Magnesium in PDB 1tmm: Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin
Enzymatic activity of Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin
All present enzymatic activity of Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin:
2.7.6.3;
Protein crystallography data
The structure of Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin, PDB code: 1tmm
was solved by
J.Blaszczyk,
Y.Li,
Y.Wu,
G.Shi,
X.Ji,
H.Yan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
1.25
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
47.992,
47.392,
71.438,
90.00,
104.13,
90.00
|
R / Rfree (%)
|
13.2 /
16.4
|
Other elements in 1tmm:
The structure of Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin
(pdb code 1tmm). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin, PDB code: 1tmm:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 1tmm
Go back to
Magnesium Binding Sites List in 1tmm
Magnesium binding site 1 out
of 5 in the Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin
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 Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg161
b:7.8
occ:1.00
|
OD1
|
A:ASP97
|
2.0
|
7.6
|
1.0
|
OD1
|
A:ASP95
|
2.1
|
7.2
|
1.0
|
O
|
A:HOH404
|
2.1
|
8.0
|
1.0
|
O
|
A:HOH408
|
2.1
|
8.3
|
1.0
|
O1B
|
A:APC171
|
2.1
|
8.8
|
1.0
|
O1A
|
A:APC171
|
2.1
|
8.7
|
1.0
|
CG
|
A:ASP95
|
3.0
|
6.7
|
1.0
|
CG
|
A:ASP97
|
3.1
|
7.0
|
1.0
|
PB
|
A:APC171
|
3.2
|
9.2
|
1.0
|
PA
|
A:APC171
|
3.2
|
9.2
|
1.0
|
OD2
|
A:ASP95
|
3.3
|
8.5
|
1.0
|
C3A
|
A:APC171
|
3.5
|
9.4
|
1.0
|
MG
|
A:MG162
|
3.5
|
8.2
|
1.0
|
OD2
|
A:ASP97
|
3.6
|
7.8
|
1.0
|
O5'
|
A:APC171
|
3.8
|
9.2
|
1.0
|
O
|
A:HOH440
|
3.9
|
23.1
|
1.0
|
O2B
|
A:APC171
|
4.0
|
11.1
|
1.0
|
NZ
|
A:LYS85
|
4.0
|
9.4
|
1.0
|
OE2
|
A:GLU77
|
4.2
|
8.7
|
1.0
|
O
|
A:LEU96
|
4.2
|
7.3
|
1.0
|
CB
|
A:ASP95
|
4.3
|
7.2
|
1.0
|
CB
|
A:ASP97
|
4.4
|
6.9
|
1.0
|
NH1
|
A:ARG82
|
4.4
|
10.1
|
1.0
|
O3B
|
A:APC171
|
4.5
|
10.3
|
1.0
|
NH2
|
A:ARG82
|
4.5
|
10.6
|
1.0
|
O2A
|
A:APC171
|
4.5
|
11.1
|
1.0
|
C
|
A:LEU96
|
4.5
|
6.0
|
1.0
|
O1G
|
A:APC171
|
4.7
|
12.0
|
1.0
|
CA
|
A:ASP97
|
4.7
|
6.0
|
1.0
|
N
|
A:LEU96
|
4.7
|
6.6
|
1.0
|
O
|
A:HOH435
|
4.7
|
9.2
|
1.0
|
O3G
|
A:APC171
|
4.7
|
9.6
|
1.0
|
CA
|
A:ASP95
|
4.7
|
7.1
|
1.0
|
O6A
|
A:HHR181
|
4.7
|
10.3
|
1.0
|
C2
|
A:APC171
|
4.8
|
6.6
|
1.0
|
N
|
A:ASP97
|
4.8
|
6.3
|
1.0
|
N3
|
A:APC171
|
4.8
|
7.3
|
1.0
|
PG
|
A:APC171
|
4.9
|
9.8
|
1.0
|
C
|
A:ASP95
|
4.9
|
6.5
|
1.0
|
CZ
|
A:ARG82
|
5.0
|
9.0
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 1tmm
Go back to
Magnesium Binding Sites List in 1tmm
Magnesium binding site 2 out
of 5 in the Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin
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 Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg162
b:8.2
occ:1.00
|
OD2
|
A:ASP97
|
2.0
|
7.8
|
1.0
|
O3G
|
A:APC171
|
2.0
|
9.6
|
1.0
|
OD2
|
A:ASP95
|
2.1
|
8.5
|
1.0
|
O
|
A:HOH496
|
2.1
|
8.9
|
1.0
|
O1B
|
A:APC171
|
2.1
|
8.8
|
1.0
|
O6A
|
A:HHR181
|
2.1
|
10.3
|
1.0
|
CG
|
A:ASP97
|
3.0
|
7.0
|
1.0
|
CG
|
A:ASP95
|
3.1
|
6.7
|
1.0
|
PG
|
A:APC171
|
3.2
|
9.8
|
1.0
|
PB
|
A:APC171
|
3.2
|
9.2
|
1.0
|
C6A
|
A:HHR181
|
3.3
|
10.4
|
1.0
|
OD1
|
A:ASP97
|
3.3
|
7.6
|
1.0
|
O3B
|
A:APC171
|
3.4
|
10.3
|
1.0
|
MG
|
A:MG161
|
3.5
|
7.8
|
1.0
|
OD1
|
A:ASP95
|
3.6
|
7.2
|
1.0
|
O1G
|
A:APC171
|
3.9
|
12.0
|
1.0
|
O2B
|
A:APC171
|
4.0
|
11.1
|
1.0
|
O
|
A:HOH414
|
4.0
|
9.6
|
1.0
|
N5
|
A:HHR181
|
4.1
|
9.9
|
1.0
|
C6
|
A:HHR181
|
4.1
|
10.6
|
1.0
|
NH1
|
A:ARG121
|
4.2
|
9.8
|
1.0
|
O
|
A:HOH469
|
4.2
|
13.3
|
1.0
|
O
|
A:HOH407
|
4.2
|
14.3
|
1.0
|
CB
|
A:ASP97
|
4.3
|
6.9
|
1.0
|
O2G
|
A:APC171
|
4.4
|
9.7
|
1.0
|
CB
|
A:ASP95
|
4.5
|
7.2
|
1.0
|
O
|
A:HOH440
|
4.6
|
23.1
|
1.0
|
O
|
A:HOH408
|
4.6
|
8.3
|
1.0
|
O
|
A:HOH481
|
4.6
|
11.5
|
1.0
|
C3A
|
A:APC171
|
4.7
|
9.4
|
1.0
|
NE2
|
A:HIS115
|
4.7
|
9.6
|
1.0
|
O1A
|
A:APC171
|
4.9
|
8.7
|
1.0
|
CE
|
A:MET124
|
5.0
|
11.4
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 1tmm
Go back to
Magnesium Binding Sites List in 1tmm
Magnesium binding site 3 out
of 5 in the Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin
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 Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg163
b:27.6
occ:1.00
|
O
|
A:HOH644
|
2.2
|
25.9
|
1.0
|
O
|
A:SER31
|
2.3
|
13.3
|
1.0
|
O
|
A:GLY26
|
2.4
|
20.1
|
1.0
|
O
|
A:HOH567
|
2.4
|
22.5
|
1.0
|
O
|
A:HOH671
|
2.6
|
27.3
|
1.0
|
O
|
A:HOH672
|
2.6
|
33.7
|
1.0
|
O
|
A:HOH935
|
3.3
|
47.2
|
1.0
|
C
|
A:SER31
|
3.5
|
13.0
|
1.0
|
C
|
A:GLY26
|
3.6
|
15.2
|
1.0
|
O
|
A:ILE28
|
3.8
|
16.9
|
1.0
|
O
|
A:HOH730
|
4.0
|
40.8
|
1.0
|
CA
|
A:HIS32
|
4.2
|
11.8
|
1.0
|
N
|
A:HIS32
|
4.3
|
10.7
|
1.0
|
CB
|
A:HIS32
|
4.3
|
13.1
|
1.0
|
CA
|
A:ASP27
|
4.4
|
16.4
|
1.0
|
N
|
A:ASP27
|
4.4
|
14.0
|
1.0
|
O
|
A:HOH983
|
4.5
|
43.9
|
1.0
|
N
|
A:SER31
|
4.5
|
13.6
|
1.0
|
O
|
A:HOH418
|
4.5
|
13.9
|
1.0
|
CA
|
A:SER31
|
4.6
|
12.2
|
1.0
|
C
|
A:ASP27
|
4.6
|
15.2
|
1.0
|
CA
|
A:GLY26
|
4.6
|
12.6
|
1.0
|
C
|
A:ILE28
|
4.8
|
14.6
|
1.0
|
N
|
A:ILE28
|
4.8
|
13.7
|
1.0
|
OXT
|
A:ACT167
|
4.8
|
21.8
|
1.0
|
O
|
A:HOH819
|
4.9
|
42.6
|
1.0
|
O
|
A:ASP27
|
5.0
|
16.4
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 1tmm
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Magnesium Binding Sites List in 1tmm
Magnesium binding site 4 out
of 5 in the Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin
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 Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg361
b:9.1
occ:1.00
|
OD1
|
B:ASP297
|
2.0
|
8.6
|
1.0
|
O1B
|
B:APC371
|
2.1
|
9.0
|
1.0
|
O
|
B:HOH431
|
2.1
|
8.4
|
1.0
|
O1A
|
B:APC371
|
2.1
|
9.2
|
1.0
|
O
|
B:HOH433
|
2.1
|
9.5
|
1.0
|
OD1
|
B:ASP295
|
2.1
|
9.0
|
1.0
|
CG
|
B:ASP295
|
3.0
|
7.9
|
1.0
|
CG
|
B:ASP297
|
3.1
|
7.8
|
1.0
|
PB
|
B:APC371
|
3.2
|
10.1
|
1.0
|
PA
|
B:APC371
|
3.2
|
10.1
|
1.0
|
OD2
|
B:ASP295
|
3.3
|
10.1
|
1.0
|
C3A
|
B:APC371
|
3.5
|
11.0
|
1.0
|
MG
|
B:MG362
|
3.5
|
9.6
|
1.0
|
OD2
|
B:ASP297
|
3.6
|
10.4
|
1.0
|
O5'
|
B:APC371
|
3.8
|
10.3
|
1.0
|
O2B
|
B:APC371
|
3.9
|
11.9
|
1.0
|
NZ
|
B:LYS285
|
4.0
|
8.4
|
0.9
|
O
|
B:HOH449
|
4.1
|
15.1
|
1.0
|
OE2
|
B:GLU277
|
4.2
|
8.7
|
1.0
|
O
|
B:LEU296
|
4.2
|
8.2
|
1.0
|
NH1
|
B:ARG282
|
4.3
|
11.9
|
1.0
|
CB
|
B:ASP295
|
4.4
|
8.1
|
1.0
|
CB
|
B:ASP297
|
4.4
|
8.1
|
1.0
|
O3B
|
B:APC371
|
4.5
|
10.7
|
1.0
|
O2A
|
B:APC371
|
4.5
|
10.6
|
1.0
|
NH2
|
B:ARG282
|
4.6
|
19.1
|
1.0
|
C
|
B:LEU296
|
4.6
|
7.4
|
1.0
|
C2
|
B:APC371
|
4.6
|
7.5
|
1.0
|
O
|
B:HOH436
|
4.7
|
9.2
|
1.0
|
CA
|
B:ASP297
|
4.7
|
8.0
|
1.0
|
O3G
|
B:APC371
|
4.7
|
12.1
|
1.0
|
N3
|
B:APC371
|
4.7
|
8.7
|
1.0
|
N
|
B:LEU296
|
4.7
|
7.2
|
1.0
|
CA
|
B:ASP295
|
4.8
|
8.2
|
1.0
|
O6A
|
B:HHR381
|
4.8
|
11.5
|
1.0
|
O1G
|
B:APC371
|
4.8
|
13.7
|
1.0
|
N
|
B:ASP297
|
4.8
|
7.0
|
1.0
|
CZ
|
B:ARG282
|
4.9
|
14.6
|
1.0
|
NH1
|
B:ARG292
|
5.0
|
24.4
|
1.0
|
C
|
B:ASP295
|
5.0
|
7.5
|
1.0
|
PG
|
B:APC371
|
5.0
|
11.4
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 1tmm
Go back to
Magnesium Binding Sites List in 1tmm
Magnesium binding site 5 out
of 5 in the Crystal Structure of Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin
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 Ternary Complex of E.Coli Hppk(W89A) with Mgampcpp and 6-Hydroxymethylpterin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg362
b:9.6
occ:1.00
|
OD2
|
B:ASP297
|
2.0
|
10.4
|
1.0
|
O3G
|
B:APC371
|
2.0
|
12.1
|
1.0
|
OD2
|
B:ASP295
|
2.1
|
10.1
|
1.0
|
O1B
|
B:APC371
|
2.2
|
9.0
|
1.0
|
O6A
|
B:HHR381
|
2.2
|
11.5
|
1.0
|
O
|
B:HOH517
|
2.2
|
13.1
|
1.0
|
CG
|
B:ASP297
|
2.9
|
7.8
|
1.0
|
CG
|
B:ASP295
|
3.2
|
7.9
|
1.0
|
PG
|
B:APC371
|
3.2
|
11.4
|
1.0
|
PB
|
B:APC371
|
3.2
|
10.1
|
1.0
|
OD1
|
B:ASP297
|
3.2
|
8.6
|
1.0
|
O3B
|
B:APC371
|
3.3
|
10.7
|
1.0
|
C6A
|
B:HHR381
|
3.4
|
15.0
|
1.0
|
MG
|
B:MG361
|
3.5
|
9.1
|
1.0
|
OD1
|
B:ASP295
|
3.6
|
9.0
|
1.0
|
O1G
|
B:APC371
|
3.9
|
13.7
|
1.0
|
O2B
|
B:APC371
|
4.0
|
11.9
|
1.0
|
O
|
B:HOH536
|
4.0
|
11.3
|
1.0
|
NH1
|
B:ARG321
|
4.0
|
10.9
|
1.0
|
O
|
B:HOH499
|
4.1
|
31.5
|
1.0
|
CB
|
B:ASP297
|
4.2
|
8.1
|
1.0
|
N5
|
B:HHR381
|
4.3
|
16.7
|
1.0
|
C6
|
B:HHR381
|
4.3
|
14.1
|
1.0
|
O
|
B:HOH464
|
4.3
|
25.8
|
1.0
|
NE2
|
B:HIS315
|
4.3
|
9.8
|
1.0
|
O2G
|
B:APC371
|
4.4
|
11.4
|
1.0
|
NH1
|
B:ARG292
|
4.4
|
24.4
|
1.0
|
CB
|
B:ASP295
|
4.5
|
8.1
|
1.0
|
O
|
B:HOH433
|
4.5
|
9.5
|
1.0
|
O
|
B:HOH449
|
4.6
|
15.1
|
1.0
|
C3A
|
B:APC371
|
4.6
|
11.0
|
1.0
|
O
|
B:HOH468
|
4.7
|
15.3
|
1.0
|
CE
|
B:MET324
|
4.9
|
13.9
|
1.0
|
O1A
|
B:APC371
|
4.9
|
9.2
|
1.0
|
|
Reference:
Y.Li,
J.Blaszczyk,
Y.Wu,
G.Shi,
X.Ji,
H.Yan.
Is the Critical Role of Loop 3 of Escherichia Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase in Catalysis Due to Loop-3 Residues Arginine-84 and Tryptophan-89? Site-Directed Mutagenesis, Biochemical, and Crystallographic Studies. Biochemistry V. 44 8590 2005.
ISSN: ISSN 0006-2960
PubMed: 15952765
DOI: 10.1021/BI0503495
Page generated: Tue Aug 13 14:35:39 2024
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