Mercury in PDB 1yp2: Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase
Enzymatic activity of Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase
All present enzymatic activity of Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase:
2.7.7.27;
Protein crystallography data
The structure of Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase, PDB code: 1yp2
was solved by
X.Jin,
M.A.Ballicora,
J.Preiss,
J.H.Geiger,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.94 /
2.11
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
79.465,
137.551,
91.623,
90.00,
112.53,
90.00
|
R / Rfree (%)
|
17.2 /
22.9
|
Mercury Binding Sites:
The binding sites of Mercury atom in the Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase
(pdb code 1yp2). This binding sites where shown within
5.0 Angstroms radius around Mercury atom.
In total 4 binding sites of Mercury where determined in the
Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase, PDB code: 1yp2:
Jump to Mercury binding site number:
1;
2;
3;
4;
Mercury binding site 1 out
of 4 in 1yp2
Go back to
Mercury Binding Sites List in 1yp2
Mercury binding site 1 out
of 4 in the Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 1 of Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg3226
b:35.4
occ:1.00
|
HG
|
A:PMB3226
|
0.0
|
35.4
|
1.0
|
O
|
A:HOH3462
|
1.7
|
6.5
|
1.0
|
C4
|
A:PMB3226
|
1.8
|
39.3
|
1.0
|
SG
|
A:CYS354
|
2.1
|
19.3
|
1.0
|
O
|
A:VAL338
|
2.2
|
19.8
|
1.0
|
C3
|
A:PMB3226
|
2.7
|
37.5
|
1.0
|
C
|
A:VAL338
|
2.9
|
22.2
|
1.0
|
C5
|
A:PMB3226
|
3.0
|
36.8
|
1.0
|
O
|
A:ILE355
|
3.4
|
23.3
|
1.0
|
CG2
|
A:VAL338
|
3.4
|
24.1
|
1.0
|
N
|
A:ILE355
|
3.6
|
23.1
|
1.0
|
CB
|
A:VAL338
|
3.6
|
21.0
|
1.0
|
N
|
A:ILE339
|
3.6
|
18.5
|
1.0
|
CB
|
A:CYS354
|
3.6
|
12.3
|
1.0
|
O
|
A:HOH3412
|
3.7
|
26.7
|
1.0
|
O
|
A:HOH3415
|
3.8
|
46.9
|
1.0
|
CA
|
A:CYS354
|
3.8
|
23.6
|
1.0
|
CG
|
A:LYS340
|
3.8
|
35.4
|
1.0
|
CA
|
A:VAL338
|
3.8
|
23.1
|
1.0
|
CA
|
A:ILE339
|
3.9
|
19.6
|
1.0
|
C2
|
A:PMB3226
|
4.0
|
39.8
|
1.0
|
C
|
A:ILE355
|
4.1
|
24.0
|
1.0
|
C
|
A:CYS354
|
4.1
|
24.1
|
1.0
|
N
|
A:LYS340
|
4.1
|
21.1
|
1.0
|
C
|
A:ILE339
|
4.2
|
21.6
|
1.0
|
C6
|
A:PMB3226
|
4.2
|
40.2
|
1.0
|
CD
|
A:LYS340
|
4.3
|
39.8
|
1.0
|
CA
|
A:ILE355
|
4.6
|
22.4
|
1.0
|
C1
|
A:PMB3226
|
4.6
|
42.8
|
1.0
|
N
|
A:VAL338
|
4.8
|
22.3
|
1.0
|
CE
|
A:LYS340
|
4.8
|
41.8
|
1.0
|
O
|
A:ILE339
|
4.9
|
20.5
|
1.0
|
N
|
A:SER356
|
5.0
|
29.3
|
1.0
|
CB
|
A:LYS340
|
5.0
|
31.5
|
1.0
|
|
Mercury binding site 2 out
of 4 in 1yp2
Go back to
Mercury Binding Sites List in 1yp2
Mercury binding site 2 out
of 4 in the Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 2 of Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Hg3227
b:35.4
occ:1.00
|
HG
|
B:PMB3227
|
0.0
|
35.4
|
1.0
|
C4
|
B:PMB3227
|
1.8
|
40.5
|
1.0
|
SG
|
B:CYS354
|
2.0
|
40.5
|
1.0
|
O
|
B:HOH3403
|
2.6
|
22.1
|
1.0
|
C3
|
B:PMB3227
|
2.7
|
26.4
|
1.0
|
CB
|
B:CYS354
|
2.9
|
21.9
|
1.0
|
C5
|
B:PMB3227
|
2.9
|
36.4
|
1.0
|
CG2
|
B:VAL338
|
3.1
|
22.1
|
1.0
|
O
|
B:HOH3251
|
3.2
|
16.5
|
1.0
|
O
|
B:VAL338
|
3.2
|
15.6
|
1.0
|
O
|
B:HOH3362
|
3.3
|
28.5
|
1.0
|
CA
|
B:CYS354
|
3.4
|
24.1
|
1.0
|
CB
|
B:VAL338
|
3.9
|
20.2
|
1.0
|
N
|
B:ILE355
|
4.0
|
21.6
|
1.0
|
NH2
|
B:ARG378
|
4.0
|
65.3
|
1.0
|
C
|
B:CYS354
|
4.1
|
23.1
|
1.0
|
C2
|
B:PMB3227
|
4.1
|
33.1
|
1.0
|
C
|
B:VAL338
|
4.1
|
18.6
|
1.0
|
C6
|
B:PMB3227
|
4.2
|
34.2
|
1.0
|
CZ
|
B:ARG378
|
4.4
|
62.5
|
1.0
|
O
|
B:ILE355
|
4.6
|
22.2
|
1.0
|
CA
|
B:VAL338
|
4.7
|
17.6
|
1.0
|
C1
|
B:PMB3227
|
4.7
|
38.5
|
1.0
|
NH1
|
B:ARG378
|
4.7
|
63.4
|
1.0
|
C
|
B:ILE355
|
4.8
|
21.2
|
1.0
|
N
|
B:CYS354
|
4.8
|
19.4
|
1.0
|
|
Mercury binding site 3 out
of 4 in 1yp2
Go back to
Mercury Binding Sites List in 1yp2
Mercury binding site 3 out
of 4 in the Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 3 of Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Hg3228
b:35.4
occ:1.00
|
HG
|
C:PMB3228
|
0.0
|
35.4
|
1.0
|
SG
|
C:CYS354
|
1.7
|
44.4
|
1.0
|
C4
|
C:PMB3228
|
1.8
|
20.7
|
1.0
|
O
|
C:HOH3428
|
2.7
|
16.5
|
1.0
|
C3
|
C:PMB3228
|
2.7
|
42.6
|
1.0
|
CB
|
C:CYS354
|
2.7
|
25.3
|
1.0
|
C5
|
C:PMB3228
|
2.9
|
44.8
|
1.0
|
O
|
C:HOH3249
|
3.0
|
20.2
|
1.0
|
CA
|
C:CYS354
|
3.2
|
20.4
|
1.0
|
O
|
C:VAL338
|
3.3
|
16.8
|
1.0
|
CG2
|
C:VAL338
|
3.3
|
23.3
|
1.0
|
NH1
|
C:ARG378
|
3.4
|
80.5
|
1.0
|
N
|
C:ILE355
|
3.5
|
21.2
|
1.0
|
C
|
C:CYS354
|
3.6
|
21.2
|
1.0
|
O
|
C:HOH3386
|
3.7
|
31.9
|
1.0
|
O
|
C:HOH3310
|
4.0
|
37.0
|
1.0
|
C2
|
C:PMB3228
|
4.1
|
46.6
|
1.0
|
CB
|
C:VAL338
|
4.2
|
19.9
|
1.0
|
O
|
C:ILE355
|
4.3
|
16.4
|
1.0
|
C
|
C:VAL338
|
4.3
|
18.7
|
1.0
|
C6
|
C:PMB3228
|
4.3
|
47.9
|
1.0
|
C
|
C:ILE355
|
4.3
|
20.3
|
1.0
|
CZ
|
C:ARG378
|
4.4
|
80.5
|
1.0
|
CA
|
C:ILE355
|
4.6
|
20.0
|
1.0
|
O
|
C:CYS354
|
4.6
|
20.5
|
1.0
|
N
|
C:CYS354
|
4.7
|
16.7
|
1.0
|
OG
|
C:SER356
|
4.7
|
24.9
|
1.0
|
C1
|
C:PMB3228
|
4.8
|
49.1
|
1.0
|
N
|
C:SER356
|
4.9
|
21.4
|
1.0
|
CA
|
C:VAL338
|
4.9
|
18.8
|
1.0
|
NH2
|
C:ARG378
|
5.0
|
80.5
|
1.0
|
|
Mercury binding site 4 out
of 4 in 1yp2
Go back to
Mercury Binding Sites List in 1yp2
Mercury binding site 4 out
of 4 in the Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 4 of Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Hg3229
b:35.4
occ:1.00
|
HG
|
D:PMB3229
|
0.0
|
35.4
|
1.0
|
C4
|
D:PMB3229
|
1.8
|
19.2
|
1.0
|
NH1
|
D:ARG378
|
2.2
|
80.6
|
1.0
|
SG
|
D:CYS354
|
2.5
|
38.6
|
1.0
|
C3
|
D:PMB3229
|
2.7
|
28.0
|
1.0
|
O
|
D:HOH3234
|
2.8
|
23.1
|
1.0
|
C5
|
D:PMB3229
|
2.9
|
24.4
|
1.0
|
O
|
D:HOH3423
|
3.1
|
38.9
|
1.0
|
CB
|
D:CYS354
|
3.2
|
28.4
|
1.0
|
O
|
D:VAL338
|
3.3
|
19.5
|
1.0
|
CZ
|
D:ARG378
|
3.4
|
80.6
|
1.0
|
CG2
|
D:VAL338
|
3.5
|
17.1
|
1.0
|
CA
|
D:CYS354
|
3.6
|
23.9
|
1.0
|
NH2
|
D:ARG378
|
3.8
|
80.6
|
1.0
|
N
|
D:ILE355
|
4.0
|
23.6
|
1.0
|
C
|
D:CYS354
|
4.1
|
25.6
|
1.0
|
CB
|
D:VAL338
|
4.1
|
16.5
|
1.0
|
C2
|
D:PMB3229
|
4.1
|
32.8
|
1.0
|
C6
|
D:PMB3229
|
4.2
|
31.3
|
1.0
|
C
|
D:VAL338
|
4.2
|
21.1
|
1.0
|
CE
|
D:LYS340
|
4.3
|
32.8
|
1.0
|
O
|
D:HOH3474
|
4.5
|
58.3
|
1.0
|
NE
|
D:ARG378
|
4.5
|
80.6
|
1.0
|
O
|
D:ILE355
|
4.6
|
20.8
|
1.0
|
C1
|
D:PMB3229
|
4.7
|
35.5
|
1.0
|
C
|
D:ILE355
|
4.8
|
23.1
|
1.0
|
CA
|
D:VAL338
|
4.8
|
20.6
|
1.0
|
CG
|
D:LYS340
|
4.8
|
22.9
|
1.0
|
|
Reference:
X.Jin,
M.A.Ballicora,
J.Preiss,
J.H.Geiger.
Crystal Structure of Potato Tuber Adp-Glucose Pyrophosphorylase. Embo J. V. 24 694 2005.
ISSN: ISSN 0261-4189
PubMed: 15692569
DOI: 10.1038/SJ.EMBOJ.7600551
Page generated: Sun Aug 11 01:58:46 2024
|