Magnesium in PDB 7v09: Crystal Structure of ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein
Protein crystallography data
The structure of Crystal Structure of ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein, PDB code: 7v09
was solved by
P.J.Stogios,
T.Skarina,
N.Mesa,
R.Di Leo,
A.Savchenko,
A.Joachimiak,
K.J.F.Satchell,
Center For Structural Genomics Of Infectious Diseases(Csgid),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.86 /
2.00
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
69.956,
67.618,
86.656,
90,
104.22,
90
|
R / Rfree (%)
|
25 /
29.6
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein
(pdb code 7v09). 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 ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein, PDB code: 7v09:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 7v09
Go back to
Magnesium Binding Sites List in 7v09
Magnesium binding site 1 out
of 5 in the Crystal Structure of ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein
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 ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg501
b:21.6
occ:1.00
|
O
|
A:PHE284
|
2.1
|
28.6
|
1.0
|
O
|
A:HOH791
|
2.3
|
28.0
|
1.0
|
OE2
|
A:GLU367
|
2.3
|
28.7
|
1.0
|
OE2
|
A:GLU164
|
2.4
|
36.0
|
1.0
|
OE1
|
A:GLU164
|
2.8
|
33.7
|
1.0
|
CD
|
A:GLU164
|
2.9
|
30.3
|
1.0
|
C
|
A:PHE284
|
3.3
|
26.8
|
1.0
|
CD
|
A:GLU367
|
3.4
|
33.5
|
1.0
|
OE1
|
A:GLU367
|
3.9
|
33.0
|
1.0
|
N
|
A:PHE284
|
4.0
|
26.9
|
1.0
|
CA
|
A:PHE284
|
4.1
|
29.2
|
1.0
|
N
|
A:VAL285
|
4.4
|
28.3
|
1.0
|
CG
|
A:GLU164
|
4.4
|
31.2
|
1.0
|
CB
|
A:PHE284
|
4.4
|
31.8
|
1.0
|
CA
|
A:VAL285
|
4.6
|
26.2
|
1.0
|
CG
|
A:GLU367
|
4.7
|
32.9
|
1.0
|
O
|
A:HOH725
|
4.7
|
29.8
|
1.0
|
OH
|
A:TYR152
|
4.8
|
29.1
|
1.0
|
CE1
|
A:TYR152
|
5.0
|
30.3
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 7v09
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Magnesium Binding Sites List in 7v09
Magnesium binding site 2 out
of 5 in the Crystal Structure of ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein
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 ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:19.5
occ:1.00
|
O
|
A:SER245
|
2.2
|
29.4
|
1.0
|
OE2
|
A:GLU250
|
2.3
|
34.5
|
1.0
|
OE1
|
B:GLU68
|
2.4
|
36.5
|
1.0
|
O
|
B:HOH643
|
2.4
|
23.3
|
0.5
|
OE2
|
B:GLU68
|
2.4
|
35.2
|
1.0
|
O
|
A:HOH726
|
2.5
|
30.2
|
1.0
|
CD
|
B:GLU68
|
2.7
|
34.3
|
1.0
|
OE1
|
A:GLU250
|
2.7
|
27.1
|
1.0
|
CD
|
A:GLU250
|
2.9
|
29.5
|
1.0
|
C
|
A:SER245
|
3.3
|
27.9
|
1.0
|
O
|
B:HOH643
|
3.6
|
26.1
|
0.5
|
N
|
A:SER245
|
4.0
|
26.0
|
1.0
|
CA
|
A:SER245
|
4.1
|
27.4
|
1.0
|
CG
|
B:GLU68
|
4.2
|
34.2
|
1.0
|
N
|
A:ASN246
|
4.3
|
28.1
|
1.0
|
OD2
|
A:ASP247
|
4.3
|
27.7
|
1.0
|
CG
|
A:GLU250
|
4.4
|
26.9
|
1.0
|
CB
|
A:SER245
|
4.4
|
26.0
|
1.0
|
CA
|
A:ASN246
|
4.5
|
27.2
|
1.0
|
OD1
|
A:ASN246
|
4.7
|
28.8
|
1.0
|
O
|
A:HOH849
|
4.9
|
33.8
|
1.0
|
OD2
|
B:ASP70
|
4.9
|
33.4
|
1.0
|
CB
|
B:GLU68
|
4.9
|
30.6
|
1.0
|
N
|
A:ASP247
|
4.9
|
27.0
|
1.0
|
C
|
A:GLY244
|
5.0
|
29.3
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 7v09
Go back to
Magnesium Binding Sites List in 7v09
Magnesium binding site 3 out
of 5 in the Crystal Structure of ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein
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 ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg503
b:30.5
occ:1.00
|
OE1
|
A:GLN307
|
2.3
|
31.9
|
1.0
|
OE2
|
A:GLU87
|
2.4
|
33.6
|
1.0
|
O
|
A:HOH731
|
2.6
|
27.0
|
0.5
|
O
|
A:HOH658
|
2.9
|
39.7
|
1.0
|
OE1
|
A:GLU311
|
2.9
|
34.7
|
1.0
|
OE2
|
A:GLU311
|
2.9
|
37.4
|
1.0
|
CD
|
A:GLU311
|
3.1
|
35.7
|
1.0
|
O
|
A:HOH664
|
3.1
|
36.2
|
1.0
|
CD
|
A:GLN307
|
3.5
|
31.8
|
1.0
|
CD
|
A:GLU87
|
3.6
|
31.1
|
1.0
|
O
|
A:HOH731
|
3.9
|
27.6
|
0.5
|
NE2
|
A:GLN307
|
4.2
|
30.0
|
1.0
|
CG
|
A:GLU311
|
4.4
|
33.2
|
1.0
|
CG
|
A:GLU87
|
4.5
|
31.5
|
1.0
|
OE1
|
A:GLU87
|
4.5
|
27.9
|
1.0
|
O
|
A:LEU85
|
4.6
|
28.3
|
1.0
|
CG
|
A:GLN307
|
4.6
|
31.4
|
1.0
|
O
|
A:HOH842
|
4.7
|
37.5
|
1.0
|
CB
|
A:GLN307
|
4.7
|
33.1
|
1.0
|
CA
|
A:GLN307
|
4.8
|
33.8
|
1.0
|
CB
|
A:GLU311
|
4.9
|
34.6
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 7v09
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Magnesium Binding Sites List in 7v09
Magnesium binding site 4 out
of 5 in the Crystal Structure of ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein
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 ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg501
b:28.2
occ:1.00
|
O
|
B:HOH696
|
2.1
|
30.6
|
1.0
|
OE2
|
B:GLU250
|
2.4
|
39.3
|
1.0
|
OE1
|
A:GLU68
|
2.4
|
39.6
|
1.0
|
O
|
A:HOH690
|
2.4
|
33.0
|
1.0
|
O
|
B:SER245
|
2.5
|
33.3
|
1.0
|
OE1
|
B:GLU250
|
2.7
|
31.3
|
1.0
|
OE2
|
A:GLU68
|
2.8
|
40.3
|
1.0
|
CD
|
B:GLU250
|
2.9
|
38.1
|
1.0
|
CD
|
A:GLU68
|
2.9
|
32.7
|
1.0
|
C
|
B:SER245
|
3.5
|
32.1
|
1.0
|
N
|
B:SER245
|
4.2
|
33.4
|
1.0
|
N
|
B:ASN246
|
4.4
|
32.2
|
1.0
|
CG
|
B:GLU250
|
4.4
|
34.5
|
1.0
|
CA
|
B:SER245
|
4.4
|
31.3
|
1.0
|
CA
|
B:ASN246
|
4.4
|
33.7
|
1.0
|
O
|
A:HOH728
|
4.4
|
36.7
|
1.0
|
CG
|
A:GLU68
|
4.4
|
33.4
|
1.0
|
OD1
|
B:ASN246
|
4.5
|
35.0
|
1.0
|
O
|
A:HOH806
|
4.6
|
32.4
|
1.0
|
OD2
|
B:ASP247
|
4.6
|
34.9
|
1.0
|
OD2
|
A:ASP70
|
4.8
|
35.5
|
1.0
|
CB
|
B:SER245
|
4.9
|
30.9
|
1.0
|
C
|
B:GLY244
|
5.0
|
32.8
|
1.0
|
N
|
B:ASP247
|
5.0
|
32.1
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 7v09
Go back to
Magnesium Binding Sites List in 7v09
Magnesium binding site 5 out
of 5 in the Crystal Structure of ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein
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 ECL_RS08780, Putative Sugar Transport System Periplasmic Sugar-Binding Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg502
b:37.2
occ:1.00
|
OE2
|
B:GLU164
|
2.0
|
52.2
|
1.0
|
O
|
B:PHE284
|
2.0
|
49.1
|
1.0
|
O
|
B:HOH632
|
2.1
|
43.5
|
1.0
|
OE2
|
B:GLU367
|
2.1
|
45.4
|
1.0
|
CD
|
B:GLU164
|
2.8
|
52.7
|
1.0
|
OE1
|
B:GLU164
|
3.1
|
57.4
|
1.0
|
C
|
B:PHE284
|
3.2
|
44.4
|
1.0
|
CD
|
B:GLU367
|
3.3
|
40.6
|
1.0
|
OE1
|
B:GLU367
|
3.8
|
41.1
|
1.0
|
O
|
B:HOH802
|
4.1
|
40.3
|
1.0
|
N
|
B:VAL285
|
4.1
|
39.9
|
1.0
|
CA
|
B:VAL285
|
4.1
|
42.8
|
1.0
|
CG
|
B:GLU164
|
4.2
|
55.4
|
1.0
|
CA
|
B:PHE284
|
4.2
|
44.7
|
1.0
|
N
|
B:PHE284
|
4.3
|
46.3
|
1.0
|
O
|
B:HOH688
|
4.3
|
37.7
|
1.0
|
CG
|
B:GLU367
|
4.5
|
42.8
|
1.0
|
CB
|
B:PHE284
|
4.6
|
40.1
|
1.0
|
CD2
|
B:PHE284
|
4.8
|
42.1
|
1.0
|
CB
|
B:VAL285
|
4.9
|
48.7
|
1.0
|
|
Reference:
P.J.Stogios,
P.J.Stogios,
T.Skarina,
N.Mesa,
R.Di Leo,
A.Savchenko,
A.Joachimiak,
K.J.F.Satchell,
Center For Structural Genomics Of Infectious Diseases(Csgid).
N/A N/A.
Page generated: Thu Oct 3 10:18:03 2024
|