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Sodium in PDB 4ru5: Crystal Structure of the Pseudomonas Phage PHI297 Tailspike GP61

Protein crystallography data

The structure of Crystal Structure of the Pseudomonas Phage PHI297 Tailspike GP61, PDB code: 4ru5 was solved by C.Browning, L.V.Sycheva, M.M.Shneider, P.G.Leiman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.37 / 1.52
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 210.617, 124.705, 83.563, 90.00, 97.93, 90.00
R / Rfree (%) 7.9 / 12

Other elements in 4ru5:

The structure of Crystal Structure of the Pseudomonas Phage PHI297 Tailspike GP61 also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Pseudomonas Phage PHI297 Tailspike GP61 (pdb code 4ru5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Crystal Structure of the Pseudomonas Phage PHI297 Tailspike GP61, PDB code: 4ru5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 4ru5

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Sodium binding site 1 out of 10 in the Crystal Structure of the Pseudomonas Phage PHI297 Tailspike GP61


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Pseudomonas Phage PHI297 Tailspike GP61 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na803

b:60.3
occ:1.00
 O C:HOH1881 1.9 40.5 1.0
O A:HOH942 3.5 17.3 1.0
O B:HOH953 3.7 18.1 1.0
O B:ALA708 3.7 17.6 1.0
O C:HOH1053 3.8 17.0 1.0
N B:ALA708 4.0 15.1 1.0
O A:ALA708 4.0 16.4 1.0
O C:ALA708 4.1 16.3 1.0
CG1 B:VAL707 4.1 17.1 1.0
O A:HOH1305 4.2 31.3 1.0
N A:ALA708 4.2 16.4 1.0
CG1 C:VAL707 4.3 16.9 1.0
CG1 A:VAL707 4.4 14.9 1.0
N C:ALA708 4.4 14.1 1.0
CB B:ALA708 4.6 15.6 1.0
C B:ALA708 4.6 12.9 1.0
CA B:ALA708 4.7 14.4 1.0
CB A:ALA708 4.7 16.0 1.0
NE2 A:GLN689 4.7 19.1 1.0
CA B:VAL707 4.7 15.1 1.0
C B:VAL707 4.7 15.3 1.0
CA A:VAL707 4.8 15.0 1.0
CA A:ALA708 4.8 15.0 1.0
C A:VAL707 4.8 14.8 1.0
NE2 C:GLN689 4.8 19.3 1.0
C A:ALA708 4.9 12.4 1.0
NE2 B:GLN689 4.9 19.7 1.0
CB C:ALA708 4.9 18.2 1.0
CA C:VAL707 5.0 17.0 1.0
C C:ALA708 5.0 13.4 1.0

Sodium binding site 2 out of 10 in 4ru5

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Sodium binding site 2 out of 10 in the Crystal Structure of the Pseudomonas Phage PHI297 Tailspike GP61


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Pseudomonas Phage PHI297 Tailspike GP61 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na804

b:58.6
occ:1.00
 OD1 A:ASP336 3.1 27.0 1.0
O A:HOH1375 3.3 47.5 1.0
CG A:ASP336 3.7 24.5 1.0
O A:HOH1171 3.9 31.8 1.0
O A:SER333 3.9 22.7 0.3
O A:GLU334 4.0 20.7 1.0
OD2 A:ASP336 4.0 25.4 1.0
C A:GLU334 4.1 20.1 1.0
C A:VAL335 4.1 18.0 1.0
O A:VAL335 4.3 20.5 1.0
CG A:PRO292 4.3 23.8 1.0
N A:VAL335 4.3 19.3 1.0
N A:ASP336 4.4 17.5 1.0
CD A:PRO292 4.4 17.9 1.0
O A:HOH1487 4.4 49.2 1.0
O A:SER333 4.5 24.1 0.7
CA A:VAL335 4.6 17.6 1.0
O A:HOH1319 4.6 36.0 1.0
CA A:GLU334 4.7 19.8 1.0
O A:HOH1590 4.8 0.2 1.0
CB A:ASP336 4.9 19.5 1.0
C A:SER333 4.9 19.6 0.3
CA A:ASP336 4.9 18.4 1.0
O A:HOH1462 4.9 41.7 1.0
O A:HOH1105 5.0 26.2 1.0

Sodium binding site 3 out of 10 in 4ru5

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Sodium binding site 3 out of 10 in the Crystal Structure of the Pseudomonas Phage PHI297 Tailspike GP61


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Pseudomonas Phage PHI297 Tailspike GP61 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na805

b:67.1
occ:1.00
 CD1 A:LEU222 4.1 16.6 1.0
OE1 A:GLN253 4.2 23.9 1.0
CD2 A:LEU251 4.3 18.6 1.0
CD A:GLN253 4.3 20.8 1.0
NE2 A:GLN253 4.3 26.8 1.0
OE2 A:GLU224 4.3 32.5 1.0
O A:HOH1700 4.3 50.3 1.0
CD2 A:LEU222 4.4 18.9 1.0
O A:HOH1317 4.6 40.2 1.0
CD A:GLU224 4.8 23.8 1.0
CG A:LEU222 4.9 15.1 1.0
O A:HOH1490 4.9 55.2 1.0

Sodium binding site 4 out of 10 in 4ru5

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Sodium binding site 4 out of 10 in the Crystal Structure of the Pseudomonas Phage PHI297 Tailspike GP61


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Pseudomonas Phage PHI297 Tailspike GP61 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na806

b:44.6
occ:1.00
 N A:ASP302 3.1 17.9 1.0
O A:HOH1854 3.3 54.2 1.0
O A:HOH1856 3.4 67.9 1.0
CA A:ARG301 3.7 16.2 0.5
CA A:ARG301 3.7 18.0 0.5
CG A:ASP302 3.8 21.2 1.0
C A:ARG301 3.9 16.1 0.5
C A:ARG301 3.9 16.6 0.5
CB A:ASP302 3.9 20.4 1.0
OD2 A:ASP302 4.0 25.1 1.0
O A:HOH1829 4.1 67.8 1.0
CA A:ASP302 4.1 18.7 1.0
CD A:ARG301 4.1 21.2 0.5
CB A:ARG301 4.2 18.9 0.5
CB A:ARG301 4.2 15.2 0.5
OD1 A:ASP302 4.3 21.2 1.0
CD A:PRO303 4.3 17.8 1.0
O A:ASP300 4.6 20.1 1.0
CG A:ARG301 4.7 23.6 0.5
O A:HOH1736 4.8 45.7 1.0
CG A:ARG301 4.8 18.3 0.5
N A:ARG301 4.9 17.6 0.5
N A:ARG301 4.9 18.6 0.5

Sodium binding site 5 out of 10 in 4ru5

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Sodium binding site 5 out of 10 in the Crystal Structure of the Pseudomonas Phage PHI297 Tailspike GP61


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Pseudomonas Phage PHI297 Tailspike GP61 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na807

b:64.5
occ:1.00
 O A:HOH1831 2.6 64.2 1.0
OD1 A:ASP280 2.9 33.7 1.0
NH2 A:ARG341 3.0 20.9 1.0
NA A:NA808 3.1 55.9 1.0
CZ A:ARG341 4.0 19.8 1.0
CG A:ASP280 4.1 32.7 1.0
NH1 A:ARG341 4.1 23.9 1.0
C A:ASP280 4.2 24.1 1.0
O A:ASP280 4.3 23.1 1.0
N A:LEU281 4.3 20.7 1.0
C A:LEU281 4.4 18.3 1.0
NH1 A:ARG339 4.4 24.3 1.0
CB A:ALA282 4.4 21.6 1.0
O A:LEU281 4.5 21.6 1.0
N A:ALA282 4.5 20.0 1.0
CA A:LEU281 4.7 18.0 1.0
CA A:ASP280 4.7 24.6 1.0
OD2 A:ASP280 4.8 42.2 1.0
O A:HOH1846 4.8 69.5 1.0
O A:HOH1880 4.9 56.2 1.0
OD2 A:ASP285 5.0 18.8 1.0

Sodium binding site 6 out of 10 in 4ru5

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Sodium binding site 6 out of 10 in the Crystal Structure of the Pseudomonas Phage PHI297 Tailspike GP61


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of the Pseudomonas Phage PHI297 Tailspike GP61 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na808

b:55.9
occ:1.00
 NH1 A:ARG341 3.0 23.9 1.0
NA A:NA807 3.1 64.5 1.0
O A:HOH1870 3.6 75.2 1.0
OD1 A:ASP280 3.7 33.7 1.0
NH1 A:ARG339 3.8 24.3 1.0
CZ A:ARG341 3.8 19.8 1.0
NH2 A:ARG341 3.8 20.9 1.0
OD2 A:ASP280 4.1 42.2 1.0
CG A:ASP280 4.3 32.7 1.0
CZ A:ARG339 4.4 21.4 1.0
NH2 A:ARG339 4.5 20.3 1.0
O A:HOH1267 4.8 36.2 1.0

Sodium binding site 7 out of 10 in 4ru5

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Sodium binding site 7 out of 10 in the Crystal Structure of the Pseudomonas Phage PHI297 Tailspike GP61


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of the Pseudomonas Phage PHI297 Tailspike GP61 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na803

b:70.2
occ:1.00
 OH B:TYR711 3.3 23.3 1.0
CE1 B:TYR711 3.5 21.6 1.0
CZ B:TYR711 3.8 19.7 1.0
OG A:SER699 3.9 22.0 1.0
O A:HOH1411 4.0 39.1 1.0
O A:HOH977 4.2 21.4 1.0
N A:SER699 4.4 18.8 1.0
O A:GLY697 4.5 19.0 1.0
CA A:GLN698 4.5 15.2 1.0
C A:GLY697 4.6 17.8 1.0
N A:GLN698 4.6 16.6 1.0
CB A:SER699 4.6 20.0 1.0
CD1 B:TYR711 4.7 17.5 1.0
C A:GLN698 4.8 18.6 1.0
O A:HOH1320 4.8 40.6 1.0

Sodium binding site 8 out of 10 in 4ru5

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Sodium binding site 8 out of 10 in the Crystal Structure of the Pseudomonas Phage PHI297 Tailspike GP61


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of the Pseudomonas Phage PHI297 Tailspike GP61 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na804

b:54.6
occ:1.00
 O B:HOH1347 3.4 40.7 1.0
O B:HOH1886 3.9 50.0 1.0
O B:HOH1757 3.9 59.2 1.0
CZ B:TYR384 3.9 13.2 1.0
CE1 B:TYR384 4.1 16.3 1.0
O B:ALA359 4.1 15.5 1.0
CE2 B:TYR384 4.1 14.5 1.0
OD2 B:ASP411 4.1 17.5 1.0
CB B:ALA359 4.2 16.3 1.0
O B:HOH1663 4.3 47.7 1.0
CD1 B:TYR384 4.3 14.3 1.0
O B:HOH1995 4.4 58.9 1.0
OH B:TYR384 4.4 16.6 1.0
CD2 B:TYR384 4.4 13.5 1.0
CG B:TYR384 4.5 11.5 1.0
O B:HOH1245 4.6 27.3 1.0
CE B:MET442 4.8 38.8 0.4
C B:ALA359 4.9 13.3 1.0
O B:HOH966 4.9 17.3 1.0
O B:HOH1683 5.0 48.7 1.0

Sodium binding site 9 out of 10 in 4ru5

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Sodium binding site 9 out of 10 in the Crystal Structure of the Pseudomonas Phage PHI297 Tailspike GP61


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of the Pseudomonas Phage PHI297 Tailspike GP61 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na803

b:38.2
occ:1.00
 O A:HOH1625 2.4 65.5 1.0
O A:HOH918 2.7 16.9 1.0
O C:HOH943 3.2 16.1 1.0
N C:MET601 3.3 13.7 0.3
N C:MET601 3.4 12.8 0.7
O C:HOH1268 3.4 27.3 1.0
CA C:MET601 4.0 15.5 0.3
CA C:MET601 4.0 13.3 0.7
OH C:TYR631 4.0 13.1 1.0
O A:HOH1041 4.1 17.8 1.0
O A:HOH1164 4.2 23.9 1.0
C C:HIS600 4.3 12.2 1.0
ND1 C:HIS600 4.3 16.0 1.0
CA C:HIS600 4.3 12.1 1.0
CE2 C:TYR631 4.5 12.9 1.0
O C:VAL599 4.5 12.1 1.0
N C:ALA602 4.5 13.5 1.0
C C:MET601 4.6 14.2 0.7
C C:MET601 4.6 14.8 0.3
O C:HOH1677 4.6 44.1 1.0
O C:ALA602 4.7 14.9 1.0
CZ C:TYR631 4.8 11.3 1.0
CE2 A:TYR624 4.8 11.2 1.0
O C:HOH1186 4.8 32.8 1.0
OH A:TYR624 4.9 13.7 1.0

Sodium binding site 10 out of 10 in 4ru5

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Sodium binding site 10 out of 10 in the Crystal Structure of the Pseudomonas Phage PHI297 Tailspike GP61


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of the Pseudomonas Phage PHI297 Tailspike GP61 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na804

b:50.9
occ:1.00
 N C:ALA176 3.1 42.6 1.0
CB C:ALA176 3.5 49.5 1.0
O C:HOH1542 3.6 44.2 1.0
N C:LEU175 3.7 34.8 1.0
CB C:THR174 3.8 45.8 1.0
CA C:ALA176 3.8 33.3 1.0
CB C:LEU175 3.9 39.2 1.0
C C:LEU175 4.0 41.3 1.0
CA C:LEU175 4.0 36.7 1.0
OG1 C:THR174 4.1 44.9 1.0
C C:THR174 4.4 40.7 1.0
O C:HOH1886 4.5 49.9 1.0
CA C:THR174 4.6 34.5 1.0
O C:HOH1547 4.7 74.7 1.0
CG2 C:THR174 4.8 41.0 1.0
CG C:LEU175 4.9 42.9 1.0

Reference:

T.Olszak, M.M.Shneider, A.Latka, B.Maciejewska, C.Browning, L.V.Sycheva, A.Cornelissen, K.Danis-Wlodarczyk, S.N.Senchenkova, A.S.Shashkov, G.Gula, M.Arabski, S.Wasik, K.A.Miroshnikov, R.Lavigne, P.G.Leiman, Y.A.Knirel, Z.Drulis-Kawa. The O-Specific Polysaccharide Lyase From the Phage LKA1 Tailspike Reduces Pseudomonas Virulence. Sci Rep V. 7 16302 2017.
ISSN: ESSN 2045-2322
PubMed: 29176754
DOI: 10.1038/S41598-017-16411-4
Page generated: Mon Oct 7 18:21:44 2024

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