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

Protein crystallography data

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

Other elements in 4ru4:

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

Sodium (Na) 21 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of the Tailspike Protein GP49 From Pseudomonas Phage LKA1, PDB code: 4ru4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4ru4

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Calcium binding site 1 out of 8 in the Crystal Structure of the Tailspike Protein GP49 From Pseudomonas Phage LKA1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca811

b:70.7
occ:1.00
 O C:HOH1056 2.3 13.8 1.0
O B:HOH977 2.4 14.1 1.0
O B:HOH1037 2.4 16.5 1.0
O C:HOH1009 2.5 18.3 1.0
O A:HOH1149 2.5 15.5 1.0
O B:HOH1172 2.6 16.1 1.0
O C:VAL715 4.0 7.5 1.0
O A:VAL715 4.0 8.3 1.0
O B:VAL715 4.0 9.0 1.0
O C:HOH923 4.1 8.5 1.0
O B:HOH901 4.2 8.0 1.0
O C:HOH987 4.2 10.3 1.0
O C:HOH1087 4.5 17.1 1.0
O B:HOH1638 4.6 43.6 1.0
O C:ALA730 4.7 10.2 1.0
O B:HOH1028 4.7 16.8 1.0
O A:ALA730 4.7 8.9 1.0
O A:HOH1140 4.7 19.3 1.0
OG1 C:THR716 4.8 7.3 1.0
O B:ALA730 4.8 10.6 1.0
OG1 B:THR716 4.8 10.3 1.0
OG1 A:THR716 4.8 8.8 1.0

Calcium binding site 2 out of 8 in 4ru4

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Calcium binding site 2 out of 8 in the Crystal Structure of the Tailspike Protein GP49 From Pseudomonas Phage LKA1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca812

b:88.9
occ:1.00
 O A:HOH1172 2.4 26.5 1.0
O A:HOH1390 2.5 34.9 1.0
O A:HOH1092 2.5 17.4 1.0
O A:HOH1822 2.5 37.4 1.0
O A:ASP561 2.6 11.5 1.0
O A:GLY535 2.7 12.4 1.0
C A:GLY535 3.5 14.3 1.0
C A:ASP561 3.5 13.0 1.0
CA A:GLY535 4.1 14.4 1.0
CA A:PRO562 4.2 8.7 1.0
N A:ASP561 4.2 9.4 1.0
N A:PRO562 4.2 11.3 1.0
O A:HOH1044 4.3 19.8 1.0
N A:GLY536 4.4 9.8 1.0
CA A:ASP561 4.5 9.0 1.0
O A:HOH1145 4.6 11.8 1.0
O A:SER534 4.6 9.2 1.0
CA A:GLY536 4.7 10.1 1.0
CD A:PRO564 4.8 12.0 1.0
C A:PRO562 4.8 9.6 1.0
O A:HOH1041 4.9 17.4 1.0
CG A:PRO564 5.0 13.4 1.0

Calcium binding site 3 out of 8 in 4ru4

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Calcium binding site 3 out of 8 in the Crystal Structure of the Tailspike Protein GP49 From Pseudomonas Phage LKA1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
B:Ca811

b:57.7
occ:1.00
 O B:HOH1331 2.4 26.7 1.0
O B:HOH985 2.5 12.4 1.0
O B:HOH1191 2.5 15.5 1.0
O B:ASP561 2.5 8.1 1.0
O B:HOH1277 2.5 29.5 1.0
O B:GLY535 2.6 14.7 1.0
C B:ASP561 3.4 11.4 1.0
C B:GLY535 3.5 14.0 1.0
CA B:PRO562 4.1 7.9 1.0
N B:ASP561 4.1 11.6 1.0
O B:HOH1530 4.1 38.8 1.0
N B:PRO562 4.1 10.0 1.0
CA B:GLY535 4.2 9.2 1.0
O B:HOH1603 4.2 48.2 1.0
O B:HOH1080 4.3 11.6 1.0
N B:GLY536 4.3 11.0 1.0
O B:HOH1182 4.3 21.4 1.0
CA B:ASP561 4.4 12.2 1.0
CA B:GLY536 4.5 8.1 1.0
O B:SER534 4.6 10.4 1.0
C B:PRO562 4.8 6.7 1.0
CD B:PRO564 4.8 8.4 1.0
O B:HOH1564 4.8 36.8 1.0
O B:HOH1354 4.9 21.1 1.0
CB B:ASP561 4.9 9.7 1.0

Calcium binding site 4 out of 8 in 4ru4

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Calcium binding site 4 out of 8 in the Crystal Structure of the Tailspike Protein GP49 From Pseudomonas Phage LKA1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
C:Ca805

b:52.3
occ:1.00
 O C:HOH1169 2.4 20.9 1.0
O C:HOH1336 2.5 34.4 1.0
O C:HOH1588 2.5 28.1 1.0
O C:HOH1033 2.5 15.4 1.0
O C:ASP561 2.5 8.2 1.0
O C:GLY535 2.6 11.4 1.0
C C:GLY535 3.5 11.4 1.0
C C:ASP561 3.5 8.2 1.0
CA C:PRO562 4.1 12.1 1.0
CA C:GLY535 4.2 8.1 1.0
N C:PRO562 4.2 12.3 1.0
N C:ASP561 4.2 9.3 1.0
O C:HOH1352 4.3 23.5 1.0
N C:GLY536 4.4 8.0 1.0
CA C:ASP561 4.5 8.9 1.0
O C:SER534 4.5 11.8 1.0
O C:HOH1062 4.6 15.3 1.0
CA C:GLY536 4.6 7.2 1.0
CD C:PRO564 4.7 11.8 1.0
O C:HOH1751 4.7 37.9 1.0
O C:HOH1708 4.8 56.4 1.0
C C:PRO562 4.8 10.7 1.0
O C:HOH1425 5.0 39.0 1.0

Calcium binding site 5 out of 8 in 4ru4

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Calcium binding site 5 out of 8 in the Crystal Structure of the Tailspike Protein GP49 From Pseudomonas Phage LKA1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
D:Ca806

b:74.0
occ:1.00
 O D:HOH1033 2.4 17.5 1.0
O F:HOH1009 2.4 18.2 1.0
O D:HOH1102 2.5 18.2 1.0
O E:HOH1601 2.5 14.7 1.0
O D:HOH1084 2.5 19.9 1.0
O F:HOH1144 2.6 17.8 1.0
O D:HOH965 4.0 8.1 1.0
O E:VAL715 4.0 9.8 1.0
O D:VAL715 4.1 10.1 1.0
O F:HOH921 4.2 10.1 1.0
O F:HOH942 4.2 9.7 1.0
O F:VAL715 4.2 10.0 1.0
O E:HOH1269 4.5 20.2 1.0
O E:ALA730 4.7 12.3 1.0
O D:ALA730 4.7 10.3 1.0
O F:HOH1045 4.7 22.4 1.0
O D:HOH1173 4.7 18.1 1.0
O F:ALA730 4.8 12.6 1.0
OG1 E:THR716 4.9 10.0 1.0
OG1 F:THR716 4.9 10.7 1.0
OG1 D:THR716 5.0 11.2 1.0

Calcium binding site 6 out of 8 in 4ru4

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Calcium binding site 6 out of 8 in the Crystal Structure of the Tailspike Protein GP49 From Pseudomonas Phage LKA1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
D:Ca807

b:59.8
occ:1.00
 O D:HOH1427 2.4 37.1 1.0
O D:ASP561 2.5 7.7 1.0
O D:HOH989 2.5 12.2 1.0
O D:HOH1309 2.5 24.9 1.0
O D:HOH1133 2.5 18.8 1.0
O D:GLY535 2.8 15.6 1.0
C D:ASP561 3.4 8.6 1.0
C D:GLY535 3.5 13.5 1.0
CA D:PRO562 4.0 7.5 1.0
N D:ASP561 4.1 9.6 1.0
CA D:GLY535 4.1 11.3 1.0
N D:PRO562 4.2 7.4 1.0
O D:HOH1363 4.3 42.9 1.0
CA D:ASP561 4.4 8.0 1.0
O D:HOH1039 4.4 23.3 1.0
O D:HOH1110 4.4 13.4 1.0
N D:GLY536 4.4 11.5 1.0
O D:HOH1693 4.4 40.0 1.0
CA D:GLY536 4.6 7.5 1.0
O D:SER534 4.6 7.8 0.6
O D:SER534 4.7 8.1 0.4
CD D:PRO564 4.8 8.2 1.0
C D:PRO562 4.8 7.7 1.0
O D:HOH1657 4.8 52.7 1.0
O D:HOH1124 4.9 15.4 1.0
CB D:ASP561 4.9 11.7 1.0

Calcium binding site 7 out of 8 in 4ru4

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Calcium binding site 7 out of 8 in the Crystal Structure of the Tailspike Protein GP49 From Pseudomonas Phage LKA1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
E:Ca808

b:59.2
occ:1.00
 O E:HOH1061 2.4 17.4 1.0
O E:HOH1122 2.5 19.1 1.0
O E:HOH1424 2.5 29.5 1.0
O E:HOH1687 2.5 38.2 1.0
O E:ASP561 2.5 12.3 1.0
O E:GLY535 2.8 15.0 1.0
C E:ASP561 3.5 10.1 1.0
C E:GLY535 3.6 13.3 1.0
N E:ASP561 4.1 7.5 1.0
CA E:GLY535 4.2 14.2 1.0
CA E:PRO562 4.3 8.2 1.0
N E:PRO562 4.3 11.6 1.0
O E:HOH1669 4.4 44.5 1.0
CA E:ASP561 4.4 7.8 1.0
O E:HOH1028 4.5 11.8 1.0
N E:GLY536 4.5 7.5 1.0
O E:SER534 4.5 8.5 1.0
O E:HOH1224 4.6 24.0 1.0
CD E:PRO564 4.7 13.1 1.0
CA E:GLY536 4.7 7.5 1.0
O E:HOH1745 4.8 46.3 1.0
C E:PRO562 4.9 11.2 1.0
CB E:ASP561 4.9 7.4 1.0
O E:HOH1067 5.0 16.4 1.0
CG E:PRO564 5.0 14.7 1.0

Calcium binding site 8 out of 8 in 4ru4

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
F:Ca804

b:59.6
occ:1.00
 O F:ASP561 2.4 8.6 1.0
O F:HOH1071 2.5 20.3 1.0
O F:HOH1204 2.5 34.4 1.0
O F:HOH1544 2.5 41.0 1.0
O F:HOH940 2.5 14.2 1.0
O F:GLY535 2.6 11.5 1.0
C F:ASP561 3.5 10.0 1.0
C F:GLY535 3.5 13.0 1.0
CA F:PRO562 4.1 8.5 1.0
CA F:GLY535 4.1 12.0 1.0
N F:ASP561 4.1 10.8 1.0
N F:PRO562 4.2 9.3 1.0
CA F:ASP561 4.4 10.6 1.0
N F:GLY536 4.4 11.3 1.0
O F:HOH1189 4.4 25.0 1.0
O F:HOH1023 4.5 15.8 1.0
O F:SER534 4.6 12.5 1.0
CA F:GLY536 4.6 8.9 1.0
CD F:PRO564 4.7 10.9 1.0
O F:HOH1552 4.7 37.7 1.0
O F:HOH1654 4.8 35.8 1.0
C F:PRO562 4.8 11.2 1.0
O F:HOH1782 4.9 47.9 1.0
CB F:ASP561 4.9 8.2 1.0
O F:HOH1259 4.9 17.8 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: Sun Jul 14 12:47:14 2024

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