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Sodium in PDB 6jpr: Crystal Structure of Phycocyanin From Nostoc Sp. R76DM

Protein crystallography data

The structure of Crystal Structure of Phycocyanin From Nostoc Sp. R76DM, PDB code: 6jpr was solved by R.R.Sonani, G.D.Gupta, R.P.Rastogi, S.N.Patel, D.Madamwar, V.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.26 / 2.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.136, 186.158, 85.532, 90.00, 94.33, 90.00
R / Rfree (%) 19.9 / 24.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Phycocyanin From Nostoc Sp. R76DM (pdb code 6jpr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Phycocyanin From Nostoc Sp. R76DM, PDB code: 6jpr:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6jpr

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Sodium binding site 1 out of 5 in the Crystal Structure of Phycocyanin From Nostoc Sp. R76DM


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 Phycocyanin From Nostoc Sp. R76DM within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:31.9
occ:1.00
 O A:ASN159 2.4 30.9 1.0
OG H:SER49 2.4 23.4 1.0
O H:HOH320 2.4 32.5 1.0
O A:SER162 2.6 25.1 1.0
O I:HOH366 2.8 33.6 1.0
C A:SER162 3.5 25.1 1.0
C A:ASN159 3.5 26.4 1.0
CB H:SER49 3.7 24.6 1.0
O I:HOH314 3.8 23.2 1.0
O H:HOH336 3.9 29.7 1.0
OXT A:SER162 3.9 18.1 1.0
O H:HOH326 3.9 23.9 1.0
NZ I:LYS120 4.1 27.2 1.0
CA A:ASN159 4.3 27.0 1.0
N A:THR160 4.5 27.6 1.0
CA H:SER49 4.6 26.1 1.0
CA A:THR160 4.6 29.4 1.0
CB A:ASN159 4.6 26.0 1.0
CA A:SER162 4.7 21.4 1.0
N A:SER162 4.7 26.1 1.0
O A:HOH305 4.8 26.7 1.0
O A:THR160 4.8 30.7 1.0
C A:THR160 4.9 32.3 1.0
OD1 A:ASN159 5.0 27.1 1.0

Sodium binding site 2 out of 5 in 6jpr

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Sodium binding site 2 out of 5 in the Crystal Structure of Phycocyanin From Nostoc Sp. R76DM


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 Phycocyanin From Nostoc Sp. R76DM within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:42.0
occ:1.00
 O A:HOH321 2.6 20.8 1.0
OG I:SER125 2.6 21.4 1.0
O A:HOH339 2.8 22.9 1.0
OG A:SER125 3.0 28.3 1.0
O A:HOH313 3.0 19.6 1.0
CB A:SER125 3.0 24.0 1.0
CA A:SER125 3.2 27.8 1.0
CB I:SER125 3.4 20.2 1.0
O A:HOH314 3.8 21.1 1.0
O A:LEU124 3.9 26.2 1.0
CD A:PRO126 3.9 19.0 1.0
CA I:SER125 3.9 17.7 1.0
CD I:PRO126 4.0 23.9 1.0
N A:SER125 4.0 24.5 1.0
C A:LEU124 4.2 22.9 1.0
C A:SER125 4.4 22.3 1.0
OD1 A:ASP123 4.4 25.5 1.0
N I:PRO126 4.5 23.2 1.0
N A:PRO126 4.6 22.5 1.0
O I:HOH336 4.6 24.1 1.0
C I:SER125 4.7 22.9 1.0
OG I:SER127 4.8 18.4 1.0
O A:HOH369 4.9 27.0 1.0

Sodium binding site 3 out of 5 in 6jpr

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Sodium binding site 3 out of 5 in the Crystal Structure of Phycocyanin From Nostoc Sp. R76DM


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 Phycocyanin From Nostoc Sp. R76DM within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na204

b:43.9
occ:1.00
 O B:ALA172 2.4 34.4 1.0
O B:ALA169 2.5 28.1 1.0
O B:HOH317 3.2 26.6 1.0
C B:ALA172 3.3 33.9 1.0
C B:ALA169 3.5 29.9 1.0
OXT B:ALA172 3.8 34.9 1.0
CA B:ALA169 3.9 28.3 1.0
NH1 B:ARG114 4.0 33.5 1.0
CA B:ALA172 4.4 25.4 1.0
CB B:ALA169 4.4 25.5 1.0
N B:ALA172 4.5 27.6 1.0
NE B:ARG114 4.6 38.1 1.0
N B:ALA170 4.7 28.1 1.0
CZ B:ARG114 4.8 44.5 1.0
CB B:ALA172 4.8 31.5 1.0
O B:ALA168 4.9 23.0 1.0

Sodium binding site 4 out of 5 in 6jpr

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Sodium binding site 4 out of 5 in the Crystal Structure of Phycocyanin From Nostoc Sp. R76DM


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 Phycocyanin From Nostoc Sp. R76DM within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na205

b:35.9
occ:1.00
 OG D:SER49 2.4 25.4 1.0
O K:ASN159 2.7 32.1 1.0
O K:SER162 2.8 30.4 1.0
O D:HOH354 3.1 35.3 1.0
O K:HOH333 3.5 22.4 1.0
CB D:SER49 3.6 28.8 1.0
C K:SER162 3.7 22.3 1.0
C K:ASN159 3.7 28.1 1.0
OXT K:SER162 4.0 23.6 1.0
O K:HOH354 4.0 33.1 1.0
O D:HOH325 4.0 26.5 1.0
NZ E:LYS120 4.1 39.3 1.0
CA K:ASN159 4.3 26.8 1.0
CA D:SER49 4.4 29.2 1.0
CB K:ASN159 4.5 27.6 1.0
OD1 K:ASN159 4.5 29.3 1.0
N K:THR160 4.7 27.5 1.0
CE E:LYS120 4.7 34.2 1.0
CG K:ASN159 4.9 34.0 1.0
CA K:SER162 4.9 21.6 1.0
N K:SER162 4.9 29.5 1.0
N D:SER49 4.9 28.1 1.0
CA K:THR160 4.9 32.2 1.0
OG K:SER162 5.0 29.0 1.0

Sodium binding site 5 out of 5 in 6jpr

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Sodium binding site 5 out of 5 in the Crystal Structure of Phycocyanin From Nostoc Sp. R76DM


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 Phycocyanin From Nostoc Sp. R76DM within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na203

b:37.7
occ:1.00
 OG F:SER49 2.5 24.2 1.0
O I:ASN159 2.6 26.6 1.0
O F:HOH353 2.6 27.3 1.0
O I:HOH361 2.9 34.6 1.0
O I:SER162 3.0 33.1 1.0
O A:HOH334 3.5 52.8 1.0
C I:ASN159 3.6 25.4 1.0
CB F:SER49 3.8 30.6 1.0
C I:SER162 3.9 29.1 1.0
O F:HOH343 4.0 26.9 1.0
OXT I:SER162 4.3 30.4 1.0
CA I:ASN159 4.4 19.2 1.0
NZ A:LYS120 4.4 40.4 1.0
N I:THR160 4.6 18.5 1.0
CB I:ASN159 4.6 24.8 1.0
CA F:SER49 4.6 26.9 1.0
CA I:THR160 4.7 20.0 1.0
CE A:LYS120 4.7 33.6 1.0
O I:HOH363 4.7 32.6 1.0
OD1 I:ASN159 4.9 25.2 1.0
O F:HOH359 4.9 30.5 1.0

Reference:

R.R.Sonani, R.P.Rastogi, S.N.Patel, M.G.Chaubey, N.K.Singh, G.D.Gupta, V.Kumar, D.Madamwar. Phylogenetic and Crystallographic Analysis of Nostoc Phycocyanin Having Blue-Shifted Spectral Properties. Sci Rep V. 9 9863 2019.
ISSN: ESSN 2045-2322
PubMed: 31285455
DOI: 10.1038/S41598-019-46288-4
Page generated: Tue Oct 8 11:28:08 2024

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