Sodium in PDB 4ru4: Crystal Structure of the Tailspike Protein GP49 From Pseudomonas Phage LKA1

The structure of Crystal Structure of the Tailspike Protein GP49 From Pseudomonas Phage LKA1, PDB code: 4ru4 was solved by C.Browning, 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)	19.99 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	114.400, 148.234, 117.582, 90.00, 90.85, 90.00
R / Rfree (%)	12.9 / 17.4

The structure of Crystal Structure of the Tailspike Protein GP49 From Pseudomonas Phage LKA1 also contains other interesting chemical elements:

Calcium

(Ca)

8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of the Tailspike Protein GP49 From Pseudomonas Phage LKA1 (pdb code 4ru4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 21 binding sites of Sodium where determined in the Crystal Structure of the Tailspike Protein GP49 From Pseudomonas Phage LKA1, PDB code: 4ru4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 21 in the Crystal Structure of the Tailspike Protein GP49 From Pseudomonas Phage LKA1


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 Tailspike Protein GP49 From Pseudomonas Phage LKA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na804 b:16.0 occ:1.00 O B:HOH1293 2.7 29.4 1.0 O A:HOH1548 3.0 32.1 1.0 OG A:SER429 3.0 7.8 0.6 O A:HOH1611 3.1 36.7 1.0 NH2 B:ARG351 3.2 10.3 1.0 CB A:SER429 3.6 7.4 0.4 NH1 B:ARG351 3.8 10.5 1.0 CB A:SER429 3.8 7.8 0.6 CA B:GLY312 3.8 8.9 1.0 OG A:SER429 4.0 7.1 0.4 CZ B:ARG351 4.0 11.9 1.0 O B:ALA311 4.1 10.9 1.0 CD1 A:ILE431 4.1 23.9 1.0 N B:GLY312 4.2 10.6 1.0 CG1 A:ILE431 4.2 19.9 1.0 CG2 A:THR406 4.2 9.0 1.0 C B:ALA311 4.3 13.2 1.0 O A:SER429 4.6 10.2 0.6 CB A:THR406 4.6 10.6 1.0 O A:HOH1342 4.7 34.5 1.0 O B:HOH1135 4.8 23.4 1.0 CB B:ALA311 4.9 17.8 1.0 O A:HOH1650 5.0 44.9 1.0 C A:SER429 5.0 9.1 0.6 CA A:SER429 5.0 8.6 0.4

Sodium binding site 2 out of 21 in the Crystal Structure of the Tailspike Protein GP49 From Pseudomonas Phage LKA1


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 Tailspike Protein GP49 From Pseudomonas Phage LKA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na805 b:46.2 occ:1.00 O A:HOH1880 2.4 57.0 1.0 O A:HOH1481 2.5 52.8 1.0 O A:SER255 3.4 19.5 0.6 O A:VAL231 3.5 10.9 1.0 O A:SER255 3.5 19.7 0.5 OG A:SER252 3.5 10.6 0.5 OG A:SER255 3.9 24.8 0.6 O A:HOH1374 3.9 31.9 1.0 O A:HOH1061 4.0 15.4 1.0 O A:HOH916 4.2 11.5 1.0 O A:HOH1073 4.2 16.9 1.0 C A:SER255 4.3 21.3 0.6 CG1 A:VAL231 4.3 11.5 1.0 C A:SER255 4.4 20.8 0.5 C A:VAL231 4.4 11.2 1.0 CA A:GLY234 4.4 16.1 1.0 CB A:SER252 4.4 10.5 0.5 CB A:SER252 4.5 10.5 0.5 O A:HOH1355 4.5 37.3 1.0 O A:HOH1539 4.5 43.5 1.0 O A:THR253 4.5 18.2 1.0 CB A:SER255 4.6 23.3 0.5 N A:GLY234 4.7 16.0 1.0 N A:SER255 4.7 26.1 0.5 N A:SER255 4.7 26.1 0.6 CA A:SER255 4.8 23.8 0.5 CA A:ASP232 4.8 14.1 1.0 CA A:SER255 4.8 24.2 0.6 CB A:SER255 4.9 22.9 0.6 O A:ASP232 4.9 15.5 1.0

Sodium binding site 3 out of 21 in the Crystal Structure of the Tailspike Protein GP49 From Pseudomonas Phage LKA1


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 Tailspike Protein GP49 From Pseudomonas Phage LKA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na806 b:7.7 occ:1.00 OG A:SER331 3.0 15.6 1.0 CB A:SER331 3.5 13.3 1.0 N A:SER331 3.5 6.7 1.0 O A:HOH1613 3.8 42.8 1.0 CB A:ARG329 3.8 6.3 1.0 N A:THR330 4.1 10.5 1.0 CB A:THR330 4.1 12.0 1.0 CD A:ARG329 4.1 10.3 1.0 CA A:SER331 4.2 9.7 1.0 O A:HOH1756 4.5 55.2 1.0 CA A:THR330 4.5 10.5 1.0 C A:THR330 4.5 7.8 1.0 C A:ARG329 4.5 13.2 1.0 CG A:ARG329 4.5 8.6 1.0 CA A:ARG329 4.6 9.6 1.0 OG1 A:THR330 4.8 19.8 1.0 O A:HOH1841 4.9 57.7 1.0

Sodium binding site 4 out of 21 in the Crystal Structure of the Tailspike Protein GP49 From Pseudomonas Phage LKA1


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 Tailspike Protein GP49 From Pseudomonas Phage LKA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na807 b:12.4 occ:1.00 O C:HOH1647 2.4 65.6 1.0 OG C:SER429 2.7 20.8 1.0 O A:HOH1264 3.1 28.9 1.0 NH2 A:ARG351 3.1 10.9 1.0 O C:HOH1048 3.1 18.9 1.0 NH1 A:ARG351 3.6 11.7 1.0 CA A:GLY312 3.7 9.8 1.0 CB C:SER429 3.7 14.6 1.0 CZ A:ARG351 3.8 9.9 1.0 O A:ALA311 4.0 13.3 1.0 N A:GLY312 4.1 11.4 1.0 C A:ALA311 4.2 12.1 1.0 CD1 C:ILE431 4.2 14.4 1.0 CG1 C:ILE431 4.3 11.1 1.0 CG2 C:THR406 4.5 16.0 1.0 O C:HOH1157 4.5 29.6 1.0 O A:HOH1415 4.6 25.5 1.0 O A:HOH1019 4.7 20.1 1.0 O C:SER429 4.7 11.4 1.0 CB C:THR406 4.7 16.2 1.0 O C:HOH1131 5.0 20.1 1.0 CA C:SER429 5.0 9.9 1.0 CB A:ALA311 5.0 10.5 1.0

Sodium binding site 5 out of 21 in the Crystal Structure of the Tailspike Protein GP49 From Pseudomonas Phage LKA1


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 Tailspike Protein GP49 From Pseudomonas Phage LKA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na808 b:12.1 occ:1.00 O A:HOH1414 3.0 29.6 1.0 O A:HOH1195 3.1 26.5 1.0 O A:HOH1281 3.2 31.0 1.0 N A:LEU218 3.2 11.9 1.0 O A:HOH1181 3.4 32.2 1.0 CA A:ALA217 3.7 8.9 1.0 CB A:LEU218 4.0 12.4 1.0 CB A:ALA217 4.0 13.7 1.0 C A:ALA217 4.0 10.9 1.0 CG A:LEU218 4.0 11.0 1.0 CA A:LEU218 4.2 11.8 1.0 CB A:LEU205 4.3 10.7 1.0 O A:HOH1131 4.4 24.0 1.0 CD1 A:LEU205 4.4 9.2 1.0 CD2 A:LEU205 4.4 8.1 1.0 CD1 A:LEU218 4.4 14.6 1.0 CG A:LEU205 4.6 9.1 1.0 O A:HOH1032 4.8 17.6 1.0 O A:HOH1836 4.9 46.8 1.0

Sodium binding site 6 out of 21 in the Crystal Structure of the Tailspike Protein GP49 From Pseudomonas Phage LKA1


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 Tailspike Protein GP49 From Pseudomonas Phage LKA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na809 b:6.8 occ:1.00 O A:HOH1208 2.9 26.4 1.0 O A:HOH945 3.2 10.7 1.0 NE2 A:GLN209 3.2 9.4 1.0 CD A:GLN209 4.3 11.8 1.0 OE1 A:GLN209 4.4 9.7 1.0 O A:ALA215 4.5 15.8 1.0 O A:HOH1335 4.9 33.4 1.0

Sodium binding site 7 out of 21 in the Crystal Structure of the Tailspike Protein GP49 From Pseudomonas Phage LKA1


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 Tailspike Protein GP49 From Pseudomonas Phage LKA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na810 b:3.8 occ:1.00 O A:HOH991 3.2 10.9 1.0 N A:THR757 3.2 7.2 1.0 CA A:VAL756 3.5 7.2 1.0 NH2 A:ARG720 3.5 9.3 1.0 CG2 A:THR757 3.6 11.4 1.0 CB A:VAL756 3.8 9.7 1.0 OG1 A:THR757 3.9 8.0 1.0 C A:VAL756 3.9 7.3 1.0 CG1 A:VAL756 4.1 10.2 1.0 CB A:THR757 4.2 9.1 1.0 CA A:THR757 4.3 10.2 1.0 O A:ALA755 4.3 11.0 1.0 CZ A:ARG720 4.5 11.4 1.0 N A:VAL756 4.7 11.9 1.0 C A:ALA755 5.0 12.4 1.0

Sodium binding site 8 out of 21 in the Crystal Structure of the Tailspike Protein GP49 From Pseudomonas Phage LKA1


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 Tailspike Protein GP49 From Pseudomonas Phage LKA1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na806 b:29.7 occ:1.00 O B:HOH944 2.7 7.7 1.0 O B:HOH942 3.5 11.4 1.0 CB B:ALA542 3.6 6.8 1.0 O B:HOH1503 3.9 36.4 1.0 O B:HOH1226 4.2 28.1 1.0 O B:HOH1094 4.3 14.4 1.0 CA B:ALA542 4.4 6.8 1.0 O B:ALA577 4.5 9.2 1.0 CB B:SER576 4.7 13.1 1.0 O B:HOH1173 4.7 22.9 1.0 O B:HOH1356 4.8 33.0 1.0 CG B:GLU543 4.9 9.9 1.0 N B:GLU543 4.9 6.9 1.0 CG2 B:VAL578 4.9 7.0 1.0 OG B:SER576 5.0 12.7 1.0

Sodium binding site 9 out of 21 in the Crystal Structure of the Tailspike Protein GP49 From Pseudomonas Phage LKA1


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 Tailspike Protein GP49 From Pseudomonas Phage LKA1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na807 b:12.2 occ:1.00 O B:HOH1129 2.7 27.9 1.0 OG B:SER429 3.0 7.9 0.7 O B:HOH1777 3.1 43.4 1.0 NH2 C:ARG351 3.1 13.7 1.0 O B:HOH1353 3.2 30.8 1.0 NH1 C:ARG351 3.7 11.6 1.0 CB B:SER429 3.7 7.7 0.3 CA C:GLY312 3.8 9.5 1.0 CB B:SER429 3.8 7.2 0.7 CZ C:ARG351 3.8 13.2 1.0 CD1 B:ILE431 3.9 18.5 1.0 O C:ALA311 4.0 8.1 1.0 OG B:SER429 4.1 8.7 0.3 N C:GLY312 4.1 8.4 1.0 C C:ALA311 4.2 10.6 1.0 CG1 B:ILE431 4.2 11.3 1.0 CG2 B:THR406 4.4 12.1 1.0 O C:HOH926 4.6 13.0 1.0 CB B:THR406 4.7 11.5 1.0 O C:HOH1258 4.8 28.9 1.0 O B:SER429 4.8 9.2 0.7 CB C:ALA311 4.9 14.8 1.0 O B:HOH1054 4.9 16.5 1.0

Sodium binding site 10 out of 21 in the Crystal Structure of the Tailspike Protein GP49 From Pseudomonas Phage LKA1


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 Tailspike Protein GP49 From Pseudomonas Phage LKA1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na808 b:4.2 occ:1.00 OG B:SER331 3.0 18.0 1.0 CG2 B:THR330 3.4 6.2 0.4 N B:SER331 3.5 6.0 1.0 CB B:SER331 3.5 10.3 1.0 CB B:ARG329 3.8 5.4 1.0 N B:THR330 4.0 9.9 0.4 N B:THR330 4.0 10.1 0.6 CB B:THR330 4.0 7.8 0.6 CA B:SER331 4.1 9.0 1.0 CD B:ARG329 4.1 8.5 1.0 CA B:THR330 4.4 9.7 0.6 C B:THR330 4.4 11.0 0.6 C B:THR330 4.5 11.0 0.4 CG B:ARG329 4.5 7.8 1.0 C B:ARG329 4.5 9.9 1.0 CA B:THR330 4.6 9.7 0.4 CA B:ARG329 4.6 8.1 1.0 CB B:THR330 4.6 9.9 0.4 OG1 B:THR330 4.7 10.5 0.6 O B:HOH1270 4.7 28.3 1.0

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