Sodium in PDB 5nb4: Atomic Resolution Structure of C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5

Protein crystallography data

The structure of Atomic Resolution Structure of C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5, PDB code: 5nb4 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) 94.62 / 1.14
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 109.046, 109.095, 117.371, 78.78, 82.32, 60.26
R / Rfree (%) 14.7 / 18.4

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Sodium atom in the Atomic Resolution Structure of C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5 (pdb code 5nb4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 16 binding sites of Sodium where determined in the Atomic Resolution Structure of C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5, PDB code: 5nb4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 16 in 5nb4

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Sodium binding site 1 out of 16 in the Atomic Resolution Structure of C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Atomic Resolution Structure of C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:18.6
occ:1.00
 O A:HOH513 2.1 33.1 1.0
O A:HOH356 2.3 41.0 1.0
O A:HOH541 2.3 16.5 1.0
O A:ASN161 2.4 9.5 1.0
O A:SER164 2.4 18.8 1.0
OG P:SER47 2.5 11.5 1.0
C A:SER164 3.3 13.9 1.0
C A:ASN161 3.5 8.2 1.0
O P:HOH573 3.6 25.2 1.0
CB P:SER47 3.7 9.3 1.0
O P:HOH470 3.8 20.7 0.5
O P:HOH319 3.8 29.7 1.0
OXT A:SER164 3.9 17.0 1.0
O A:HOH316 4.0 15.3 1.0
CA A:ASN161 4.2 9.1 1.0
CA A:SER164 4.3 12.4 1.0
N A:SER164 4.3 11.9 1.0
O P:HOH320 4.3 21.5 0.5
O F:HOH314 4.4 46.2 1.0
CB A:ASN161 4.5 8.9 1.0
N A:SER162 4.5 7.8 1.0
CB A:SER164 4.6 15.6 1.0
O P:HOH531 4.6 17.1 1.0
O A:HOH586 4.7 38.0 1.0
OD1 A:ASN161 4.7 11.4 1.0
CA A:SER162 4.7 8.3 1.0
CA P:SER47 4.7 7.9 1.0
C A:SER162 4.8 9.5 1.0

Sodium binding site 2 out of 16 in 5nb4

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Sodium binding site 2 out of 16 in the Atomic Resolution Structure of C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Atomic Resolution Structure of C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na205

b:21.6
occ:1.00
 O B:HOH515 2.3 24.4 1.0
O B:HOH493 2.3 36.3 1.0
O B:ASN161 2.4 9.8 1.0
OG Q:SER47 2.6 12.4 1.0
O B:SER164 2.7 20.4 1.0
O B:HOH509 3.1 40.0 1.0
C B:SER164 3.3 15.8 1.0
O B:HOH562 3.5 34.0 1.0
C B:ASN161 3.5 9.6 1.0
O Q:HOH310 3.8 58.1 1.0
OXT B:SER164 3.8 16.1 1.0
CB Q:SER47 3.8 10.7 1.0
O Q:HOH487 3.8 17.8 0.5
O D:HOH388 4.0 30.0 1.0
O B:HOH322 4.0 18.9 1.0
CA B:ASN161 4.2 8.5 1.0
CA B:SER164 4.2 12.4 1.0
N B:SER164 4.3 12.2 1.0
O Q:HOH373 4.3 40.6 0.5
CB B:ASN161 4.5 9.6 1.0
CB B:SER164 4.5 15.3 1.0
N B:SER162 4.6 9.1 1.0
O Q:HOH539 4.6 20.9 1.0
CA B:SER162 4.7 8.7 1.0
O B:HOH326 4.7 26.2 1.0
OD1 B:ASN161 4.8 13.1 1.0
CA Q:SER47 4.8 9.3 1.0
C B:SER162 4.9 8.9 1.0
OE2 Q:GLU85 5.0 25.3 1.0

Sodium binding site 3 out of 16 in 5nb4

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Sodium binding site 3 out of 16 in the Atomic Resolution Structure of C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Atomic Resolution Structure of C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na205

b:19.7
occ:1.00
 O C:HOH505 2.1 52.1 1.0
O C:ASN161 2.4 12.4 1.0
O C:HOH534 2.4 23.2 1.0
OG R:SER47 2.4 16.6 1.0
O C:HOH525 2.5 32.2 1.0
O C:SER164 2.6 22.5 1.0
C C:SER164 3.4 17.1 1.0
O C:HOH310 3.5 44.9 1.0
C C:ASN161 3.5 12.1 1.0
CB R:SER47 3.6 14.3 1.0
O R:HOH552 3.6 31.8 1.0
O R:HOH311 3.8 43.4 1.0
O R:HOH488 3.9 53.9 1.0
OXT C:SER164 4.0 22.0 1.0
O C:HOH321 4.0 19.4 1.0
CA C:ASN161 4.2 12.9 1.0
N C:SER164 4.2 15.4 1.0
CA C:SER164 4.2 17.3 1.0
CB C:SER164 4.5 18.9 1.0
O C:HOH586 4.5 64.8 1.0
N C:SER162 4.5 12.3 1.0
CB C:ASN161 4.5 11.8 1.0
O C:HOH392 4.6 35.5 1.0
CA R:SER47 4.6 12.0 1.0
OD1 C:ASN161 4.7 14.4 1.0
CA C:SER162 4.7 12.2 1.0
O R:HOH524 4.8 24.6 1.0
C C:SER162 4.8 11.7 1.0

Sodium binding site 4 out of 16 in 5nb4

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Sodium binding site 4 out of 16 in the Atomic Resolution Structure of C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Atomic Resolution Structure of C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na205

b:18.5
occ:1.00
 O D:HOH498 2.0 26.6 0.5
O M:HOH533 2.4 19.5 1.0
O D:HOH514 2.4 22.6 1.0
O D:ASN161 2.4 8.4 1.0
OG M:SER47 2.5 11.6 1.0
O D:SER164 2.6 18.1 1.0
C D:SER164 3.4 13.3 1.0
C D:ASN161 3.5 8.1 1.0
O M:HOH342 3.6 34.2 1.0
O D:HOH599 3.6 20.3 1.0
CB M:SER47 3.7 9.8 1.0
O M:HOH451 3.7 24.1 0.5
O D:HOH555 3.8 32.0 0.5
OXT D:SER164 3.8 15.7 1.0
O D:HOH319 4.0 13.6 1.0
O B:HOH460 4.2 13.7 0.5
CA D:ASN161 4.2 9.1 1.0
CA D:SER164 4.2 11.6 1.0
N D:SER164 4.3 10.1 1.0
O M:HOH314 4.3 29.3 0.5
N D:SER162 4.5 7.8 1.0
CB D:ASN161 4.5 9.7 1.0
CB D:SER164 4.5 14.6 1.0
O D:HOH302 4.6 25.7 0.9
O M:HOH608 4.6 29.3 1.0
O M:HOH566 4.7 15.9 1.0
OD1 D:ASN161 4.7 11.7 1.0
CA D:SER162 4.7 8.8 1.0
CA M:SER47 4.8 8.4 1.0
C D:SER162 4.8 8.8 1.0

Sodium binding site 5 out of 16 in 5nb4

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Sodium binding site 5 out of 16 in the Atomic Resolution Structure of C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Atomic Resolution Structure of C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na204

b:19.6
occ:1.00
 O E:HOH502 2.3 22.0 1.0
O E:HOH488 2.3 38.1 1.0
O E:HOH493 2.4 37.8 1.0
O E:ASN161 2.4 12.3 1.0
OG N:SER47 2.5 13.2 1.0
O E:SER164 2.5 22.5 1.0
C E:SER164 3.3 17.2 1.0
C E:ASN161 3.4 12.4 1.0
CB N:SER47 3.7 12.2 1.0
OXT E:SER164 3.8 20.5 1.0
O N:HOH325 3.8 91.0 1.0
O C:HOH538 3.8 33.6 1.0
O E:HOH342 3.9 20.1 1.0
O N:HOH522 4.0 60.9 1.0
CA E:ASN161 4.1 11.5 1.0
N E:SER164 4.2 15.4 1.0
CA E:SER164 4.2 15.1 1.0
O N:HOH617 4.3 30.8 1.0
CB E:ASN161 4.5 11.9 1.0
N E:SER162 4.5 10.7 1.0
CB E:SER164 4.5 18.1 1.0
O N:HOH565 4.5 18.9 1.0
CA E:SER162 4.7 11.2 1.0
OD1 E:ASN161 4.7 13.3 1.0
CA N:SER47 4.7 10.8 1.0
O E:HOH354 4.8 29.7 0.5
C E:SER162 4.8 12.0 1.0

Sodium binding site 6 out of 16 in 5nb4

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Sodium binding site 6 out of 16 in the Atomic Resolution Structure of C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Atomic Resolution Structure of C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na204

b:17.9
occ:1.00
 O F:HOH527 2.3 19.3 1.0
O F:HOH517 2.3 36.0 1.0
O F:ASN161 2.4 11.1 1.0
OG O:SER47 2.5 11.8 1.0
O F:SER164 2.5 20.3 1.0
O F:HOH516 2.5 23.2 1.0
C F:SER164 3.3 16.6 1.0
C F:ASN161 3.5 10.1 1.0
O O:HOH601 3.6 24.6 1.0
CB O:SER47 3.7 10.8 1.0
OXT F:SER164 3.8 17.0 1.0
O F:HOH315 3.9 14.8 1.0
O O:HOH353 4.0 65.1 1.0
O O:HOH309 4.1 0.9 0.5
O O:HOH625 4.1 36.9 0.5
CA F:ASN161 4.2 9.4 1.0
CA F:SER164 4.3 14.3 1.0
N F:SER164 4.3 12.6 1.0
O F:HOH567 4.3 24.9 0.5
CB F:ASN161 4.5 11.0 1.0
N F:SER162 4.6 9.6 1.0
O O:HOH575 4.6 18.4 1.0
OD1 F:ASN161 4.6 12.1 1.0
CB F:SER164 4.7 17.4 1.0
CA O:SER47 4.7 9.2 1.0
O F:HOH377 4.7 29.3 0.5
CA F:SER162 4.7 10.1 1.0
C F:SER162 4.9 11.3 1.0
CG F:ASN161 5.0 11.4 1.0

Sodium binding site 7 out of 16 in 5nb4

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Sodium binding site 7 out of 16 in the Atomic Resolution Structure of C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Atomic Resolution Structure of C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na204

b:16.9
occ:1.00
 O G:HOH502 2.3 34.8 1.0
O L:HOH528 2.3 20.0 1.0
O G:ASN161 2.4 9.5 1.0
OG V:SER47 2.5 11.7 1.0
OXT G:SER164 2.6 20.8 1.0
O L:HOH506 2.6 20.5 1.0
NA V:NA206 2.9 25.4 0.7
C G:SER164 3.3 14.9 1.0
C G:ASN161 3.5 9.1 1.0
CB V:SER47 3.7 9.5 1.0
O L:HOH309 3.7 24.5 1.0
O G:HOH569 3.8 45.7 1.0
O G:SER164 3.9 16.2 1.0
O G:HOH325 3.9 15.7 1.0
NH1 L:ARG118 4.1 12.3 0.3
O V:HOH519 4.1 41.8 1.0
CA G:ASN161 4.1 9.1 1.0
CA G:SER164 4.2 13.1 1.0
N G:SER164 4.3 11.7 1.0
O V:HOH448 4.3 39.7 1.0
O G:HOH321 4.4 39.7 1.0
CB G:ASN161 4.4 9.7 1.0
O G:HOH567 4.4 29.4 1.0
CB G:SER164 4.5 16.3 1.0
N G:SER162 4.5 8.8 1.0
O V:HOH558 4.6 18.1 1.0
OD1 G:ASN161 4.6 10.4 1.0
CA V:SER47 4.7 8.6 1.0
CA G:SER162 4.7 8.5 1.0
C G:SER162 4.9 9.7 1.0
CG G:ASN161 4.9 9.9 1.0

Sodium binding site 8 out of 16 in 5nb4

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Sodium binding site 8 out of 16 in the Atomic Resolution Structure of C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Atomic Resolution Structure of C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na204

b:21.0
occ:1.00
 O H:HOH485 2.2 34.8 1.0
O H:HOH488 2.3 25.8 0.5
O H:HOH515 2.3 22.8 1.0
O H:ASN161 2.4 11.4 1.0
O H:SER164 2.4 20.6 1.0
OG W:SER47 2.5 12.9 1.0
C H:SER164 3.3 16.7 1.0
C H:ASN161 3.4 11.3 1.0
O W:HOH336 3.5 38.4 1.0
O H:HOH560 3.7 27.0 1.0
CB W:SER47 3.7 10.3 1.0
OXT H:SER164 3.7 18.4 1.0
O H:HOH534 3.9 22.4 0.5
O H:HOH336 4.0 16.9 1.0
O W:HOH533 4.1 46.5 1.0
CA H:ASN161 4.1 11.5 1.0
CA H:SER164 4.2 14.5 1.0
N H:SER164 4.2 13.3 1.0
O J:HOH333 4.3 38.1 1.0
CB H:SER164 4.4 18.4 1.0
N H:SER162 4.5 10.4 1.0
CB H:ASN161 4.5 11.6 1.0
O W:HOH566 4.6 17.5 1.0
OD1 H:ASN161 4.7 12.6 1.0
CA H:SER162 4.7 10.8 1.0
CA W:SER47 4.7 9.5 1.0
C H:SER162 4.8 11.2 1.0

Sodium binding site 9 out of 16 in 5nb4

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Sodium binding site 9 out of 16 in the Atomic Resolution Structure of C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Atomic Resolution Structure of C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na205

b:20.1
occ:1.00
 O I:HOH498 1.9 39.0 1.0
O X:HOH535 2.3 19.2 1.0
O I:ASN161 2.4 9.9 1.0
O I:HOH509 2.4 26.0 1.0
OG X:SER47 2.5 13.0 1.0
O I:SER164 2.7 17.7 1.0
C I:SER164 3.3 15.2 1.0
C I:ASN161 3.5 8.7 1.0
O K:HOH549 3.6 25.9 1.0
CB X:SER47 3.7 10.9 1.0
OXT I:SER164 3.8 15.2 1.0
O X:HOH335 3.8 34.6 1.0
O X:HOH519 3.9 35.5 1.0
O I:HOH556 4.0 37.6 1.0
O I:HOH320 4.0 15.0 1.0
CA I:ASN161 4.2 9.4 1.0
CA I:SER164 4.2 14.4 1.0
N I:SER164 4.2 12.3 1.0
O K:HOH304 4.3 29.8 1.0
CB I:SER164 4.4 15.9 1.0
CB I:ASN161 4.5 11.1 1.0
N I:SER162 4.5 9.2 1.0
OD1 I:ASN161 4.7 12.8 1.0
O I:HOH390 4.7 29.5 0.5
CA I:SER162 4.7 10.0 1.0
O X:HOH559 4.7 17.7 1.0
CA X:SER47 4.7 9.9 1.0
C I:SER162 4.8 10.1 1.0

Sodium binding site 10 out of 16 in 5nb4

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Sodium binding site 10 out of 16 in the Atomic Resolution Structure of C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Atomic Resolution Structure of C-Phycoerythrin From Marine Cyanobacterium Phormidium Sp. A09DM at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na205

b:17.9
occ:1.00
 O J:HOH507 2.2 31.7 1.0
O J:HOH528 2.3 20.0 1.0
O J:ASN161 2.4 12.1 1.0
OG S:SER47 2.4 14.7 1.0
O J:HOH514 2.5 33.6 1.0
O J:SER164 2.5 18.6 1.0
C J:SER164 3.3 15.7 1.0
C J:ASN161 3.5 10.7 1.0
O H:HOH519 3.5 32.6 1.0
CB S:SER47 3.6 10.7 1.0
OXT J:SER164 3.9 17.6 1.0
O S:HOH317 3.9 70.7 1.0
O J:HOH573 4.0 24.9 0.5
O J:HOH316 4.0 16.1 1.0
CA J:ASN161 4.2 10.2 1.0
O S:HOH421 4.2 38.8 1.0
CA J:SER164 4.2 14.6 1.0
N J:SER164 4.2 13.5 1.0
O J:HOH577 4.3 32.8 1.0
CB J:SER164 4.4 17.1 1.0
N J:SER162 4.5 10.4 1.0
CB J:ASN161 4.5 9.9 1.0
O J:HOH383 4.6 26.3 0.6
CA S:SER47 4.6 10.3 1.0
OD1 J:ASN161 4.7 13.3 1.0
CA J:SER162 4.7 11.1 1.0
O S:HOH533 4.8 19.2 1.0
C J:SER162 4.8 10.8 1.0
O S:HOH574 4.8 32.6 0.5

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: Tue Dec 15 11:20:40 2020

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