Atomistry » Manganese » PDB 4u87-4wiu » 4urr
Atomistry »
  Manganese »
    PDB 4u87-4wiu »
      4urr »

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

Go back to Manganese Binding Sites List in 4urr
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

Go back to Manganese Binding Sites List in 4urr
Manganese binding site 2 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 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

Go back to Manganese Binding Sites List in 4urr
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

Go back to Manganese Binding Sites List in 4urr
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

Go back to Manganese Binding Sites List in 4urr
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

Go back to Manganese Binding Sites List in 4urr
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

Go back to Manganese Binding Sites List in 4urr
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

Go back to Manganese Binding Sites List in 4urr
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

Go back to Manganese Binding Sites List in 4urr
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

Go back to Manganese Binding Sites List in 4urr
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy