Magnesium in PDB 3ct7: Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12
Protein crystallography data
The structure of Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12, PDB code: 3ct7
was solved by
A.A.Fedorov,
E.V.Fedorov,
K.K.Chan,
J.A.Gerlt,
S.C.Almo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
24.90 /
2.50
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
75.462,
129.209,
154.451,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.2 /
24.9
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12
(pdb code 3ct7). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12, PDB code: 3ct7:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 3ct7
Go back to
Magnesium Binding Sites List in 3ct7
Magnesium binding site 1 out
of 6 in the Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12
![](/pictures/MG/pdb/ct/3ct7-MG-sphere_01.jpg) Mono view
![](/pictures/MG/pdb/ct/3ct7-MG-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg232
b:36.3
occ:1.00
|
OD2
|
A:ASP32
|
2.3
|
34.9
|
1.0
|
ND1
|
A:HIS63
|
2.3
|
30.9
|
1.0
|
NE2
|
A:HIS30
|
2.4
|
31.9
|
1.0
|
OD1
|
A:ASP173
|
2.5
|
44.9
|
1.0
|
CE1
|
A:HIS63
|
3.0
|
31.8
|
1.0
|
CG
|
A:ASP32
|
3.1
|
33.9
|
1.0
|
CE1
|
A:HIS30
|
3.3
|
32.3
|
1.0
|
CD2
|
A:HIS30
|
3.4
|
30.7
|
1.0
|
OD1
|
A:ASP32
|
3.4
|
35.6
|
1.0
|
CG
|
A:HIS63
|
3.5
|
30.5
|
1.0
|
CG
|
A:ASP173
|
3.5
|
45.1
|
1.0
|
CE
|
A:MET65
|
3.9
|
31.7
|
1.0
|
OD2
|
A:ASP173
|
3.9
|
47.0
|
1.0
|
CB
|
A:HIS63
|
3.9
|
29.6
|
1.0
|
NE2
|
A:HIS63
|
4.2
|
32.7
|
1.0
|
ND1
|
A:HIS30
|
4.4
|
33.0
|
1.0
|
CD2
|
A:HIS63
|
4.5
|
32.4
|
1.0
|
CB
|
A:ASP32
|
4.5
|
30.1
|
1.0
|
CG
|
A:HIS30
|
4.5
|
32.7
|
1.0
|
CB
|
A:ASP173
|
4.8
|
45.0
|
1.0
|
CD1
|
A:ILE112
|
4.8
|
28.7
|
1.0
|
SD
|
A:MET65
|
4.9
|
29.3
|
1.0
|
SD
|
A:MET135
|
4.9
|
37.1
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 3ct7
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Magnesium Binding Sites List in 3ct7
Magnesium binding site 2 out
of 6 in the Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12
![](/pictures/MG/pdb/ct/3ct7-MG-sphere_02.jpg) Mono view
![](/pictures/MG/pdb/ct/3ct7-MG-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg232
b:35.9
occ:1.00
|
OD2
|
B:ASP32
|
2.2
|
40.4
|
1.0
|
NE2
|
B:HIS30
|
2.4
|
28.3
|
1.0
|
OD1
|
B:ASP173
|
2.5
|
42.1
|
1.0
|
ND1
|
B:HIS63
|
2.5
|
29.5
|
1.0
|
CG
|
B:ASP32
|
3.1
|
37.6
|
1.0
|
CE1
|
B:HIS63
|
3.1
|
30.9
|
1.0
|
OD1
|
B:ASP32
|
3.3
|
42.0
|
1.0
|
CD2
|
B:HIS30
|
3.4
|
30.0
|
1.0
|
CE1
|
B:HIS30
|
3.4
|
30.9
|
1.0
|
CG
|
B:ASP173
|
3.5
|
45.1
|
1.0
|
CG
|
B:HIS63
|
3.6
|
27.0
|
1.0
|
OD2
|
B:ASP173
|
3.8
|
44.6
|
1.0
|
CE
|
B:MET65
|
3.9
|
28.9
|
1.0
|
CB
|
B:HIS63
|
4.1
|
24.9
|
1.0
|
NE2
|
B:HIS63
|
4.4
|
29.7
|
1.0
|
CB
|
B:ASP32
|
4.5
|
35.0
|
1.0
|
ND1
|
B:HIS30
|
4.5
|
30.4
|
1.0
|
CG
|
B:HIS30
|
4.5
|
30.3
|
1.0
|
CD2
|
B:HIS63
|
4.6
|
29.4
|
1.0
|
CB
|
B:ASP173
|
4.8
|
42.5
|
1.0
|
SD
|
B:MET65
|
4.9
|
32.3
|
1.0
|
CD1
|
B:ILE112
|
4.9
|
24.6
|
1.0
|
CD1
|
B:ILE193
|
5.0
|
25.6
|
1.0
|
SD
|
B:MET135
|
5.0
|
33.6
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 3ct7
Go back to
Magnesium Binding Sites List in 3ct7
Magnesium binding site 3 out
of 6 in the Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12
![](/pictures/MG/pdb/ct/3ct7-MG-sphere_03.jpg) Mono view
![](/pictures/MG/pdb/ct/3ct7-MG-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg301
b:42.3
occ:1.00
|
OD1
|
C:ASP173
|
2.4
|
42.8
|
1.0
|
OD2
|
C:ASP32
|
2.4
|
34.9
|
1.0
|
NE2
|
C:HIS30
|
2.4
|
27.3
|
1.0
|
ND1
|
C:HIS63
|
2.5
|
36.4
|
1.0
|
CE1
|
C:HIS63
|
3.1
|
38.3
|
1.0
|
CG
|
C:ASP32
|
3.2
|
33.2
|
1.0
|
OD1
|
C:ASP32
|
3.4
|
32.2
|
1.0
|
CD2
|
C:HIS30
|
3.4
|
29.7
|
1.0
|
CG
|
C:ASP173
|
3.4
|
40.4
|
1.0
|
CE1
|
C:HIS30
|
3.4
|
27.2
|
1.0
|
CG
|
C:HIS63
|
3.7
|
35.6
|
1.0
|
OD2
|
C:ASP173
|
3.7
|
40.5
|
1.0
|
CE
|
C:MET65
|
3.9
|
31.8
|
1.0
|
CB
|
C:HIS63
|
4.2
|
29.3
|
1.0
|
NE2
|
C:HIS63
|
4.4
|
39.3
|
1.0
|
ND1
|
C:HIS30
|
4.5
|
28.9
|
1.0
|
CG
|
C:HIS30
|
4.5
|
29.4
|
1.0
|
CB
|
C:ASP32
|
4.6
|
30.9
|
1.0
|
CD2
|
C:HIS63
|
4.6
|
36.7
|
1.0
|
CB
|
C:ASP173
|
4.7
|
40.8
|
1.0
|
CD1
|
C:ILE112
|
4.9
|
29.1
|
1.0
|
SD
|
C:MET135
|
4.9
|
39.5
|
1.0
|
CD1
|
C:ILE193
|
4.9
|
30.1
|
1.0
|
SD
|
C:MET65
|
4.9
|
30.0
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 3ct7
Go back to
Magnesium Binding Sites List in 3ct7
Magnesium binding site 4 out
of 6 in the Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12
![](/pictures/MG/pdb/ct/3ct7-MG-sphere_04.jpg) Mono view
![](/pictures/MG/pdb/ct/3ct7-MG-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg401
b:33.9
occ:1.00
|
OD2
|
D:ASP32
|
2.2
|
32.8
|
1.0
|
ND1
|
D:HIS63
|
2.3
|
34.0
|
1.0
|
NE2
|
D:HIS30
|
2.4
|
36.9
|
1.0
|
OD1
|
D:ASP173
|
2.5
|
43.0
|
1.0
|
CE1
|
D:HIS63
|
2.9
|
33.0
|
1.0
|
CG
|
D:ASP32
|
3.1
|
30.1
|
1.0
|
CE1
|
D:HIS30
|
3.3
|
37.5
|
1.0
|
OD1
|
D:ASP32
|
3.4
|
32.1
|
1.0
|
CG
|
D:HIS63
|
3.4
|
32.2
|
1.0
|
CD2
|
D:HIS30
|
3.4
|
36.3
|
1.0
|
CG
|
D:ASP173
|
3.5
|
43.2
|
1.0
|
CE
|
D:MET65
|
3.8
|
32.6
|
1.0
|
CB
|
D:HIS63
|
4.0
|
30.4
|
1.0
|
OD2
|
D:ASP173
|
4.0
|
44.6
|
1.0
|
NE2
|
D:HIS63
|
4.2
|
33.9
|
1.0
|
O
|
D:HOH806
|
4.3
|
38.5
|
1.0
|
CD2
|
D:HIS63
|
4.4
|
32.7
|
1.0
|
CB
|
D:ASP32
|
4.5
|
27.0
|
1.0
|
ND1
|
D:HIS30
|
4.5
|
38.5
|
1.0
|
CG
|
D:HIS30
|
4.6
|
36.5
|
1.0
|
CD1
|
D:ILE112
|
4.8
|
23.1
|
1.0
|
CB
|
D:ASP173
|
4.8
|
41.5
|
1.0
|
SD
|
D:MET65
|
4.8
|
36.2
|
1.0
|
SD
|
D:MET135
|
4.9
|
32.6
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 3ct7
Go back to
Magnesium Binding Sites List in 3ct7
Magnesium binding site 5 out
of 6 in the Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12
![](/pictures/MG/pdb/ct/3ct7-MG-sphere_05.jpg) Mono view
![](/pictures/MG/pdb/ct/3ct7-MG-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg501
b:29.8
occ:1.00
|
OD2
|
E:ASP32
|
2.3
|
40.0
|
1.0
|
OD1
|
E:ASP173
|
2.4
|
50.3
|
1.0
|
NE2
|
E:HIS30
|
2.4
|
37.5
|
1.0
|
ND1
|
E:HIS63
|
2.5
|
28.3
|
1.0
|
CG
|
E:ASP32
|
3.1
|
40.5
|
1.0
|
CE1
|
E:HIS63
|
3.2
|
27.0
|
1.0
|
OD1
|
E:ASP32
|
3.3
|
40.0
|
1.0
|
CD2
|
E:HIS30
|
3.3
|
37.3
|
1.0
|
CE1
|
E:HIS30
|
3.4
|
37.7
|
1.0
|
CG
|
E:ASP173
|
3.4
|
47.8
|
1.0
|
CG
|
E:HIS63
|
3.7
|
27.5
|
1.0
|
OD2
|
E:ASP173
|
3.7
|
50.0
|
1.0
|
CE
|
E:MET65
|
4.0
|
30.8
|
1.0
|
CB
|
E:HIS63
|
4.2
|
25.5
|
1.0
|
O
|
E:HOH826
|
4.3
|
37.6
|
1.0
|
NE2
|
E:HIS63
|
4.4
|
27.2
|
1.0
|
ND1
|
E:HIS30
|
4.5
|
38.7
|
1.0
|
CG
|
E:HIS30
|
4.5
|
36.6
|
1.0
|
CB
|
E:ASP32
|
4.5
|
36.6
|
1.0
|
CD2
|
E:HIS63
|
4.7
|
27.9
|
1.0
|
CB
|
E:ASP173
|
4.7
|
46.0
|
1.0
|
SD
|
E:MET135
|
4.9
|
34.0
|
1.0
|
SD
|
E:MET65
|
4.9
|
28.5
|
1.0
|
CD1
|
E:ILE112
|
4.9
|
31.8
|
1.0
|
CD1
|
E:ILE193
|
5.0
|
28.2
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 3ct7
Go back to
Magnesium Binding Sites List in 3ct7
Magnesium binding site 6 out
of 6 in the Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12
![](/pictures/MG/pdb/ct/3ct7-MG-sphere_06.jpg) Mono view
![](/pictures/MG/pdb/ct/3ct7-MG-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Crystal Structure of D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg601
b:42.7
occ:1.00
|
OD2
|
F:ASP32
|
2.3
|
39.9
|
1.0
|
OD1
|
F:ASP173
|
2.5
|
45.1
|
1.0
|
ND1
|
F:HIS63
|
2.7
|
32.0
|
1.0
|
NE2
|
F:HIS30
|
2.7
|
33.9
|
1.0
|
CG
|
F:ASP32
|
3.0
|
38.4
|
1.0
|
OD1
|
F:ASP32
|
3.1
|
41.3
|
1.0
|
CE1
|
F:HIS63
|
3.2
|
31.1
|
1.0
|
CG
|
F:ASP173
|
3.5
|
43.2
|
1.0
|
CD2
|
F:HIS30
|
3.6
|
32.4
|
1.0
|
CE
|
F:MET65
|
3.7
|
21.9
|
1.0
|
OD2
|
F:ASP173
|
3.7
|
42.5
|
1.0
|
CE1
|
F:HIS30
|
3.8
|
33.4
|
1.0
|
CG
|
F:HIS63
|
3.9
|
30.3
|
1.0
|
CB
|
F:ASP32
|
4.4
|
34.8
|
1.0
|
CB
|
F:HIS63
|
4.4
|
28.5
|
1.0
|
NE2
|
F:HIS63
|
4.5
|
31.5
|
1.0
|
O
|
F:HOH816
|
4.6
|
40.4
|
1.0
|
SD
|
F:MET65
|
4.7
|
26.4
|
1.0
|
CD2
|
F:HIS63
|
4.8
|
30.3
|
1.0
|
CG
|
F:HIS30
|
4.8
|
34.0
|
1.0
|
CB
|
F:ASP173
|
4.8
|
41.8
|
1.0
|
ND1
|
F:HIS30
|
4.9
|
33.5
|
1.0
|
SD
|
F:MET135
|
4.9
|
34.6
|
1.0
|
|
Reference:
K.K.Chan,
A.A.Fedorov,
E.V.Fedorov,
S.C.Almo,
J.A.Gerlt.
Structural Basis For Substrate Specificity in Phosphate Binding (Beta/Alpha)8-Barrels: D-Allulose 6-Phosphate 3-Epimerase From Escherichia Coli K-12. Biochemistry V. 47 9608 2008.
ISSN: ISSN 0006-2960
PubMed: 18700786
DOI: 10.1021/BI800821V
Page generated: Wed Aug 14 11:52:45 2024
|