Phosphorus in PDB 1a5z: Lactate Dehydrogenase From Thermotoga Maritima (Tmldh)
Enzymatic activity of Lactate Dehydrogenase From Thermotoga Maritima (Tmldh)
All present enzymatic activity of Lactate Dehydrogenase From Thermotoga Maritima (Tmldh):
1.1.1.27;
Protein crystallography data
The structure of Lactate Dehydrogenase From Thermotoga Maritima (Tmldh), PDB code: 1a5z
was solved by
G.Auerbach,
R.Ostendorp,
L.Prade,
I.Korndoerfer,
T.Dams,
R.Huber,
R.Jaenicke,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
8.00 /
2.10
|
Space group
|
I 41 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
105.480,
105.480,
187.700,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20 /
28.6
|
Phosphorus Binding Sites:
The binding sites of Phosphorus atom in the Lactate Dehydrogenase From Thermotoga Maritima (Tmldh)
(pdb code 1a5z). This binding sites where shown within
5.0 Angstroms radius around Phosphorus atom.
In total 6 binding sites of Phosphorus where determined in the
Lactate Dehydrogenase From Thermotoga Maritima (Tmldh), PDB code: 1a5z:
Jump to Phosphorus binding site number:
1;
2;
3;
4;
5;
6;
Phosphorus binding site 1 out
of 6 in 1a5z
Go back to
Phosphorus Binding Sites List in 1a5z
Phosphorus binding site 1 out
of 6 in the Lactate Dehydrogenase From Thermotoga Maritima (Tmldh)
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 1 of Lactate Dehydrogenase From Thermotoga Maritima (Tmldh) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P353
b:37.0
occ:0.50
|
P1
|
A:FBP353
|
0.0
|
37.0
|
0.5
|
O2P
|
A:FBP353
|
1.5
|
37.4
|
0.5
|
O3P
|
A:FBP353
|
1.5
|
47.2
|
0.5
|
O1
|
A:FBP353
|
1.5
|
37.1
|
0.5
|
O1P
|
A:FBP353
|
1.6
|
44.5
|
0.5
|
C1
|
A:FBP353
|
2.5
|
41.4
|
0.5
|
O
|
A:HOH542
|
3.6
|
54.7
|
1.0
|
C2
|
A:FBP353
|
3.7
|
38.9
|
0.5
|
O4
|
A:FBP353
|
3.7
|
44.9
|
0.5
|
OG
|
A:SER186
|
3.8
|
45.0
|
1.0
|
O
|
A:HOH441
|
3.9
|
38.2
|
1.0
|
O2
|
A:FBP353
|
4.0
|
46.8
|
0.5
|
O5
|
A:FBP353
|
4.3
|
41.0
|
0.5
|
CA
|
A:SER186
|
4.4
|
47.5
|
1.0
|
CB
|
A:SER186
|
4.5
|
43.4
|
1.0
|
O
|
A:ARG185
|
4.7
|
44.4
|
1.0
|
C4
|
A:FBP353
|
4.8
|
42.0
|
0.5
|
C3
|
A:FBP353
|
4.9
|
45.2
|
0.5
|
|
Phosphorus binding site 2 out
of 6 in 1a5z
Go back to
Phosphorus Binding Sites List in 1a5z
Phosphorus binding site 2 out
of 6 in the Lactate Dehydrogenase From Thermotoga Maritima (Tmldh)
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 2 of Lactate Dehydrogenase From Thermotoga Maritima (Tmldh) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P353
b:29.3
occ:0.50
|
P2
|
A:FBP353
|
0.0
|
29.3
|
0.5
|
O5P
|
A:FBP353
|
1.5
|
41.1
|
0.5
|
O6P
|
A:FBP353
|
1.5
|
43.3
|
0.5
|
O4P
|
A:FBP353
|
1.5
|
42.1
|
0.5
|
O6
|
A:FBP353
|
1.5
|
33.2
|
0.5
|
C6
|
A:FBP353
|
2.7
|
42.7
|
0.5
|
ND1
|
A:HIS188
|
3.2
|
43.3
|
1.0
|
C5
|
A:FBP353
|
3.3
|
41.7
|
0.5
|
O5
|
A:FBP353
|
3.7
|
41.0
|
0.5
|
NH1
|
A:ARG173
|
3.8
|
43.2
|
1.0
|
CG
|
A:HIS188
|
4.0
|
45.8
|
1.0
|
CB
|
A:HIS188
|
4.0
|
39.8
|
1.0
|
CE1
|
A:HIS188
|
4.2
|
41.1
|
1.0
|
CA
|
A:HIS188
|
4.6
|
36.5
|
1.0
|
O3
|
A:FBP353
|
4.6
|
44.1
|
0.5
|
CZ
|
A:ARG173
|
4.7
|
41.2
|
1.0
|
C4
|
A:FBP353
|
4.7
|
42.0
|
0.5
|
O
|
A:VAL187
|
4.8
|
48.4
|
1.0
|
NH2
|
A:ARG173
|
4.8
|
38.8
|
1.0
|
|
Phosphorus binding site 3 out
of 6 in 1a5z
Go back to
Phosphorus Binding Sites List in 1a5z
Phosphorus binding site 3 out
of 6 in the Lactate Dehydrogenase From Thermotoga Maritima (Tmldh)
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 3 of Lactate Dehydrogenase From Thermotoga Maritima (Tmldh) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P354
b:25.0
occ:1.00
|
P1
|
A:FBP354
|
0.0
|
25.0
|
1.0
|
O2P
|
A:FBP354
|
1.5
|
44.4
|
1.0
|
O3P
|
A:FBP354
|
1.5
|
36.7
|
1.0
|
O1
|
A:FBP354
|
1.5
|
50.4
|
1.0
|
O1P
|
A:FBP354
|
1.5
|
50.3
|
1.0
|
C1
|
A:FBP354
|
2.5
|
70.0
|
1.0
|
OE2
|
A:GLU60
|
2.9
|
68.4
|
1.0
|
O
|
A:HOH391
|
3.4
|
38.0
|
1.0
|
CD
|
A:GLU60
|
3.6
|
65.8
|
1.0
|
CG
|
A:GLU60
|
3.6
|
63.2
|
1.0
|
O
|
A:HOH551
|
3.7
|
68.0
|
1.0
|
C2
|
A:FBP354
|
3.8
|
75.9
|
1.0
|
O2
|
A:FBP354
|
4.0
|
90.1
|
1.0
|
O5
|
A:FBP354
|
4.3
|
69.1
|
1.0
|
O
|
A:ALA80
|
4.3
|
55.2
|
1.0
|
OE1
|
A:GLU60
|
4.6
|
67.7
|
1.0
|
CB
|
A:GLU60
|
4.7
|
51.0
|
1.0
|
|
Phosphorus binding site 4 out
of 6 in 1a5z
Go back to
Phosphorus Binding Sites List in 1a5z
Phosphorus binding site 4 out
of 6 in the Lactate Dehydrogenase From Thermotoga Maritima (Tmldh)
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 4 of Lactate Dehydrogenase From Thermotoga Maritima (Tmldh) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P354
b:46.3
occ:1.00
|
P2
|
A:FBP354
|
0.0
|
46.3
|
1.0
|
O6P
|
A:FBP354
|
1.5
|
66.7
|
1.0
|
O4P
|
A:FBP354
|
1.5
|
62.1
|
1.0
|
O5P
|
A:FBP354
|
1.5
|
59.2
|
1.0
|
O6
|
A:FBP354
|
1.5
|
56.6
|
1.0
|
C6
|
A:FBP354
|
2.7
|
70.3
|
1.0
|
OD1
|
A:ASP87
|
3.1
|
66.8
|
1.0
|
OD2
|
A:ASP87
|
3.1
|
63.8
|
1.0
|
CG
|
A:ASP87
|
3.5
|
64.4
|
1.0
|
C5
|
A:FBP354
|
3.5
|
70.9
|
1.0
|
O
|
A:HOH547
|
3.8
|
67.8
|
1.0
|
O5
|
A:FBP354
|
4.2
|
69.1
|
1.0
|
OD2
|
A:ASP84
|
4.3
|
66.4
|
1.0
|
OD1
|
A:ASP84
|
4.4
|
59.5
|
1.0
|
CG
|
A:ASP84
|
4.6
|
58.8
|
1.0
|
N
|
A:ASP84
|
4.8
|
46.4
|
1.0
|
CA
|
A:GLY83
|
4.8
|
46.1
|
1.0
|
C4
|
A:FBP354
|
5.0
|
73.6
|
1.0
|
CB
|
A:ASP87
|
5.0
|
57.7
|
1.0
|
|
Phosphorus binding site 5 out
of 6 in 1a5z
Go back to
Phosphorus Binding Sites List in 1a5z
Phosphorus binding site 5 out
of 6 in the Lactate Dehydrogenase From Thermotoga Maritima (Tmldh)
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 5 of Lactate Dehydrogenase From Thermotoga Maritima (Tmldh) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P352
b:79.1
occ:1.00
|
PA
|
A:NAD352
|
0.0
|
79.1
|
1.0
|
O1A
|
A:NAD352
|
1.5
|
90.0
|
1.0
|
O2A
|
A:NAD352
|
1.5
|
87.4
|
1.0
|
O3
|
A:NAD352
|
1.6
|
85.2
|
1.0
|
O5B
|
A:NAD352
|
1.6
|
80.3
|
1.0
|
C5B
|
A:NAD352
|
2.8
|
63.8
|
1.0
|
PN
|
A:NAD352
|
3.0
|
80.6
|
1.0
|
O1N
|
A:NAD352
|
3.4
|
83.2
|
1.0
|
C4B
|
A:NAD352
|
3.5
|
51.6
|
1.0
|
O
|
A:HOH637
|
3.5
|
65.5
|
1.0
|
O2N
|
A:NAD352
|
3.7
|
83.4
|
1.0
|
CA
|
A:GLY30
|
3.9
|
35.0
|
1.0
|
O
|
A:HOH472
|
4.0
|
46.2
|
1.0
|
O5D
|
A:NAD352
|
4.1
|
86.4
|
1.0
|
C3B
|
A:NAD352
|
4.2
|
49.5
|
1.0
|
N
|
A:ARG31
|
4.3
|
32.6
|
1.0
|
O3D
|
A:NAD352
|
4.4
|
60.0
|
1.0
|
O
|
A:HOH467
|
4.5
|
56.0
|
1.0
|
C
|
A:GLY30
|
4.6
|
36.9
|
1.0
|
O
|
A:HOH626
|
4.7
|
67.4
|
1.0
|
O
|
A:HOH369
|
4.7
|
35.8
|
1.0
|
C3D
|
A:NAD352
|
4.7
|
73.9
|
1.0
|
O
|
A:HOH618
|
4.7
|
48.6
|
1.0
|
CG
|
A:ARG31
|
4.7
|
37.8
|
1.0
|
O4B
|
A:NAD352
|
4.8
|
47.3
|
1.0
|
C5D
|
A:NAD352
|
4.8
|
79.2
|
1.0
|
N
|
A:GLY30
|
4.9
|
41.9
|
1.0
|
O
|
A:GLY99
|
5.0
|
47.9
|
1.0
|
O3B
|
A:NAD352
|
5.0
|
42.5
|
1.0
|
|
Phosphorus binding site 6 out
of 6 in 1a5z
Go back to
Phosphorus Binding Sites List in 1a5z
Phosphorus binding site 6 out
of 6 in the Lactate Dehydrogenase From Thermotoga Maritima (Tmldh)
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 6 of Lactate Dehydrogenase From Thermotoga Maritima (Tmldh) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P352
b:80.6
occ:1.00
|
PN
|
A:NAD352
|
0.0
|
80.6
|
1.0
|
O1N
|
A:NAD352
|
1.5
|
83.2
|
1.0
|
O2N
|
A:NAD352
|
1.5
|
83.4
|
1.0
|
O3
|
A:NAD352
|
1.6
|
85.2
|
1.0
|
O5D
|
A:NAD352
|
1.6
|
86.4
|
1.0
|
C5D
|
A:NAD352
|
2.7
|
79.2
|
1.0
|
PA
|
A:NAD352
|
3.0
|
79.1
|
1.0
|
O1A
|
A:NAD352
|
3.4
|
90.0
|
1.0
|
O2A
|
A:NAD352
|
3.6
|
87.4
|
1.0
|
CG2
|
A:VAL32
|
3.8
|
37.4
|
1.0
|
C4D
|
A:NAD352
|
3.8
|
75.8
|
1.0
|
C3D
|
A:NAD352
|
3.9
|
73.9
|
1.0
|
O
|
A:HOH369
|
4.0
|
35.8
|
1.0
|
N
|
A:VAL32
|
4.1
|
32.3
|
1.0
|
N
|
A:ARG31
|
4.1
|
32.6
|
1.0
|
O5B
|
A:NAD352
|
4.1
|
80.3
|
1.0
|
O7N
|
A:NAD352
|
4.3
|
67.9
|
1.0
|
CB
|
A:VAL32
|
4.3
|
35.2
|
1.0
|
O3D
|
A:NAD352
|
4.4
|
60.0
|
1.0
|
C2N
|
A:NAD352
|
4.4
|
74.6
|
1.0
|
CB
|
A:ARG31
|
4.5
|
34.3
|
1.0
|
CG
|
A:ARG31
|
4.6
|
37.8
|
1.0
|
O
|
A:HOH436
|
4.6
|
68.9
|
1.0
|
C5B
|
A:NAD352
|
4.7
|
63.8
|
1.0
|
CA
|
A:ARG31
|
4.7
|
30.9
|
1.0
|
O
|
A:HOH618
|
4.7
|
48.6
|
1.0
|
C
|
A:GLY30
|
4.7
|
36.9
|
1.0
|
O4D
|
A:NAD352
|
4.8
|
74.2
|
1.0
|
CA
|
A:GLY30
|
4.8
|
35.0
|
1.0
|
CA
|
A:VAL32
|
4.8
|
29.7
|
1.0
|
C
|
A:ARG31
|
4.9
|
32.3
|
1.0
|
O
|
A:ALA97
|
4.9
|
40.7
|
1.0
|
O
|
A:HOH626
|
4.9
|
67.4
|
1.0
|
C7N
|
A:NAD352
|
4.9
|
71.1
|
1.0
|
|
Reference:
G.Auerbach,
R.Ostendorp,
L.Prade,
I.Korndorfer,
T.Dams,
R.Huber,
R.Jaenicke.
Lactate Dehydrogenase From the Hyperthermophilic Bacterium Thermotoga Maritima: the Crystal Structure at 2.1 A Resolution Reveals Strategies For Intrinsic Protein Stabilization. Structure V. 6 769 1998.
ISSN: ISSN 0969-2126
PubMed: 9655830
DOI: 10.1016/S0969-2126(98)00078-1
Page generated: Fri Sep 25 12:16:55 2020
|