Magnesium in PDB 6f45: Crystal Structure of the GP37-GP38 Adhesin Tip Complex of the Bacteriophage S16 Long Tail Fiber
Protein crystallography data
The structure of Crystal Structure of the GP37-GP38 Adhesin Tip Complex of the Bacteriophage S16 Long Tail Fiber, PDB code: 6f45
was solved by
M.Dunne,
P.Leiman,
J.Klumpp,
M.J.Loessner,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.76 /
1.70
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
81.337,
98.904,
140.036,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.2 /
18.5
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of the GP37-GP38 Adhesin Tip Complex of the Bacteriophage S16 Long Tail Fiber
(pdb code 6f45). 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 the GP37-GP38 Adhesin Tip Complex of the Bacteriophage S16 Long Tail Fiber, PDB code: 6f45:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 6f45
Go back to
Magnesium Binding Sites List in 6f45
Magnesium binding site 1 out
of 6 in the Crystal Structure of the GP37-GP38 Adhesin Tip Complex of the Bacteriophage S16 Long Tail Fiber
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 the GP37-GP38 Adhesin Tip Complex of the Bacteriophage S16 Long Tail Fiber within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg301
b:31.4
occ:1.00
|
O
|
D:HOH607
|
2.1
|
29.8
|
1.0
|
O
|
D:HOH561
|
2.2
|
24.8
|
1.0
|
O
|
D:HOH421
|
2.2
|
30.5
|
1.0
|
OD1
|
D:ASN240
|
3.9
|
24.9
|
1.0
|
ND2
|
D:ASN240
|
4.2
|
24.8
|
1.0
|
O
|
D:HOH482
|
4.2
|
32.3
|
1.0
|
O
|
D:HOH423
|
4.3
|
39.6
|
1.0
|
O
|
D:HOH644
|
4.3
|
32.7
|
1.0
|
O
|
D:HOH609
|
4.4
|
36.1
|
1.0
|
CA
|
D:GLY242
|
4.5
|
20.1
|
1.0
|
CG
|
D:ASN240
|
4.5
|
22.4
|
1.0
|
N
|
D:GLY242
|
4.6
|
23.2
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 6f45
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Magnesium Binding Sites List in 6f45
Magnesium binding site 2 out
of 6 in the Crystal Structure of the GP37-GP38 Adhesin Tip Complex of the Bacteriophage S16 Long Tail Fiber
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 the GP37-GP38 Adhesin Tip Complex of the Bacteriophage S16 Long Tail Fiber within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg801
b:35.3
occ:1.00
|
OD1
|
A:ASN595
|
2.1
|
32.4
|
0.6
|
OD2
|
A:ASP579
|
2.2
|
32.3
|
0.4
|
O
|
A:HOH907
|
2.2
|
37.0
|
1.0
|
OD2
|
A:ASP579
|
2.3
|
30.7
|
0.6
|
O
|
A:HOH968
|
2.3
|
45.2
|
1.0
|
O
|
A:HOH967
|
2.4
|
41.5
|
1.0
|
O
|
B:HOH906
|
2.6
|
41.2
|
1.0
|
CG
|
A:ASP579
|
2.9
|
29.4
|
0.4
|
OD1
|
A:ASP579
|
3.0
|
24.4
|
0.4
|
CG
|
A:ASN595
|
3.2
|
36.6
|
0.6
|
OD1
|
A:ASN595
|
3.3
|
30.9
|
0.4
|
CG
|
A:ASP579
|
3.3
|
28.5
|
0.6
|
CB
|
A:ASP579
|
3.7
|
21.6
|
0.6
|
ND2
|
A:ASN595
|
3.8
|
35.0
|
0.6
|
CG
|
A:ASN595
|
3.9
|
27.4
|
0.4
|
OD1
|
B:ASP587
|
4.1
|
31.7
|
1.0
|
O
|
A:HOH909
|
4.2
|
30.9
|
1.0
|
O
|
A:HOH959
|
4.2
|
48.7
|
1.0
|
OD2
|
B:ASP587
|
4.2
|
30.2
|
1.0
|
CB
|
A:ASP579
|
4.4
|
27.7
|
0.4
|
OD1
|
A:ASP579
|
4.4
|
25.0
|
0.6
|
OD1
|
A:ASP577
|
4.4
|
26.6
|
1.0
|
CB
|
A:ASN595
|
4.5
|
30.7
|
0.6
|
CB
|
A:ASN595
|
4.5
|
30.6
|
0.4
|
CA
|
A:ASN595
|
4.6
|
23.7
|
0.6
|
CA
|
A:ASN595
|
4.6
|
23.8
|
0.4
|
CG
|
B:ASP587
|
4.6
|
34.7
|
1.0
|
ND2
|
A:ASN596
|
4.7
|
37.6
|
1.0
|
ND2
|
A:ASN595
|
4.7
|
30.0
|
0.4
|
O
|
A:HOH941
|
4.8
|
40.4
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 6f45
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Magnesium Binding Sites List in 6f45
Magnesium binding site 3 out
of 6 in the Crystal Structure of the GP37-GP38 Adhesin Tip Complex of the Bacteriophage S16 Long Tail Fiber
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 the GP37-GP38 Adhesin Tip Complex of the Bacteriophage S16 Long Tail Fiber within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg802
b:32.3
occ:0.46
|
O
|
A:HOH957
|
1.9
|
42.1
|
1.0
|
O
|
A:HOH920
|
2.1
|
48.1
|
1.0
|
O
|
A:HOH980
|
2.1
|
43.3
|
1.0
|
O
|
A:HOH979
|
2.3
|
44.6
|
1.0
|
O
|
A:HOH937
|
4.1
|
37.7
|
1.0
|
OE2
|
A:GLU610
|
4.3
|
27.0
|
1.0
|
OE1
|
A:GLU610
|
4.4
|
31.5
|
1.0
|
O
|
A:HOH985
|
4.5
|
42.7
|
1.0
|
CD
|
A:GLU610
|
4.7
|
29.2
|
1.0
|
O
|
A:HOH954
|
4.7
|
55.1
|
1.0
|
NE2
|
A:GLN591
|
5.0
|
32.7
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 6f45
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Magnesium Binding Sites List in 6f45
Magnesium binding site 4 out
of 6 in the Crystal Structure of the GP37-GP38 Adhesin Tip Complex of the Bacteriophage S16 Long Tail Fiber
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 the GP37-GP38 Adhesin Tip Complex of the Bacteriophage S16 Long Tail Fiber within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg803
b:27.7
occ:0.61
|
OD1
|
A:ASP579
|
2.0
|
25.0
|
0.6
|
O
|
A:HOH941
|
2.1
|
40.4
|
1.0
|
O
|
A:HOH924
|
2.1
|
39.0
|
1.0
|
O
|
A:HOH983
|
2.2
|
35.5
|
1.0
|
O
|
A:HOH910
|
2.2
|
37.8
|
1.0
|
O
|
A:HOH943
|
2.2
|
40.0
|
1.0
|
CG
|
A:ASP579
|
3.0
|
28.5
|
0.6
|
OD2
|
A:ASP579
|
3.4
|
30.7
|
0.6
|
CB
|
A:ASP579
|
3.8
|
27.7
|
0.4
|
OD1
|
A:ASN578
|
3.8
|
27.1
|
1.0
|
OD2
|
A:ASP579
|
3.9
|
32.3
|
0.4
|
OD1
|
A:ASN596
|
4.2
|
34.8
|
1.0
|
ND2
|
A:ASN596
|
4.2
|
37.6
|
1.0
|
CG
|
A:ASP579
|
4.2
|
29.4
|
0.4
|
O
|
A:HOH978
|
4.3
|
53.1
|
1.0
|
CB
|
A:ASP579
|
4.3
|
21.6
|
0.6
|
CG
|
A:ASN578
|
4.4
|
30.8
|
1.0
|
O
|
A:ASN578
|
4.4
|
28.5
|
1.0
|
ND2
|
A:ASN578
|
4.5
|
43.0
|
1.0
|
CG
|
A:ASN596
|
4.6
|
30.4
|
1.0
|
CA
|
A:ASP579
|
4.7
|
23.5
|
0.6
|
CA
|
A:ASP579
|
4.7
|
23.3
|
0.4
|
N
|
A:ASP579
|
4.8
|
21.1
|
1.0
|
C
|
A:ASN578
|
4.8
|
23.9
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 6f45
Go back to
Magnesium Binding Sites List in 6f45
Magnesium binding site 5 out
of 6 in the Crystal Structure of the GP37-GP38 Adhesin Tip Complex of the Bacteriophage S16 Long Tail Fiber
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 the GP37-GP38 Adhesin Tip Complex of the Bacteriophage S16 Long Tail Fiber within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg801
b:71.3
occ:1.00
|
O
|
B:HOH954
|
2.0
|
68.8
|
1.0
|
O
|
C:HOH943
|
2.1
|
66.0
|
1.0
|
O
|
B:HOH936
|
2.2
|
55.2
|
1.0
|
OD1
|
B:ASN595
|
2.4
|
40.3
|
1.0
|
OD1
|
B:ASP579
|
2.4
|
44.4
|
1.0
|
OD1
|
B:ASP577
|
2.7
|
47.6
|
1.0
|
CG
|
B:ASP577
|
3.0
|
52.3
|
1.0
|
CG
|
B:ASP579
|
3.3
|
56.1
|
1.0
|
OD2
|
B:ASP577
|
3.3
|
47.8
|
1.0
|
OD2
|
B:ASP579
|
3.5
|
69.7
|
1.0
|
CG
|
B:ASN595
|
3.6
|
51.1
|
1.0
|
CB
|
B:ASP577
|
3.9
|
39.6
|
1.0
|
OD1
|
C:ASP587
|
4.0
|
44.3
|
1.0
|
CA
|
B:ASN595
|
4.3
|
31.8
|
1.0
|
OG1
|
B:THR580
|
4.3
|
27.2
|
1.0
|
ND2
|
B:ASN595
|
4.5
|
50.0
|
1.0
|
CB
|
B:ASN595
|
4.5
|
37.3
|
1.0
|
CB
|
B:ASP579
|
4.6
|
44.5
|
1.0
|
N
|
B:ASP579
|
4.7
|
31.2
|
1.0
|
O
|
B:HOH901
|
4.9
|
35.5
|
1.0
|
N
|
B:ASN595
|
4.9
|
30.2
|
1.0
|
N
|
C:GLY588
|
4.9
|
38.4
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 6f45
Go back to
Magnesium Binding Sites List in 6f45
Magnesium binding site 6 out
of 6 in the Crystal Structure of the GP37-GP38 Adhesin Tip Complex of the Bacteriophage S16 Long Tail Fiber
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Crystal Structure of the GP37-GP38 Adhesin Tip Complex of the Bacteriophage S16 Long Tail Fiber within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg801
b:62.5
occ:1.00
|
O
|
A:HOH915
|
2.1
|
62.7
|
1.0
|
O
|
C:HOH901
|
2.2
|
57.2
|
1.0
|
O
|
A:HOH901
|
2.2
|
63.5
|
1.0
|
O
|
C:HOH903
|
2.2
|
63.0
|
1.0
|
O
|
A:HOH904
|
2.7
|
58.0
|
1.0
|
O
|
C:HOH973
|
2.8
|
72.0
|
1.0
|
OD1
|
C:ASN595
|
3.3
|
41.1
|
0.6
|
OD1
|
A:ASP587
|
3.7
|
58.2
|
1.0
|
OD2
|
C:ASP577
|
3.7
|
62.1
|
1.0
|
OD1
|
C:ASN595
|
3.8
|
31.1
|
0.4
|
OD2
|
C:ASP579
|
3.9
|
59.5
|
1.0
|
CG
|
C:ASN595
|
4.0
|
38.7
|
0.6
|
O
|
C:HOH902
|
4.2
|
42.5
|
1.0
|
O
|
C:HOH909
|
4.2
|
54.4
|
1.0
|
ND2
|
C:ASN595
|
4.5
|
31.4
|
0.6
|
CG
|
C:ASN595
|
4.5
|
36.1
|
0.4
|
CG
|
A:ASP587
|
4.6
|
44.8
|
1.0
|
OD2
|
A:ASP587
|
4.6
|
64.8
|
1.0
|
CG
|
C:ASP577
|
4.6
|
52.8
|
1.0
|
OD1
|
C:ASP577
|
4.8
|
60.6
|
1.0
|
CG
|
C:ASP579
|
4.8
|
50.0
|
1.0
|
CB
|
C:ASP579
|
4.9
|
32.7
|
1.0
|
|
Reference:
M.Dunne,
J.M.Denyes,
H.Arndt,
M.J.Loessner,
P.G.Leiman,
J.Klumpp.
Salmonella Phage S16 Tail Fiber Adhesin Features A Rare Polyglycine Rich Domain For Host Recognition. Structure V. 26 1573 2018.
ISSN: ISSN 1878-4186
PubMed: 30244968
DOI: 10.1016/J.STR.2018.07.017
Page generated: Tue Oct 1 00:06:31 2024
|