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Sodium in PDB 2ynq: Crystal Structure of Geobacillus Thermodenitrificans Essb Extracellular Fragment

Protein crystallography data

The structure of Crystal Structure of Geobacillus Thermodenitrificans Essb Extracellular Fragment, PDB code: 2ynq was solved by M.Zoltner, P.K.Fyfe, W.N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 94.782 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 132.890, 110.620, 97.410, 90.00, 103.34, 90.00
R / Rfree (%) 18.62 / 22.15

Other elements in 2ynq:

The structure of Crystal Structure of Geobacillus Thermodenitrificans Essb Extracellular Fragment also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Geobacillus Thermodenitrificans Essb Extracellular Fragment (pdb code 2ynq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Geobacillus Thermodenitrificans Essb Extracellular Fragment, PDB code: 2ynq:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 2ynq

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Sodium binding site 1 out of 5 in the Crystal Structure of Geobacillus Thermodenitrificans Essb Extracellular Fragment


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 Geobacillus Thermodenitrificans Essb Extracellular Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1392

b:39.8
occ:1.00
 O A:HOH2026 2.2 39.6 1.0
O A:HOH2017 2.3 39.0 1.0
O A:ILE305 2.4 47.0 1.0
O7 A:MLI1391 2.4 41.8 1.0
O A:SER302 2.4 50.0 1.0
O A:HOH2025 2.6 55.2 1.0
C A:SER302 3.4 50.7 1.0
C2 A:MLI1391 3.5 45.2 1.0
C A:ILE305 3.5 48.2 1.0
OH A:TYR281 3.8 39.7 1.0
O6 A:MLI1391 3.8 45.6 1.0
CA A:ASN303 4.0 53.4 1.0
N A:ASN303 4.1 52.2 1.0
CE1 A:TYR281 4.1 39.6 1.0
N A:ILE305 4.3 49.8 1.0
CA A:ILE305 4.3 48.3 1.0
C A:ASN303 4.3 53.9 1.0
CZ A:TYR281 4.4 41.2 1.0
ND2 A:ASN303 4.5 55.5 1.0
CA A:SER302 4.5 50.0 1.0
CB A:ILE305 4.5 47.8 1.0
O A:ASN303 4.5 55.4 1.0
N A:THR306 4.5 48.0 1.0
CB A:SER302 4.6 49.7 1.0
CA A:THR306 4.7 48.7 1.0
C1 A:MLI1391 4.7 45.2 1.0
OG A:SER302 4.8 52.5 1.0
OG A:SER285 4.9 42.1 1.0
N A:ASN304 5.0 53.1 1.0

Sodium binding site 2 out of 5 in 2ynq

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Sodium binding site 2 out of 5 in the Crystal Structure of Geobacillus Thermodenitrificans Essb Extracellular Fragment


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 Geobacillus Thermodenitrificans Essb Extracellular Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1393

b:56.5
occ:1.00
 O A:HOH2070 2.4 75.3 1.0
O A:HOH2071 2.5 55.3 1.0
O D:GLN257 2.5 41.5 1.0
OE1 A:GLN372 2.5 49.5 1.0
O A:HOH2051 2.7 49.7 1.0
O A:HOH2050 3.1 62.8 1.0
CD A:GLN372 3.5 50.2 1.0
O A:HOH2069 3.7 74.6 1.0
C D:GLN257 3.7 41.6 1.0
CB A:GLN372 3.9 48.0 1.0
CG A:GLN372 3.9 47.5 1.0
CB D:GLN257 4.3 42.1 1.0
ND2 D:ASN258 4.4 40.3 1.0
CA D:GLN257 4.4 41.8 1.0
CB D:ASN258 4.5 40.1 1.0
NE2 A:GLN372 4.6 51.2 1.0
N D:ASN258 4.8 40.7 1.0
CG D:LYS259 4.8 41.5 1.0
O A:HOH2052 4.8 57.9 1.0
CA A:GLN372 4.9 46.6 1.0
CE D:LYS259 4.9 47.0 1.0
CG D:GLN257 4.9 43.8 1.0
C D:ASN258 5.0 39.7 1.0
CG D:ASN258 5.0 41.2 1.0
CA D:ASN258 5.0 39.9 1.0

Sodium binding site 3 out of 5 in 2ynq

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Sodium binding site 3 out of 5 in the Crystal Structure of Geobacillus Thermodenitrificans Essb Extracellular Fragment


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 Geobacillus Thermodenitrificans Essb Extracellular Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1391

b:44.0
occ:1.00
 O B:ILE305 2.4 45.9 1.0
O7 B:MLI1390 2.4 46.3 1.0
O B:SER302 2.4 46.1 1.0
O B:HOH2042 2.4 49.1 1.0
O B:HOH2033 2.5 43.3 1.0
O B:HOH2043 2.6 43.4 1.0
C2 B:MLI1390 3.3 46.3 1.0
C B:SER302 3.5 46.0 1.0
O6 B:MLI1390 3.5 42.9 1.0
C B:ILE305 3.5 46.8 1.0
OH B:TYR281 4.0 40.5 1.0
CA B:ASN303 4.0 49.6 1.0
N B:ASN303 4.1 47.5 1.0
O B:ASN303 4.1 50.1 1.0
C B:ASN303 4.2 49.5 1.0
CE1 B:TYR281 4.3 38.4 1.0
N B:ILE305 4.3 46.9 1.0
CA B:ILE305 4.3 46.0 1.0
CB B:ILE305 4.5 45.4 1.0
CA B:SER302 4.5 45.2 1.0
N B:THR306 4.5 47.1 1.0
ND2 B:ASN303 4.6 54.7 1.0
CZ B:TYR281 4.6 38.4 1.0
CA B:THR306 4.7 47.0 1.0
C1 B:MLI1390 4.7 45.2 1.0
CB B:SER302 4.8 44.4 1.0
OG B:SER285 4.9 40.5 1.0
OG B:SER302 4.9 46.6 1.0

Sodium binding site 4 out of 5 in 2ynq

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Sodium binding site 4 out of 5 in the Crystal Structure of Geobacillus Thermodenitrificans Essb Extracellular Fragment


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 Geobacillus Thermodenitrificans Essb Extracellular Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1391

b:39.5
occ:1.00
 O C:HOH2028 2.2 35.5 1.0
O C:HOH2015 2.3 44.4 1.0
O C:ILE305 2.4 40.9 1.0
O C:SER302 2.5 44.9 1.0
O C:HOH2029 2.5 40.3 1.0
O7 C:MLI1390 2.7 38.0 1.0
O C:HOH2058 3.4 38.2 1.0
C C:ILE305 3.6 42.1 1.0
C C:SER302 3.6 44.8 1.0
C2 C:MLI1390 3.6 40.7 1.0
O6 C:MLI1390 3.9 42.0 1.0
OH C:TYR281 4.2 38.3 1.0
O C:HOH2030 4.2 54.9 1.0
O C:HOH2059 4.3 45.5 1.0
CA C:ASN303 4.3 48.1 1.0
O C:ASN303 4.4 49.0 1.0
CA C:ILE305 4.4 42.3 1.0
N C:ASN303 4.4 46.3 1.0
CB C:ILE305 4.4 41.7 1.0
N C:ILE305 4.4 44.2 1.0
C C:ASN303 4.5 48.4 1.0
CE1 C:TYR281 4.5 37.1 1.0
CA C:SER302 4.5 43.9 1.0
N C:THR306 4.6 42.2 1.0
CA C:THR306 4.8 42.7 1.0
CZ C:TYR281 4.8 35.7 1.0
CB C:SER302 4.9 43.1 1.0
CG2 C:ILE305 4.9 38.8 1.0
OG C:SER285 4.9 35.2 1.0
C1 C:MLI1390 4.9 39.2 1.0

Sodium binding site 5 out of 5 in 2ynq

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Sodium binding site 5 out of 5 in the Crystal Structure of Geobacillus Thermodenitrificans Essb Extracellular Fragment


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 Geobacillus Thermodenitrificans Essb Extracellular Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1391

b:57.4
occ:1.00
 O D:ARG298 2.2 56.1 1.0
O D:VAL301 2.4 53.7 1.0
O D:HOH2025 2.5 51.7 1.0
O D:HOH2026 2.5 59.4 1.0
OD1 D:ASN303 2.6 51.6 1.0
O D:HOH2027 3.0 66.0 1.0
C D:ARG298 3.5 56.3 1.0
C D:VAL301 3.7 52.7 1.0
CG D:ASN303 3.7 51.2 1.0
O D:GLN299 4.1 60.3 1.0
C D:GLN299 4.1 59.7 1.0
N D:ASN303 4.1 51.1 1.0
CA D:GLN299 4.2 60.2 1.0
N D:VAL301 4.2 55.1 1.0
N D:GLN299 4.3 58.3 1.0
ND2 D:ASN303 4.5 48.5 1.0
CA D:ARG298 4.5 55.2 1.0
CA D:VAL301 4.5 52.7 1.0
N D:SER302 4.6 51.9 1.0
N D:THR300 4.6 59.1 1.0
CB D:ASN303 4.7 50.3 1.0
CA D:SER302 4.7 51.8 1.0
CG2 D:VAL301 4.8 49.8 1.0
C D:THR300 4.8 57.3 1.0
O A:HOH2062 4.9 80.1 1.0
CA D:ASN303 5.0 50.2 1.0
C D:SER302 5.0 51.0 1.0

Reference:

M.Zoltner, D.G.Norman, P.K.Fyfe, H.El Mkami, T.Palmer, W.N.Hunter. The Architecture of Essb, An Integral Membrane Component of the Type VII Secretion System. Structure V. 21 595 2013.
ISSN: ISSN 0969-2126
PubMed: 23499020
DOI: 10.1016/J.STR.2013.02.007
Page generated: Mon Oct 7 05:27:16 2024

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