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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

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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 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 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 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

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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

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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

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