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Sodium in PDB 7c3f: Crystal Structure of Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex

Enzymatic activity of Crystal Structure of Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex

All present enzymatic activity of Crystal Structure of Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex:
1.8.7.2;

Protein crystallography data

The structure of Crystal Structure of Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex, PDB code: 7c3f was solved by G.Kurisu, L.Juniar, H.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.57 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 174.262, 137.209, 192.457, 90.00, 90.21, 90.00
R / Rfree (%) 21 / 24.5

Other elements in 7c3f:

The structure of Crystal Structure of Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex also contains other interesting chemical elements:

Iron (Fe) 28 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex (pdb code 7c3f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Crystal Structure of Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex, PDB code: 7c3f:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 7c3f

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Sodium binding site 1 out of 10 in the Crystal Structure of Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex


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 Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:52.4
occ:1.00
OG1 A:THR35 2.6 40.7 1.0
O A:LEU88 2.7 44.5 1.0
O A:MET87 2.8 41.4 1.0
N A:CYS29 2.9 47.2 1.0
CA A:LEU88 3.2 39.8 1.0
C A:LEU88 3.3 46.4 1.0
CA A:PHE28 3.3 45.6 1.0
CB A:THR35 3.6 43.5 1.0
CB A:PHE28 3.6 43.1 1.0
C A:PHE28 3.6 49.4 1.0
CB A:CYS29 3.7 53.0 1.0
C A:MET87 3.7 41.1 1.0
CD1 A:PHE28 3.7 48.7 1.0
CA A:CYS29 3.9 51.6 1.0
CG2 A:THR35 3.9 42.4 1.0
N A:LEU88 3.9 34.3 1.0
CA A:THR35 4.0 45.2 1.0
CG A:PHE28 4.1 51.9 1.0
CD1 A:LEU88 4.1 35.1 1.0
N A:THR35 4.3 38.4 1.0
CB A:LEU88 4.4 35.0 1.0
N A:PHE89 4.5 46.9 1.0
N A:PHE28 4.6 52.8 1.0
O A:TYR27 4.7 45.7 1.0
CG A:LEU88 4.8 43.2 1.0
O A:PHE28 4.8 50.8 1.0
CE1 A:PHE28 4.8 42.5 1.0
C A:CYS29 4.9 52.3 1.0
O A:CYS29 4.9 47.0 1.0

Sodium binding site 2 out of 10 in 7c3f

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Sodium binding site 2 out of 10 in the Crystal Structure of Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex


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 Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:57.4
occ:1.00
O C:SER16 2.7 43.1 1.0
OG C:SER20 2.7 50.7 1.0
N C:SER20 3.2 41.2 1.0
CA C:THR17 3.3 45.6 1.0
CB C:SER20 3.4 46.4 1.0
C C:THR17 3.5 36.0 1.0
C C:SER16 3.6 40.8 1.0
CE D:MET115 3.7 47.9 1.0
NZ F:LYS42 3.7 67.7 1.0
O C:THR17 3.7 40.6 1.0
N C:ASP19 3.8 41.4 1.0
O F:HOH201 3.8 44.4 1.0
N C:THR17 3.9 41.3 1.0
CB C:ASP19 3.9 47.0 1.0
CA C:SER20 3.9 40.0 1.0
O C:HOH316 4.0 39.7 1.0
N C:TRP18 4.0 40.7 1.0
C C:ASP19 4.1 40.8 1.0
CA C:ASP19 4.1 43.7 1.0
CG D:MET115 4.4 64.1 1.0
CB C:THR17 4.5 38.0 1.0
CE F:LYS42 4.6 71.2 1.0
C C:TRP18 4.6 42.0 1.0
SD D:MET115 4.7 60.1 1.0
OD2 C:ASP19 4.8 61.0 1.0
CD F:LYS42 4.8 56.4 1.0
CG2 C:THR17 4.9 41.9 1.0
CG C:ASP19 4.9 58.0 1.0
CA C:TRP18 5.0 41.8 1.0

Sodium binding site 3 out of 10 in 7c3f

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Sodium binding site 3 out of 10 in the Crystal Structure of Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex


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 Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na202

b:51.4
occ:1.00
N D:CYS29 2.6 47.3 1.0
OG1 D:THR35 2.7 41.5 1.0
O D:LEU88 2.7 44.5 1.0
O D:MET87 2.8 46.9 1.0
CA D:PHE28 3.2 44.0 1.0
CA D:LEU88 3.3 38.5 1.0
C D:LEU88 3.4 43.6 1.0
C D:PHE28 3.4 47.7 1.0
CB D:CYS29 3.4 40.6 1.0
CB D:PHE28 3.6 42.3 1.0
CA D:CYS29 3.6 50.8 1.0
CB D:THR35 3.7 43.8 1.0
C D:MET87 3.7 42.2 1.0
CD1 D:PHE28 3.9 41.7 1.0
CG2 D:THR35 3.9 42.6 1.0
N D:LEU88 4.0 40.4 1.0
CA D:THR35 4.1 40.7 1.0
CG D:PHE28 4.1 49.8 1.0
CD1 D:LEU88 4.3 36.9 1.0
N D:THR35 4.4 50.5 1.0
N D:PHE28 4.5 42.4 1.0
CB D:LEU88 4.6 36.5 1.0
N D:PHE89 4.6 36.2 1.0
O D:TYR27 4.6 44.5 1.0
O D:PHE28 4.6 47.6 1.0
C D:CYS29 4.7 53.1 1.0
O D:CYS29 4.8 52.0 1.0
CG D:LEU88 5.0 46.2 1.0
CE1 D:PHE28 5.0 41.6 1.0

Sodium binding site 4 out of 10 in 7c3f

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Sodium binding site 4 out of 10 in the Crystal Structure of Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex


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 Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na201

b:58.1
occ:1.00
O E:VAL46 2.8 50.4 1.0
O E:VAL52 2.9 74.7 1.0
C E:TYR47 3.0 49.1 1.0
CA E:TYR47 3.0 48.6 1.0
N E:VAL49 3.1 49.4 1.0
N E:HIS48 3.2 50.8 1.0
C E:VAL46 3.3 51.3 1.0
N E:TYR47 3.4 48.5 1.0
CB E:VAL49 3.5 55.6 1.0
CG2 E:VAL49 3.6 53.4 1.0
O E:TYR47 3.6 51.1 1.0
O E:PRO53 3.7 64.4 1.0
CG2 E:VAL55 3.7 55.0 1.0
CA E:VAL49 3.8 49.5 1.0
C E:PRO53 3.8 62.4 1.0
N E:GLU54 3.8 54.9 1.0
CA E:GLU54 3.9 54.3 1.0
N E:VAL55 3.9 50.9 1.0
C E:HIS48 4.0 46.0 1.0
C E:GLU54 4.1 55.9 1.0
O E:VAL49 4.1 53.2 1.0
C E:VAL52 4.1 61.9 1.0
CA E:HIS48 4.1 54.3 1.0
O E:HOH305 4.2 48.0 1.0
CG2 E:VAL46 4.2 50.3 1.0
CB E:VAL55 4.3 53.5 1.0
C E:VAL49 4.4 55.3 1.0
CB E:TYR47 4.5 44.1 1.0
CA E:PRO53 4.6 60.2 1.0
CA E:VAL46 4.6 48.9 1.0
CA E:VAL55 4.7 49.6 1.0
N E:PRO53 4.8 62.5 1.0
CB E:VAL46 4.8 57.7 1.0
CG1 E:VAL49 4.8 58.3 1.0
O E:GLU54 4.9 63.4 1.0
ND1 E:HIS48 4.9 50.1 1.0

Sodium binding site 5 out of 10 in 7c3f

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Sodium binding site 5 out of 10 in the Crystal Structure of Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex


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 Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na202

b:56.2
occ:1.00
OG1 G:THR35 2.6 51.5 1.0
O G:MET87 2.8 48.0 1.0
N G:CYS29 2.8 54.9 1.0
O G:LEU88 2.9 56.2 1.0
CA G:LEU88 3.3 42.3 1.0
C G:LEU88 3.5 49.0 1.0
CB G:THR35 3.5 51.4 1.0
CA G:PHE28 3.5 52.4 1.0
CB G:CYS29 3.5 45.0 1.0
CG2 G:THR35 3.6 43.4 1.0
C G:PHE28 3.6 54.2 1.0
CB G:PHE28 3.7 50.7 1.0
CA G:CYS29 3.8 48.4 1.0
C G:MET87 3.8 47.1 1.0
CA G:THR35 3.8 51.1 1.0
CD1 G:PHE28 4.0 49.3 1.0
N G:LEU88 4.0 44.5 1.0
CD1 G:LEU88 4.1 39.7 1.0
CG G:PHE28 4.2 53.6 1.0
N G:THR35 4.2 49.9 1.0
CB G:LEU88 4.5 38.3 1.0
N G:PHE89 4.7 41.8 1.0
N G:PHE28 4.8 52.5 1.0
C G:CYS29 4.8 53.8 1.0
O G:PHE28 4.8 59.8 1.0
CG G:LEU88 4.8 42.4 1.0
O G:TYR27 4.9 51.4 1.0
O G:CYS29 4.9 49.9 1.0

Sodium binding site 6 out of 10 in 7c3f

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Sodium binding site 6 out of 10 in the Crystal Structure of Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na202

b:52.6
occ:1.00
O J:MET87 2.5 48.2 1.0
OG1 J:THR35 2.7 45.1 1.0
N J:CYS29 2.8 54.9 1.0
O J:LEU88 2.8 48.4 1.0
CA J:LEU88 3.2 52.5 1.0
C J:LEU88 3.3 48.4 1.0
CB J:CYS29 3.4 50.9 1.0
CA J:PHE28 3.5 51.9 1.0
C J:MET87 3.5 50.1 1.0
C J:PHE28 3.6 57.8 1.0
CA J:CYS29 3.7 58.7 1.0
CB J:THR35 3.7 57.2 1.0
CB J:PHE28 3.8 44.5 1.0
N J:LEU88 3.8 41.3 1.0
CG2 J:THR35 3.9 42.0 1.0
CA J:THR35 4.0 46.5 1.0
CD1 J:PHE28 4.1 41.8 1.0
CD1 J:LEU88 4.3 36.6 1.0
N J:THR35 4.3 47.2 1.0
CG J:PHE28 4.4 47.5 1.0
CB J:LEU88 4.5 47.3 1.0
N J:PHE89 4.5 47.8 1.0
O J:PHE28 4.8 55.7 1.0
O J:TYR27 4.8 57.2 1.0
N J:PHE28 4.8 47.4 1.0
C J:CYS29 4.8 51.4 1.0
CA J:MET87 4.9 49.4 1.0
O J:CYS29 4.9 56.1 1.0
CG J:LEU88 4.9 46.4 1.0
CG1 J:VAL34 4.9 41.7 1.0

Sodium binding site 7 out of 10 in 7c3f

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Sodium binding site 7 out of 10 in the Crystal Structure of Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na201

b:52.7
occ:1.00
O L:ASP15 2.6 41.4 1.0
O O:HOH310 2.7 50.7 1.0
O O:HOH347 2.9 35.3 1.0
N L:ASP19 3.1 42.5 1.0
N L:TRP18 3.5 39.7 1.0
O L:SER16 3.6 45.5 1.0
CB L:ASP19 3.6 48.7 1.0
CB L:TRP18 3.7 36.7 1.0
O O:LYS42 3.7 51.5 1.0
C L:ASP15 3.8 38.6 1.0
C L:SER16 3.9 44.2 1.0
CA L:TRP18 3.9 41.3 1.0
O L:HOH326 3.9 51.8 1.0
C L:TRP18 3.9 46.7 1.0
CA L:ASP19 3.9 50.2 1.0
CB O:ASP45 4.0 43.0 1.0
CD O:PRO46 4.1 37.4 1.0
CG O:PRO46 4.1 42.7 1.0
C L:THR17 4.3 40.8 1.0
N L:THR17 4.3 39.6 1.0
CA L:SER16 4.4 42.2 1.0
N L:SER16 4.6 38.6 1.0
OD2 O:ASP45 4.7 61.8 1.0
CA L:THR17 4.7 35.8 1.0
CG L:TRP18 4.7 42.1 1.0
O O:HOH334 4.8 48.7 1.0
C O:LYS42 4.8 45.4 1.0
N O:PRO46 4.9 39.6 1.0
CG O:ASP45 4.9 56.7 1.0
CD1 L:TRP18 4.9 45.1 1.0
CA L:ASP15 4.9 43.9 1.0

Sodium binding site 8 out of 10 in 7c3f

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Sodium binding site 8 out of 10 in the Crystal Structure of Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Na202

b:61.1
occ:1.00
O M:LEU88 2.5 49.0 1.0
OG1 M:THR35 2.7 52.3 1.0
O M:MET87 2.9 54.1 1.0
N M:CYS29 2.9 58.8 1.0
CA M:LEU88 3.1 41.3 1.0
C M:LEU88 3.1 47.8 1.0
CA M:PHE28 3.3 54.2 1.0
CB M:THR35 3.6 54.5 1.0
CG2 M:THR35 3.6 48.6 1.0
CB M:PHE28 3.6 50.8 1.0
C M:PHE28 3.6 57.6 1.0
CD1 M:PHE28 3.7 57.4 1.0
CD1 M:LEU88 3.8 44.6 1.0
C M:MET87 3.8 48.6 1.0
CB M:CYS29 3.8 47.6 1.0
N M:LEU88 3.9 43.9 1.0
CA M:THR35 4.0 53.8 1.0
CA M:CYS29 4.0 56.2 1.0
CG M:PHE28 4.0 60.7 1.0
CB M:LEU88 4.2 46.8 1.0
N M:PHE89 4.4 48.6 1.0
N M:THR35 4.5 55.0 1.0
CG M:LEU88 4.5 47.7 1.0
N M:PHE28 4.6 57.0 1.0
O M:TYR27 4.6 57.0 1.0
CE1 M:PHE28 4.7 53.7 1.0
O M:PHE28 4.8 51.6 1.0

Sodium binding site 9 out of 10 in 7c3f

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Sodium binding site 9 out of 10 in the Crystal Structure of Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Na201

b:53.0
occ:1.00
OG1 O:THR66 2.7 43.0 1.0
OD1 O:ASP67 3.1 78.7 1.0
CD2 M:HIS58 3.1 43.3 1.0
O M:HOH308 3.3 53.7 1.0
CB O:THR66 3.5 41.9 1.0
O O:THR66 3.6 41.0 1.0
C O:THR66 3.7 45.1 1.0
CB M:HIS58 3.7 47.3 1.0
CG M:HIS58 3.7 52.3 1.0
CA M:HIS58 3.8 45.3 1.0
N O:ASP67 3.9 44.4 1.0
CG O:ASP67 4.0 63.0 1.0
O M:ARG57 4.0 50.1 1.0
CA O:THR66 4.2 42.2 1.0
CA O:ASP67 4.3 50.5 1.0
NE2 M:HIS58 4.3 57.8 1.0
N M:HIS58 4.5 44.5 1.0
CB O:ALA35 4.5 37.8 1.0
C M:ARG57 4.6 45.7 1.0
CB O:ASP67 4.7 49.9 1.0
OD2 O:ASP67 4.8 77.1 1.0
CG2 O:THR66 4.8 32.7 1.0
C M:HIS58 5.0 44.1 1.0

Sodium binding site 10 out of 10 in 7c3f

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Sodium binding site 10 out of 10 in the Crystal Structure of Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Ferredoxin: Thioredoxin Reductase and Thioredoxin M2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na202

b:60.5
occ:1.00
NE P:ARG57 2.7 39.9 1.0
NH1 P:ARG57 2.8 49.8 1.0
O P:HIS58 3.0 50.2 1.0
OG Q:SER77 3.0 58.7 1.0
CZ P:ARG57 3.1 49.7 1.0
CB P:ARG57 3.4 49.6 1.0
CB Q:SER77 3.5 56.3 1.0
CD R:ARG79 3.6 63.5 1.0
CD1 P:TYR59 3.8 55.9 1.0
O Q:SER77 3.8 64.2 1.0
C P:HIS58 3.8 55.0 1.0
CE1 P:TYR59 3.8 53.5 1.0
CD P:ARG57 3.9 45.9 1.0
N P:HIS58 4.0 52.3 1.0
O R:ARG79 4.1 52.1 1.0
CG P:ARG57 4.1 46.7 1.0
CB R:ARG79 4.1 56.8 1.0
NE1 P:TRP71 4.3 50.0 1.0
CA P:ARG57 4.3 52.7 1.0
CG R:ARG79 4.3 56.1 1.0
CA R:ARG79 4.4 56.9 1.0
C P:ARG57 4.4 55.7 1.0
NH2 P:ARG57 4.4 45.2 1.0
C R:ARG79 4.5 52.7 1.0
NE R:ARG79 4.5 56.5 1.0
NH2 R:ARG79 4.5 61.9 1.0
CA P:HIS58 4.6 53.8 1.0
CD1 P:TRP71 4.6 48.3 1.0
N P:TYR59 4.6 55.0 1.0
CG P:TYR59 4.7 57.1 1.0
C Q:SER77 4.7 66.3 1.0
CA Q:SER77 4.7 65.4 1.0
CA P:TYR59 4.8 60.6 1.0
CZ P:TYR59 4.8 58.0 1.0
CE2 P:TRP71 4.8 43.0 1.0
CZ R:ARG79 4.9 63.5 1.0

Reference:

L.Juniar, H.Tanaka, K.Yoshida, T.Hisabori, G.Kurisu. Structural Basis For Thioredoxin Isoform-Based Fine-Tuning of Ferredoxin-Thioredoxin Reductase Activity. Protein Sci. V. 29 2538 2020.
ISSN: ESSN 1469-896X
PubMed: 33015914
DOI: 10.1002/PRO.3964
Page generated: Tue Dec 15 17:34:47 2020

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