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Sodium in PDB 3fo3: Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Dithionite (Sulfite Complex)

Protein crystallography data

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Dithionite (Sulfite Complex), PDB code: 3fo3 was solved by A.A.Trofimov, K.M.Polyakov, K.M.Boyko, A.Slutsky, T.V.Tikhonova, A.N.Antipov, R.A.Zvyagilskaya, A.N.Popov, V.S.Lamzin, G.P.Bourenkov, V.O.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.00 / 1.40
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 193.790, 193.790, 193.790, 90.00, 90.00, 90.00
R / Rfree (%) 12.6 / 13.9

Other elements in 3fo3:

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Dithionite (Sulfite Complex) also contains other interesting chemical elements:

Iron (Fe) 16 atoms
Calcium (Ca) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Dithionite (Sulfite Complex) (pdb code 3fo3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Dithionite (Sulfite Complex), PDB code: 3fo3:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 3fo3

Go back to Sodium Binding Sites List in 3fo3
Sodium binding site 1 out of 5 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Dithionite (Sulfite Complex)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Dithionite (Sulfite Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na531

b:23.9
occ:0.33
O A:HOH1167 2.2 20.4 0.5
O A:HOH1132 2.5 32.8 1.0
O A:HOH554 2.6 24.2 0.5
O A:HOH1120 3.7 18.2 0.5
OD2 A:ASP450 4.1 23.9 1.0
C3 A:TRS533 4.1 14.0 0.1
O1 A:TRS533 4.3 13.4 0.1
O2 A:TRS533 4.4 12.3 0.1
NZ A:LYS102 4.6 20.8 0.5
C2 A:TRS533 4.8 13.7 0.1
C A:TRS533 4.9 13.0 0.1
O A:HOH1080 4.9 31.0 1.0
O A:HOH1026 4.9 37.0 1.0
CG A:ASP450 5.0 20.4 1.0

Sodium binding site 2 out of 5 in 3fo3

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Sodium binding site 2 out of 5 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Dithionite (Sulfite Complex)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Dithionite (Sulfite Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na544

b:23.2
occ:0.50
O A:HOH749 2.1 24.5 1.0
O A:HOH852 2.3 32.4 1.0
O A:HOH1050 2.4 30.5 1.0
O A:HOH1146 2.4 14.5 1.0
O A:HOH598 2.4 29.6 0.5
HA A:SER84 3.4 12.1 1.0
HH11 A:ARG81 3.5 13.3 1.0
O A:HOH1042 3.7 33.2 1.0
O A:HOH733 3.9 18.2 1.0
H A:HIS85 4.1 13.2 1.0
O A:HOH851 4.1 32.7 1.0
NH1 A:ARG81 4.2 13.3 1.0
CA A:CA528 4.2 18.7 0.5
O1A A:HEC1007 4.2 14.1 0.5
HH12 A:ARG81 4.2 13.1 1.0
O A:GLU83 4.2 13.6 1.0
O A:HOH726 4.3 20.7 1.0
O1A A:HEC1007 4.3 14.4 0.5
CA A:SER84 4.4 12.0 1.0
O2A A:HEC1007 4.5 15.0 0.5
OG A:SER84 4.6 13.1 1.0
HD2 A:HIS85 4.6 22.2 1.0
OE1 A:GLU115 4.6 19.9 1.0
O A:HOH1085 4.7 34.8 1.0
CGA A:HEC1007 4.8 13.2 0.5
N A:HIS85 4.9 13.2 1.0
O2A A:HEC1007 4.9 14.0 0.5
CD2 A:HIS85 4.9 22.5 1.0
CB A:SER84 4.9 12.3 1.0
HB3 A:SER84 5.0 12.1 1.0

Sodium binding site 3 out of 5 in 3fo3

Go back to Sodium Binding Sites List in 3fo3
Sodium binding site 3 out of 5 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Dithionite (Sulfite Complex)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Dithionite (Sulfite Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na531

b:23.9
occ:0.33
O B:HOH1173 2.0 19.4 0.5
O B:HOH1138 2.3 28.0 1.0
O B:HOH554 2.7 20.4 0.5
N B:TRS533 3.0 15.8 0.1
O B:HOH1126 3.7 17.8 0.5
OD2 B:ASP450 3.8 23.4 1.0
O2 B:TRS533 4.4 15.1 0.1
O B:HOH702 4.4 19.0 0.5
NZ B:LYS102 4.4 17.8 0.5
C B:TRS533 4.5 15.5 0.1
O3 B:TRS533 4.6 15.9 0.1
O1 B:TRS533 4.7 15.7 0.1
O B:HOH1208 4.7 38.5 1.0
O B:HOH1033 4.8 34.6 1.0
CG B:ASP450 4.8 19.9 1.0
O B:HOH1086 4.8 17.2 0.5
C2 B:TRS533 5.0 15.6 0.1

Sodium binding site 4 out of 5 in 3fo3

Go back to Sodium Binding Sites List in 3fo3
Sodium binding site 4 out of 5 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Dithionite (Sulfite Complex)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Dithionite (Sulfite Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na548

b:24.8
occ:0.50
O B:HOH672 2.2 25.4 1.0
O B:HOH858 2.3 30.6 1.0
O B:HOH1057 2.4 33.3 1.0
O B:HOH598 2.4 32.9 0.5
O B:HOH1152 2.4 14.3 1.0
HA B:SER84 3.5 12.0 1.0
HH11 B:ARG81 3.5 13.2 1.0
O B:HOH1049 3.6 32.1 1.0
O B:HOH656 3.9 17.8 1.0
O B:HOH857 4.0 33.1 1.0
O1A B:HEC1007 4.1 14.4 0.5
CA B:CA528 4.1 18.2 0.5
NH1 B:ARG81 4.2 13.1 1.0
H B:HIS85 4.2 12.7 1.0
HH12 B:ARG81 4.2 12.9 1.0
O1A B:HEC1007 4.3 14.3 0.5
O B:HOH649 4.3 21.1 1.0
O B:GLU83 4.3 13.2 1.0
O2A B:HEC1007 4.4 13.3 0.5
CA B:SER84 4.5 11.9 1.0
OE1 B:GLU115 4.6 19.1 1.0
OG B:SER84 4.6 12.8 1.0
HD2 B:HIS85 4.6 23.1 1.0
O B:HOH1091 4.7 30.8 1.0
CGA B:HEC1007 4.7 11.6 0.5
HB3 B:SER84 4.9 12.3 1.0
N B:HIS85 4.9 12.5 1.0
O2A B:HEC1007 4.9 13.1 0.5
CB B:SER84 4.9 12.3 1.0
CGA B:HEC1007 5.0 12.7 0.5
CD2 B:HIS85 5.0 23.1 1.0

Sodium binding site 5 out of 5 in 3fo3

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Sodium binding site 5 out of 5 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Dithionite (Sulfite Complex)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Dithionite (Sulfite Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na549

b:30.6
occ:0.50
O B:HOH783 2.4 34.8 0.5
O B:ASN375 2.4 16.7 1.0
O B:HOH723 2.4 51.6 1.0
O B:HOH722 3.1 41.5 1.0
C2 B:PG4540 3.1 29.9 0.5
O1 B:PG4540 3.2 32.0 0.5
C B:ASN375 3.5 15.1 1.0
O B:HOH745 3.5 35.9 0.5
HB3 B:ASN375 3.8 15.4 1.0
C1 B:PG4540 3.8 31.3 0.5
HA3 B:GLY376 3.8 13.9 1.0
O B:HOH1222 3.9 41.4 1.0
HA B:ASN375 4.0 14.9 1.0
CA B:ASN375 4.2 14.9 1.0
O B:HOH746 4.3 34.4 0.5
N B:GLY376 4.4 13.7 1.0
O2 B:PG4540 4.4 31.9 0.5
CB B:ASN375 4.5 15.4 1.0
CA B:GLY376 4.5 13.9 1.0
OD1 B:ASN375 4.8 21.1 1.0

Reference:

A.A.Trofimov, K.M.Polyakov, K.M.Boyko, T.V.Tikhonova, T.N.Safonova, A.V.Tikhonov, A.N.Popov, V.O.Popov. Structures of Complexes of Octahaem Cytochrome C Nitrite Reductase From Thioalkalivibrio Nitratireducens with Sulfite and Cyanide Acta Crystallogr.,Sect.D V. 66 1043 2010.
ISSN: ISSN 0907-4449
PubMed: 20944237
DOI: 10.1107/S0907444910031665
Page generated: Tue Dec 15 06:10:56 2020

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