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Manganese in PDB 4urr: Tailspike Protein of SF6 Bacteriophage Bound to Shigella Flexneri O-Antigen Octasaccharide Fragment

Protein crystallography data

The structure of Tailspike Protein of SF6 Bacteriophage Bound to Shigella Flexneri O-Antigen Octasaccharide Fragment, PDB code: 4urr was solved by U.Gohlke, U.Heinemann, R.Seckler, S.Barbirz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.33 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.987, 138.895, 136.073, 90.00, 92.05, 90.00
R / Rfree (%) 19.57 / 23.58

Manganese Binding Sites:

The binding sites of Manganese atom in the Tailspike Protein of SF6 Bacteriophage Bound to Shigella Flexneri O-Antigen Octasaccharide Fragment (pdb code 4urr). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 10 binding sites of Manganese where determined in the Tailspike Protein of SF6 Bacteriophage Bound to Shigella Flexneri O-Antigen Octasaccharide Fragment, PDB code: 4urr:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 10 in 4urr

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Manganese binding site 1 out of 10 in the Tailspike Protein of SF6 Bacteriophage Bound to Shigella Flexneri O-Antigen Octasaccharide Fragment


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Tailspike Protein of SF6 Bacteriophage Bound to Shigella Flexneri O-Antigen Octasaccharide Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1623

b:13.8
occ:1.00
 O A:HOH2016 2.0 5.0 1.0
OD1 A:ASP135 2.1 10.6 1.0
O A:HOH2018 2.2 8.4 1.0
O A:HOH2015 2.2 10.6 1.0
ND1 A:HIS153 2.3 19.7 1.0
O A:HOH2020 2.3 3.0 1.0
CG A:ASP135 3.2 11.4 1.0
CE1 A:HIS153 3.3 18.5 1.0
CG A:HIS153 3.3 19.0 1.0
OD2 A:ASP135 3.5 9.9 1.0
CB A:HIS153 3.5 15.4 1.0
O B:LYS141 3.9 16.2 1.0
OE1 A:GLN123 4.1 31.4 1.0
CA A:HIS153 4.2 13.7 1.0
O A:HOH2033 4.2 8.9 1.0
N B:LYS141 4.3 9.7 1.0
NE2 A:HIS153 4.4 19.1 1.0
CD2 A:HIS153 4.4 20.0 1.0
O B:GLY139 4.4 11.5 1.0
N A:ALA136 4.4 16.1 1.0
O A:LYS133 4.5 12.9 1.0
CB A:ASP135 4.5 14.2 1.0
O A:ASN131 4.5 20.2 1.0
N A:ASP135 4.6 12.6 1.0
C B:LYS141 4.8 15.1 1.0
CA A:ASP135 4.9 13.5 1.0
CA B:VAL140 4.9 9.9 1.0
C A:ASP135 4.9 18.7 1.0
CB A:ALA136 5.0 15.8 1.0

Manganese binding site 2 out of 10 in 4urr

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Manganese binding site 2 out of 10 in the Tailspike Protein of SF6 Bacteriophage Bound to Shigella Flexneri O-Antigen Octasaccharide Fragment


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Tailspike Protein of SF6 Bacteriophage Bound to Shigella Flexneri O-Antigen Octasaccharide Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1624

b:4.8
occ:0.33
 O A:HOH2202 2.0 18.9 1.0
OE2 B:GLU394 2.0 8.5 1.0
OE2 A:GLU394 2.1 12.6 1.0
O A:HOH2313 2.1 5.2 1.0
OE2 C:GLU394 2.2 6.6 1.0
O A:HOH2193 2.2 7.8 1.0
CD B:GLU394 3.2 24.3 1.0
CD A:GLU394 3.2 21.8 1.0
CD C:GLU394 3.3 21.6 1.0
OE1 A:GLU394 3.7 24.9 1.0
OE1 B:GLU394 3.7 32.9 1.0
OE1 C:GLU394 3.8 29.4 1.0
OE1 A:GLN395 3.9 12.4 1.0
OE1 B:GLN395 4.0 16.0 1.0
OE1 C:GLN395 4.1 11.0 1.0
NE2 A:GLN395 4.2 24.7 1.0
OD2 B:ASP371 4.3 9.1 1.0
MN A:MN1625 4.3 14.2 0.3
OD2 C:ASP371 4.4 9.2 1.0
OD2 A:ASP371 4.4 8.3 1.0
NE2 B:GLN395 4.4 21.7 1.0
CG B:GLU394 4.4 16.2 1.0
CG A:GLU394 4.4 9.3 1.0
CD A:GLN395 4.4 20.3 1.0
NE2 C:GLN395 4.4 11.7 1.0
CG C:GLU394 4.5 10.0 1.0
CD B:GLN395 4.6 18.2 1.0
CD C:GLN395 4.7 12.9 1.0
CB B:ASP371 4.7 8.8 1.0
CB A:ASP371 4.8 8.0 1.0
CB C:ASP371 4.8 8.4 1.0
CG B:ASP371 4.9 11.0 1.0
CG A:ASP371 5.0 12.1 1.0

Manganese binding site 3 out of 10 in 4urr

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Manganese binding site 3 out of 10 in the Tailspike Protein of SF6 Bacteriophage Bound to Shigella Flexneri O-Antigen Octasaccharide Fragment


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Tailspike Protein of SF6 Bacteriophage Bound to Shigella Flexneri O-Antigen Octasaccharide Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1625

b:14.2
occ:0.33
 OE1 A:GLU394 2.0 24.9 1.0
OE1 B:GLU394 2.2 32.9 1.0
OE1 C:GLU394 2.2 29.4 1.0
CD A:GLU394 3.1 21.8 1.0
CD B:GLU394 3.3 24.3 1.0
CD C:GLU394 3.3 21.6 1.0
OE2 A:GLU394 3.7 12.6 1.0
OE2 B:GLU394 3.8 8.5 1.0
OE2 C:GLU394 3.8 6.6 1.0
O A:HOH2203 4.3 22.1 1.0
MN A:MN1624 4.3 4.8 0.3
CG A:GLU394 4.3 9.3 1.0
CB A:GLU394 4.5 5.6 1.0
CG B:GLU394 4.6 16.2 1.0
O A:HOH2130 4.6 15.7 1.0
CG C:GLU394 4.6 10.0 1.0
CB B:GLU394 4.8 8.8 1.0
CB C:GLU394 4.8 10.0 1.0
ND2 A:ASN419 4.9 10.5 1.0

Manganese binding site 4 out of 10 in 4urr

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Manganese binding site 4 out of 10 in the Tailspike Protein of SF6 Bacteriophage Bound to Shigella Flexneri O-Antigen Octasaccharide Fragment


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Tailspike Protein of SF6 Bacteriophage Bound to Shigella Flexneri O-Antigen Octasaccharide Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1624

b:13.7
occ:1.00
 O B:HOH2016 2.1 14.1 1.0
O B:HOH2015 2.2 14.6 1.0
OD1 B:ASP135 2.2 12.8 1.0
O B:HOH2023 2.2 10.1 1.0
ND1 B:HIS153 2.3 18.2 1.0
O B:HOH2021 2.6 10.2 1.0
CG B:ASP135 3.2 11.4 1.0
CE1 B:HIS153 3.3 19.5 1.0
CG B:HIS153 3.4 16.3 1.0
OD2 B:ASP135 3.6 10.6 1.0
CB B:HIS153 3.6 12.4 1.0
O C:LYS141 3.8 14.1 1.0
OE1 B:GLN123 3.9 29.6 1.0
N C:LYS141 4.2 14.0 1.0
CA B:HIS153 4.4 10.9 1.0
O B:HOH2035 4.4 13.4 1.0
O C:GLY139 4.4 17.4 1.0
O B:ASN131 4.4 16.3 1.0
O B:LYS133 4.4 19.6 1.0
N B:ALA136 4.5 11.8 1.0
NE2 B:HIS153 4.5 19.8 1.0
CD2 B:HIS153 4.5 19.1 1.0
N B:ASP135 4.5 10.7 1.0
CB B:ASP135 4.5 10.6 1.0
C C:LYS141 4.7 16.0 1.0
CA B:ASP135 4.9 10.2 1.0
CA C:VAL140 4.9 11.2 1.0
CA C:LYS141 5.0 13.0 1.0
C B:ASP135 5.0 13.4 1.0
CB B:ALA136 5.0 10.4 1.0

Manganese binding site 5 out of 10 in 4urr

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Manganese binding site 5 out of 10 in the Tailspike Protein of SF6 Bacteriophage Bound to Shigella Flexneri O-Antigen Octasaccharide Fragment


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Tailspike Protein of SF6 Bacteriophage Bound to Shigella Flexneri O-Antigen Octasaccharide Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1623

b:19.7
occ:1.00
 OD1 C:ASP135 2.1 12.7 1.0
O C:HOH2017 2.2 17.2 1.0
O A:HOH2024 2.3 25.1 1.0
O A:HOH2023 2.4 14.3 1.0
ND1 C:HIS153 2.5 20.5 1.0
O A:HOH2022 2.5 7.3 1.0
CG C:ASP135 3.1 13.8 1.0
CE1 C:HIS153 3.4 19.1 1.0
OD2 C:ASP135 3.5 10.9 1.0
CG C:HIS153 3.5 18.1 1.0
CB C:HIS153 3.7 13.9 1.0
O A:LYS141 3.8 21.0 1.0
OE1 C:GLN123 4.0 59.5 1.0
N A:LYS141 4.1 20.7 1.0
O A:GLY139 4.3 17.2 1.0
CA C:HIS153 4.4 12.6 1.0
O A:HOH2026 4.4 22.7 1.0
CB C:ASP135 4.5 12.9 1.0
N C:ASP135 4.5 12.4 1.0
N C:ALA136 4.6 16.1 1.0
O C:LYS133 4.6 22.7 1.0
NE2 C:HIS153 4.6 19.6 1.0
CD2 C:HIS153 4.6 20.6 1.0
C A:LYS141 4.7 23.6 1.0
CA A:VAL140 4.7 15.4 1.0
O C:ASN131 4.7 34.8 1.0
CA C:ASP135 4.9 11.7 1.0
CA A:LYS141 4.9 20.9 1.0
C A:VAL140 4.9 23.9 1.0

Manganese binding site 6 out of 10 in 4urr

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Manganese binding site 6 out of 10 in the Tailspike Protein of SF6 Bacteriophage Bound to Shigella Flexneri O-Antigen Octasaccharide Fragment


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Tailspike Protein of SF6 Bacteriophage Bound to Shigella Flexneri O-Antigen Octasaccharide Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1623

b:32.8
occ:1.00
 O D:HOH2017 2.1 16.5 1.0
OD1 D:ASP135 2.2 28.5 1.0
ND1 D:HIS153 2.2 32.8 1.0
O D:HOH2015 2.3 17.1 1.0
O D:HOH2011 2.4 15.9 1.0
O D:HOH2012 2.4 12.0 1.0
CE1 D:HIS153 3.2 31.6 1.0
CG D:ASP135 3.2 31.4 1.0
CG D:HIS153 3.2 31.1 1.0
CB D:HIS153 3.5 27.2 1.0
OD2 D:ASP135 3.6 38.0 1.0
O E:LYS141 3.8 38.2 1.0
OE1 D:GLN123 4.1 38.6 1.0
CA D:HIS153 4.2 25.5 1.0
NE2 D:HIS153 4.4 31.6 1.0
N E:LYS141 4.4 29.3 1.0
CD2 D:HIS153 4.4 32.4 1.0
N D:ALA136 4.4 24.4 1.0
O D:HOH2018 4.5 20.0 1.0
O D:ASN131 4.5 36.9 1.0
CB D:ASP135 4.5 24.6 1.0
O D:LYS133 4.6 31.4 1.0
N D:ASP135 4.6 23.6 1.0
O E:GLY139 4.6 36.9 1.0
C E:LYS141 4.8 36.3 1.0
CA D:ASP135 4.9 23.6 1.0
C D:ASP135 4.9 27.6 1.0
CB D:ALA136 5.0 25.3 1.0

Manganese binding site 7 out of 10 in 4urr

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Manganese binding site 7 out of 10 in the Tailspike Protein of SF6 Bacteriophage Bound to Shigella Flexneri O-Antigen Octasaccharide Fragment


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Tailspike Protein of SF6 Bacteriophage Bound to Shigella Flexneri O-Antigen Octasaccharide Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1624

b:6.2
occ:0.33
 O D:HOH2116 2.1 9.2 1.0
OE2 D:GLU394 2.1 24.2 1.0
O D:HOH2245 2.2 5.5 1.0
OE2 E:GLU394 2.2 13.6 1.0
OE2 F:GLU394 2.2 19.0 1.0
O D:HOH2117 2.2 12.8 1.0
CD D:GLU394 3.3 34.8 1.0
CD F:GLU394 3.3 32.7 1.0
CD E:GLU394 3.3 25.3 1.0
OE1 F:GLU394 3.8 18.3 1.0
OE1 D:GLU394 3.8 54.1 1.0
OE1 E:GLU394 3.9 34.9 1.0
OE1 D:GLN395 3.9 11.1 1.0
OE1 F:GLN395 4.0 13.9 1.0
OE1 E:GLN395 4.1 16.9 1.0
OD2 E:ASP371 4.2 15.5 1.0
OD2 D:ASP371 4.2 22.2 1.0
NE2 D:GLN395 4.3 21.9 1.0
NE2 F:GLN395 4.3 21.1 1.0
OD2 F:ASP371 4.3 16.4 1.0
CG D:GLU394 4.5 18.1 1.0
NE2 E:GLN395 4.5 11.6 1.0
MN D:MN1625 4.5 23.6 0.3
CD D:GLN395 4.5 16.9 1.0
CG E:GLU394 4.5 11.1 1.0
CG F:GLU394 4.6 11.0 1.0
CD F:GLN395 4.6 22.7 1.0
CB D:ASP371 4.7 10.8 1.0
CD E:GLN395 4.7 12.5 1.0
CB E:ASP371 4.7 12.8 1.0
CG D:ASP371 4.8 23.2 1.0
CB F:ASP371 4.8 6.8 1.0
CG E:ASP371 4.9 18.2 1.0
CG F:ASP371 5.0 13.4 1.0

Manganese binding site 8 out of 10 in 4urr

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Manganese binding site 8 out of 10 in the Tailspike Protein of SF6 Bacteriophage Bound to Shigella Flexneri O-Antigen Octasaccharide Fragment


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Tailspike Protein of SF6 Bacteriophage Bound to Shigella Flexneri O-Antigen Octasaccharide Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1625

b:23.6
occ:0.33
 OE1 F:GLU394 2.0 18.3 1.0
OE1 E:GLU394 2.0 34.9 1.0
O D:HOH2246 2.4 19.8 1.0
OE1 D:GLU394 2.6 54.1 1.0
O D:HOH2131 3.0 14.8 1.0
CD F:GLU394 3.1 32.7 1.0
CD E:GLU394 3.2 25.3 1.0
CD D:GLU394 3.6 34.8 1.0
OE2 F:GLU394 3.6 19.0 1.0
OE2 E:GLU394 3.7 13.6 1.0
O D:HOH2132 3.9 16.9 1.0
OE2 D:GLU394 3.9 24.2 1.0
CG F:GLU394 4.3 11.0 1.0
CG E:GLU394 4.4 11.1 1.0
CB F:GLU394 4.5 8.5 1.0
MN D:MN1624 4.5 6.2 0.3
CB E:GLU394 4.6 8.1 1.0
ND2 E:ASN419 4.7 15.5 1.0
NE2 E:GLN395 4.8 11.6 1.0
CG D:GLU394 4.9 18.1 1.0
O D:HOH2133 5.0 17.8 1.0

Manganese binding site 9 out of 10 in 4urr

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Manganese binding site 9 out of 10 in the Tailspike Protein of SF6 Bacteriophage Bound to Shigella Flexneri O-Antigen Octasaccharide Fragment


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Tailspike Protein of SF6 Bacteriophage Bound to Shigella Flexneri O-Antigen Octasaccharide Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn1623

b:26.8
occ:1.00
 OD1 E:ASP135 2.0 44.0 1.0
O E:HOH2022 2.2 20.3 1.0
ND1 E:HIS153 2.3 31.1 1.0
O E:HOH2020 2.6 28.2 1.0
CG E:ASP135 3.1 41.0 1.0
CG E:HIS153 3.3 29.1 1.0
CE1 E:HIS153 3.4 30.1 1.0
OD2 E:ASP135 3.5 40.9 1.0
CB E:HIS153 3.5 25.2 1.0
O F:LYS141 4.0 32.0 1.0
OE1 E:GLN123 4.1 53.3 1.0
CA E:HIS153 4.2 24.7 1.0
O E:HOH2027 4.2 20.5 1.0
N E:ALA136 4.3 31.2 1.0
O F:GLY139 4.3 37.3 1.0
N F:LYS141 4.4 33.9 1.0
CB E:ASP135 4.4 33.7 1.0
N E:ASP135 4.4 34.7 1.0
O E:LYS133 4.4 40.8 1.0
CD2 E:HIS153 4.4 31.3 1.0
NE2 E:HIS153 4.5 30.4 1.0
O E:ASN131 4.5 45.6 1.0
CA E:ASP135 4.7 33.3 1.0
C E:ASP135 4.8 34.9 1.0
CA F:VAL140 4.9 35.6 1.0
CB E:ALA136 4.9 32.6 1.0
C F:LYS141 4.9 36.0 1.0

Manganese binding site 10 out of 10 in 4urr

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Manganese binding site 10 out of 10 in the Tailspike Protein of SF6 Bacteriophage Bound to Shigella Flexneri O-Antigen Octasaccharide Fragment


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Tailspike Protein of SF6 Bacteriophage Bound to Shigella Flexneri O-Antigen Octasaccharide Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn1624

b:28.1
occ:1.00
 O D:HOH2019 2.2 18.1 1.0
OD1 F:ASP135 2.2 37.2 1.0
O D:HOH2021 2.2 24.2 1.0
O F:HOH2012 2.2 17.7 1.0
O D:HOH2020 2.3 21.4 1.0
ND1 F:HIS153 2.4 34.6 1.0
CG F:ASP135 3.3 37.2 1.0
CE1 F:HIS153 3.3 33.9 1.0
CG F:HIS153 3.4 33.3 1.0
OD2 F:ASP135 3.6 40.8 1.0
CB F:HIS153 3.7 30.8 1.0
O D:LYS141 3.8 26.6 1.0
OE1 F:GLN123 3.9 40.0 1.0
N D:LYS141 4.3 25.9 1.0
O D:HOH2023 4.4 9.8 1.0
O F:LYS133 4.4 29.6 1.0
O F:ASN131 4.4 35.9 1.0
CA F:HIS153 4.4 30.8 1.0
N F:ALA136 4.5 28.6 1.0
O D:GLY139 4.5 25.4 1.0
N F:ASP135 4.5 29.6 1.0
NE2 F:HIS153 4.5 34.1 1.0
CD2 F:HIS153 4.6 34.4 1.0
CB F:ASP135 4.6 30.0 1.0
C D:LYS141 4.7 28.6 1.0
CA F:ASP135 4.9 29.2 1.0
CA D:VAL140 4.9 23.4 1.0
CA D:LYS141 5.0 25.6 1.0
CD F:GLN123 5.0 49.8 1.0
CB F:ALA136 5.0 27.9 1.0

Reference:

Y.Kang, U.Gohlke, T.Scheid, S.Kunstmann, U.Heinemann, R.Seckler, R.Lipowsky, M.Santer, S.Barbirz. Shigella Flexneri O-Polysaccharide Fragments Interacting with the Tailspike Protein of Bacteriophage SF6 To Be Published.
Page generated: Sat Oct 5 21:23:30 2024

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