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Chlorine in PDB 5nb3: High Resolution C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5

Protein crystallography data

The structure of High Resolution C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5, PDB code: 5nb3 was solved by R.R.Sonani, A.W.Roszak, C.Ortmann De Percin Northumberland, D.Madamwar, R.J.Cogdell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 95.42 / 1.38
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 110.046, 110.170, 118.516, 78.76, 82.28, 60.43
R / Rfree (%) 15.5 / 21.1

Other elements in 5nb3:

The structure of High Resolution C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5 also contains other interesting chemical elements:

Sodium (Na) 19 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the High Resolution C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5 (pdb code 5nb3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the High Resolution C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5, PDB code: 5nb3:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5nb3

Go back to Chlorine Binding Sites List in 5nb3
Chlorine binding site 1 out of 6 in the High Resolution C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of High Resolution C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:30.4
occ:1.00
 O F:HOH304 2.4 21.2 0.5
O A:HOH306 2.4 26.9 0.5
O F:HOH478 2.8 15.0 1.0
O A:HOH470 2.9 15.2 1.0
N A:THR124 3.5 8.7 0.5
N F:THR124 3.5 10.1 0.4
N A:THR124 3.5 8.8 0.5
N F:THR124 3.6 9.4 0.6
CA F:PRO123 3.6 10.0 1.0
CA A:PRO123 3.6 9.1 1.0
CB F:PRO123 3.9 11.4 1.0
CB A:PRO123 4.0 9.5 1.0
OG1 A:THR124 4.1 12.8 0.5
OG1 F:THR124 4.1 14.7 0.4
C F:PRO123 4.1 9.7 1.0
C A:PRO123 4.1 9.1 1.0
OG1 A:THR124 4.2 12.3 0.5
OG1 F:THR124 4.2 10.7 0.6
CB F:THR124 4.2 11.8 0.4
CB A:THR124 4.3 10.9 0.5
O F:HOH503 4.3 23.9 1.0
O F:HOH461 4.3 42.3 1.0
O A:HOH511 4.3 28.1 1.0
O A:HOH345 4.3 33.8 1.0
O F:HOH412 4.5 24.7 1.0
CA F:THR124 4.5 10.7 0.4
CA A:THR124 4.5 9.0 0.5
O A:HOH510 4.6 30.7 1.0
O F:HOH491 4.7 35.0 1.0
CA A:THR124 4.7 8.7 0.5
CA F:THR124 4.7 9.2 0.6
N F:PRO123 4.7 10.1 1.0
O F:LEU122 4.7 12.3 1.0
N A:PRO123 4.8 9.3 1.0
O A:LEU122 4.9 12.4 1.0
CB A:THR124 4.9 9.3 0.5
CB F:THR124 4.9 9.1 0.6
N F:ALA125 5.0 9.7 1.0
N A:ALA125 5.0 9.0 1.0

Chlorine binding site 2 out of 6 in 5nb3

Go back to Chlorine Binding Sites List in 5nb3
Chlorine binding site 2 out of 6 in the High Resolution C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of High Resolution C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl204

b:31.2
occ:1.00
 O D:HOH302 2.4 20.6 0.5
O D:HOH479 2.8 15.6 1.0
O B:HOH458 2.8 15.1 1.0
N B:THR124 3.4 10.6 0.5
N D:THR124 3.5 10.6 0.5
N B:THR124 3.5 10.4 0.5
CA B:PRO123 3.5 10.0 1.0
CA D:PRO123 3.6 9.6 1.0
N D:THR124 3.6 10.5 0.5
CB B:PRO123 3.9 11.1 1.0
CB D:PRO123 3.9 10.8 1.0
OG1 B:THR124 4.0 14.6 0.5
C B:PRO123 4.0 10.2 1.0
OG1 D:THR124 4.1 16.4 0.5
C D:PRO123 4.1 10.4 1.0
OG1 B:THR124 4.2 11.4 0.5
O D:HOH503 4.3 25.9 1.0
CB B:THR124 4.3 12.6 0.5
CB D:THR124 4.4 12.8 0.5
OG1 D:THR124 4.4 9.6 0.5
O B:HOH393 4.4 38.1 1.0
O D:HOH314 4.4 37.4 1.0
O D:HOH347 4.4 29.0 1.0
O B:HOH499 4.5 18.6 1.0
CA B:THR124 4.5 11.3 0.5
CA D:THR124 4.6 10.1 0.5
O B:HOH402 4.6 28.4 1.0
O D:HOH469 4.6 32.3 1.0
CA B:THR124 4.7 10.3 0.5
N D:PRO123 4.8 10.2 1.0
CA D:THR124 4.8 9.0 0.5
N B:PRO123 4.8 10.1 1.0
N B:ALA125 4.9 10.4 1.0
O B:HOH501 4.9 31.4 1.0
O D:LEU122 5.0 13.9 1.0
O B:LEU122 5.0 12.2 1.0
CB B:THR124 5.0 9.6 0.5

Chlorine binding site 3 out of 6 in 5nb3

Go back to Chlorine Binding Sites List in 5nb3
Chlorine binding site 3 out of 6 in the High Resolution C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of High Resolution C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl205

b:32.6
occ:1.00
 O C:HOH465 2.8 21.4 1.0
O E:HOH440 2.9 17.8 1.0
N C:THR124 3.5 9.3 0.5
N E:THR124 3.5 12.4 0.5
CA C:PRO123 3.6 14.1 1.0
N C:THR124 3.6 8.4 0.5
CA E:PRO123 3.6 12.8 1.0
N E:THR124 3.6 12.4 0.5
CB C:PRO123 3.9 14.7 1.0
CB E:PRO123 4.0 14.2 1.0
OG1 C:THR124 4.0 15.2 0.5
C C:PRO123 4.1 12.7 1.0
C E:PRO123 4.1 12.5 1.0
OG1 E:THR124 4.2 16.7 0.5
O E:HOH493 4.2 24.4 1.0
OG1 C:THR124 4.2 13.9 0.5
O E:HOH397 4.3 32.9 1.0
CB C:THR124 4.3 14.5 0.5
OG1 E:THR124 4.3 11.9 0.5
O C:HOH372 4.4 29.4 1.0
CB E:THR124 4.4 15.7 0.5
O C:HOH489 4.4 27.8 1.0
CA C:THR124 4.5 13.3 0.5
O E:HOH470 4.6 37.5 1.0
O C:HOH359 4.6 27.9 0.5
CA E:THR124 4.6 13.0 0.5
CA C:THR124 4.7 12.5 0.5
O E:HOH508 4.7 35.3 1.0
N C:PRO123 4.7 14.4 1.0
N E:PRO123 4.8 12.2 1.0
O C:LEU122 4.8 16.4 1.0
O C:HOH501 4.8 33.8 1.0
O E:LEU122 4.8 14.0 1.0
CA E:THR124 4.8 11.8 0.5
CB C:THR124 4.9 13.2 0.5
N C:ALA125 4.9 14.5 1.0

Chlorine binding site 4 out of 6 in 5nb3

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Chlorine binding site 4 out of 6 in the High Resolution C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of High Resolution C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl204

b:36.2
occ:1.00
 O I:HOH321 2.4 24.0 0.5
O K:HOH306 2.4 22.8 0.5
O I:HOH461 2.8 18.4 1.0
O K:HOH441 2.8 18.3 1.0
N K:THR124 3.5 16.7 0.5
N I:THR124 3.5 14.4 0.5
N I:THR124 3.5 14.8 0.5
N K:THR124 3.6 12.0 0.5
CA I:PRO123 3.6 15.3 1.0
CA K:PRO123 3.6 14.0 1.0
CB I:PRO123 3.8 16.5 1.0
CB K:PRO123 3.8 14.2 1.0
C K:PRO123 4.1 14.9 1.0
C I:PRO123 4.1 16.2 1.0
OG1 I:THR124 4.2 17.9 0.5
OG1 I:THR124 4.2 15.3 0.5
OG1 K:THR124 4.2 13.2 0.5
O I:HOH533 4.3 30.9 1.0
OG1 K:THR124 4.3 17.4 0.5
O K:HOH498 4.3 25.4 1.0
O K:HOH437 4.3 40.2 1.0
O I:HOH320 4.4 24.2 0.5
CB I:THR124 4.4 14.7 0.5
CB K:THR124 4.4 17.5 0.5
O K:HOH400 4.5 28.2 1.0
CA I:THR124 4.5 14.8 0.5
CA K:THR124 4.5 15.3 0.5
O I:HOH355 4.5 29.2 1.0
CA I:THR124 4.7 14.8 0.5
CA K:THR124 4.8 13.5 0.5
O K:HOH486 4.8 34.3 1.0
O I:HOH500 4.8 36.8 1.0
N K:PRO123 4.8 14.8 1.0
N I:PRO123 4.8 16.3 1.0
CB I:THR124 4.9 15.3 0.5
N I:ALA125 4.9 14.0 1.0
N K:ALA125 4.9 13.4 1.0
O I:LEU122 4.9 15.7 1.0
CB K:THR124 5.0 13.5 0.5
O K:LEU122 5.0 16.2 1.0

Chlorine binding site 5 out of 6 in 5nb3

Go back to Chlorine Binding Sites List in 5nb3
Chlorine binding site 5 out of 6 in the High Resolution C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of High Resolution C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl206

b:33.9
occ:1.00
 O H:HOH306 2.4 17.7 0.5
O J:HOH304 2.6 22.2 0.5
O J:HOH454 2.8 18.4 1.0
O H:HOH477 2.9 16.2 1.0
N J:THR124 3.5 14.4 0.5
CA J:PRO123 3.5 10.2 1.0
N H:THR124 3.5 13.4 0.5
N J:THR124 3.5 11.7 0.5
CA H:PRO123 3.6 12.2 1.0
N H:THR124 3.7 11.7 0.5
CB J:PRO123 3.8 14.0 1.0
CB H:PRO123 3.9 13.9 1.0
C J:PRO123 4.1 13.6 1.0
C H:PRO123 4.1 11.1 1.0
OG1 H:THR124 4.2 14.3 0.5
O H:HOH497 4.2 25.0 1.0
O J:HOH506 4.2 25.4 1.0
OG1 J:THR124 4.3 12.2 0.5
CB H:THR124 4.3 15.6 0.5
CB J:THR124 4.3 15.9 0.5
OG1 J:THR124 4.3 18.8 0.5
O J:HOH436 4.4 36.6 1.0
OG1 H:THR124 4.4 20.2 0.5
O J:HOH359 4.4 32.4 1.0
O H:HOH377 4.5 24.9 1.0
CA J:THR124 4.5 15.0 0.5
O H:HOH488 4.5 32.5 1.0
CA H:THR124 4.6 12.9 0.5
O H:HOH451 4.6 37.0 1.0
CA J:THR124 4.7 12.9 0.5
N J:PRO123 4.7 12.8 1.0
N H:PRO123 4.8 12.1 1.0
O J:HOH499 4.8 26.5 1.0
CA H:THR124 4.8 11.2 0.5
O J:LEU122 4.9 15.6 1.0
CB J:THR124 4.9 12.4 0.5
O H:LEU122 4.9 14.0 1.0
N J:ALA125 4.9 14.7 1.0

Chlorine binding site 6 out of 6 in 5nb3

Go back to Chlorine Binding Sites List in 5nb3
Chlorine binding site 6 out of 6 in the High Resolution C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of High Resolution C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl204

b:27.9
occ:1.00
 O L:HOH302 2.4 38.0 1.0
O G:HOH311 2.5 30.6 1.0
O G:HOH472 2.8 14.7 1.0
O L:HOH468 2.8 16.2 1.0
N L:THR124 3.4 9.6 0.5
N G:THR124 3.5 11.0 0.5
N L:THR124 3.5 9.7 0.5
CA L:PRO123 3.5 10.1 1.0
N G:THR124 3.6 10.2 0.5
CA G:PRO123 3.7 11.0 1.0
CB L:PRO123 3.9 9.4 1.0
CB G:PRO123 4.0 11.7 1.0
C L:PRO123 4.0 9.4 1.0
OG1 L:THR124 4.1 13.8 0.5
OG1 G:THR124 4.1 9.9 0.5
C G:PRO123 4.1 10.7 1.0
OG1 L:THR124 4.2 11.9 0.5
O L:HOH493 4.2 25.0 1.0
CB L:THR124 4.2 10.9 0.5
CB G:THR124 4.3 13.4 0.5
O G:HOH396 4.3 42.8 1.0
OG1 G:THR124 4.4 16.1 0.5
O L:HOH430 4.4 37.6 1.0
O G:HOH496 4.4 22.0 1.0
O L:HOH406 4.4 30.2 1.0
CA L:THR124 4.5 10.4 0.5
O G:HOH392 4.5 27.2 1.0
CA G:THR124 4.5 11.2 0.5
O L:HOH499 4.6 30.2 1.0
O L:LEU122 4.7 11.7 1.0
CA L:THR124 4.7 9.9 0.5
N L:PRO123 4.7 9.6 1.0
CA G:THR124 4.7 9.4 0.5
O G:HOH504 4.8 28.6 1.0
N G:PRO123 4.9 10.8 1.0
CB G:THR124 4.9 9.9 0.5
CB L:THR124 4.9 9.9 0.5
O G:LEU122 4.9 11.2 1.0
N G:ALA125 5.0 9.7 1.0
N L:ALA125 5.0 10.0 1.0

Reference:

R.R.Sonani, A.W.Roszak, C.Ortmann De Percin Northumberland, D.Madamwar, R.J.Cogdell. An Improved Crystal Structure of C-Phycoerythrin From the Marine Cyanobacterium Phormidium Sp. A09DM. Photosyn. Res. V. 135 65 2018.
ISSN: ISSN 1573-5079
PubMed: 28918447
DOI: 10.1007/S11120-017-0443-2
Page generated: Fri Jul 26 13:23:49 2024

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