Sodium in PDB 1a5u: Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate
Enzymatic activity of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate
All present enzymatic activity of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate:
2.7.1.40;
Protein crystallography data
The structure of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate, PDB code: 1a5u
was solved by
T.M.Larsen,
M.M.Benning,
I.Rayment,
G.H.Reed,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
30.00 /
2.35
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
95.300,
216.500,
258.600,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
n/a /
n/a
|
Other elements in 1a5u:
The structure of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate
(pdb code 1a5u). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the
Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate, PDB code: 1a5u:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Sodium binding site 1 out
of 8 in 1a5u
Go back to
Sodium Binding Sites List in 1a5u
Sodium binding site 1 out
of 8 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na532
b:43.4
occ:1.00
|
O
|
A:THR113
|
2.6
|
32.1
|
1.0
|
|
OG
|
A:SER76
|
2.6
|
32.8
|
1.0
|
|
OD1
|
A:ASP112
|
2.8
|
51.4
|
1.0
|
|
OD1
|
A:ASN74
|
2.8
|
22.9
|
1.0
|
|
O3G
|
A:ATP535
|
2.9
|
17.4
|
1.0
|
|
OG
|
A:SER242
|
3.4
|
37.3
|
1.0
|
|
CB
|
A:SER76
|
3.6
|
19.8
|
1.0
|
|
CG
|
A:ASN74
|
3.7
|
24.4
|
1.0
|
|
C
|
A:THR113
|
3.8
|
19.7
|
1.0
|
|
CG
|
A:ASP112
|
3.9
|
38.4
|
1.0
|
|
ND2
|
A:ASN74
|
4.0
|
10.9
|
1.0
|
|
NZ
|
A:LYS269
|
4.2
|
31.8
|
1.0
|
|
O
|
A:HOH6743
|
4.2
|
24.8
|
1.0
|
|
PG
|
A:ATP535
|
4.3
|
52.9
|
1.0
|
|
O
|
A:ASP112
|
4.3
|
38.3
|
1.0
|
|
NH2
|
A:ARG119
|
4.3
|
38.2
|
1.0
|
|
N
|
A:SER76
|
4.3
|
29.1
|
1.0
|
|
C
|
A:ASP112
|
4.4
|
53.4
|
1.0
|
|
OE1
|
A:GLU117
|
4.4
|
38.1
|
1.0
|
|
CB
|
A:SER242
|
4.5
|
32.0
|
1.0
|
|
O
|
A:LYS114
|
4.5
|
57.5
|
1.0
|
|
CA
|
A:LYS114
|
4.5
|
36.0
|
1.0
|
|
CA
|
A:SER76
|
4.6
|
24.3
|
1.0
|
|
OE2
|
A:GLU117
|
4.6
|
92.2
|
1.0
|
|
OD2
|
A:ASP112
|
4.6
|
38.4
|
1.0
|
|
N
|
A:LYS114
|
4.6
|
53.6
|
1.0
|
|
N
|
A:THR113
|
4.6
|
41.4
|
1.0
|
|
NH2
|
A:ARG72
|
4.6
|
38.0
|
1.0
|
|
CB
|
A:ASP112
|
4.7
|
41.4
|
1.0
|
|
O3B
|
A:ATP535
|
4.7
|
18.8
|
1.0
|
|
CA
|
A:THR113
|
4.8
|
28.6
|
1.0
|
|
O2G
|
A:ATP535
|
4.9
|
31.7
|
1.0
|
|
C
|
A:LYS114
|
4.9
|
24.2
|
1.0
|
|
CD
|
A:GLU117
|
4.9
|
61.0
|
1.0
|
|
N
|
A:PHE75
|
5.0
|
53.0
|
1.0
|
|
Sodium binding site 2 out
of 8 in 1a5u
Go back to
Sodium Binding Sites List in 1a5u
Sodium binding site 2 out
of 8 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na1132
b:52.5
occ:1.00
|
OD1
|
B:ASP712
|
2.6
|
25.7
|
1.0
|
|
OD1
|
B:ASN674
|
2.6
|
39.8
|
1.0
|
|
O
|
B:HOH6139
|
2.8
|
30.8
|
1.0
|
|
O
|
B:THR713
|
3.0
|
15.8
|
1.0
|
|
OG
|
B:SER676
|
3.3
|
36.7
|
1.0
|
|
O
|
B:HOH6608
|
3.4
|
79.0
|
1.0
|
|
C
|
B:THR713
|
3.6
|
41.5
|
1.0
|
|
CG
|
B:ASP712
|
3.6
|
25.7
|
1.0
|
|
O
|
B:ASP712
|
3.6
|
29.4
|
1.0
|
|
CG
|
B:ASN674
|
3.7
|
13.3
|
1.0
|
|
CB
|
B:SER676
|
3.7
|
16.2
|
1.0
|
|
NZ
|
B:LYS869
|
3.8
|
11.1
|
1.0
|
|
C
|
B:ASP712
|
3.9
|
46.2
|
1.0
|
|
OG
|
B:SER842
|
4.0
|
14.8
|
1.0
|
|
N
|
B:LYS714
|
4.1
|
7.7
|
1.0
|
|
CB
|
B:ASP712
|
4.1
|
27.7
|
1.0
|
|
N
|
B:SER676
|
4.1
|
35.8
|
1.0
|
|
CA
|
B:LYS714
|
4.2
|
31.8
|
1.0
|
|
NH2
|
B:ARG672
|
4.2
|
15.6
|
1.0
|
|
ND2
|
B:ASN674
|
4.3
|
24.8
|
1.0
|
|
O
|
B:HOH6063
|
4.3
|
37.1
|
1.0
|
|
N
|
B:THR713
|
4.3
|
92.5
|
1.0
|
|
CA
|
B:SER676
|
4.4
|
20.2
|
1.0
|
|
N
|
B:PHE675
|
4.5
|
33.1
|
1.0
|
|
OD2
|
B:ASP712
|
4.5
|
37.9
|
1.0
|
|
CA
|
B:THR713
|
4.5
|
11.0
|
1.0
|
|
O
|
B:LYS714
|
4.6
|
21.7
|
1.0
|
|
CA
|
B:ASP712
|
4.6
|
16.2
|
1.0
|
|
CA
|
B:ASN674
|
4.7
|
33.2
|
1.0
|
|
C
|
B:LYS714
|
4.7
|
16.1
|
1.0
|
|
CB
|
B:ASN674
|
4.7
|
10.0
|
1.0
|
|
C
|
B:ASN674
|
4.8
|
47.7
|
1.0
|
|
Sodium binding site 3 out
of 8 in 1a5u
Go back to
Sodium Binding Sites List in 1a5u
Sodium binding site 3 out
of 8 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na1732
b:56.0
occ:1.00
|
O
|
C:THR1313
|
2.5
|
30.3
|
1.0
|
|
OD1
|
C:ASN1274
|
2.8
|
49.1
|
1.0
|
|
OG
|
C:SER1276
|
2.8
|
52.6
|
1.0
|
|
OD1
|
C:ASP1312
|
3.0
|
33.8
|
1.0
|
|
O3G
|
C:ATP1735
|
3.2
|
14.7
|
1.0
|
|
OG
|
C:SER1442
|
3.4
|
33.2
|
1.0
|
|
CG
|
C:ASN1274
|
3.6
|
32.3
|
1.0
|
|
C
|
C:THR1313
|
3.6
|
0.0
|
1.0
|
|
CB
|
C:SER1276
|
3.7
|
19.5
|
1.0
|
|
ND2
|
C:ASN1274
|
3.8
|
31.3
|
1.0
|
|
CG
|
C:ASP1312
|
3.9
|
53.5
|
1.0
|
|
NZ
|
C:LYS1469
|
4.0
|
76.7
|
1.0
|
|
O
|
C:LYS1314
|
4.2
|
47.3
|
1.0
|
|
CB
|
C:SER1442
|
4.2
|
10.9
|
1.0
|
|
N
|
C:SER1276
|
4.3
|
29.0
|
1.0
|
|
CA
|
C:LYS1314
|
4.3
|
15.6
|
1.0
|
|
NH2
|
C:ARG1272
|
4.3
|
66.6
|
1.0
|
|
N
|
C:LYS1314
|
4.4
|
29.8
|
1.0
|
|
OD2
|
C:ASP1312
|
4.4
|
26.5
|
1.0
|
|
OE1
|
C:GLU1317
|
4.5
|
72.3
|
1.0
|
|
C
|
C:ASP1312
|
4.5
|
57.6
|
1.0
|
|
PG
|
C:ATP1735
|
4.5
|
54.0
|
1.0
|
|
N
|
C:THR1313
|
4.5
|
31.0
|
1.0
|
|
NH1
|
C:ARG1319
|
4.6
|
52.6
|
1.0
|
|
CA
|
C:SER1276
|
4.6
|
44.3
|
1.0
|
|
O
|
C:ASP1312
|
4.6
|
37.5
|
1.0
|
|
CA
|
C:THR1313
|
4.7
|
29.4
|
1.0
|
|
C
|
C:LYS1314
|
4.7
|
28.4
|
1.0
|
|
CB
|
C:ASP1312
|
4.7
|
20.5
|
1.0
|
|
OE2
|
C:GLU1317
|
4.8
|
65.5
|
1.0
|
|
N
|
C:PHE1275
|
4.9
|
20.0
|
1.0
|
|
O3B
|
C:ATP1735
|
5.0
|
38.1
|
1.0
|
|
CB
|
C:ASN1274
|
5.0
|
37.3
|
1.0
|
|
Sodium binding site 4 out
of 8 in 1a5u
Go back to
Sodium Binding Sites List in 1a5u
Sodium binding site 4 out
of 8 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na2332
b:27.3
occ:1.00
|
OD1
|
D:ASP1912
|
2.5
|
26.2
|
1.0
|
|
OG
|
D:SER1876
|
2.6
|
23.8
|
1.0
|
|
O
|
D:HOH7433
|
2.6
|
30.8
|
1.0
|
|
OD1
|
D:ASN1874
|
2.7
|
30.8
|
1.0
|
|
O3G
|
D:ATP2335
|
2.7
|
32.8
|
1.0
|
|
O
|
D:THR1913
|
2.8
|
39.6
|
1.0
|
|
CG
|
D:ASN1874
|
3.4
|
20.9
|
1.0
|
|
ND2
|
D:ASN1874
|
3.5
|
22.6
|
1.0
|
|
OG
|
D:SER2042
|
3.5
|
23.2
|
1.0
|
|
CB
|
D:SER1876
|
3.6
|
24.0
|
1.0
|
|
CG
|
D:ASP1912
|
3.8
|
17.1
|
1.0
|
|
C
|
D:THR1913
|
3.9
|
20.3
|
1.0
|
|
O
|
D:HOH6430
|
4.0
|
18.1
|
1.0
|
|
PG
|
D:ATP2335
|
4.1
|
17.7
|
1.0
|
|
NZ
|
D:LYS2069
|
4.1
|
18.9
|
1.0
|
|
N
|
D:SER1876
|
4.4
|
39.7
|
1.0
|
|
OD2
|
D:ASP1912
|
4.4
|
27.6
|
1.0
|
|
CA
|
D:LYS1914
|
4.4
|
13.8
|
1.0
|
|
NH1
|
D:ARG1919
|
4.5
|
25.3
|
1.0
|
|
O
|
D:ASP1912
|
4.5
|
11.4
|
1.0
|
|
OE1
|
D:GLU1917
|
4.5
|
24.8
|
1.0
|
|
CA
|
D:SER1876
|
4.5
|
14.9
|
1.0
|
|
CB
|
D:SER2042
|
4.5
|
10.8
|
1.0
|
|
N
|
D:LYS1914
|
4.6
|
23.7
|
1.0
|
|
C
|
D:ASP1912
|
4.7
|
20.5
|
1.0
|
|
CB
|
D:ASP1912
|
4.7
|
23.0
|
1.0
|
|
OE2
|
D:GLU1917
|
4.7
|
24.7
|
1.0
|
|
O2G
|
D:ATP2335
|
4.7
|
14.9
|
1.0
|
|
NH2
|
D:ARG1872
|
4.7
|
23.5
|
1.0
|
|
O3B
|
D:ATP2335
|
4.7
|
18.5
|
1.0
|
|
CB
|
D:ASN1874
|
4.7
|
5.8
|
1.0
|
|
O1G
|
D:ATP2335
|
4.8
|
31.3
|
1.0
|
|
O
|
D:LYS1914
|
4.8
|
18.3
|
1.0
|
|
N
|
D:THR1913
|
4.8
|
27.8
|
1.0
|
|
CA
|
D:THR1913
|
4.9
|
15.3
|
1.0
|
|
CD
|
D:GLU1917
|
5.0
|
27.6
|
1.0
|
|
Sodium binding site 5 out
of 8 in 1a5u
Go back to
Sodium Binding Sites List in 1a5u
Sodium binding site 5 out
of 8 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na3532
b:29.6
occ:1.00
|
O
|
E:HOH7689
|
2.3
|
31.1
|
1.0
|
|
OD1
|
E:ASP3112
|
2.5
|
21.5
|
1.0
|
|
O
|
E:THR3113
|
2.6
|
33.9
|
1.0
|
|
OD1
|
E:ASN3074
|
2.6
|
33.9
|
1.0
|
|
O3G
|
E:ATP3535
|
2.9
|
27.8
|
1.0
|
|
OG
|
E:SER3076
|
3.0
|
18.2
|
1.0
|
|
OG
|
E:SER3242
|
3.4
|
8.3
|
1.0
|
|
CB
|
E:SER3076
|
3.5
|
7.6
|
1.0
|
|
CG
|
E:ASN3074
|
3.6
|
17.3
|
1.0
|
|
CG
|
E:ASP3112
|
3.7
|
22.2
|
1.0
|
|
C
|
E:THR3113
|
3.7
|
42.5
|
1.0
|
|
ND2
|
E:ASN3074
|
4.0
|
15.4
|
1.0
|
|
O
|
E:ASP3112
|
4.1
|
12.9
|
1.0
|
|
NH2
|
E:ARG3119
|
4.1
|
29.4
|
1.0
|
|
N
|
E:SER3076
|
4.2
|
23.4
|
1.0
|
|
O
|
E:HOH6954
|
4.2
|
30.3
|
1.0
|
|
NZ
|
E:LYS3269
|
4.2
|
5.4
|
1.0
|
|
CA
|
E:LYS3114
|
4.2
|
16.6
|
1.0
|
|
PG
|
E:ATP3535
|
4.3
|
22.2
|
1.0
|
|
OD2
|
E:ASP3112
|
4.3
|
27.0
|
1.0
|
|
CB
|
E:SER3242
|
4.4
|
1.0
|
1.0
|
|
CA
|
E:SER3076
|
4.4
|
25.7
|
1.0
|
|
N
|
E:LYS3114
|
4.4
|
37.8
|
1.0
|
|
C
|
E:ASP3112
|
4.4
|
34.3
|
1.0
|
|
O
|
E:LYS3114
|
4.6
|
20.9
|
1.0
|
|
OE2
|
E:GLU3117
|
4.6
|
12.7
|
1.0
|
|
CB
|
E:ASP3112
|
4.6
|
5.0
|
1.0
|
|
NH2
|
E:ARG3072
|
4.7
|
20.8
|
1.0
|
|
N
|
E:THR3113
|
4.7
|
32.6
|
1.0
|
|
OE1
|
E:GLU3117
|
4.8
|
30.3
|
1.0
|
|
C
|
E:LYS3114
|
4.8
|
29.0
|
1.0
|
|
CA
|
E:THR3113
|
4.8
|
16.1
|
1.0
|
|
O3B
|
E:ATP3535
|
4.9
|
48.8
|
1.0
|
|
CB
|
E:ASN3074
|
4.9
|
23.9
|
1.0
|
|
N
|
E:PHE3075
|
5.0
|
33.3
|
1.0
|
|
O2G
|
E:ATP3535
|
5.0
|
6.9
|
1.0
|
|
Sodium binding site 6 out
of 8 in 1a5u
Go back to
Sodium Binding Sites List in 1a5u
Sodium binding site 6 out
of 8 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Na4132
b:40.0
occ:1.00
|
O3G
|
F:ATP4135
|
2.4
|
28.8
|
1.0
|
|
OD1
|
F:ASN3674
|
2.6
|
33.3
|
1.0
|
|
O
|
F:HOH6481
|
2.8
|
28.5
|
1.0
|
|
OG
|
F:SER3676
|
2.8
|
30.3
|
1.0
|
|
OD1
|
F:ASP3712
|
3.0
|
25.8
|
1.0
|
|
O
|
F:THR3713
|
3.0
|
32.4
|
1.0
|
|
CG
|
F:ASN3674
|
3.4
|
40.5
|
1.0
|
|
CB
|
F:SER3676
|
3.5
|
8.3
|
1.0
|
|
ND2
|
F:ASN3674
|
3.5
|
26.8
|
1.0
|
|
OG
|
F:SER3842
|
3.6
|
22.0
|
1.0
|
|
PG
|
F:ATP4135
|
3.7
|
52.6
|
1.0
|
|
NZ
|
F:LYS3869
|
3.9
|
29.1
|
1.0
|
|
O
|
F:HOH6450
|
3.9
|
20.4
|
1.0
|
|
C
|
F:THR3713
|
3.9
|
21.9
|
1.0
|
|
CG
|
F:ASP3712
|
4.0
|
82.6
|
1.0
|
|
O3B
|
F:ATP4135
|
4.2
|
38.8
|
1.0
|
|
N
|
F:SER3676
|
4.4
|
31.4
|
1.0
|
|
O2G
|
F:ATP4135
|
4.4
|
20.2
|
1.0
|
|
NH2
|
F:ARG3672
|
4.4
|
34.0
|
1.0
|
|
CA
|
F:LYS3714
|
4.5
|
37.5
|
1.0
|
|
CA
|
F:SER3676
|
4.5
|
25.0
|
1.0
|
|
O
|
F:ASP3712
|
4.5
|
43.7
|
1.0
|
|
N
|
F:LYS3714
|
4.6
|
43.6
|
1.0
|
|
OD2
|
F:ASP3712
|
4.6
|
25.6
|
1.0
|
|
O
|
F:LYS3714
|
4.6
|
54.0
|
1.0
|
|
C
|
F:ASP3712
|
4.6
|
29.1
|
1.0
|
|
OE2
|
F:GLU3717
|
4.7
|
0.0
|
1.0
|
|
O1G
|
F:ATP4135
|
4.7
|
54.9
|
1.0
|
|
CB
|
F:ASP3712
|
4.7
|
15.5
|
1.0
|
|
CB
|
F:ASN3674
|
4.8
|
43.5
|
1.0
|
|
N
|
F:THR3713
|
4.8
|
26.6
|
1.0
|
|
CB
|
F:SER3842
|
4.8
|
45.6
|
1.0
|
|
CD
|
F:GLU3717
|
4.9
|
52.1
|
1.0
|
|
NH2
|
F:ARG3719
|
4.9
|
0.0
|
1.0
|
|
OE1
|
F:GLU3717
|
4.9
|
56.3
|
1.0
|
|
O3
|
F:OXL4133
|
5.0
|
42.2
|
1.0
|
|
CA
|
F:THR3713
|
5.0
|
25.3
|
1.0
|
|
C
|
F:LYS3714
|
5.0
|
17.4
|
1.0
|
|
Sodium binding site 7 out
of 8 in 1a5u
Go back to
Sodium Binding Sites List in 1a5u
Sodium binding site 7 out
of 8 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Na4732
b:31.2
occ:1.00
|
O
|
G:HOH7008
|
2.2
|
28.3
|
1.0
|
|
OD1
|
G:ASN4274
|
2.5
|
21.1
|
1.0
|
|
OD1
|
G:ASP4312
|
2.6
|
24.4
|
1.0
|
|
OG
|
G:SER4276
|
2.8
|
30.3
|
1.0
|
|
O3G
|
G:ATP4735
|
2.8
|
22.6
|
1.0
|
|
O
|
G:THR4313
|
2.8
|
25.0
|
1.0
|
|
CB
|
G:SER4276
|
3.4
|
29.6
|
1.0
|
|
CG
|
G:ASN4274
|
3.4
|
38.3
|
1.0
|
|
OG
|
G:SER4442
|
3.6
|
31.7
|
1.0
|
|
ND2
|
G:ASN4274
|
3.7
|
16.1
|
1.0
|
|
CG
|
G:ASP4312
|
3.7
|
23.0
|
1.0
|
|
O
|
G:HOH6654
|
3.8
|
32.1
|
1.0
|
|
C
|
G:THR4313
|
3.8
|
45.0
|
1.0
|
|
NH2
|
G:ARG4319
|
4.0
|
0.0
|
1.0
|
|
PG
|
G:ATP4735
|
4.1
|
32.1
|
1.0
|
|
NZ
|
G:LYS4469
|
4.1
|
26.2
|
1.0
|
|
OE1
|
G:GLU4317
|
4.2
|
58.2
|
1.0
|
|
N
|
G:SER4276
|
4.2
|
31.2
|
1.0
|
|
CA
|
G:SER4276
|
4.3
|
26.7
|
1.0
|
|
CA
|
G:LYS4314
|
4.4
|
16.6
|
1.0
|
|
OD2
|
G:ASP4312
|
4.4
|
31.5
|
1.0
|
|
O2G
|
G:ATP4735
|
4.5
|
3.0
|
1.0
|
|
NH2
|
G:ARG4272
|
4.5
|
15.4
|
1.0
|
|
N
|
G:LYS4314
|
4.5
|
45.3
|
1.0
|
|
CB
|
G:SER4442
|
4.5
|
19.7
|
1.0
|
|
O
|
G:LYS4314
|
4.6
|
36.1
|
1.0
|
|
OE2
|
G:GLU4317
|
4.6
|
30.1
|
1.0
|
|
CB
|
G:ASP4312
|
4.6
|
12.3
|
1.0
|
|
C
|
G:ASP4312
|
4.7
|
42.1
|
1.0
|
|
O
|
G:ASP4312
|
4.7
|
25.4
|
1.0
|
|
CD
|
G:GLU4317
|
4.7
|
31.9
|
1.0
|
|
N
|
G:THR4313
|
4.7
|
41.9
|
1.0
|
|
CB
|
G:ASN4274
|
4.8
|
10.2
|
1.0
|
|
O3
|
G:OXL4733
|
4.8
|
55.8
|
1.0
|
|
CA
|
G:THR4313
|
4.8
|
23.3
|
1.0
|
|
O3B
|
G:ATP4735
|
4.9
|
30.6
|
1.0
|
|
C
|
G:LYS4314
|
4.9
|
40.3
|
1.0
|
|
O1G
|
G:ATP4735
|
5.0
|
35.7
|
1.0
|
|
Sodium binding site 8 out
of 8 in 1a5u
Go back to
Sodium Binding Sites List in 1a5u
Sodium binding site 8 out
of 8 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Na5332
b:57.1
occ:1.00
|
OD1
|
H:ASN4874
|
2.6
|
22.4
|
1.0
|
|
OG
|
H:SER4876
|
2.9
|
41.0
|
1.0
|
|
OD1
|
H:ASP4912
|
3.0
|
21.3
|
1.0
|
|
O
|
H:HOH6813
|
3.1
|
42.2
|
1.0
|
|
O
|
H:THR4913
|
3.2
|
31.9
|
1.0
|
|
CG
|
H:ASN4874
|
3.5
|
15.8
|
1.0
|
|
O
|
H:HOH6932
|
3.6
|
39.7
|
1.0
|
|
CG
|
H:ASP4912
|
3.8
|
27.7
|
1.0
|
|
NZ
|
H:LYS5069
|
3.9
|
19.7
|
1.0
|
|
C
|
H:THR4913
|
3.9
|
5.8
|
1.0
|
|
NH2
|
H:ARG4872
|
3.9
|
31.1
|
1.0
|
|
O
|
H:ASP4912
|
4.0
|
31.5
|
1.0
|
|
ND2
|
H:ASN4874
|
4.0
|
25.9
|
1.0
|
|
OG
|
H:SER5042
|
4.1
|
28.5
|
1.0
|
|
CB
|
H:SER4876
|
4.1
|
16.8
|
1.0
|
|
O
|
H:HOH7233
|
4.2
|
44.9
|
1.0
|
|
C
|
H:ASP4912
|
4.3
|
23.7
|
1.0
|
|
N
|
H:SER4876
|
4.3
|
26.9
|
1.0
|
|
CB
|
H:ASP4912
|
4.4
|
1.0
|
1.0
|
|
CA
|
H:LYS4914
|
4.4
|
19.2
|
1.0
|
|
N
|
H:LYS4914
|
4.5
|
66.9
|
1.0
|
|
OD2
|
H:ASP4912
|
4.5
|
39.8
|
1.0
|
|
CB
|
H:ASN4874
|
4.7
|
20.2
|
1.0
|
|
CA
|
H:ASN4874
|
4.7
|
9.9
|
1.0
|
|
N
|
H:PHE4875
|
4.7
|
32.4
|
1.0
|
|
CA
|
H:SER4876
|
4.7
|
18.0
|
1.0
|
|
N
|
H:THR4913
|
4.8
|
29.7
|
1.0
|
|
O
|
H:HOH7232
|
4.8
|
30.4
|
1.0
|
|
O
|
H:LYS4914
|
4.8
|
16.3
|
1.0
|
|
O3
|
H:OXL5333
|
4.8
|
65.3
|
1.0
|
|
O
|
H:HOH6478
|
4.9
|
32.6
|
1.0
|
|
CA
|
H:THR4913
|
4.9
|
34.5
|
1.0
|
|
CA
|
H:ASP4912
|
4.9
|
10.5
|
1.0
|
|
CZ
|
H:ARG4872
|
5.0
|
38.1
|
1.0
|
|
C
|
H:ASN4874
|
5.0
|
14.9
|
1.0
|
|
C
|
H:LYS4914
|
5.0
|
24.9
|
1.0
|
|
Reference:
T.M.Larsen,
M.M.Benning,
I.Rayment,
G.H.Reed.
Structure of the Bis(MG2+)-Atp-Oxalate Complex of the Rabbit Muscle Pyruvate Kinase at 2.1 A Resolution: Atp Binding Over A Barrel. Biochemistry V. 37 6247 1998.
ISSN: ISSN 0006-2960
PubMed: 9572839
DOI: 10.1021/BI980243S
Page generated: Tue Dec 15 05:21:44 2020
|
