Atomistry » Chlorine » PDB 5n6s-5ncu » 5nb3
Atomistry »
  Chlorine »
    PDB 5n6s-5ncu »
      5nb3 »

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

Go back to Chlorine Binding Sites List in 5nb3
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: Sat Dec 12 12:09:08 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy