Magnesium in PDB 3hqp: Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate
Enzymatic activity of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate
All present enzymatic activity of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate:
2.7.1.40;
Protein crystallography data
The structure of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate, PDB code: 3hqp
was solved by
H.P.Morgan,
M.D.Walkinshaw,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
34.46 /
2.30
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
127.486,
151.140,
160.319,
89.73,
80.17,
71.64
|
R / Rfree (%)
|
19.8 /
25.2
|
Other elements in 3hqp:
The structure of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate also contains other interesting chemical elements:
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
30;
Binding sites:
The binding sites of Magnesium atom in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate
(pdb code 3hqp). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 30 binding sites of Magnesium where determined in the
Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate, PDB code: 3hqp:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 30 in 3hqp
Go back to
Magnesium Binding Sites List in 3hqp
Magnesium binding site 1 out
of 30 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg500
b:77.7
occ:1.00
|
O1G
|
A:ATP1001
|
2.1
|
74.7
|
1.0
|
O1A
|
A:ATP1001
|
2.1
|
80.6
|
1.0
|
O
|
A:HOH1024
|
2.1
|
53.2
|
1.0
|
O1B
|
A:ATP1001
|
2.4
|
78.3
|
1.0
|
PG
|
A:ATP1001
|
3.3
|
74.7
|
1.0
|
PA
|
A:ATP1001
|
3.4
|
81.4
|
1.0
|
PB
|
A:ATP1001
|
3.5
|
78.3
|
1.0
|
C2
|
A:OXL510
|
3.7
|
65.9
|
1.0
|
C1
|
A:OXL510
|
3.7
|
65.3
|
1.0
|
O3B
|
A:ATP1001
|
3.7
|
76.5
|
1.0
|
O4
|
A:OXL510
|
3.8
|
66.3
|
1.0
|
O1
|
A:OXL510
|
3.8
|
65.6
|
1.0
|
O3A
|
A:ATP1001
|
3.8
|
79.8
|
1.0
|
O2G
|
A:ATP1001
|
3.8
|
70.1
|
1.0
|
OG1
|
A:THR296
|
3.8
|
39.1
|
1.0
|
OD2
|
A:ASP145
|
3.8
|
60.0
|
1.0
|
CG2
|
A:THR296
|
4.0
|
39.0
|
1.0
|
O5'
|
A:ATP1001
|
4.0
|
82.5
|
1.0
|
O
|
A:HOH540
|
4.0
|
60.5
|
1.0
|
OG
|
A:SER330
|
4.0
|
37.9
|
1.0
|
O3
|
A:OXL510
|
4.3
|
63.2
|
1.0
|
O2
|
A:OXL510
|
4.3
|
66.2
|
1.0
|
CB
|
A:SER330
|
4.4
|
37.4
|
1.0
|
CB
|
A:THR296
|
4.5
|
39.2
|
1.0
|
O3G
|
A:ATP1001
|
4.6
|
73.5
|
1.0
|
O2A
|
A:ATP1001
|
4.7
|
81.2
|
1.0
|
O
|
A:HOH1120
|
4.8
|
59.4
|
1.0
|
O2B
|
A:ATP1001
|
4.9
|
78.9
|
1.0
|
CG
|
A:ASP145
|
4.9
|
59.4
|
1.0
|
NH2
|
A:ARG49
|
4.9
|
54.5
|
1.0
|
|
Magnesium binding site 2 out
of 30 in 3hqp
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Magnesium Binding Sites List in 3hqp
Magnesium binding site 2 out
of 30 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:58.3
occ:1.00
|
O3
|
A:OXL510
|
2.1
|
63.2
|
1.0
|
OD2
|
A:ASP264
|
2.1
|
48.0
|
1.0
|
OE1
|
A:GLU240
|
2.1
|
50.4
|
1.0
|
O2G
|
A:ATP1001
|
2.1
|
70.1
|
1.0
|
O2
|
A:OXL510
|
2.6
|
66.2
|
1.0
|
C1
|
A:OXL510
|
3.0
|
65.3
|
1.0
|
CD
|
A:GLU240
|
3.1
|
46.8
|
1.0
|
CG
|
A:ASP264
|
3.2
|
43.2
|
1.0
|
C2
|
A:OXL510
|
3.2
|
65.9
|
1.0
|
OE2
|
A:GLU240
|
3.4
|
46.6
|
1.0
|
PG
|
A:ATP1001
|
3.4
|
74.7
|
1.0
|
NZ
|
A:LYS238
|
3.6
|
42.6
|
1.0
|
O3G
|
A:ATP1001
|
3.9
|
73.5
|
1.0
|
CB
|
A:ASP264
|
3.9
|
41.5
|
1.0
|
O
|
A:HOH2123
|
4.1
|
46.9
|
1.0
|
OD1
|
A:ASP264
|
4.1
|
44.5
|
1.0
|
O1G
|
A:ATP1001
|
4.2
|
74.7
|
1.0
|
O1
|
A:OXL510
|
4.2
|
65.6
|
1.0
|
CE2
|
A:PHE212
|
4.4
|
41.5
|
1.0
|
CG
|
A:GLU240
|
4.4
|
45.1
|
1.0
|
K
|
A:K504
|
4.4
|
0.5
|
1.0
|
O
|
A:HOH540
|
4.5
|
60.5
|
1.0
|
CE
|
A:LYS238
|
4.5
|
42.3
|
1.0
|
O4
|
A:OXL510
|
4.5
|
66.3
|
1.0
|
O3B
|
A:ATP1001
|
4.6
|
76.5
|
1.0
|
CZ
|
A:PHE212
|
4.7
|
41.4
|
1.0
|
CB
|
A:GLU240
|
4.7
|
43.9
|
1.0
|
CB
|
A:ALA261
|
4.7
|
36.9
|
1.0
|
N
|
A:ASP264
|
5.0
|
40.4
|
1.0
|
|
Magnesium binding site 3 out
of 30 in 3hqp
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Magnesium Binding Sites List in 3hqp
Magnesium binding site 3 out
of 30 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg500
b:35.1
occ:1.00
|
O
|
B:HOH1724
|
1.9
|
38.3
|
1.0
|
O
|
B:HOH1574
|
2.0
|
32.8
|
1.0
|
O
|
B:HOH511
|
2.0
|
26.1
|
1.0
|
O1B
|
B:ATP1001
|
2.1
|
35.3
|
1.0
|
O1G
|
B:ATP1001
|
2.1
|
33.4
|
1.0
|
O1A
|
B:ATP1001
|
2.2
|
33.9
|
1.0
|
PB
|
B:ATP1001
|
3.2
|
34.9
|
1.0
|
PG
|
B:ATP1001
|
3.3
|
35.0
|
1.0
|
PA
|
B:ATP1001
|
3.5
|
33.3
|
1.0
|
O3B
|
B:ATP1001
|
3.6
|
35.3
|
1.0
|
O3A
|
B:ATP1001
|
3.7
|
33.0
|
1.0
|
O2G
|
B:ATP1001
|
3.9
|
33.2
|
1.0
|
O
|
B:HOH1882
|
4.0
|
38.5
|
1.0
|
C2
|
B:OXL510
|
4.0
|
33.1
|
1.0
|
OD2
|
B:ASP145
|
4.1
|
31.1
|
1.0
|
O4
|
B:OXL510
|
4.1
|
32.2
|
1.0
|
OG
|
B:SER330
|
4.1
|
19.9
|
1.0
|
C1
|
B:OXL510
|
4.1
|
32.6
|
1.0
|
O
|
B:HOH552
|
4.1
|
49.0
|
1.0
|
OG1
|
B:THR296
|
4.2
|
21.2
|
1.0
|
O
|
B:HOH575
|
4.2
|
37.9
|
1.0
|
O3
|
B:OXL510
|
4.3
|
32.9
|
1.0
|
CB
|
B:SER330
|
4.3
|
19.4
|
1.0
|
CG2
|
B:THR296
|
4.4
|
21.3
|
1.0
|
O2
|
B:OXL510
|
4.4
|
33.0
|
1.0
|
O
|
B:HOH571
|
4.5
|
35.9
|
1.0
|
O5'
|
B:ATP1001
|
4.5
|
35.0
|
1.0
|
O
|
B:HOH902
|
4.5
|
38.2
|
1.0
|
O2A
|
B:ATP1001
|
4.6
|
31.4
|
1.0
|
C5'
|
B:ATP1001
|
4.6
|
36.1
|
1.0
|
O1
|
B:OXL510
|
4.6
|
30.9
|
1.0
|
O3G
|
B:ATP1001
|
4.6
|
34.1
|
1.0
|
O2B
|
B:ATP1001
|
4.6
|
34.5
|
1.0
|
NH1
|
B:ARG49
|
4.6
|
24.8
|
1.0
|
CB
|
B:THR296
|
4.9
|
20.7
|
1.0
|
|
Magnesium binding site 4 out
of 30 in 3hqp
Go back to
Magnesium Binding Sites List in 3hqp
Magnesium binding site 4 out
of 30 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg502
b:29.0
occ:1.00
|
O2
|
B:OXL510
|
2.0
|
33.0
|
1.0
|
OD2
|
B:ASP264
|
2.0
|
20.8
|
1.0
|
O1
|
B:OXL510
|
2.1
|
30.9
|
1.0
|
OE1
|
B:GLU240
|
2.2
|
23.6
|
1.0
|
O
|
B:HOH1726
|
2.2
|
26.2
|
1.0
|
O2G
|
B:ATP1001
|
2.2
|
33.2
|
1.0
|
C2
|
B:OXL510
|
2.8
|
33.1
|
1.0
|
C1
|
B:OXL510
|
2.8
|
32.6
|
1.0
|
CG
|
B:ASP264
|
3.2
|
20.3
|
1.0
|
CD
|
B:GLU240
|
3.2
|
21.6
|
1.0
|
PG
|
B:ATP1001
|
3.2
|
35.0
|
1.0
|
OE2
|
B:GLU240
|
3.5
|
21.9
|
1.0
|
O3G
|
B:ATP1001
|
3.6
|
34.1
|
1.0
|
CB
|
B:ASP264
|
3.7
|
19.9
|
1.0
|
O1G
|
B:ATP1001
|
3.8
|
33.4
|
1.0
|
NZ
|
B:LYS238
|
3.8
|
18.5
|
1.0
|
O
|
B:HOH584
|
4.0
|
46.5
|
1.0
|
O3
|
B:OXL510
|
4.0
|
32.9
|
1.0
|
O4
|
B:OXL510
|
4.1
|
32.2
|
1.0
|
O
|
B:HOH511
|
4.1
|
26.1
|
1.0
|
OD1
|
B:ASP264
|
4.2
|
21.5
|
1.0
|
CE
|
B:LYS238
|
4.2
|
19.9
|
1.0
|
N
|
B:ASP264
|
4.5
|
19.5
|
1.0
|
O
|
B:HOH505
|
4.5
|
30.5
|
1.0
|
CG
|
B:GLU240
|
4.6
|
20.6
|
1.0
|
O3B
|
B:ATP1001
|
4.6
|
35.3
|
1.0
|
O
|
B:HOH552
|
4.6
|
49.0
|
1.0
|
CE2
|
B:PHE212
|
4.7
|
20.8
|
1.0
|
CZ
|
B:PHE212
|
4.7
|
20.5
|
1.0
|
CA
|
B:ASP264
|
4.7
|
20.0
|
1.0
|
CB
|
B:ALA261
|
4.8
|
19.2
|
1.0
|
CB
|
B:GLU240
|
4.8
|
20.4
|
1.0
|
O
|
B:HOH1882
|
4.9
|
38.5
|
1.0
|
|
Magnesium binding site 5 out
of 30 in 3hqp
Go back to
Magnesium Binding Sites List in 3hqp
Magnesium binding site 5 out
of 30 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg500
b:45.3
occ:1.00
|
O1G
|
C:ATP1001
|
2.0
|
44.7
|
1.0
|
O
|
C:HOH1651
|
2.1
|
47.9
|
1.0
|
O1B
|
C:ATP1001
|
2.1
|
46.4
|
1.0
|
O1A
|
C:ATP1001
|
2.1
|
47.8
|
1.0
|
O
|
C:HOH580
|
2.3
|
35.4
|
1.0
|
PG
|
C:ATP1001
|
2.9
|
46.7
|
1.0
|
O2G
|
C:ATP1001
|
3.0
|
46.4
|
1.0
|
PB
|
C:ATP1001
|
3.1
|
47.6
|
1.0
|
PA
|
C:ATP1001
|
3.3
|
48.2
|
1.0
|
O3B
|
C:ATP1001
|
3.4
|
46.7
|
1.0
|
O3A
|
C:ATP1001
|
3.6
|
47.6
|
1.0
|
C1
|
C:OXL510
|
4.2
|
40.2
|
1.0
|
C2
|
C:OXL510
|
4.2
|
41.3
|
1.0
|
O2
|
C:OXL510
|
4.2
|
41.6
|
1.0
|
O3
|
C:OXL510
|
4.2
|
39.4
|
1.0
|
OG
|
C:SER330
|
4.2
|
36.1
|
1.0
|
OD2
|
C:ASP145
|
4.2
|
36.9
|
1.0
|
O2A
|
C:ATP1001
|
4.2
|
46.8
|
1.0
|
O3G
|
C:ATP1001
|
4.3
|
44.0
|
1.0
|
O
|
C:HOH1181
|
4.4
|
55.9
|
1.0
|
CG2
|
C:THR296
|
4.4
|
37.6
|
1.0
|
OG1
|
C:THR296
|
4.5
|
37.5
|
1.0
|
O2B
|
C:ATP1001
|
4.5
|
48.9
|
1.0
|
O5'
|
C:ATP1001
|
4.5
|
48.5
|
1.0
|
CB
|
C:SER330
|
4.6
|
36.9
|
1.0
|
O
|
C:HOH2012
|
4.6
|
51.0
|
1.0
|
O1
|
C:OXL510
|
4.7
|
39.6
|
1.0
|
O
|
C:HOH1133
|
4.7
|
49.2
|
1.0
|
NH1
|
C:ARG49
|
4.7
|
44.3
|
1.0
|
O4
|
C:OXL510
|
4.7
|
41.9
|
1.0
|
C5'
|
C:ATP1001
|
4.7
|
50.8
|
1.0
|
NH2
|
C:ARG49
|
4.8
|
45.5
|
1.0
|
O
|
C:HOH511
|
5.0
|
28.4
|
1.0
|
|
Magnesium binding site 6 out
of 30 in 3hqp
Go back to
Magnesium Binding Sites List in 3hqp
Magnesium binding site 6 out
of 30 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg502
b:38.9
occ:1.00
|
OD2
|
C:ASP264
|
2.1
|
37.6
|
1.0
|
OE1
|
C:GLU240
|
2.1
|
34.8
|
1.0
|
O4
|
C:OXL510
|
2.1
|
41.9
|
1.0
|
O
|
C:HOH1778
|
2.1
|
44.8
|
1.0
|
O1
|
C:OXL510
|
2.3
|
39.6
|
1.0
|
O2G
|
C:ATP1001
|
2.7
|
46.4
|
1.0
|
C2
|
C:OXL510
|
3.0
|
41.3
|
1.0
|
CD
|
C:GLU240
|
3.1
|
34.4
|
1.0
|
C1
|
C:OXL510
|
3.1
|
40.2
|
1.0
|
CG
|
C:ASP264
|
3.2
|
36.6
|
1.0
|
OE2
|
C:GLU240
|
3.4
|
32.9
|
1.0
|
O3G
|
C:ATP1001
|
3.5
|
44.0
|
1.0
|
PG
|
C:ATP1001
|
3.6
|
46.7
|
1.0
|
CB
|
C:ASP264
|
3.7
|
35.5
|
1.0
|
O
|
C:HOH511
|
3.9
|
28.4
|
1.0
|
NZ
|
C:LYS238
|
4.0
|
33.9
|
1.0
|
O2
|
C:OXL510
|
4.2
|
41.6
|
1.0
|
OD1
|
C:ASP264
|
4.2
|
37.6
|
1.0
|
CE2
|
C:PHE212
|
4.3
|
30.1
|
1.0
|
CZ
|
C:PHE212
|
4.3
|
30.0
|
1.0
|
CE
|
C:LYS238
|
4.3
|
33.2
|
1.0
|
O3
|
C:OXL510
|
4.3
|
39.4
|
1.0
|
CG
|
C:GLU240
|
4.4
|
36.5
|
1.0
|
O
|
C:HOH1131
|
4.5
|
45.1
|
1.0
|
N
|
C:ASP264
|
4.6
|
34.9
|
1.0
|
O
|
C:HOH1651
|
4.6
|
47.9
|
1.0
|
O1G
|
C:ATP1001
|
4.6
|
44.7
|
1.0
|
CB
|
C:GLU240
|
4.7
|
37.0
|
1.0
|
CA
|
C:ASP264
|
4.8
|
35.3
|
1.0
|
O3B
|
C:ATP1001
|
4.8
|
46.7
|
1.0
|
CB
|
C:ALA261
|
4.8
|
33.7
|
1.0
|
O
|
C:HOH1277
|
4.8
|
53.4
|
1.0
|
OG
|
C:SER211
|
5.0
|
32.7
|
1.0
|
|
Magnesium binding site 7 out
of 30 in 3hqp
Go back to
Magnesium Binding Sites List in 3hqp
Magnesium binding site 7 out
of 30 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg500
b:37.2
occ:1.00
|
O
|
D:HOH1872
|
2.0
|
37.7
|
1.0
|
O1A
|
D:ATP1001
|
2.1
|
39.7
|
1.0
|
O1B
|
D:ATP1001
|
2.2
|
38.1
|
1.0
|
O
|
D:HOH1943
|
2.3
|
33.5
|
1.0
|
O
|
D:HOH609
|
2.4
|
46.0
|
1.0
|
O1G
|
D:ATP1001
|
2.5
|
37.0
|
1.0
|
PA
|
D:ATP1001
|
3.3
|
40.2
|
1.0
|
PB
|
D:ATP1001
|
3.4
|
38.3
|
1.0
|
O5'
|
D:ATP1001
|
3.6
|
41.8
|
1.0
|
PG
|
D:ATP1001
|
3.7
|
38.4
|
1.0
|
O3A
|
D:ATP1001
|
3.8
|
39.9
|
1.0
|
O3B
|
D:ATP1001
|
3.9
|
38.7
|
1.0
|
OG
|
D:SER330
|
4.0
|
22.5
|
1.0
|
OD2
|
D:ASP145
|
4.0
|
39.6
|
1.0
|
O
|
D:HOH625
|
4.0
|
40.6
|
1.0
|
CG2
|
D:THR296
|
4.1
|
21.4
|
1.0
|
OG1
|
D:THR296
|
4.1
|
22.8
|
1.0
|
CB
|
D:SER330
|
4.1
|
22.7
|
1.0
|
O
|
D:HOH624
|
4.2
|
29.1
|
1.0
|
O2G
|
D:ATP1001
|
4.4
|
35.5
|
1.0
|
C2
|
D:OXL510
|
4.5
|
38.6
|
1.0
|
O4
|
D:OXL510
|
4.5
|
40.0
|
1.0
|
C1
|
D:OXL510
|
4.5
|
39.2
|
1.0
|
O1
|
D:OXL510
|
4.6
|
39.6
|
1.0
|
O2A
|
D:ATP1001
|
4.7
|
39.7
|
1.0
|
O
|
D:HOH1942
|
4.7
|
45.6
|
1.0
|
CB
|
D:THR296
|
4.7
|
22.5
|
1.0
|
O2B
|
D:ATP1001
|
4.7
|
39.8
|
1.0
|
O
|
D:HOH1486
|
4.8
|
43.5
|
1.0
|
O3G
|
D:ATP1001
|
4.9
|
37.9
|
1.0
|
O2
|
D:OXL510
|
4.9
|
37.9
|
1.0
|
C5'
|
D:ATP1001
|
5.0
|
42.8
|
1.0
|
O3
|
D:OXL510
|
5.0
|
38.1
|
1.0
|
|
Magnesium binding site 8 out
of 30 in 3hqp
Go back to
Magnesium Binding Sites List in 3hqp
Magnesium binding site 8 out
of 30 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg502
b:34.5
occ:1.00
|
O
|
D:HOH736
|
2.0
|
50.6
|
1.0
|
OD2
|
D:ASP264
|
2.1
|
27.9
|
1.0
|
O2G
|
D:ATP1001
|
2.1
|
35.5
|
1.0
|
O2
|
D:OXL510
|
2.1
|
37.9
|
1.0
|
O3
|
D:OXL510
|
2.1
|
38.1
|
1.0
|
OE1
|
D:GLU240
|
2.1
|
28.1
|
1.0
|
C2
|
D:OXL510
|
2.8
|
38.6
|
1.0
|
C1
|
D:OXL510
|
2.9
|
39.2
|
1.0
|
CD
|
D:GLU240
|
3.1
|
26.2
|
1.0
|
CG
|
D:ASP264
|
3.2
|
24.2
|
1.0
|
OE2
|
D:GLU240
|
3.4
|
26.2
|
1.0
|
PG
|
D:ATP1001
|
3.4
|
38.4
|
1.0
|
CB
|
D:ASP264
|
3.8
|
22.7
|
1.0
|
O
|
D:HOH527
|
3.8
|
27.4
|
1.0
|
NZ
|
D:LYS238
|
3.9
|
15.7
|
1.0
|
O4
|
D:OXL510
|
4.1
|
40.0
|
1.0
|
O1G
|
D:ATP1001
|
4.1
|
37.0
|
1.0
|
O1
|
D:OXL510
|
4.1
|
39.6
|
1.0
|
O3G
|
D:ATP1001
|
4.2
|
37.9
|
1.0
|
OD1
|
D:ASP264
|
4.2
|
25.8
|
1.0
|
O
|
D:HOH1872
|
4.2
|
37.7
|
1.0
|
CE
|
D:LYS238
|
4.4
|
17.0
|
1.0
|
N
|
D:ASP264
|
4.5
|
22.0
|
1.0
|
CG
|
D:GLU240
|
4.5
|
24.9
|
1.0
|
O
|
D:HOH501
|
4.5
|
35.2
|
1.0
|
O3B
|
D:ATP1001
|
4.6
|
38.7
|
1.0
|
CE2
|
D:PHE212
|
4.7
|
19.8
|
1.0
|
CZ
|
D:PHE212
|
4.7
|
21.0
|
1.0
|
CB
|
D:ALA261
|
4.7
|
21.0
|
1.0
|
CA
|
D:ASP264
|
4.8
|
22.3
|
1.0
|
CB
|
D:GLU240
|
4.8
|
24.5
|
1.0
|
O
|
D:HOH1613
|
4.8
|
48.1
|
1.0
|
O
|
D:HOH625
|
4.9
|
40.6
|
1.0
|
|
Magnesium binding site 9 out
of 30 in 3hqp
Go back to
Magnesium Binding Sites List in 3hqp
Magnesium binding site 9 out
of 30 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg500
b:55.5
occ:1.00
|
O
|
E:HOH2013
|
2.1
|
39.5
|
1.0
|
O1B
|
E:ATP1001
|
2.1
|
54.8
|
1.0
|
O1A
|
E:ATP1001
|
2.1
|
55.2
|
1.0
|
O1G
|
E:ATP1001
|
2.1
|
54.2
|
1.0
|
O
|
E:HOH1659
|
2.2
|
51.6
|
1.0
|
PB
|
E:ATP1001
|
3.3
|
55.4
|
1.0
|
PG
|
E:ATP1001
|
3.3
|
53.3
|
1.0
|
PA
|
E:ATP1001
|
3.4
|
56.3
|
1.0
|
O3B
|
E:ATP1001
|
3.8
|
54.7
|
1.0
|
O3A
|
E:ATP1001
|
3.8
|
55.9
|
1.0
|
O2G
|
E:ATP1001
|
3.8
|
52.3
|
1.0
|
OG
|
E:SER330
|
3.9
|
39.9
|
1.0
|
C1
|
E:OXL510
|
4.0
|
49.7
|
1.0
|
OG1
|
E:THR296
|
4.0
|
42.3
|
1.0
|
O1
|
E:OXL510
|
4.1
|
49.6
|
1.0
|
OD2
|
E:ASP145
|
4.2
|
52.7
|
1.0
|
C2
|
E:OXL510
|
4.2
|
49.4
|
1.0
|
CB
|
E:SER330
|
4.2
|
39.7
|
1.0
|
CG2
|
E:THR296
|
4.2
|
42.2
|
1.0
|
O3
|
E:OXL510
|
4.3
|
49.3
|
1.0
|
NH1
|
E:ARG49
|
4.4
|
46.7
|
1.0
|
O2A
|
E:ATP1001
|
4.4
|
55.9
|
1.0
|
O
|
E:HOH685
|
4.4
|
61.1
|
1.0
|
O2
|
E:OXL510
|
4.5
|
50.0
|
1.0
|
NH2
|
E:ARG49
|
4.5
|
46.1
|
1.0
|
O5'
|
E:ATP1001
|
4.5
|
57.1
|
1.0
|
O4
|
E:OXL510
|
4.6
|
48.6
|
1.0
|
O3G
|
E:ATP1001
|
4.6
|
54.4
|
1.0
|
C5'
|
E:ATP1001
|
4.6
|
58.4
|
1.0
|
O2B
|
E:ATP1001
|
4.7
|
54.5
|
1.0
|
CB
|
E:THR296
|
4.7
|
42.4
|
1.0
|
CZ
|
E:ARG49
|
5.0
|
46.7
|
1.0
|
|
Magnesium binding site 10 out
of 30 in 3hqp
Go back to
Magnesium Binding Sites List in 3hqp
Magnesium binding site 10 out
of 30 in the Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Crystal Structure of Leishmania Mexicana Pyruvate Kinase (Lmpyk) in Complex with Atp, Oxalate and Fructose 2,6 Bisphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg502
b:48.2
occ:1.00
|
O2G
|
E:ATP1001
|
2.1
|
52.3
|
1.0
|
OD2
|
E:ASP264
|
2.1
|
43.5
|
1.0
|
O3
|
E:OXL510
|
2.1
|
49.3
|
1.0
|
O4
|
E:OXL510
|
2.1
|
48.6
|
1.0
|
O
|
E:HOH556
|
2.2
|
52.6
|
1.0
|
OE1
|
E:GLU240
|
2.4
|
38.6
|
1.0
|
C2
|
E:OXL510
|
2.8
|
49.4
|
1.0
|
C1
|
E:OXL510
|
2.8
|
49.7
|
1.0
|
PG
|
E:ATP1001
|
3.2
|
53.3
|
1.0
|
CG
|
E:ASP264
|
3.3
|
41.0
|
1.0
|
CD
|
E:GLU240
|
3.5
|
39.7
|
1.0
|
O
|
E:HOH1822
|
3.6
|
48.3
|
1.0
|
O3G
|
E:ATP1001
|
3.6
|
54.4
|
1.0
|
OE2
|
E:GLU240
|
3.8
|
40.3
|
1.0
|
O1G
|
E:ATP1001
|
3.9
|
54.2
|
1.0
|
NZ
|
E:LYS238
|
3.9
|
38.4
|
1.0
|
CB
|
E:ASP264
|
3.9
|
39.7
|
1.0
|
O2
|
E:OXL510
|
4.0
|
50.0
|
1.0
|
O1
|
E:OXL510
|
4.1
|
49.6
|
1.0
|
CE
|
E:LYS238
|
4.3
|
38.2
|
1.0
|
OD1
|
E:ASP264
|
4.3
|
41.6
|
1.0
|
O3B
|
E:ATP1001
|
4.4
|
54.7
|
1.0
|
O
|
E:HOH737
|
4.5
|
52.5
|
1.0
|
N
|
E:ASP264
|
4.6
|
39.0
|
1.0
|
CE2
|
E:PHE212
|
4.7
|
38.7
|
1.0
|
CB
|
E:ALA261
|
4.8
|
37.7
|
1.0
|
CG
|
E:GLU240
|
4.8
|
40.3
|
1.0
|
CZ
|
E:PHE212
|
4.8
|
38.7
|
1.0
|
CA
|
E:ASP264
|
4.9
|
39.5
|
1.0
|
|
Reference:
H.P.Morgan,
I.W.Mcnae,
M.W.Nowicki,
V.Hannaert,
P.A.M.Michels,
L.A.Fothergill-Gilmore,
M.D.Walkinshaw.
The Allosteric Mechanism of Pryuvate Kinase From Leishmania Mexicana: A Rock and Lock Model J.Biol.Chem. V. 285 12892 2010.
ISSN: ISSN 0021-9258
PubMed: 20123988
DOI: 10.1074/JBC.M109.079905
Page generated: Wed Aug 14 15:18:07 2024
|