Magnesium in PDB 1ru1: Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form)
Enzymatic activity of Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form)
All present enzymatic activity of Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form):
2.7.6.3;
Protein crystallography data
The structure of Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form), PDB code: 1ru1
was solved by
J.Blaszczyk,
X.Ji,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
1.40
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
52.797,
68.752,
36.491,
90.00,
90.50,
90.00
|
R / Rfree (%)
|
15 /
19.8
|
Other elements in 1ru1:
The structure of Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form) also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form)
(pdb code 1ru1). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form), PDB code: 1ru1:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 1ru1
Go back to
Magnesium Binding Sites List in 1ru1
Magnesium binding site 1 out
of 4 in the Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form)
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 A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg161
b:13.4
occ:1.00
|
OD1
|
A:ASP95
|
2.0
|
15.3
|
1.0
|
O1A
|
A:APC171
|
2.0
|
13.8
|
1.0
|
O
|
A:HOH413
|
2.1
|
14.6
|
1.0
|
O1B
|
A:APC171
|
2.1
|
12.1
|
1.0
|
OD1
|
A:ASP97
|
2.1
|
10.9
|
1.0
|
O
|
A:HOH423
|
2.1
|
12.0
|
1.0
|
CG
|
A:ASP95
|
2.9
|
14.3
|
1.0
|
OD2
|
A:ASP95
|
3.1
|
14.8
|
1.0
|
CG
|
A:ASP97
|
3.1
|
11.5
|
1.0
|
PB
|
A:APC171
|
3.2
|
14.5
|
1.0
|
PA
|
A:APC171
|
3.2
|
16.2
|
1.0
|
MG
|
A:MG162
|
3.5
|
13.3
|
1.0
|
C3A
|
A:APC171
|
3.5
|
17.4
|
1.0
|
OD2
|
A:ASP97
|
3.6
|
12.7
|
1.0
|
O5'
|
A:APC171
|
3.7
|
18.1
|
1.0
|
O2B
|
A:APC171
|
3.9
|
14.3
|
1.0
|
OE2
|
A:GLU77
|
4.1
|
14.0
|
1.0
|
CB
|
A:ASP95
|
4.3
|
12.5
|
1.0
|
O
|
A:HOH681
|
4.4
|
28.0
|
1.0
|
O
|
A:LEU96
|
4.4
|
11.9
|
1.0
|
CB
|
A:ASP97
|
4.5
|
10.2
|
1.0
|
O2A
|
A:APC171
|
4.5
|
14.9
|
1.0
|
O
|
A:HOH539
|
4.5
|
24.5
|
1.0
|
O3B
|
A:APC171
|
4.5
|
14.5
|
1.0
|
O
|
A:HOH682
|
4.6
|
34.2
|
1.0
|
C
|
A:LEU96
|
4.6
|
11.2
|
1.0
|
O3G
|
A:APC171
|
4.6
|
12.8
|
1.0
|
O
|
A:HOH442
|
4.7
|
19.1
|
1.0
|
N
|
A:LEU96
|
4.7
|
12.1
|
1.0
|
O4
|
A:PH2181
|
4.7
|
17.2
|
1.0
|
N3
|
A:APC171
|
4.7
|
11.8
|
1.0
|
CA
|
A:ASP97
|
4.7
|
10.5
|
1.0
|
O1G
|
A:APC171
|
4.7
|
15.2
|
1.0
|
C2
|
A:APC171
|
4.7
|
10.4
|
1.0
|
N
|
A:ASP97
|
4.8
|
12.1
|
1.0
|
CA
|
A:ASP95
|
4.8
|
12.4
|
1.0
|
PG
|
A:APC171
|
4.9
|
13.9
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 1ru1
Go back to
Magnesium Binding Sites List in 1ru1
Magnesium binding site 2 out
of 4 in the Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form)
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 A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg162
b:13.3
occ:1.00
|
OD2
|
A:ASP95
|
2.0
|
14.8
|
1.0
|
OD2
|
A:ASP97
|
2.0
|
12.7
|
1.0
|
O3G
|
A:APC171
|
2.1
|
12.8
|
1.0
|
O
|
A:HOH403
|
2.1
|
18.7
|
1.0
|
O1B
|
A:APC171
|
2.1
|
12.1
|
1.0
|
O4
|
A:PH2181
|
2.1
|
17.2
|
1.0
|
CG
|
A:ASP97
|
3.0
|
11.5
|
1.0
|
CG
|
A:ASP95
|
3.1
|
14.3
|
1.0
|
PB
|
A:APC171
|
3.2
|
14.5
|
1.0
|
PG
|
A:APC171
|
3.2
|
13.9
|
1.0
|
OD1
|
A:ASP97
|
3.3
|
10.9
|
1.0
|
C11
|
A:PH2181
|
3.3
|
31.9
|
1.0
|
O3B
|
A:APC171
|
3.4
|
14.5
|
1.0
|
MG
|
A:MG161
|
3.5
|
13.4
|
1.0
|
OD1
|
A:ASP95
|
3.6
|
15.3
|
1.0
|
O1G
|
A:APC171
|
3.9
|
15.2
|
1.0
|
O
|
A:HOH419
|
4.0
|
22.2
|
1.0
|
O2B
|
A:APC171
|
4.0
|
14.3
|
1.0
|
NH1
|
A:ARG121
|
4.1
|
15.5
|
1.0
|
NE2
|
A:HIS115
|
4.2
|
12.9
|
1.0
|
CB
|
A:ASP97
|
4.3
|
10.2
|
1.0
|
C2
|
A:PH2181
|
4.3
|
38.1
|
1.0
|
O
|
A:HOH708
|
4.4
|
35.6
|
1.0
|
CB
|
A:ASP95
|
4.4
|
12.5
|
1.0
|
O2G
|
A:APC171
|
4.4
|
15.8
|
1.0
|
N1
|
A:PH2181
|
4.4
|
38.2
|
1.0
|
O
|
A:HOH423
|
4.5
|
12.0
|
1.0
|
O
|
A:HOH713
|
4.6
|
37.4
|
1.0
|
C3A
|
A:APC171
|
4.7
|
17.4
|
1.0
|
O
|
A:HOH682
|
4.9
|
34.2
|
1.0
|
O1A
|
A:APC171
|
4.9
|
13.8
|
1.0
|
O
|
A:HOH539
|
5.0
|
24.5
|
1.0
|
O
|
A:HOH519
|
5.0
|
27.1
|
1.0
|
CD2
|
A:HIS115
|
5.0
|
14.1
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 1ru1
Go back to
Magnesium Binding Sites List in 1ru1
Magnesium binding site 3 out
of 4 in the Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form)
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 A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg361
b:10.1
occ:1.00
|
OD1
|
B:ASP297
|
2.1
|
11.9
|
1.0
|
O1B
|
B:APC371
|
2.1
|
11.2
|
1.0
|
O
|
B:HOH668
|
2.1
|
13.6
|
1.0
|
OD1
|
B:ASP295
|
2.1
|
12.5
|
1.0
|
O
|
B:HOH426
|
2.1
|
12.6
|
1.0
|
O1A
|
B:APC371
|
2.1
|
12.2
|
1.0
|
CG
|
B:ASP295
|
3.0
|
13.0
|
1.0
|
CG
|
B:ASP297
|
3.1
|
12.7
|
1.0
|
PA
|
B:APC371
|
3.2
|
11.6
|
1.0
|
PB
|
B:APC371
|
3.2
|
11.9
|
1.0
|
OD2
|
B:ASP295
|
3.3
|
11.4
|
1.0
|
C3A
|
B:APC371
|
3.4
|
10.9
|
1.0
|
OD2
|
B:ASP297
|
3.5
|
11.7
|
1.0
|
MG
|
B:MG362
|
3.5
|
11.6
|
1.0
|
O5'
|
B:APC371
|
3.8
|
12.2
|
1.0
|
O2B
|
B:APC371
|
4.0
|
13.5
|
1.0
|
OE2
|
B:GLU277
|
4.2
|
14.4
|
1.0
|
O
|
B:HOH425
|
4.2
|
14.8
|
1.0
|
O
|
B:LEU296
|
4.2
|
10.6
|
1.0
|
O
|
B:HOH510
|
4.4
|
19.2
|
1.0
|
O
|
B:HOH420
|
4.4
|
19.6
|
1.0
|
CB
|
B:ASP295
|
4.4
|
11.5
|
1.0
|
O3B
|
B:APC371
|
4.4
|
11.5
|
1.0
|
CB
|
B:ASP297
|
4.4
|
10.3
|
1.0
|
O2A
|
B:APC371
|
4.5
|
12.7
|
1.0
|
N3
|
B:APC371
|
4.5
|
10.8
|
1.0
|
O
|
B:HOH415
|
4.6
|
11.2
|
1.0
|
C
|
B:LEU296
|
4.6
|
10.4
|
1.0
|
C2
|
B:APC371
|
4.6
|
9.9
|
1.0
|
O1G
|
B:APC371
|
4.6
|
12.8
|
1.0
|
O
|
B:HOH772
|
4.6
|
31.1
|
1.0
|
O3G
|
B:APC371
|
4.6
|
11.2
|
1.0
|
N
|
B:LEU296
|
4.6
|
9.3
|
1.0
|
CA
|
B:ASP297
|
4.7
|
10.4
|
1.0
|
O4
|
B:PH2381
|
4.7
|
12.7
|
1.0
|
CA
|
B:ASP295
|
4.8
|
12.0
|
1.0
|
N
|
B:ASP297
|
4.8
|
10.4
|
1.0
|
PG
|
B:APC371
|
4.9
|
12.4
|
1.0
|
C
|
B:ASP295
|
5.0
|
10.1
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 1ru1
Go back to
Magnesium Binding Sites List in 1ru1
Magnesium binding site 4 out
of 4 in the Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form)
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 A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg362
b:11.6
occ:1.00
|
OD2
|
B:ASP297
|
2.0
|
11.7
|
1.0
|
O3G
|
B:APC371
|
2.0
|
11.2
|
1.0
|
O
|
B:HOH401
|
2.1
|
11.2
|
1.0
|
OD2
|
B:ASP295
|
2.1
|
11.4
|
1.0
|
O4
|
B:PH2381
|
2.1
|
12.7
|
1.0
|
O1B
|
B:APC371
|
2.2
|
11.2
|
1.0
|
CG
|
B:ASP297
|
2.9
|
12.7
|
1.0
|
CG
|
B:ASP295
|
3.1
|
13.0
|
1.0
|
PG
|
B:APC371
|
3.2
|
12.4
|
1.0
|
PB
|
B:APC371
|
3.2
|
11.9
|
1.0
|
C11
|
B:PH2381
|
3.3
|
14.0
|
1.0
|
OD1
|
B:ASP297
|
3.3
|
11.9
|
1.0
|
O3B
|
B:APC371
|
3.3
|
11.5
|
1.0
|
MG
|
B:MG361
|
3.5
|
10.1
|
1.0
|
OD1
|
B:ASP295
|
3.6
|
12.5
|
1.0
|
O1G
|
B:APC371
|
3.9
|
12.8
|
1.0
|
O2B
|
B:APC371
|
4.0
|
13.5
|
1.0
|
O
|
B:HOH407
|
4.0
|
13.0
|
1.0
|
NH1
|
B:ARG321
|
4.1
|
12.3
|
1.0
|
N1
|
B:PH2381
|
4.1
|
13.5
|
1.0
|
C2
|
B:PH2381
|
4.2
|
15.7
|
1.0
|
O
|
B:HOH588
|
4.2
|
25.5
|
1.0
|
CB
|
B:ASP297
|
4.3
|
10.3
|
1.0
|
NE2
|
B:HIS315
|
4.3
|
10.9
|
1.0
|
O2G
|
B:APC371
|
4.3
|
14.6
|
1.0
|
CB
|
B:ASP295
|
4.4
|
11.5
|
1.0
|
O
|
B:HOH461
|
4.4
|
18.1
|
1.0
|
O
|
B:HOH426
|
4.6
|
12.6
|
1.0
|
C3A
|
B:APC371
|
4.7
|
10.9
|
1.0
|
O
|
B:HOH446
|
4.9
|
18.1
|
1.0
|
O
|
B:HOH772
|
5.0
|
31.1
|
1.0
|
|
Reference:
J.Blaszczyk,
Y.Li,
Y.Wu,
G.Shi,
X.Ji,
H.Yan.
Essential Roles of A Dynamic Loop in the Catalysis of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase. Biochemistry V. 43 1469 2004.
ISSN: ISSN 0006-2960
PubMed: 14769023
DOI: 10.1021/BI036053L
Page generated: Tue Aug 13 13:08:03 2024
|