Manganese in PDB 2vgi: Human Erythrocyte Pyruvate Kinase: R486W Mutant
Enzymatic activity of Human Erythrocyte Pyruvate Kinase: R486W Mutant
All present enzymatic activity of Human Erythrocyte Pyruvate Kinase: R486W Mutant:
2.7.1.40;
Protein crystallography data
The structure of Human Erythrocyte Pyruvate Kinase: R486W Mutant, PDB code: 2vgi
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 /
2.87
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
73.705,
171.164,
85.050,
90.00,
91.61,
90.00
|
R / Rfree (%)
|
25.7 /
31.1
|
Other elements in 2vgi:
The structure of Human Erythrocyte Pyruvate Kinase: R486W Mutant also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Human Erythrocyte Pyruvate Kinase: R486W Mutant
(pdb code 2vgi). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the
Human Erythrocyte Pyruvate Kinase: R486W Mutant, PDB code: 2vgi:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 2vgi
Go back to
Manganese Binding Sites List in 2vgi
Manganese binding site 1 out
of 4 in the Human Erythrocyte Pyruvate Kinase: R486W Mutant
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Human Erythrocyte Pyruvate Kinase: R486W Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn1577
b:2.0
occ:1.00
|
OE2
|
A:GLU315
|
1.6
|
2.0
|
1.0
|
OD2
|
A:ASP339
|
1.7
|
2.0
|
1.0
|
O1P
|
A:PGA1575
|
2.2
|
2.0
|
1.0
|
O1
|
A:PGA1575
|
2.4
|
2.0
|
1.0
|
O4P
|
A:PGA1575
|
2.6
|
2.0
|
1.0
|
CD
|
A:GLU315
|
2.9
|
2.0
|
1.0
|
CG
|
A:ASP339
|
2.9
|
2.0
|
1.0
|
P
|
A:PGA1575
|
3.0
|
2.0
|
1.0
|
C1
|
A:PGA1575
|
3.0
|
2.0
|
1.0
|
C2
|
A:PGA1575
|
3.1
|
2.0
|
1.0
|
OD1
|
A:ASP339
|
3.6
|
2.0
|
1.0
|
OE1
|
A:GLU315
|
3.8
|
2.0
|
1.0
|
CG
|
A:GLU315
|
3.8
|
2.0
|
1.0
|
CB
|
A:ASP339
|
4.0
|
2.0
|
1.0
|
O3P
|
A:PGA1575
|
4.0
|
2.0
|
1.0
|
CZ
|
A:PHE287
|
4.0
|
2.0
|
1.0
|
O2P
|
A:PGA1575
|
4.1
|
2.0
|
1.0
|
O2
|
A:PGA1575
|
4.2
|
2.0
|
1.0
|
NZ
|
A:LYS313
|
4.2
|
2.0
|
1.0
|
CE
|
A:LYS313
|
4.3
|
2.0
|
1.0
|
CE1
|
A:PHE287
|
4.4
|
2.0
|
1.0
|
N
|
A:ASP339
|
4.5
|
2.0
|
1.0
|
CE2
|
A:PHE287
|
4.8
|
2.0
|
1.0
|
CA
|
A:ASP339
|
4.9
|
2.0
|
1.0
|
CB
|
A:ALA336
|
4.9
|
2.0
|
1.0
|
|
Manganese binding site 2 out
of 4 in 2vgi
Go back to
Manganese Binding Sites List in 2vgi
Manganese binding site 2 out
of 4 in the Human Erythrocyte Pyruvate Kinase: R486W Mutant
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Human Erythrocyte Pyruvate Kinase: R486W Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn1577
b:2.0
occ:1.00
|
OD2
|
B:ASP339
|
1.5
|
2.0
|
1.0
|
OE2
|
B:GLU315
|
1.7
|
2.0
|
1.0
|
O1
|
B:PGA1575
|
2.0
|
2.0
|
1.0
|
O1P
|
B:PGA1575
|
2.3
|
2.0
|
1.0
|
O4P
|
B:PGA1575
|
2.6
|
2.0
|
1.0
|
CG
|
B:ASP339
|
2.7
|
2.0
|
1.0
|
C1
|
B:PGA1575
|
2.8
|
2.0
|
1.0
|
CD
|
B:GLU315
|
2.9
|
2.0
|
1.0
|
P
|
B:PGA1575
|
3.0
|
2.0
|
1.0
|
C2
|
B:PGA1575
|
3.0
|
2.0
|
1.0
|
OD1
|
B:ASP339
|
3.5
|
2.0
|
1.0
|
CG
|
B:GLU315
|
3.6
|
2.0
|
1.0
|
CB
|
B:ASP339
|
3.8
|
2.0
|
1.0
|
O3P
|
B:PGA1575
|
3.8
|
2.0
|
1.0
|
OE1
|
B:GLU315
|
3.9
|
2.0
|
1.0
|
O2
|
B:PGA1575
|
3.9
|
2.0
|
1.0
|
CZ
|
B:PHE287
|
4.2
|
2.0
|
1.0
|
O2P
|
B:PGA1575
|
4.3
|
2.0
|
1.0
|
N
|
B:ASP339
|
4.3
|
2.0
|
1.0
|
CE1
|
B:PHE287
|
4.5
|
2.0
|
1.0
|
CA
|
B:ASP339
|
4.6
|
2.0
|
1.0
|
CE
|
B:LYS313
|
4.7
|
2.0
|
1.0
|
NZ
|
B:LYS313
|
4.7
|
2.0
|
1.0
|
CB
|
B:ALA336
|
4.9
|
2.0
|
1.0
|
CE2
|
B:PHE287
|
4.9
|
2.0
|
1.0
|
CB
|
B:GLU315
|
4.9
|
2.0
|
1.0
|
|
Manganese binding site 3 out
of 4 in 2vgi
Go back to
Manganese Binding Sites List in 2vgi
Manganese binding site 3 out
of 4 in the Human Erythrocyte Pyruvate Kinase: R486W Mutant
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Human Erythrocyte Pyruvate Kinase: R486W Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn1577
b:2.0
occ:1.00
|
OE2
|
C:GLU315
|
1.7
|
2.0
|
1.0
|
OD2
|
C:ASP339
|
1.8
|
2.0
|
1.0
|
O1
|
C:PGA1575
|
1.9
|
2.0
|
1.0
|
O1P
|
C:PGA1575
|
2.0
|
2.0
|
1.0
|
O4P
|
C:PGA1575
|
2.3
|
2.0
|
1.0
|
C1
|
C:PGA1575
|
2.4
|
2.0
|
1.0
|
C2
|
C:PGA1575
|
2.6
|
2.0
|
1.0
|
P
|
C:PGA1575
|
2.6
|
2.0
|
1.0
|
CD
|
C:GLU315
|
2.9
|
2.0
|
1.0
|
CG
|
C:ASP339
|
3.1
|
2.0
|
1.0
|
O3P
|
C:PGA1575
|
3.4
|
2.0
|
1.0
|
OE1
|
C:GLU315
|
3.7
|
2.0
|
1.0
|
CG
|
C:GLU315
|
3.7
|
2.0
|
1.0
|
OD1
|
C:ASP339
|
3.9
|
2.0
|
1.0
|
O2P
|
C:PGA1575
|
4.0
|
2.0
|
1.0
|
O2
|
C:PGA1575
|
4.0
|
2.0
|
1.0
|
CB
|
C:ASP339
|
4.0
|
2.0
|
1.0
|
CE
|
C:LYS313
|
4.3
|
2.0
|
1.0
|
CZ
|
C:PHE287
|
4.3
|
2.0
|
1.0
|
CE1
|
C:PHE287
|
4.5
|
2.0
|
1.0
|
NZ
|
C:LYS313
|
4.5
|
2.0
|
1.0
|
N
|
C:ASP339
|
4.5
|
2.0
|
1.0
|
CB
|
C:ALA336
|
4.8
|
2.0
|
1.0
|
CA
|
C:ASP339
|
4.9
|
2.0
|
1.0
|
CB
|
C:GLU315
|
4.9
|
2.0
|
1.0
|
|
Manganese binding site 4 out
of 4 in 2vgi
Go back to
Manganese Binding Sites List in 2vgi
Manganese binding site 4 out
of 4 in the Human Erythrocyte Pyruvate Kinase: R486W Mutant
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Human Erythrocyte Pyruvate Kinase: R486W Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn1577
b:2.0
occ:1.00
|
OE2
|
D:GLU315
|
1.7
|
2.0
|
1.0
|
OD2
|
D:ASP339
|
1.9
|
2.0
|
1.0
|
O1P
|
D:PGA1575
|
2.0
|
2.0
|
1.0
|
O1
|
D:PGA1575
|
2.5
|
2.0
|
1.0
|
C2
|
D:PGA1575
|
2.9
|
2.0
|
1.0
|
CD
|
D:GLU315
|
2.9
|
2.0
|
1.0
|
C1
|
D:PGA1575
|
3.0
|
2.0
|
1.0
|
P
|
D:PGA1575
|
3.1
|
2.0
|
1.0
|
CG
|
D:ASP339
|
3.1
|
2.0
|
1.0
|
O4P
|
D:PGA1575
|
3.2
|
2.0
|
1.0
|
CG
|
D:GLU315
|
3.8
|
2.0
|
1.0
|
OE1
|
D:GLU315
|
3.8
|
2.0
|
1.0
|
OD1
|
D:ASP339
|
3.9
|
2.0
|
1.0
|
O2P
|
D:PGA1575
|
4.0
|
2.0
|
1.0
|
CB
|
D:ASP339
|
4.1
|
2.0
|
1.0
|
O2
|
D:PGA1575
|
4.2
|
2.0
|
1.0
|
CE
|
D:LYS313
|
4.2
|
2.0
|
1.0
|
O3P
|
D:PGA1575
|
4.2
|
2.0
|
1.0
|
CZ
|
D:PHE287
|
4.4
|
2.0
|
1.0
|
NZ
|
D:LYS313
|
4.5
|
2.0
|
1.0
|
CE1
|
D:PHE287
|
4.5
|
2.0
|
1.0
|
N
|
D:ASP339
|
4.6
|
2.0
|
1.0
|
CB
|
D:ALA336
|
4.7
|
2.0
|
1.0
|
CA
|
D:ASP339
|
5.0
|
2.0
|
1.0
|
OG
|
D:SER286
|
5.0
|
2.0
|
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: Sat Oct 5 15:16:25 2024
|