Atomistry » Sodium » PDB 6jbu-6kcb » 6jpr
Atomistry »
  Sodium »
    PDB 6jbu-6kcb »
      6jpr »

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

Go back to Sodium Binding Sites List in 6jpr
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

Go back to Sodium Binding Sites List in 6jpr
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

Go back to Sodium Binding Sites List in 6jpr
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

Go back to Sodium Binding Sites List in 6jpr
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

Go back to Sodium Binding Sites List in 6jpr
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy