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Sodium in PDB 6gas: Crystal Structure of Oxidised Ferredoxin/Flavodoxin Nadp+ Oxidoreductase 2 (FNR2) From Bacillus Cereus

Enzymatic activity of Crystal Structure of Oxidised Ferredoxin/Flavodoxin Nadp+ Oxidoreductase 2 (FNR2) From Bacillus Cereus

All present enzymatic activity of Crystal Structure of Oxidised Ferredoxin/Flavodoxin Nadp+ Oxidoreductase 2 (FNR2) From Bacillus Cereus:
1.18.1.2;

Protein crystallography data

The structure of Crystal Structure of Oxidised Ferredoxin/Flavodoxin Nadp+ Oxidoreductase 2 (FNR2) From Bacillus Cereus, PDB code: 6gas was solved by I.Gudim, H.-P.Hersleth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.60 / 2.40
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 109.660, 109.660, 242.519, 90.00, 90.00, 120.00
R / Rfree (%) 20.7 / 26.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Oxidised Ferredoxin/Flavodoxin Nadp+ Oxidoreductase 2 (FNR2) From Bacillus Cereus (pdb code 6gas). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Oxidised Ferredoxin/Flavodoxin Nadp+ Oxidoreductase 2 (FNR2) From Bacillus Cereus, PDB code: 6gas:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6gas

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Sodium binding site 1 out of 4 in the Crystal Structure of Oxidised Ferredoxin/Flavodoxin Nadp+ Oxidoreductase 2 (FNR2) From Bacillus Cereus


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 Oxidised Ferredoxin/Flavodoxin Nadp+ Oxidoreductase 2 (FNR2) From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1002

b:45.4
occ:1.00
 O A:THR120 2.6 38.7 1.0
N A:GLY18 2.7 38.8 1.0
O1P A:FAD1001 2.7 41.5 1.0
CA A:GLY18 3.1 37.8 1.0
N A:GLY21 3.1 42.8 1.0
O A:GLY16 3.1 41.4 1.0
OG1 A:THR120 3.4 32.6 1.0
C A:GLY16 3.4 44.8 1.0
CB A:THR120 3.5 39.4 1.0
C A:GLY18 3.5 42.0 1.0
CA A:GLY21 3.6 34.5 1.0
O A:GLY18 3.6 36.8 1.0
C A:THR120 3.7 42.1 1.0
C5B A:FAD1001 3.7 40.1 1.0
O5B A:FAD1001 3.7 34.3 1.0
C A:GLY17 3.8 39.0 1.0
P A:FAD1001 3.9 41.1 1.0
N A:GLY17 3.9 41.1 1.0
C4B A:FAD1001 4.1 42.1 1.0
CA A:GLY16 4.1 37.7 1.0
N A:THR20 4.1 39.7 1.0
CA A:GLY17 4.1 36.6 1.0
C A:THR20 4.2 45.0 1.0
CA A:THR120 4.2 38.8 1.0
CB A:THR20 4.3 37.8 1.0
N A:PRO19 4.4 44.4 1.0
O3P A:FAD1001 4.4 49.4 1.0
O2P A:FAD1001 4.4 40.3 1.0
CA A:THR20 4.4 38.7 1.0
O4B A:FAD1001 4.6 41.1 1.0
CG2 A:THR120 4.7 41.3 1.0
PA A:FAD1001 4.7 36.0 1.0
C A:GLY21 4.8 43.1 1.0
O A:GLY17 4.8 39.2 1.0
N A:ALA121 4.8 34.5 1.0
CD A:PRO19 4.9 38.1 1.0
C A:PRO19 4.9 44.5 1.0
N A:LEU22 5.0 44.8 1.0
O A:HOH1112 5.0 40.5 1.0

Sodium binding site 2 out of 4 in 6gas

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Sodium binding site 2 out of 4 in the Crystal Structure of Oxidised Ferredoxin/Flavodoxin Nadp+ Oxidoreductase 2 (FNR2) From Bacillus Cereus


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 Oxidised Ferredoxin/Flavodoxin Nadp+ Oxidoreductase 2 (FNR2) From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1002

b:56.8
occ:1.00
 O B:SER204 2.3 49.0 1.0
O B:MET202 2.3 46.5 1.0
N B:SER204 3.3 55.5 1.0
C B:SER204 3.4 49.8 1.0
C B:MET202 3.5 56.0 1.0
C B:ASN203 3.9 57.1 1.0
CA B:SER204 4.0 50.8 1.0
CA B:ASN203 4.1 54.8 1.0
N B:ASN203 4.2 45.5 1.0
O B:ALA206 4.4 53.5 1.0
O B:LEU201 4.4 44.2 1.0
N B:ARG205 4.5 49.4 1.0
CA B:MET202 4.6 56.6 1.0
O B:ASN203 4.6 57.2 1.0
CA B:ARG205 4.9 54.9 1.0

Sodium binding site 3 out of 4 in 6gas

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Sodium binding site 3 out of 4 in the Crystal Structure of Oxidised Ferredoxin/Flavodoxin Nadp+ Oxidoreductase 2 (FNR2) From Bacillus Cereus


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 Oxidised Ferredoxin/Flavodoxin Nadp+ Oxidoreductase 2 (FNR2) From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1002

b:54.3
occ:1.00
 O2P C:FAD1001 2.4 45.5 1.0
N C:ASP287 2.9 44.0 1.0
O C:ALA285 3.0 40.2 1.0
N C:GLY122 3.1 47.9 1.0
C C:GLY286 3.2 41.9 1.0
CA C:GLY286 3.2 44.9 1.0
N C:ILE288 3.3 41.3 1.0
C C:THR120 3.5 45.1 1.0
CA C:GLY122 3.6 47.0 1.0
P C:FAD1001 3.6 49.6 1.0
N C:ALA121 3.7 41.1 1.0
CG2 C:ILE288 3.7 41.2 1.0
O C:THR120 3.8 41.5 1.0
CA C:THR120 3.8 36.3 1.0
CA C:ASP287 3.9 45.1 1.0
C C:ALA285 3.9 37.6 1.0
O3P C:FAD1001 3.9 59.7 1.0
CB C:ILE288 4.0 45.6 1.0
N C:GLY286 4.0 39.9 1.0
C C:ASP287 4.1 45.1 1.0
O C:GLY286 4.1 43.0 1.0
C C:ALA121 4.2 47.8 1.0
CB C:ASP287 4.2 52.1 1.0
CA C:ILE288 4.3 41.5 1.0
CB C:THR120 4.3 39.0 1.0
OG1 C:THR20 4.3 40.7 1.0
O1P C:FAD1001 4.5 47.3 1.0
CA C:ALA121 4.5 40.5 1.0
CB C:THR20 4.5 43.1 1.0
C C:GLY122 4.8 53.9 1.0
O5' C:FAD1001 4.8 50.1 1.0
O C:HOH1117 4.8 45.9 1.0
CG2 C:THR20 4.9 36.3 1.0
O C:GLY122 4.9 50.8 1.0

Sodium binding site 4 out of 4 in 6gas

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Sodium binding site 4 out of 4 in the Crystal Structure of Oxidised Ferredoxin/Flavodoxin Nadp+ Oxidoreductase 2 (FNR2) From Bacillus Cereus


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 Oxidised Ferredoxin/Flavodoxin Nadp+ Oxidoreductase 2 (FNR2) From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1002

b:55.7
occ:1.00
 O D:THR120 2.4 44.2 1.0
O1P D:FAD1001 2.8 46.2 1.0
O D:GLY16 3.0 50.7 1.0
N D:GLY18 3.0 49.4 1.0
N D:GLY21 3.2 51.5 1.0
OG1 D:THR120 3.2 43.5 1.0
CB D:THR120 3.4 43.4 1.0
CA D:GLY18 3.4 51.6 1.0
C D:GLY16 3.4 49.9 1.0
C D:THR120 3.5 43.0 1.0
C D:GLY18 3.7 53.2 1.0
O D:GLY18 3.7 45.7 1.0
O5B D:FAD1001 3.8 49.4 1.0
CA D:GLY21 3.8 43.4 1.0
C5B D:FAD1001 3.9 47.2 1.0
P D:FAD1001 3.9 47.6 1.0
C D:GLY17 4.0 47.6 1.0
N D:GLY17 4.0 45.4 1.0
CA D:THR120 4.0 39.2 1.0
CA D:GLY16 4.1 42.7 1.0
CB D:THR20 4.1 41.2 1.0
N D:THR20 4.1 47.3 1.0
C4B D:FAD1001 4.2 49.7 1.0
C D:THR20 4.2 49.2 1.0
CA D:GLY17 4.3 46.1 1.0
CA D:THR20 4.3 46.7 1.0
O3P D:FAD1001 4.4 57.6 1.0
O2P D:FAD1001 4.4 49.5 1.0
O4B D:FAD1001 4.5 50.8 1.0
N D:PRO19 4.5 54.2 1.0
N D:ALA121 4.6 44.4 1.0
CG2 D:THR120 4.7 39.1 1.0
PA D:FAD1001 4.8 53.3 1.0
O D:HOH1117 4.9 40.2 1.0
C D:PRO19 5.0 47.1 1.0
CG2 D:THR20 5.0 41.6 1.0
OG1 D:THR20 5.0 40.2 1.0
O D:ILE15 5.0 42.3 1.0

Reference:

I.Gudim, M.Hammerstad, M.Lofstad, H.P.Hersleth. The Characterization of Different Flavodoxin Reductase-Flavodoxin (Fnr-Fld) Interactions Reveals An Efficient Fnr-Fld Redox Pair and Identifies A Novel Fnr Subclass. Biochemistry V. 57 5427 2018.
ISSN: ISSN 1520-4995
PubMed: 30142264
DOI: 10.1021/ACS.BIOCHEM.8B00674
Page generated: Tue Oct 8 08:59:20 2024

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