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Potassium in PDB 2vgf: Human Erythrocyte Pyruvate Kinase: T384M Mutant

Enzymatic activity of Human Erythrocyte Pyruvate Kinase: T384M Mutant

All present enzymatic activity of Human Erythrocyte Pyruvate Kinase: T384M Mutant:
2.7.1.40;

Protein crystallography data

The structure of Human Erythrocyte Pyruvate Kinase: T384M Mutant, PDB code: 2vgf was solved by G.Valentini, L.R.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 / 2.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.296, 172.976, 85.779, 90.00, 93.12, 90.00
R / Rfree (%) 26.8 / 30.3

Other elements in 2vgf:

The structure of Human Erythrocyte Pyruvate Kinase: T384M Mutant 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: T384M Mutant (pdb code 2vgf). 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: T384M Mutant, PDB code: 2vgf:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 2vgf

Go back to Potassium Binding Sites List in 2vgf
Potassium binding site 1 out of 4 in the Human Erythrocyte Pyruvate Kinase: T384M Mutant


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: T384M Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K582

b:52.7
occ:1.00
O2P A:PGA581 2.7 86.6 1.0
O A:THR157 2.9 11.4 1.0
OD1 A:ASP156 3.0 12.3 1.0
OD1 A:ASN118 3.4 13.1 1.0
OG A:SER286 3.4 12.4 1.0
OG A:SER120 3.6 18.1 1.0
CB A:SER120 3.8 16.8 1.0
NZ A:LYS313 3.8 10.7 1.0
C A:THR157 3.9 11.8 1.0
O A:LYS158 4.0 11.8 1.0
CA A:LYS158 4.0 11.6 1.0
CG A:ASP156 4.1 12.1 1.0
P A:PGA581 4.2 85.7 1.0
N A:LYS158 4.4 11.6 1.0
C A:LYS158 4.4 11.6 1.0
O A:ASP156 4.5 11.9 1.0
CG A:ASN118 4.5 11.8 1.0
CB A:SER286 4.6 11.6 1.0
N A:SER120 4.6 15.3 1.0
NH2 A:ARG116 4.6 12.5 1.0
O4P A:PGA581 4.6 86.5 1.0
CA A:SER120 4.7 16.4 1.0
OD2 A:ASP156 4.7 11.7 1.0
O1P A:PGA581 4.8 86.5 1.0
CE A:LYS313 4.9 11.3 1.0
C A:ASP156 4.9 11.6 1.0
MN A:MN583 4.9 64.1 1.0
ND2 A:ASN118 5.0 11.4 1.0

Potassium binding site 2 out of 4 in 2vgf

Go back to Potassium Binding Sites List in 2vgf
Potassium binding site 2 out of 4 in the Human Erythrocyte Pyruvate Kinase: T384M Mutant


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: T384M Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K586

b:33.5
occ:1.00
OD1 B:ASP156 2.5 12.0 1.0
O2P B:PGA581 2.7 86.5 1.0
OD1 B:ASN118 2.9 12.5 1.0
O B:THR157 2.9 11.7 1.0
OG B:SER286 3.4 11.9 1.0
NZ B:LYS313 3.5 10.8 1.0
CG B:ASP156 3.5 11.8 1.0
OE2 B:GLU161 3.8 12.5 1.0
C B:THR157 3.9 11.6 1.0
CB B:SER120 4.0 16.6 1.0
CG B:ASN118 4.0 11.8 1.0
O B:ASP156 4.1 11.6 1.0
OD2 B:ASP156 4.1 11.7 1.0
NH2 B:ARG116 4.1 11.7 1.0
P B:PGA581 4.2 85.7 1.0
OG B:SER120 4.3 18.2 1.0
CA B:LYS158 4.3 11.7 1.0
C B:ASP156 4.4 11.5 1.0
O B:LYS158 4.4 11.8 1.0
N B:LYS158 4.5 11.3 1.0
CB B:ASP156 4.5 11.1 1.0
N B:SER120 4.5 15.2 1.0
ND2 B:ASN118 4.7 11.4 1.0
N B:THR157 4.7 11.6 1.0
O1P B:PGA581 4.7 86.5 1.0
CE B:LYS313 4.7 11.1 1.0
CB B:SER286 4.7 11.7 1.0
CD B:GLU161 4.8 12.4 1.0
CA B:SER120 4.8 16.3 1.0
C B:LYS158 4.8 11.8 1.0
CA B:THR157 4.9 11.6 1.0
O4P B:PGA581 4.9 86.5 1.0
O3P B:PGA581 5.0 86.2 1.0

Potassium binding site 3 out of 4 in 2vgf

Go back to Potassium Binding Sites List in 2vgf
Potassium binding site 3 out of 4 in the Human Erythrocyte Pyruvate Kinase: T384M Mutant


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: T384M Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K590

b:41.5
occ:1.00
O2P C:PGA581 2.7 86.6 1.0
O C:THR157 2.8 11.2 1.0
OD1 C:ASP156 3.0 12.1 1.0
OD1 C:ASN118 3.2 12.2 1.0
OE2 C:GLU161 3.3 16.5 1.0
OG C:SER286 3.4 11.9 1.0
OG C:SER120 3.6 17.8 1.0
CB C:SER120 3.8 16.6 1.0
NZ C:LYS313 3.8 10.8 1.0
C C:THR157 3.9 11.5 1.0
CG C:ASP156 4.0 11.7 1.0
CA C:LYS158 4.1 11.7 1.0
O C:LYS158 4.1 11.7 1.0
P C:PGA581 4.2 85.7 1.0
CG C:ASN118 4.3 11.5 1.0
N C:LYS158 4.4 11.6 1.0
CD C:GLU161 4.4 15.7 1.0
O C:ASP156 4.5 11.7 1.0
OD2 C:ASP156 4.5 11.9 1.0
N C:SER120 4.5 15.1 1.0
C C:LYS158 4.5 11.5 1.0
CB C:SER286 4.6 11.5 1.0
NH2 C:ARG116 4.6 11.8 1.0
CA C:SER120 4.6 16.3 1.0
ND2 C:ASN118 4.8 11.1 1.0
O4P C:PGA581 4.8 86.5 1.0
O1P C:PGA581 4.8 86.5 1.0
C C:ASP156 4.8 11.4 1.0
CE C:LYS313 4.9 11.2 1.0
CB C:ASP156 5.0 11.1 1.0

Potassium binding site 4 out of 4 in 2vgf

Go back to Potassium Binding Sites List in 2vgf
Potassium binding site 4 out of 4 in the Human Erythrocyte Pyruvate Kinase: T384M Mutant


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: T384M Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K594

b:77.2
occ:1.00
OD1 D:ASN118 2.5 12.3 1.0
O2P D:PGA581 2.7 86.6 1.0
OD1 D:ASP156 2.7 12.1 1.0
O D:THR157 3.2 11.5 1.0
CG D:ASP156 3.5 11.8 1.0
CG D:ASN118 3.6 11.6 1.0
NH2 D:ARG116 3.7 11.9 1.0
OG D:SER120 3.8 18.3 1.0
NZ D:LYS313 3.8 11.0 1.0
CB D:SER120 3.8 16.9 1.0
OG D:SER286 4.0 12.2 1.0
OD2 D:ASP156 4.1 11.7 1.0
O D:ASP156 4.2 11.5 1.0
ND2 D:ASN118 4.2 11.2 1.0
P D:PGA581 4.2 85.8 1.0
C D:THR157 4.2 11.5 1.0
N D:SER120 4.3 15.2 1.0
CB D:ASP156 4.4 11.3 1.0
C D:ASP156 4.6 11.4 1.0
CA D:SER120 4.6 16.4 1.0
CA D:LYS158 4.7 11.7 1.0
OE2 D:GLU161 4.7 17.9 1.0
CB D:ASN118 4.8 11.5 1.0
O3P D:PGA581 4.8 86.3 1.0
N D:LYS158 4.9 11.7 1.0
CZ D:ARG116 4.9 11.6 1.0
N D:PHE119 4.9 12.1 1.0
O1P D:PGA581 4.9 86.5 1.0
O D:LYS158 5.0 11.9 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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