Magnesium 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:
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
14;
Binding sites:
The binding sites of Magnesium 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 Magnesium atom.
In total 14 binding sites of Magnesium where determined in the
Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate, PDB code: 1a5u:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 14 in 1a5u
Go back to
Magnesium Binding Sites List in 1a5u
Magnesium binding site 1 out
of 14 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg 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:Mg534
b:19.5
occ:1.00
|
O
|
A:HOH6743
|
1.8
|
24.8
|
1.0
|
|
OD2
|
A:ASP295
|
2.0
|
25.4
|
1.0
|
|
O3
|
A:OXL533
|
2.0
|
33.3
|
1.0
|
|
O4
|
A:OXL533
|
2.1
|
42.9
|
1.0
|
|
OE1
|
A:GLU271
|
2.2
|
20.8
|
1.0
|
|
O2G
|
A:ATP535
|
2.5
|
31.7
|
1.0
|
|
C1
|
A:OXL533
|
2.8
|
45.5
|
1.0
|
|
C2
|
A:OXL533
|
2.9
|
27.2
|
1.0
|
|
CG
|
A:ASP295
|
2.9
|
69.9
|
1.0
|
|
CD
|
A:GLU271
|
3.3
|
25.6
|
1.0
|
|
CB
|
A:ASP295
|
3.3
|
24.3
|
1.0
|
|
PG
|
A:ATP535
|
3.5
|
52.9
|
1.0
|
|
O3G
|
A:ATP535
|
3.8
|
17.4
|
1.0
|
|
O
|
A:HOH6003
|
3.8
|
27.7
|
1.0
|
|
OE2
|
A:GLU271
|
3.9
|
23.9
|
1.0
|
|
O1
|
A:OXL533
|
4.1
|
72.1
|
1.0
|
|
O2
|
A:OXL533
|
4.1
|
40.2
|
1.0
|
|
NZ
|
A:LYS269
|
4.1
|
31.8
|
1.0
|
|
O
|
A:HOH6459
|
4.2
|
11.7
|
1.0
|
|
OD1
|
A:ASP295
|
4.2
|
48.2
|
1.0
|
|
N
|
A:ASP295
|
4.3
|
1.9
|
1.0
|
|
O1G
|
A:ATP535
|
4.3
|
37.8
|
1.0
|
|
CA
|
A:ASP295
|
4.4
|
44.3
|
1.0
|
|
CZ
|
A:PHE243
|
4.5
|
34.5
|
1.0
|
|
CE2
|
A:PHE243
|
4.5
|
48.1
|
1.0
|
|
CG
|
A:GLU271
|
4.5
|
13.3
|
1.0
|
|
CB
|
A:GLU271
|
4.6
|
12.8
|
1.0
|
|
CB
|
A:ALA292
|
4.6
|
38.6
|
1.0
|
|
MG
|
A:MG536
|
4.9
|
25.1
|
1.0
|
|
CE
|
A:LYS269
|
4.9
|
14.8
|
1.0
|
|
O3B
|
A:ATP535
|
4.9
|
18.8
|
1.0
|
|
OG
|
A:SER242
|
5.0
|
37.3
|
1.0
|
|
Magnesium binding site 2 out
of 14 in 1a5u
Go back to
Magnesium Binding Sites List in 1a5u
Magnesium binding site 2 out
of 14 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg 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
|
A:Mg536
b:25.1
occ:1.00
|
O1G
|
A:ATP535
|
1.9
|
37.8
|
1.0
|
|
O
|
A:HOH6079
|
2.0
|
12.6
|
1.0
|
|
O1A
|
A:ATP535
|
2.3
|
26.3
|
1.0
|
|
O
|
A:HOH6459
|
2.3
|
11.7
|
1.0
|
|
PG
|
A:ATP535
|
2.7
|
52.9
|
1.0
|
|
O2B
|
A:ATP535
|
2.8
|
18.7
|
1.0
|
|
O2G
|
A:ATP535
|
3.1
|
31.7
|
1.0
|
|
PB
|
A:ATP535
|
3.3
|
27.5
|
1.0
|
|
O3B
|
A:ATP535
|
3.3
|
18.8
|
1.0
|
|
PA
|
A:ATP535
|
3.4
|
33.9
|
1.0
|
|
O3A
|
A:ATP535
|
3.7
|
56.2
|
1.0
|
|
C1
|
A:OXL533
|
3.8
|
45.5
|
1.0
|
|
O1
|
A:OXL533
|
3.9
|
72.1
|
1.0
|
|
OG1
|
A:THR327
|
3.9
|
37.4
|
1.0
|
|
C2
|
A:OXL533
|
3.9
|
27.2
|
1.0
|
|
O
|
A:HOH6598
|
4.0
|
30.6
|
1.0
|
|
O3G
|
A:ATP535
|
4.0
|
17.4
|
1.0
|
|
O2
|
A:OXL533
|
4.1
|
40.2
|
1.0
|
|
O2A
|
A:ATP535
|
4.2
|
7.8
|
1.0
|
|
O3
|
A:OXL533
|
4.2
|
33.3
|
1.0
|
|
OG
|
A:SER361
|
4.3
|
25.7
|
1.0
|
|
OD2
|
A:ASP177
|
4.3
|
27.7
|
1.0
|
|
NH2
|
A:ARG72
|
4.3
|
38.0
|
1.0
|
|
NH1
|
A:ARG72
|
4.4
|
56.5
|
1.0
|
|
O4
|
A:OXL533
|
4.4
|
42.9
|
1.0
|
|
O
|
A:HOH6358
|
4.5
|
41.2
|
1.0
|
|
CB
|
A:SER361
|
4.6
|
25.6
|
1.0
|
|
O5'
|
A:ATP535
|
4.7
|
33.8
|
1.0
|
|
O1B
|
A:ATP535
|
4.7
|
43.2
|
1.0
|
|
CG2
|
A:THR327
|
4.8
|
21.2
|
1.0
|
|
MG
|
A:MG534
|
4.9
|
19.5
|
1.0
|
|
CZ
|
A:ARG72
|
4.9
|
35.4
|
1.0
|
|
C5'
|
A:ATP535
|
4.9
|
60.8
|
1.0
|
|
CB
|
A:THR327
|
4.9
|
18.8
|
1.0
|
|
Magnesium binding site 3 out
of 14 in 1a5u
Go back to
Magnesium Binding Sites List in 1a5u
Magnesium binding site 3 out
of 14 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg 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
|
B:Mg1134
b:26.2
occ:1.00
|
O
|
B:HOH6992
|
2.0
|
39.4
|
1.0
|
|
OD2
|
B:ASP895
|
2.2
|
21.4
|
1.0
|
|
O3
|
B:OXL1133
|
2.3
|
33.6
|
1.0
|
|
OE1
|
B:GLU871
|
2.4
|
56.7
|
1.0
|
|
O4
|
B:OXL1133
|
2.7
|
21.8
|
1.0
|
|
C1
|
B:OXL1133
|
3.2
|
30.0
|
1.0
|
|
CG
|
B:ASP895
|
3.3
|
0.0
|
1.0
|
|
C2
|
B:OXL1133
|
3.4
|
35.0
|
1.0
|
|
CD
|
B:GLU871
|
3.5
|
20.7
|
1.0
|
|
OE2
|
B:GLU871
|
3.9
|
34.8
|
1.0
|
|
O
|
B:HOH6139
|
4.0
|
30.8
|
1.0
|
|
O
|
B:HOH6608
|
4.0
|
79.0
|
1.0
|
|
CB
|
B:ASP895
|
4.2
|
18.1
|
1.0
|
|
NZ
|
B:LYS869
|
4.2
|
11.1
|
1.0
|
|
OD1
|
B:ASP895
|
4.4
|
33.3
|
1.0
|
|
O
|
B:HOH6417
|
4.4
|
86.4
|
1.0
|
|
O1
|
B:OXL1133
|
4.4
|
34.8
|
1.0
|
|
CE
|
B:LYS869
|
4.6
|
18.8
|
1.0
|
|
O2
|
B:OXL1133
|
4.6
|
34.2
|
1.0
|
|
CG
|
B:GLU871
|
4.8
|
26.1
|
1.0
|
|
O
|
B:HOH6840
|
4.9
|
35.8
|
1.0
|
|
N
|
B:ASP895
|
4.9
|
28.8
|
1.0
|
|
Magnesium binding site 4 out
of 14 in 1a5u
Go back to
Magnesium Binding Sites List in 1a5u
Magnesium binding site 4 out
of 14 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg 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
|
C:Mg1734
b:35.7
occ:1.00
|
O4
|
C:OXL1733
|
2.0
|
40.0
|
1.0
|
|
O3
|
C:OXL1733
|
2.0
|
72.0
|
1.0
|
|
OD2
|
C:ASP1495
|
2.2
|
34.9
|
1.0
|
|
OE1
|
C:GLU1471
|
2.2
|
33.8
|
1.0
|
|
O2G
|
C:ATP1735
|
2.4
|
31.4
|
1.0
|
|
C2
|
C:OXL1733
|
2.7
|
39.3
|
1.0
|
|
C1
|
C:OXL1733
|
2.7
|
29.8
|
1.0
|
|
CD
|
C:GLU1471
|
3.2
|
29.0
|
1.0
|
|
PG
|
C:ATP1735
|
3.2
|
54.0
|
1.0
|
|
O3G
|
C:ATP1735
|
3.3
|
14.7
|
1.0
|
|
CG
|
C:ASP1495
|
3.3
|
15.7
|
1.0
|
|
OE2
|
C:GLU1471
|
3.5
|
25.4
|
1.0
|
|
NZ
|
C:LYS1469
|
3.6
|
76.7
|
1.0
|
|
O1
|
C:OXL1733
|
4.0
|
37.3
|
1.0
|
|
O2
|
C:OXL1733
|
4.0
|
29.6
|
1.0
|
|
O1G
|
C:ATP1735
|
4.0
|
46.1
|
1.0
|
|
CB
|
C:ASP1495
|
4.2
|
22.1
|
1.0
|
|
CE
|
C:LYS1469
|
4.3
|
28.6
|
1.0
|
|
OD1
|
C:ASP1495
|
4.3
|
30.0
|
1.0
|
|
O
|
C:HOH6006
|
4.5
|
27.4
|
1.0
|
|
CE2
|
C:PHE1443
|
4.5
|
23.0
|
1.0
|
|
CB
|
C:ALA1492
|
4.6
|
14.0
|
1.0
|
|
CG
|
C:GLU1471
|
4.6
|
13.9
|
1.0
|
|
O
|
C:HOH6005
|
4.6
|
40.0
|
1.0
|
|
O3B
|
C:ATP1735
|
4.7
|
38.1
|
1.0
|
|
N
|
C:ASP1495
|
4.9
|
19.1
|
1.0
|
|
CB
|
C:GLU1471
|
4.9
|
27.2
|
1.0
|
|
NH2
|
C:ARG1272
|
4.9
|
66.6
|
1.0
|
|
CZ
|
C:PHE1443
|
4.9
|
39.5
|
1.0
|
|
O
|
C:HOH6647
|
5.0
|
19.7
|
1.0
|
|
Magnesium binding site 5 out
of 14 in 1a5u
Go back to
Magnesium Binding Sites List in 1a5u
Magnesium binding site 5 out
of 14 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg 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
|
C:Mg1736
b:25.6
occ:1.00
|
O
|
C:HOH6006
|
1.9
|
27.4
|
1.0
|
|
O1A
|
C:ATP1735
|
1.9
|
16.6
|
1.0
|
|
O
|
C:HOH6571
|
2.0
|
26.9
|
1.0
|
|
O
|
C:HOH6647
|
2.1
|
19.7
|
1.0
|
|
O1G
|
C:ATP1735
|
2.2
|
46.1
|
1.0
|
|
O2B
|
C:ATP1735
|
2.3
|
24.2
|
1.0
|
|
PA
|
C:ATP1735
|
3.1
|
34.7
|
1.0
|
|
PB
|
C:ATP1735
|
3.2
|
38.9
|
1.0
|
|
PG
|
C:ATP1735
|
3.2
|
54.0
|
1.0
|
|
O3A
|
C:ATP1735
|
3.4
|
58.9
|
1.0
|
|
O3B
|
C:ATP1735
|
3.5
|
38.1
|
1.0
|
|
O2G
|
C:ATP1735
|
3.8
|
31.4
|
1.0
|
|
O
|
C:HOH6851
|
3.9
|
25.4
|
1.0
|
|
O
|
C:HOH6734
|
3.9
|
35.1
|
1.0
|
|
O
|
C:HOH7372
|
4.0
|
33.1
|
1.0
|
|
O2A
|
C:ATP1735
|
4.1
|
21.2
|
1.0
|
|
CB
|
C:SER1561
|
4.1
|
36.9
|
1.0
|
|
O5'
|
C:ATP1735
|
4.1
|
27.2
|
1.0
|
|
C5'
|
C:ATP1735
|
4.2
|
35.6
|
1.0
|
|
OG
|
C:SER1561
|
4.2
|
31.0
|
1.0
|
|
OG1
|
C:THR1527
|
4.4
|
44.2
|
1.0
|
|
OD2
|
C:ASP1377
|
4.4
|
54.1
|
1.0
|
|
O3G
|
C:ATP1735
|
4.4
|
14.7
|
1.0
|
|
NH1
|
C:ARG1272
|
4.4
|
62.3
|
1.0
|
|
O1B
|
C:ATP1735
|
4.5
|
91.7
|
1.0
|
|
C1
|
C:OXL1733
|
4.6
|
29.8
|
1.0
|
|
O1
|
C:OXL1733
|
4.6
|
37.3
|
1.0
|
|
CG2
|
C:THR1527
|
4.7
|
41.4
|
1.0
|
|
C2
|
C:OXL1733
|
4.7
|
39.3
|
1.0
|
|
O3
|
C:OXL1733
|
4.9
|
72.0
|
1.0
|
|
NH2
|
C:ARG1272
|
4.9
|
66.6
|
1.0
|
|
O2
|
C:OXL1733
|
4.9
|
29.6
|
1.0
|
|
Magnesium binding site 6 out
of 14 in 1a5u
Go back to
Magnesium Binding Sites List in 1a5u
Magnesium binding site 6 out
of 14 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg 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
|
D:Mg2334
b:23.9
occ:1.00
|
OD2
|
D:ASP2095
|
2.0
|
11.6
|
1.0
|
|
O3
|
D:OXL2333
|
2.0
|
15.1
|
1.0
|
|
O
|
D:HOH6430
|
2.0
|
18.1
|
1.0
|
|
O4
|
D:OXL2333
|
2.1
|
23.6
|
1.0
|
|
OE1
|
D:GLU2071
|
2.2
|
37.2
|
1.0
|
|
O2G
|
D:ATP2335
|
2.3
|
14.9
|
1.0
|
|
C1
|
D:OXL2333
|
2.7
|
32.5
|
1.0
|
|
C2
|
D:OXL2333
|
2.8
|
19.0
|
1.0
|
|
CG
|
D:ASP2095
|
3.0
|
6.4
|
1.0
|
|
PG
|
D:ATP2335
|
3.3
|
17.7
|
1.0
|
|
CD
|
D:GLU2071
|
3.4
|
25.7
|
1.0
|
|
CB
|
D:ASP2095
|
3.6
|
24.9
|
1.0
|
|
O
|
D:HOH6004
|
3.7
|
29.9
|
1.0
|
|
O3G
|
D:ATP2335
|
3.8
|
32.8
|
1.0
|
|
NZ
|
D:LYS2069
|
3.9
|
18.9
|
1.0
|
|
O
|
D:HOH6045
|
3.9
|
11.2
|
1.0
|
|
OE2
|
D:GLU2071
|
3.9
|
32.0
|
1.0
|
|
O2
|
D:OXL2333
|
4.0
|
17.5
|
1.0
|
|
O1
|
D:OXL2333
|
4.0
|
12.4
|
1.0
|
|
O1G
|
D:ATP2335
|
4.0
|
31.3
|
1.0
|
|
OD1
|
D:ASP2095
|
4.2
|
28.6
|
1.0
|
|
N
|
D:ASP2095
|
4.3
|
39.4
|
1.0
|
|
CE
|
D:LYS2069
|
4.4
|
30.7
|
1.0
|
|
CA
|
D:ASP2095
|
4.6
|
20.4
|
1.0
|
|
CB
|
D:ALA2092
|
4.6
|
9.7
|
1.0
|
|
O3B
|
D:ATP2335
|
4.6
|
18.5
|
1.0
|
|
O
|
D:HOH7433
|
4.6
|
30.8
|
1.0
|
|
CG
|
D:GLU2071
|
4.7
|
34.6
|
1.0
|
|
CE1
|
D:PHE2043
|
4.7
|
39.3
|
1.0
|
|
O
|
D:HOH6382
|
4.8
|
32.8
|
1.0
|
|
MG
|
D:MG2336
|
4.9
|
24.4
|
1.0
|
|
CB
|
D:GLU2071
|
4.9
|
15.8
|
1.0
|
|
Magnesium binding site 7 out
of 14 in 1a5u
Go back to
Magnesium Binding Sites List in 1a5u
Magnesium binding site 7 out
of 14 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg 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
|
D:Mg2336
b:24.4
occ:1.00
|
O
|
D:HOH6378
|
1.8
|
22.6
|
1.0
|
|
O
|
D:HOH6045
|
1.9
|
11.2
|
1.0
|
|
O1A
|
D:ATP2335
|
2.1
|
12.8
|
1.0
|
|
O2B
|
D:ATP2335
|
2.1
|
33.3
|
1.0
|
|
O
|
D:HOH7302
|
2.1
|
22.6
|
1.0
|
|
O1G
|
D:ATP2335
|
2.1
|
31.3
|
1.0
|
|
PG
|
D:ATP2335
|
2.9
|
17.7
|
1.0
|
|
PB
|
D:ATP2335
|
3.0
|
27.7
|
1.0
|
|
O3B
|
D:ATP2335
|
3.1
|
18.5
|
1.0
|
|
PA
|
D:ATP2335
|
3.2
|
23.4
|
1.0
|
|
O2G
|
D:ATP2335
|
3.4
|
14.9
|
1.0
|
|
O3A
|
D:ATP2335
|
3.4
|
7.9
|
1.0
|
|
OD2
|
D:ASP1977
|
4.0
|
26.4
|
1.0
|
|
C1
|
D:OXL2333
|
4.0
|
32.5
|
1.0
|
|
C2
|
D:OXL2333
|
4.1
|
19.0
|
1.0
|
|
O3G
|
D:ATP2335
|
4.1
|
32.8
|
1.0
|
|
O2A
|
D:ATP2335
|
4.2
|
12.5
|
1.0
|
|
NH2
|
D:ARG1872
|
4.2
|
23.5
|
1.0
|
|
OG
|
D:SER2161
|
4.2
|
28.4
|
1.0
|
|
O1
|
D:OXL2333
|
4.3
|
12.4
|
1.0
|
|
O1B
|
D:ATP2335
|
4.3
|
9.7
|
1.0
|
|
O3
|
D:OXL2333
|
4.4
|
15.1
|
1.0
|
|
O
|
D:HOH6004
|
4.4
|
29.9
|
1.0
|
|
OG1
|
D:THR2127
|
4.4
|
12.0
|
1.0
|
|
CB
|
D:SER2161
|
4.4
|
23.1
|
1.0
|
|
O5'
|
D:ATP2335
|
4.4
|
20.6
|
1.0
|
|
O4
|
D:OXL2333
|
4.4
|
23.6
|
1.0
|
|
O2
|
D:OXL2333
|
4.4
|
17.5
|
1.0
|
|
O
|
D:HOH6606
|
4.5
|
29.6
|
1.0
|
|
C5'
|
D:ATP2335
|
4.5
|
40.4
|
1.0
|
|
NH1
|
D:ARG1872
|
4.7
|
72.3
|
1.0
|
|
O
|
D:HOH6087
|
4.7
|
16.1
|
1.0
|
|
O
|
D:HOH6138
|
4.7
|
16.8
|
1.0
|
|
CG2
|
D:THR2127
|
4.9
|
11.2
|
1.0
|
|
MG
|
D:MG2334
|
4.9
|
23.9
|
1.0
|
|
CZ
|
D:ARG1872
|
4.9
|
18.1
|
1.0
|
|
ND2
|
D:ASN1874
|
4.9
|
22.6
|
1.0
|
|
Magnesium binding site 8 out
of 14 in 1a5u
Go back to
Magnesium Binding Sites List in 1a5u
Magnesium binding site 8 out
of 14 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg 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
|
E:Mg3534
b:19.2
occ:1.00
|
OD2
|
E:ASP3295
|
2.0
|
19.6
|
1.0
|
|
O
|
E:HOH6954
|
2.1
|
30.3
|
1.0
|
|
O3
|
E:OXL3533
|
2.1
|
38.5
|
1.0
|
|
O4
|
E:OXL3533
|
2.1
|
34.2
|
1.0
|
|
OE1
|
E:GLU3271
|
2.2
|
26.3
|
1.0
|
|
O2G
|
E:ATP3535
|
2.3
|
6.9
|
1.0
|
|
C2
|
E:OXL3533
|
2.8
|
19.2
|
1.0
|
|
C1
|
E:OXL3533
|
2.8
|
21.9
|
1.0
|
|
CG
|
E:ASP3295
|
3.0
|
49.3
|
1.0
|
|
CD
|
E:GLU3271
|
3.1
|
5.9
|
1.0
|
|
PG
|
E:ATP3535
|
3.3
|
22.2
|
1.0
|
|
OE2
|
E:GLU3271
|
3.4
|
57.2
|
1.0
|
|
O3G
|
E:ATP3535
|
3.5
|
27.8
|
1.0
|
|
CB
|
E:ASP3295
|
3.6
|
30.8
|
1.0
|
|
O1G
|
E:ATP3535
|
3.8
|
23.1
|
1.0
|
|
O
|
E:HOH6156
|
3.9
|
18.4
|
1.0
|
|
O2
|
E:OXL3533
|
4.0
|
19.8
|
1.0
|
|
O1
|
E:OXL3533
|
4.0
|
21.4
|
1.0
|
|
OD1
|
E:ASP3295
|
4.2
|
35.6
|
1.0
|
|
NZ
|
E:LYS3269
|
4.2
|
5.4
|
1.0
|
|
O
|
E:HOH6341
|
4.2
|
40.5
|
1.0
|
|
N
|
E:ASP3295
|
4.5
|
13.2
|
1.0
|
|
CG
|
E:GLU3271
|
4.5
|
29.7
|
1.0
|
|
O
|
E:HOH7689
|
4.5
|
31.1
|
1.0
|
|
CB
|
E:ALA3292
|
4.5
|
13.9
|
1.0
|
|
CE
|
E:LYS3269
|
4.5
|
25.3
|
1.0
|
|
CE2
|
E:PHE3243
|
4.6
|
18.0
|
1.0
|
|
CZ
|
E:PHE3243
|
4.7
|
25.3
|
1.0
|
|
CA
|
E:ASP3295
|
4.7
|
9.0
|
1.0
|
|
O3B
|
E:ATP3535
|
4.7
|
48.8
|
1.0
|
|
CB
|
E:GLU3271
|
4.8
|
8.0
|
1.0
|
|
Magnesium binding site 9 out
of 14 in 1a5u
Go back to
Magnesium Binding Sites List in 1a5u
Magnesium binding site 9 out
of 14 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg3536
b:26.2
occ:1.00
|
O
|
E:HOH6341
|
1.8
|
40.5
|
1.0
|
|
O
|
E:HOH7379
|
2.0
|
22.3
|
1.0
|
|
O1A
|
E:ATP3535
|
2.0
|
11.0
|
1.0
|
|
O1G
|
E:ATP3535
|
2.1
|
23.1
|
1.0
|
|
O2B
|
E:ATP3535
|
2.2
|
22.5
|
1.0
|
|
O
|
E:HOH6159
|
2.3
|
14.6
|
1.0
|
|
PG
|
E:ATP3535
|
3.1
|
22.2
|
1.0
|
|
PB
|
E:ATP3535
|
3.1
|
23.0
|
1.0
|
|
PA
|
E:ATP3535
|
3.1
|
26.9
|
1.0
|
|
O3B
|
E:ATP3535
|
3.3
|
48.8
|
1.0
|
|
O3A
|
E:ATP3535
|
3.4
|
19.1
|
1.0
|
|
O2G
|
E:ATP3535
|
3.5
|
6.9
|
1.0
|
|
O
|
E:HOH6310
|
3.9
|
21.8
|
1.0
|
|
C1
|
E:OXL3533
|
4.0
|
21.9
|
1.0
|
|
OG
|
E:SER3361
|
4.1
|
15.2
|
1.0
|
|
O2A
|
E:ATP3535
|
4.1
|
14.9
|
1.0
|
|
O1
|
E:OXL3533
|
4.1
|
21.4
|
1.0
|
|
OD2
|
E:ASP3177
|
4.1
|
21.4
|
1.0
|
|
O3G
|
E:ATP3535
|
4.3
|
27.8
|
1.0
|
|
CB
|
E:SER3361
|
4.3
|
36.3
|
1.0
|
|
O5'
|
E:ATP3535
|
4.3
|
23.8
|
1.0
|
|
O3
|
E:OXL3533
|
4.3
|
38.5
|
1.0
|
|
C2
|
E:OXL3533
|
4.4
|
19.2
|
1.0
|
|
C5'
|
E:ATP3535
|
4.4
|
5.3
|
1.0
|
|
O1B
|
E:ATP3535
|
4.4
|
22.1
|
1.0
|
|
OG1
|
E:THR3327
|
4.5
|
34.9
|
1.0
|
|
NH2
|
E:ARG3072
|
4.5
|
20.8
|
1.0
|
|
O
|
E:HOH7696
|
4.5
|
52.7
|
1.0
|
|
O
|
E:HOH6156
|
4.6
|
18.4
|
1.0
|
|
O
|
E:HOH6271
|
4.6
|
22.9
|
1.0
|
|
O2
|
E:OXL3533
|
4.7
|
19.8
|
1.0
|
|
CG2
|
E:THR3327
|
4.7
|
25.6
|
1.0
|
|
NH1
|
E:ARG3072
|
4.8
|
12.2
|
1.0
|
|
O4
|
E:OXL3533
|
4.8
|
34.2
|
1.0
|
|
Magnesium binding site 10 out
of 14 in 1a5u
Go back to
Magnesium Binding Sites List in 1a5u
Magnesium binding site 10 out
of 14 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg4134
b:18.1
occ:1.00
|
OD2
|
F:ASP3895
|
2.0
|
38.2
|
1.0
|
|
O
|
F:HOH6450
|
2.0
|
20.4
|
1.0
|
|
OE1
|
F:GLU3871
|
2.1
|
31.1
|
1.0
|
|
O2G
|
F:ATP4135
|
2.1
|
20.2
|
1.0
|
|
O3
|
F:OXL4133
|
2.1
|
42.2
|
1.0
|
|
O4
|
F:OXL4133
|
2.2
|
25.1
|
1.0
|
|
C2
|
F:OXL4133
|
2.9
|
36.7
|
1.0
|
|
C1
|
F:OXL4133
|
2.9
|
29.2
|
1.0
|
|
CG
|
F:ASP3895
|
3.1
|
19.2
|
1.0
|
|
CD
|
F:GLU3871
|
3.1
|
18.6
|
1.0
|
|
PG
|
F:ATP4135
|
3.3
|
52.6
|
1.0
|
|
OE2
|
F:GLU3871
|
3.5
|
25.7
|
1.0
|
|
O3G
|
F:ATP4135
|
3.6
|
28.8
|
1.0
|
|
O1G
|
F:ATP4135
|
3.8
|
54.9
|
1.0
|
|
CB
|
F:ASP3895
|
3.8
|
17.4
|
1.0
|
|
NZ
|
F:LYS3869
|
3.9
|
29.1
|
1.0
|
|
O
|
F:HOH7013
|
4.0
|
16.8
|
1.0
|
|
O2
|
F:OXL4133
|
4.1
|
31.4
|
1.0
|
|
O1
|
F:OXL4133
|
4.1
|
23.9
|
1.0
|
|
OD1
|
F:ASP3895
|
4.1
|
43.2
|
1.0
|
|
O
|
F:HOH6481
|
4.2
|
28.5
|
1.0
|
|
CE
|
F:LYS3869
|
4.2
|
23.1
|
1.0
|
|
CZ
|
F:PHE3843
|
4.4
|
31.2
|
1.0
|
|
CG
|
F:GLU3871
|
4.5
|
14.0
|
1.0
|
|
N
|
F:ASP3895
|
4.5
|
10.1
|
1.0
|
|
CE1
|
F:PHE3843
|
4.7
|
9.4
|
1.0
|
|
CB
|
F:ALA3892
|
4.7
|
26.1
|
1.0
|
|
O3B
|
F:ATP4135
|
4.7
|
38.8
|
1.0
|
|
CB
|
F:GLU3871
|
4.7
|
10.5
|
1.0
|
|
CA
|
F:ASP3895
|
4.8
|
29.1
|
1.0
|
|
OG
|
F:SER3842
|
4.8
|
22.0
|
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
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