Potassium in PDB 6gg6: Crystal Structure of M2 Pyk in Complex with Serine.
Enzymatic activity of Crystal Structure of M2 Pyk in Complex with Serine.
All present enzymatic activity of Crystal Structure of M2 Pyk in Complex with Serine.:
2.7.1.40;
Protein crystallography data
The structure of Crystal Structure of M2 Pyk in Complex with Serine., PDB code: 6gg6
was solved by
I.W.Mcnae,
M.Yuan,
M.D.Walkinshaw,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
116.50 /
2.96
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
93.350,
108.940,
124.340,
89.72,
71.13,
66.94
|
R / Rfree (%)
|
23.6 /
25.2
|
Other elements in 6gg6:
The structure of Crystal Structure of M2 Pyk in Complex with Serine. also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of M2 Pyk in Complex with Serine.
(pdb code 6gg6). 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 M2 Pyk in Complex with Serine., PDB code: 6gg6:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Potassium binding site 1 out
of 8 in 6gg6
Go back to
Potassium Binding Sites List in 6gg6
Potassium binding site 1 out
of 8 in the Crystal Structure of M2 Pyk in Complex with Serine.
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 M2 Pyk in Complex with Serine. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K601
b:93.0
occ:1.00
|
OD1
|
A:ASN75
|
2.7
|
78.9
|
1.0
|
OD1
|
A:ASP113
|
2.8
|
78.8
|
1.0
|
OG
|
A:SER77
|
2.9
|
94.9
|
1.0
|
O
|
A:THR114
|
3.1
|
79.1
|
1.0
|
OE2
|
A:GLU118
|
3.6
|
91.7
|
1.0
|
OG
|
A:SER243
|
3.8
|
71.1
|
1.0
|
CG
|
A:ASN75
|
3.9
|
80.7
|
1.0
|
CG
|
A:ASP113
|
3.9
|
77.2
|
1.0
|
CB
|
A:SER77
|
4.1
|
94.6
|
1.0
|
C
|
A:THR114
|
4.2
|
80.8
|
1.0
|
NZ
|
A:LYS270
|
4.2
|
65.4
|
1.0
|
O
|
A:LYS115
|
4.2
|
84.2
|
1.0
|
NH2
|
A:ARG73
|
4.3
|
70.0
|
1.0
|
O
|
A:ASP113
|
4.4
|
79.5
|
1.0
|
ND2
|
A:ASN75
|
4.5
|
81.9
|
1.0
|
CA
|
A:LYS115
|
4.5
|
86.1
|
1.0
|
OD2
|
A:ASP113
|
4.6
|
75.5
|
1.0
|
N
|
A:LYS115
|
4.7
|
84.0
|
1.0
|
C
|
A:LYS115
|
4.7
|
85.4
|
1.0
|
N
|
A:SER77
|
4.8
|
92.8
|
1.0
|
C
|
A:ASP113
|
4.8
|
78.2
|
1.0
|
CB
|
A:SER243
|
4.8
|
72.0
|
1.0
|
CD
|
A:GLU118
|
4.9
|
90.5
|
1.0
|
CB
|
A:ASP113
|
4.9
|
76.8
|
1.0
|
|
Potassium binding site 2 out
of 8 in 6gg6
Go back to
Potassium Binding Sites List in 6gg6
Potassium binding site 2 out
of 8 in the Crystal Structure of M2 Pyk in Complex with Serine.
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 M2 Pyk in Complex with Serine. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K601
b:94.9
occ:1.00
|
OG
|
B:SER77
|
2.9
|
97.3
|
1.0
|
OD1
|
B:ASP113
|
3.0
|
86.2
|
1.0
|
OD1
|
B:ASN75
|
3.0
|
83.4
|
1.0
|
O
|
B:THR114
|
3.1
|
88.8
|
1.0
|
OE2
|
B:GLU118
|
3.3
|
97.3
|
1.0
|
OG
|
B:SER243
|
3.6
|
96.7
|
1.0
|
O
|
B:LYS115
|
4.0
|
90.7
|
1.0
|
CB
|
B:SER77
|
4.1
|
97.6
|
1.0
|
CG
|
B:ASP113
|
4.2
|
86.6
|
1.0
|
CG
|
B:ASN75
|
4.2
|
83.3
|
1.0
|
C
|
B:THR114
|
4.2
|
90.6
|
1.0
|
NZ
|
B:LYS270
|
4.2
|
82.0
|
1.0
|
CA
|
B:LYS115
|
4.3
|
92.7
|
1.0
|
C
|
B:LYS115
|
4.5
|
91.8
|
1.0
|
CD
|
B:GLU118
|
4.5
|
97.6
|
1.0
|
NH2
|
B:ARG73
|
4.6
|
73.6
|
1.0
|
O
|
B:ASP113
|
4.6
|
87.7
|
1.0
|
CB
|
B:SER243
|
4.6
|
94.7
|
1.0
|
N
|
B:LYS115
|
4.7
|
92.6
|
1.0
|
ND2
|
B:ASN75
|
4.7
|
83.1
|
1.0
|
OD2
|
B:ASP113
|
4.8
|
86.7
|
1.0
|
N
|
B:SER77
|
4.9
|
94.8
|
1.0
|
|
Potassium binding site 3 out
of 8 in 6gg6
Go back to
Potassium Binding Sites List in 6gg6
Potassium binding site 3 out
of 8 in the Crystal Structure of M2 Pyk in Complex with Serine.
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 M2 Pyk in Complex with Serine. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K601
b:70.6
occ:1.00
|
OG
|
C:SER77
|
2.9
|
78.5
|
1.0
|
OD1
|
C:ASP113
|
2.9
|
82.9
|
1.0
|
O
|
C:THR114
|
3.0
|
71.5
|
1.0
|
OD1
|
C:ASN75
|
3.2
|
72.1
|
1.0
|
OE2
|
C:GLU118
|
3.3
|
86.7
|
1.0
|
OG
|
C:SER243
|
3.5
|
71.4
|
1.0
|
O
|
C:LYS115
|
3.8
|
80.0
|
1.0
|
C
|
C:THR114
|
4.1
|
75.1
|
1.0
|
NZ
|
C:LYS270
|
4.1
|
62.0
|
1.0
|
CG
|
C:ASP113
|
4.1
|
78.5
|
1.0
|
CB
|
C:SER77
|
4.2
|
80.2
|
1.0
|
CA
|
C:LYS115
|
4.3
|
80.3
|
1.0
|
CG
|
C:ASN75
|
4.3
|
72.8
|
1.0
|
C
|
C:LYS115
|
4.4
|
80.2
|
1.0
|
CD
|
C:GLU118
|
4.5
|
85.8
|
1.0
|
CB
|
C:SER243
|
4.5
|
70.3
|
1.0
|
O
|
C:ASP113
|
4.6
|
74.9
|
1.0
|
N
|
C:LYS115
|
4.6
|
78.2
|
1.0
|
NH2
|
C:ARG73
|
4.7
|
66.0
|
1.0
|
OD2
|
C:ASP113
|
4.8
|
77.1
|
1.0
|
ND2
|
C:ASN75
|
4.8
|
75.1
|
1.0
|
C
|
C:ASP113
|
5.0
|
73.9
|
1.0
|
N
|
C:SER77
|
5.0
|
77.7
|
1.0
|
|
Potassium binding site 4 out
of 8 in 6gg6
Go back to
Potassium Binding Sites List in 6gg6
Potassium binding site 4 out
of 8 in the Crystal Structure of M2 Pyk in Complex with Serine.
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 M2 Pyk in Complex with Serine. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K601
b:77.6
occ:1.00
|
OG
|
D:SER77
|
2.9
|
99.6
|
1.0
|
OD1
|
D:ASP113
|
3.0
|
82.5
|
1.0
|
OD1
|
D:ASN75
|
3.0
|
80.7
|
1.0
|
O
|
D:THR114
|
3.2
|
95.1
|
1.0
|
OE2
|
D:GLU118
|
3.6
|
1.0
|
1.0
|
OG
|
D:SER243
|
3.7
|
86.2
|
1.0
|
O
|
D:LYS115
|
4.0
|
0.8
|
1.0
|
CG
|
D:ASN75
|
4.1
|
80.2
|
1.0
|
NZ
|
D:LYS270
|
4.2
|
74.5
|
1.0
|
CB
|
D:SER77
|
4.2
|
0.5
|
1.0
|
CG
|
D:ASP113
|
4.2
|
84.1
|
1.0
|
C
|
D:THR114
|
4.2
|
96.1
|
1.0
|
CA
|
D:LYS115
|
4.4
|
0.1
|
1.0
|
C
|
D:LYS115
|
4.6
|
0.3
|
1.0
|
NH2
|
D:ARG73
|
4.6
|
70.1
|
1.0
|
ND2
|
D:ASN75
|
4.6
|
80.5
|
1.0
|
CB
|
D:SER243
|
4.6
|
85.6
|
1.0
|
O
|
D:ASP113
|
4.7
|
90.5
|
1.0
|
N
|
D:LYS115
|
4.7
|
99.8
|
1.0
|
CD
|
D:GLU118
|
4.8
|
0.6
|
1.0
|
OD2
|
D:ASP113
|
4.9
|
83.1
|
1.0
|
N
|
D:SER77
|
4.9
|
98.0
|
1.0
|
|
Potassium binding site 5 out
of 8 in 6gg6
Go back to
Potassium Binding Sites List in 6gg6
Potassium binding site 5 out
of 8 in the Crystal Structure of M2 Pyk in Complex with Serine.
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 M2 Pyk in Complex with Serine. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:K601
b:72.5
occ:1.00
|
OD1
|
E:ASP113
|
2.6
|
78.7
|
1.0
|
OD1
|
E:ASN75
|
2.9
|
64.5
|
1.0
|
O
|
E:THR114
|
2.9
|
77.7
|
1.0
|
OG
|
E:SER77
|
3.0
|
82.7
|
1.0
|
OE2
|
E:GLU118
|
3.5
|
94.2
|
1.0
|
OG
|
E:SER243
|
3.6
|
72.8
|
1.0
|
CG
|
E:ASP113
|
3.8
|
78.7
|
1.0
|
C
|
E:THR114
|
4.0
|
80.9
|
1.0
|
CG
|
E:ASN75
|
4.0
|
65.6
|
1.0
|
O
|
E:LYS115
|
4.1
|
82.3
|
1.0
|
NZ
|
E:LYS270
|
4.1
|
75.5
|
1.0
|
CB
|
E:SER77
|
4.2
|
81.2
|
1.0
|
O
|
E:ASP113
|
4.3
|
79.9
|
1.0
|
CA
|
E:LYS115
|
4.4
|
83.6
|
1.0
|
NH2
|
E:ARG73
|
4.4
|
61.8
|
1.0
|
OD2
|
E:ASP113
|
4.5
|
79.0
|
1.0
|
N
|
E:LYS115
|
4.6
|
82.8
|
1.0
|
C
|
E:LYS115
|
4.6
|
83.1
|
1.0
|
ND2
|
E:ASN75
|
4.6
|
67.9
|
1.0
|
C
|
E:ASP113
|
4.6
|
80.5
|
1.0
|
CB
|
E:SER243
|
4.7
|
72.7
|
1.0
|
CB
|
E:ASP113
|
4.8
|
78.5
|
1.0
|
CD
|
E:GLU118
|
4.8
|
94.1
|
1.0
|
N
|
E:SER77
|
4.8
|
76.5
|
1.0
|
N
|
E:THR114
|
5.0
|
81.0
|
1.0
|
|
Potassium binding site 6 out
of 8 in 6gg6
Go back to
Potassium Binding Sites List in 6gg6
Potassium binding site 6 out
of 8 in the Crystal Structure of M2 Pyk in Complex with Serine.
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 M2 Pyk in Complex with Serine. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:K601
b:83.8
occ:1.00
|
OD1
|
F:ASN75
|
2.7
|
85.4
|
1.0
|
OD1
|
F:ASP113
|
2.8
|
86.7
|
1.0
|
OG
|
F:SER77
|
2.9
|
96.0
|
1.0
|
O
|
F:THR114
|
3.2
|
94.2
|
1.0
|
OE2
|
F:GLU118
|
3.6
|
99.0
|
1.0
|
OG
|
F:SER243
|
3.8
|
79.1
|
1.0
|
CG
|
F:ASN75
|
3.8
|
85.3
|
1.0
|
CG
|
F:ASP113
|
3.9
|
86.3
|
1.0
|
CB
|
F:SER77
|
4.1
|
94.5
|
1.0
|
C
|
F:THR114
|
4.2
|
97.9
|
1.0
|
NZ
|
F:LYS270
|
4.2
|
71.0
|
1.0
|
O
|
F:LYS115
|
4.2
|
0.1
|
1.0
|
NH2
|
F:ARG73
|
4.3
|
77.9
|
1.0
|
O
|
F:ASP113
|
4.4
|
91.6
|
1.0
|
ND2
|
F:ASN75
|
4.4
|
86.0
|
1.0
|
CA
|
F:LYS115
|
4.5
|
0.8
|
1.0
|
OD2
|
F:ASP113
|
4.6
|
84.9
|
1.0
|
N
|
F:LYS115
|
4.7
|
0.4
|
1.0
|
N
|
F:SER77
|
4.7
|
90.8
|
1.0
|
C
|
F:LYS115
|
4.8
|
0.4
|
1.0
|
C
|
F:ASP113
|
4.8
|
90.7
|
1.0
|
CD
|
F:GLU118
|
4.9
|
98.8
|
1.0
|
CB
|
F:ASP113
|
4.9
|
87.0
|
1.0
|
CB
|
F:SER243
|
4.9
|
80.2
|
1.0
|
|
Potassium binding site 7 out
of 8 in 6gg6
Go back to
Potassium Binding Sites List in 6gg6
Potassium binding site 7 out
of 8 in the Crystal Structure of M2 Pyk in Complex with Serine.
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 M2 Pyk in Complex with Serine. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:K601
b:86.6
occ:1.00
|
OG
|
G:SER77
|
2.9
|
90.0
|
1.0
|
OD1
|
G:ASP113
|
2.9
|
84.4
|
1.0
|
OD1
|
G:ASN75
|
2.9
|
77.6
|
1.0
|
O
|
G:THR114
|
3.2
|
82.7
|
1.0
|
OE2
|
G:GLU118
|
3.4
|
95.0
|
1.0
|
OG
|
G:SER243
|
3.7
|
77.7
|
1.0
|
CG
|
G:ASN75
|
4.1
|
77.0
|
1.0
|
O
|
G:LYS115
|
4.1
|
92.1
|
1.0
|
CG
|
G:ASP113
|
4.1
|
83.1
|
1.0
|
NZ
|
G:LYS270
|
4.2
|
68.5
|
1.0
|
CB
|
G:SER77
|
4.2
|
91.4
|
1.0
|
C
|
G:THR114
|
4.2
|
84.3
|
1.0
|
CA
|
G:LYS115
|
4.4
|
92.5
|
1.0
|
NH2
|
G:ARG73
|
4.5
|
66.1
|
1.0
|
O
|
G:ASP113
|
4.6
|
84.7
|
1.0
|
ND2
|
G:ASN75
|
4.6
|
78.1
|
1.0
|
C
|
G:LYS115
|
4.7
|
92.5
|
1.0
|
CD
|
G:GLU118
|
4.7
|
94.0
|
1.0
|
CB
|
G:SER243
|
4.7
|
77.1
|
1.0
|
N
|
G:LYS115
|
4.8
|
89.0
|
1.0
|
OD2
|
G:ASP113
|
4.8
|
82.3
|
1.0
|
N
|
G:SER77
|
4.9
|
89.3
|
1.0
|
C
|
G:ASP113
|
5.0
|
83.1
|
1.0
|
|
Potassium binding site 8 out
of 8 in 6gg6
Go back to
Potassium Binding Sites List in 6gg6
Potassium binding site 8 out
of 8 in the Crystal Structure of M2 Pyk in Complex with Serine.
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 M2 Pyk in Complex with Serine. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:K601
b:80.0
occ:1.00
|
OG
|
H:SER77
|
2.8
|
88.7
|
1.0
|
OD1
|
H:ASN75
|
2.8
|
75.6
|
1.0
|
OD1
|
H:ASP113
|
2.9
|
80.0
|
1.0
|
O
|
H:THR114
|
3.1
|
79.1
|
1.0
|
OE2
|
H:GLU118
|
3.4
|
91.5
|
1.0
|
OG
|
H:SER243
|
3.8
|
81.5
|
1.0
|
CG
|
H:ASN75
|
4.0
|
74.8
|
1.0
|
CG
|
H:ASP113
|
4.1
|
79.7
|
1.0
|
CB
|
H:SER77
|
4.1
|
88.7
|
1.0
|
O
|
H:LYS115
|
4.1
|
82.5
|
1.0
|
C
|
H:THR114
|
4.2
|
80.6
|
1.0
|
NZ
|
H:LYS270
|
4.2
|
70.2
|
1.0
|
CA
|
H:LYS115
|
4.4
|
83.6
|
1.0
|
NH2
|
H:ARG73
|
4.5
|
65.6
|
1.0
|
O
|
H:ASP113
|
4.5
|
78.2
|
1.0
|
ND2
|
H:ASN75
|
4.5
|
75.1
|
1.0
|
C
|
H:LYS115
|
4.6
|
82.7
|
1.0
|
CD
|
H:GLU118
|
4.7
|
90.1
|
1.0
|
N
|
H:LYS115
|
4.7
|
81.9
|
1.0
|
OD2
|
H:ASP113
|
4.8
|
80.3
|
1.0
|
N
|
H:SER77
|
4.8
|
87.0
|
1.0
|
CB
|
H:SER243
|
4.8
|
79.2
|
1.0
|
C
|
H:ASP113
|
4.9
|
77.7
|
1.0
|
|
Reference:
M.Yuan,
I.W.Mcnae,
Y.Chen,
E.A.Blackburn,
M.A.Wear,
P.A.M.Michels,
L.A.Fothergill-Gilmore,
T.Hupp,
M.D.Walkinshaw.
An Allostatic Mechanism For M2 Pyruvate Kinase As An Amino-Acid Sensor. Biochem. J. V. 475 1821 2018.
ISSN: ESSN 1470-8728
PubMed: 29748232
DOI: 10.1042/BCJ20180171
Page generated: Mon Aug 12 16:09:32 2024
|