Sodium in PDB 6tr1: Native Cytochrome C6 From Thermosynechococcus Elongatus in Space Group H3

The structure of Native Cytochrome C6 From Thermosynechococcus Elongatus in Space Group H3, PDB code: 6tr1 was solved by S.Falke, C.G.Feiler, I.Sarrou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.53 / 1.70
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	94.800, 94.800, 160.220, 90.00, 90.00, 120.00
R / Rfree (%)	18.6 / 20.8

The structure of Native Cytochrome C6 From Thermosynechococcus Elongatus in Space Group H3 also contains other interesting chemical elements:

Iron

(Fe)

3 atoms

The binding sites of Sodium atom in the Native Cytochrome C6 From Thermosynechococcus Elongatus in Space Group H3 (pdb code 6tr1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Native Cytochrome C6 From Thermosynechococcus Elongatus in Space Group H3, PDB code: 6tr1:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Native Cytochrome C6 From Thermosynechococcus Elongatus in Space Group H3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Native Cytochrome C6 From Thermosynechococcus Elongatus in Space Group H3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:37.1 occ:1.00 OE1 A:GLU44 2.5 31.6 1.0 O A:HOH205 2.9 27.2 1.0 CD A:GLU44 3.6 28.4 1.0 CB A:ALA75 3.9 20.1 1.0 CB A:GLU44 3.9 20.0 1.0 CA A:ALA75 3.9 17.0 1.0 CE2 E:TYR42 4.1 22.2 1.0 OH E:TYR42 4.2 28.4 1.0 CG A:GLU44 4.2 26.2 1.0 CD1 A:LEU78 4.2 25.2 1.0 CZ E:TYR42 4.5 24.8 1.0 O E:HOH206 4.6 18.9 1.0 OE2 A:GLU44 4.7 38.4 1.0 O A:ALA75 4.7 18.9 1.0 CB A:LEU78 4.7 22.1 1.0 N A:ALA75 4.9 19.1 1.0 C A:ALA75 4.9 16.0 1.0

Sodium binding site 2 out of 5 in the Native Cytochrome C6 From Thermosynechococcus Elongatus in Space Group H3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Native Cytochrome C6 From Thermosynechococcus Elongatus in Space Group H3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na102 b:33.2 occ:1.00 NH1 C:ARG64 2.5 40.7 1.0 OD1 C:ASN13 2.7 16.1 1.0 O C:HOH208 3.0 22.9 1.0 CZ C:ARG64 3.6 38.2 1.0 CE1 C:PHE61 3.6 13.7 1.0 CG C:ASN13 3.7 14.3 1.0 NH2 C:ARG64 3.9 36.4 1.0 CB C:ASN13 4.1 12.2 1.0 CA C:ASN13 4.2 13.9 1.0 CD1 C:PHE61 4.2 13.0 1.0 O C:GLY12 4.6 14.4 1.0 NE C:ARG64 4.7 26.4 1.0 CZ C:PHE61 4.7 17.2 1.0 O C:ASN13 4.7 12.0 1.0 ND2 C:ASN13 4.9 16.3 1.0

Sodium binding site 3 out of 5 in the Native Cytochrome C6 From Thermosynechococcus Elongatus in Space Group H3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Native Cytochrome C6 From Thermosynechococcus Elongatus in Space Group H3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na103 b:36.0 occ:1.00 NZ C:LYS33 2.3 47.1 1.0 OE2 C:GLU37 2.5 26.1 1.0 O A:ALA4 2.6 20.1 1.0 C A:ALA4 3.4 22.3 1.0 CE C:LYS33 3.4 42.1 1.0 CD C:GLU37 3.4 22.8 1.0 CA A:ALA4 3.7 24.3 1.0 OE1 C:GLU37 3.7 26.2 1.0 CB A:ALA7 3.8 18.4 1.0 CB A:ALA4 3.9 26.8 1.0 N A:LYS8 3.9 14.7 1.0 CB A:LYS8 4.4 20.2 1.0 CD C:LYS33 4.5 32.5 1.0 N A:ASN5 4.5 21.4 1.0 C A:ALA7 4.6 14.8 1.0 CA A:LYS8 4.6 20.2 1.0 CA A:ALA7 4.7 17.8 1.0 CG C:GLU37 4.8 20.8 1.0 CG C:LYS33 4.9 30.6 1.0 CE2 C:TYR42 4.9 23.6 1.0 N A:ALA7 5.0 16.5 1.0

Sodium binding site 4 out of 5 in the Native Cytochrome C6 From Thermosynechococcus Elongatus in Space Group H3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Native Cytochrome C6 From Thermosynechococcus Elongatus in Space Group H3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na104 b:36.9 occ:1.00 ND2 C:ASN28 2.5 24.8 1.0 NZ C:LYS29 3.5 33.1 1.0 CG C:ASN28 3.7 29.2 1.0 OD1 C:ASN28 4.0 30.3 1.0 CG1 A:VAL86 4.6 26.4 1.0 CE C:MET26 4.8 24.3 1.0

Sodium binding site 5 out of 5 in the Native Cytochrome C6 From Thermosynechococcus Elongatus in Space Group H3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Native Cytochrome C6 From Thermosynechococcus Elongatus in Space Group H3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na105 b:40.2 occ:1.00 NE2 C:GLN50 2.4 21.9 1.0 SD C:MET58 2.5 15.3 1.0 CB C:MET58 2.8 16.3 1.0 CG C:MET58 2.9 12.8 1.0 CB C:LYS55 3.1 21.8 1.0 CD C:GLN50 3.2 20.4 1.0 N C:LYS55 3.5 18.6 1.0 CE C:MET58 3.5 16.7 1.0 CG C:GLN50 3.5 26.0 1.0 C4D C:HEC101 3.5 14.5 1.0 O C:LYS55 3.6 17.5 1.0 CHA C:HEC101 3.7 13.0 1.0 CA C:LYS55 3.8 19.9 1.0 ND C:HEC101 3.9 11.7 1.0 C C:GLY54 4.0 18.7 1.0 CBD C:HEC101 4.0 15.9 1.0 C1A C:HEC101 4.1 14.1 1.0 C3D C:HEC101 4.1 14.2 1.0 CA C:MET58 4.1 15.0 1.0 C C:LYS55 4.2 17.2 1.0 OE1 C:GLN50 4.2 19.5 1.0 CG C:LYS55 4.2 29.7 1.0 NA C:HEC101 4.3 14.2 1.0 FE C:HEC101 4.3 15.1 1.0 CA C:GLY54 4.4 18.3 1.0 C1D C:HEC101 4.5 14.2 1.0 O C:GLY54 4.6 20.7 1.0 O C:GLN50 4.6 15.6 1.0 O C:MET58 4.6 12.9 1.0 N C:MET58 4.7 17.3 1.0 CAD C:HEC101 4.7 13.7 1.0 C2D C:HEC101 4.7 14.7 1.0 C C:MET58 4.7 14.3 1.0 C2A C:HEC101 4.9 13.6 1.0 CB C:GLN50 5.0 19.7 1.0

S.Falke, C.G.Feiler, I.Sarrou. Native Cytochrome C6 From Thermosynechococcus Elongatus in Space Group H3 To Be Published.