 37.9 1.0
OG D:SER120 3.5 41.9 1.0
CG D:ASP156 3.6 36.5 1.0
NZ D:LYS313 3.6 33.7 1.0
CB D:SER120 3.7 41.3 1.0
OG D:SER286 3.8 40.2 1.0
CG D:ASN118 3.9 39.8 1.0
C D:THR157 3.9 37.1 1.0
NH2 D:ARG116 4.0 34.4 1.0
O D:ASP156 4.1 36.5 1.0
OD2 D:ASP156 4.2 34.0 1.0
N D:SER120 4.3 41.1 1.0
CA D:LYS158 4.3 38.2 1.0
P D:PGA581 4.3 0.8 1.0
OE2 D:GLU161 4.3 37.3 1.0
ND2 D:ASN118 4.4 37.9 1.0
O D:LYS158 4.4 39.7 1.0
C D:ASP156 4.5 36.3 1.0
N D:LYS158 4.5 38.0 1.0
CB D:ASP156 4.5 36.3 1.0
CA D:SER120 4.6 41.4 1.0
N D:THR157 4.8 36.3 1.0
C D:LYS158 4.8 38.6 1.0
O1P D:PGA581 4.8 0.5 1.0
CA D:THR157 5.0 36.6 1.0
N D:PHE119 5.0 39.7 1.0

Reference:

G.Valentini, L.R.Chiarelli, R.Fortin, M.Dolzan, A.Galizzi, D.J.Abraham, C.Wang, P.Bianchi, A.Zanella, A.Mattevi. Structure and Function of Human Erythrocyte Pyruvate Kinase. Molecular Basis of Nonspherocytic Hemolytic Anemia. J.Biol.Chem. V. 277 23807 2002.
ISSN: ISSN 0021-9258
PubMed: 11960989
DOI: 10.1074/JBC.M202107200
Page generated: Sun Dec 13 23:12:36 2020

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