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Sodium in PDB 3lg1: Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Borohydride (in Complex with Sulfite)

Protein crystallography data

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Borohydride (in Complex with Sulfite), PDB code: 3lg1 was solved by A.A.Trofimov, K.M.Polyakov, K.M.Boyko, A.A.Filimonenkov, P.V.Dorovatovsky, T.V.Tikhonova, V.O.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.90 / 1.95
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 192.620, 192.620, 192.620, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 18.3

Other elements in 3lg1:

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Borohydride (in Complex with Sulfite) 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 Borohydride (in Complex with Sulfite) (pdb code 3lg1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Borohydride (in Complex with Sulfite), PDB code: 3lg1:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 3lg1

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Sodium binding site 1 out of 8 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Borohydride (in Complex with Sulfite)


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 Borohydride (in Complex with Sulfite) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na529

b:28.0
occ:0.50
O A:HOH550 2.3 38.4 1.0
O A:GLU390 2.3 18.1 1.0
O A:HOH1049 2.4 20.6 1.0
O A:HOH1055 3.3 22.5 1.0
C A:GLU390 3.5 18.7 1.0
O B:HOH568 3.8 39.4 1.0
O B:HOH588 4.2 19.9 1.0
O A:LEU389 4.2 21.5 1.0
CA A:GLU390 4.3 18.7 1.0
OD1 A:ASN391 4.3 16.5 1.0
N A:ASN391 4.4 17.4 1.0
O B:HOH842 4.4 35.6 1.0
O A:HOH627 4.5 30.1 1.0
OD1 B:ASP147 4.5 18.3 1.0
CA A:ASN391 4.5 17.9 1.0
CG A:ASN391 4.8 16.8 1.0

Sodium binding site 2 out of 8 in 3lg1

Go back to Sodium Binding Sites List in 3lg1
Sodium binding site 2 out of 8 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Borohydride (in Complex with Sulfite)


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 Borohydride (in Complex with Sulfite) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na530

b:29.9
occ:1.00
O4 A:PG6532 2.3 44.2 1.0
O A:HOH936 2.4 29.4 1.0
O A:THR94 2.4 17.0 1.0
O5 A:PG6532 2.6 45.5 1.0
O6 A:PG6532 2.7 43.5 1.0
C10 A:PG6532 2.9 41.4 1.0
O3 A:PG6532 3.0 34.8 1.0
C6 A:PG6532 3.1 35.7 1.0
C5 A:PG6532 3.1 33.1 1.0
C11 A:PG6532 3.1 42.6 1.0
C7 A:PG6532 3.2 36.5 1.0
C9 A:PG6532 3.3 42.2 1.0
C8 A:PG6532 3.3 41.5 1.0
C A:THR94 3.6 16.4 1.0
O A:HOH928 4.1 29.9 1.0
O A:HOH931 4.3 28.0 1.0
O A:HOH1018 4.3 18.4 0.5
CA A:SER95 4.4 15.1 1.0
O A:HOH880 4.4 29.8 1.0
N A:SER95 4.5 15.7 1.0
CA A:THR94 4.6 16.5 1.0
C4 A:PG6532 4.6 28.9 1.0
CB A:THR94 4.6 17.1 1.0

Sodium binding site 3 out of 8 in 3lg1

Go back to Sodium Binding Sites List in 3lg1
Sodium binding site 3 out of 8 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Borohydride (in Complex with Sulfite)


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 Borohydride (in Complex with Sulfite) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na531

b:43.3
occ:0.33
O A:HOH879 2.3 40.8 1.0
O A:HOH906 2.9 24.8 1.0
OD2 A:ASP450 4.0 27.0 1.0
S A:SO3537 4.3 38.3 0.1
O A:HOH858 4.6 25.3 1.0
O A:HOH831 4.7 39.1 1.0
NZ A:LYS102 4.7 25.6 1.0
O2 A:SO3537 4.9 38.2 0.1
O1 A:SO3537 4.9 38.2 0.1
CG A:ASP450 4.9 23.5 1.0

Sodium binding site 4 out of 8 in 3lg1

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Sodium binding site 4 out of 8 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Borohydride (in Complex with Sulfite)


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 Borohydride (in Complex with Sulfite) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na535

b:13.1
occ:0.50
O A:HOH842 2.2 26.6 1.0
O A:HOH883 2.3 14.5 1.0
O A:HOH603 2.4 13.5 0.5
O A:HOH688 2.5 21.3 0.5
O A:HOH1025 3.4 25.2 0.5
O A:HOH589 3.5 16.5 1.0
O A:HOH1018 3.9 18.4 0.5
O A:HOH583 3.9 13.7 0.5
CA A:CA528 3.9 16.8 0.5
O1A A:HEC1007 4.2 15.5 0.5
OE1 A:GLU115 4.2 19.5 1.0
CD2 A:HIS85 4.2 21.7 1.0
O2A A:HEC1007 4.3 16.3 0.5
O A:HOH687 4.3 18.2 0.5
NH1 A:ARG81 4.3 11.8 1.0
CA A:SER84 4.5 14.5 1.0
OG A:SER84 4.6 13.6 1.0
O A:GLU83 4.6 13.2 1.0
O A:HOH861 4.7 42.3 1.0
O A:HOH552 4.7 42.7 1.0
CGA A:HEC1007 4.7 14.8 0.5
N A:HIS85 4.8 14.7 1.0
CB A:SER84 4.9 14.2 1.0
NE2 A:HIS85 4.9 22.7 1.0
O A:HOH942 5.0 36.4 1.0

Sodium binding site 5 out of 8 in 3lg1

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Sodium binding site 5 out of 8 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Borohydride (in Complex with Sulfite)


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 Borohydride (in Complex with Sulfite) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na536

b:38.6
occ:1.00
O A:GLU265 2.4 25.6 1.0
O A:HOH899 2.5 46.6 1.0
O A:HOH1027 2.5 25.2 0.5
OD2 A:ASP288 2.5 20.6 1.0
O A:HOH817 2.6 47.9 1.0
C A:GLU265 3.5 25.9 1.0
CG A:ASP288 3.5 21.9 1.0
OE2 A:GLU265 3.8 49.5 1.0
OD1 A:ASP288 3.9 22.4 1.0
O A:HOH875 4.0 23.2 0.5
N A:GLY268 4.1 20.3 1.0
CA A:GLU265 4.1 26.9 1.0
CA A:GLY268 4.2 20.6 1.0
CD A:GLU265 4.4 45.0 1.0
N A:GLN266 4.6 24.7 1.0
CG A:GLU265 4.6 35.3 1.0
O A:SER264 4.6 24.4 1.0
C A:GLN266 4.8 23.1 1.0
CA A:GLN266 4.8 25.1 1.0
CB A:ASP288 4.8 19.7 1.0
C A:GLY268 4.9 20.3 1.0

Sodium binding site 6 out of 8 in 3lg1

Go back to Sodium Binding Sites List in 3lg1
Sodium binding site 6 out of 8 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Borohydride (in Complex with Sulfite)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Borohydride (in Complex with Sulfite) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na529

b:29.6
occ:1.00
O4 B:PG6531 2.3 45.3 1.0
O B:THR94 2.4 16.3 1.0
O B:HOH952 2.4 28.4 1.0
O5 B:PG6531 2.8 46.6 1.0
O6 B:PG6531 2.9 42.0 1.0
C10 B:PG6531 3.0 43.6 1.0
C6 B:PG6531 3.0 40.4 1.0
C5 B:PG6531 3.1 36.6 1.0
O3 B:PG6531 3.1 40.8 1.0
C7 B:PG6531 3.2 39.6 1.0
C8 B:PG6531 3.2 42.7 1.0
C9 B:PG6531 3.2 43.8 1.0
C11 B:PG6531 3.3 42.7 1.0
C B:THR94 3.6 16.6 1.0
O B:HOH944 4.0 36.2 1.0
O B:HOH947 4.2 33.2 1.0
CA B:SER95 4.5 15.3 1.0
N B:SER95 4.5 14.7 1.0
O B:HOH896 4.5 35.3 1.0
CA B:THR94 4.5 16.1 1.0
C4 B:PG6531 4.6 36.5 1.0
CB B:THR94 4.6 16.7 1.0

Sodium binding site 7 out of 8 in 3lg1

Go back to Sodium Binding Sites List in 3lg1
Sodium binding site 7 out of 8 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Borohydride (in Complex with Sulfite)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Borohydride (in Complex with Sulfite) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na530

b:40.4
occ:0.33
O B:HOH895 2.2 39.8 1.0
O B:HOH922 2.6 27.6 1.0
S B:SO3536 4.0 37.3 0.1
OD2 B:ASP450 4.0 27.9 1.0
O B:HOH875 4.5 24.7 1.0
NZ B:LYS102 4.6 20.6 1.0
O1 B:SO3536 4.6 37.6 0.1
O2 B:SO3536 4.7 37.6 0.1
O3 B:SO3536 4.7 37.6 0.1
O B:HOH848 4.9 37.8 1.0
O B:HOH912 4.9 28.9 1.0
O B:HOH1000 5.0 13.3 0.5
CG B:ASP450 5.0 22.9 1.0

Sodium binding site 8 out of 8 in 3lg1

Go back to Sodium Binding Sites List in 3lg1
Sodium binding site 8 out of 8 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Borohydride (in Complex with Sulfite)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase Reduced By Sodium Borohydride (in Complex with Sulfite) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na535

b:17.2
occ:0.50
O B:HOH899 2.3 13.6 1.0
O B:HOH705 2.4 15.5 0.5
O B:HOH859 2.5 28.6 1.0
O B:HOH620 2.5 17.2 0.5
O B:HOH606 3.3 15.9 1.0
CA B:CA528 3.8 16.1 0.5
O B:HOH600 3.9 10.0 0.5
OE1 B:GLU115 4.1 20.0 1.0
O1A B:HEC1007 4.1 15.2 0.5
O2A B:HEC1007 4.2 13.9 0.5
NH1 B:ARG81 4.3 13.1 1.0
CD2 B:HIS85 4.3 22.6 1.0
O B:HOH877 4.4 37.4 1.0
CA B:SER84 4.5 13.7 1.0
OG B:SER84 4.5 13.4 1.0
O B:HOH704 4.6 21.8 0.5
CGA B:HEC1007 4.6 13.8 0.5
O B:GLU83 4.7 14.0 1.0
O3 B:PG4532 4.8 33.6 0.5
N B:HIS85 4.8 14.6 1.0
CB B:SER84 4.8 14.0 1.0

Reference:

A.A.Trofimov, K.M.Polyakov, T.V.Tikhonova, A.V.Tikhonov, T.N.Safonova, K.M.Boyko, P.V.Dorovatovskii, V.O.Popov. Covalent Modifications of the Catalytic Tyrosine in Octahaem Cytochrome C Nitrite Reductase and Their Effect on the Enzyme Activity. Acta Crystallogr.,Sect.D V. 68 144 2012.
ISSN: ISSN 0907-4449
PubMed: 22281743
DOI: 10.1107/S0907444911052632
Page generated: Tue Dec 15 06:16:47 2020

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