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Sodium in PDB 2ga4: STX2 with Adenine

Enzymatic activity of STX2 with Adenine

All present enzymatic activity of STX2 with Adenine:
3.2.2.22;

Protein crystallography data

The structure of STX2 with Adenine, PDB code: 2ga4 was solved by M.E.Fraser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 200.00 / 1.80
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 144.550, 144.550, 59.420, 90.00, 90.00, 120.00
R / Rfree (%) 15.6 / 18.3

Sodium Binding Sites:

The binding sites of Sodium atom in the STX2 with Adenine (pdb code 2ga4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the STX2 with Adenine, PDB code: 2ga4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 2ga4

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Sodium binding site 1 out of 5 in the STX2 with Adenine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of STX2 with Adenine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na713

b:40.4
occ:1.00
OD1 A:ASN279 2.0 25.9 1.0
O1 A:FMT709 2.4 34.9 1.0
O C:HOH729 2.5 23.0 1.0
O A:HOH838 2.5 16.5 1.0
O A:ARG266 2.6 14.2 1.0
CG A:ASN279 3.1 22.7 1.0
OG A:SER278 3.2 21.8 1.0
O A:HOH760 3.4 18.9 1.0
C A:FMT709 3.4 33.5 1.0
C A:ARG266 3.4 15.7 1.0
ND2 A:ASN279 3.6 20.5 1.0
O A:PRO267 3.7 13.8 1.0
CA A:PRO267 3.7 15.3 1.0
O2 A:FMT709 3.8 29.9 1.0
N A:PRO267 4.0 15.6 1.0
C A:PRO267 4.0 15.2 1.0
N A:ASN279 4.1 10.4 1.0
ND2 A:ASN207 4.2 15.5 1.0
N A:ARG266 4.3 16.1 1.0
CB A:SER278 4.3 15.3 1.0
O A:THR263 4.3 15.4 1.0
OG1 C:THR45 4.3 22.1 1.0
N A:SER278 4.4 11.4 1.0
CB A:ASN279 4.4 16.2 1.0
CA A:ARG266 4.5 15.2 1.0
CG A:GLU277 4.5 11.8 1.0
CA A:SER278 4.7 13.5 1.0
O A:HOH727 4.8 16.8 1.0
CA A:ASN279 4.8 13.2 1.0
O A:HOH764 4.8 22.3 1.0
C A:SER278 4.9 12.6 1.0

Sodium binding site 2 out of 5 in 2ga4

Go back to Sodium Binding Sites List in 2ga4
Sodium binding site 2 out of 5 in the STX2 with Adenine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of STX2 with Adenine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na714

b:27.1
occ:1.00
O A:HOH791 2.3 22.3 1.0
O A:THR22 2.3 17.1 1.0
O A:HOH895 2.3 30.2 1.0
O A:SER25 2.4 15.2 1.0
O A:HOH767 2.5 21.9 1.0
O A:HOH961 2.5 30.8 1.0
C A:THR22 3.4 16.6 1.0
C A:SER25 3.6 13.8 1.0
CA A:THR22 4.1 16.6 1.0
O A:HOH750 4.1 18.9 1.0
OG1 A:THR26 4.3 17.1 1.0
CG2 A:THR22 4.3 23.7 1.0
CA A:THR26 4.3 15.2 1.0
N A:SER25 4.4 12.2 1.0
N A:THR26 4.4 13.8 1.0
O A:HOH950 4.5 42.7 1.0
N A:GLU23 4.5 15.5 1.0
O A:ARG21 4.6 13.6 1.0
CA A:SER25 4.6 11.7 1.0
OD1 A:ASN42 4.7 20.7 1.0
C A:GLU23 4.7 17.3 1.0
O A:GLU23 4.7 16.7 1.0
CA A:GLU23 4.7 16.8 1.0
CD A:PRO27 4.8 14.9 1.0
CB A:THR22 4.9 17.6 1.0
CB A:THR26 4.9 16.4 1.0

Sodium binding site 3 out of 5 in 2ga4

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Sodium binding site 3 out of 5 in the STX2 with Adenine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of STX2 with Adenine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na715

b:37.8
occ:1.00
OG A:SER19 2.2 16.8 1.0
O A:HOH832 2.2 18.9 1.0
O A:HOH825 2.3 26.2 1.0
O A:SER15 2.4 10.9 1.0
OG A:SER15 2.4 16.3 1.0
O A:HOH943 2.5 35.4 1.0
C A:SER15 3.0 11.2 1.0
CB A:SER19 3.4 16.8 1.0
CB A:SER15 3.5 14.0 1.0
CA A:SER15 3.5 11.0 1.0
O A:HOH847 3.7 24.6 1.0
N A:SER19 3.9 13.0 1.0
N A:SER16 4.0 11.2 1.0
CA A:SER19 4.1 13.7 1.0
O A:HOH798 4.4 22.4 1.0
CA A:SER16 4.5 11.3 1.0
C A:ASN18 4.9 12.8 1.0
N A:SER15 4.9 11.2 1.0
CB A:ASN18 5.0 13.3 1.0
O A:HOH796 5.0 21.9 1.0
C A:SER16 5.0 12.2 1.0

Sodium binding site 4 out of 5 in 2ga4

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Sodium binding site 4 out of 5 in the STX2 with Adenine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of STX2 with Adenine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na712

b:42.7
occ:1.00
O B:GLY61 2.3 28.6 1.0
OG B:SER53 2.4 34.7 1.0
O B:THR55 2.5 46.3 1.0
OG B:SER60 2.8 38.5 1.0
CB B:SER53 3.3 30.8 1.0
C B:GLY61 3.6 26.4 1.0
C B:THR55 3.6 44.7 1.0
OG1 B:THR55 3.6 47.4 1.0
O B:HOH762 3.6 36.3 1.0
CB B:SER60 3.7 36.0 1.0
N B:GLY61 3.9 29.6 1.0
C B:SER60 4.3 32.8 1.0
CA B:GLY61 4.3 28.6 1.0
N B:THR55 4.3 43.4 1.0
CA B:THR55 4.4 45.0 1.0
O B:HOH736 4.4 44.6 1.0
CB B:THR55 4.4 45.6 1.0
N B:CYS56 4.5 43.2 1.0
CA B:CYS56 4.6 42.9 1.0
N B:PHE62 4.6 20.7 1.0
CA B:SER60 4.6 35.1 1.0
CA B:SER53 4.7 29.6 1.0
CA B:PHE62 4.7 18.0 1.0
CG2 B:THR55 4.7 47.0 1.0
O B:SER60 4.9 29.9 1.0

Sodium binding site 5 out of 5 in 2ga4

Go back to Sodium Binding Sites List in 2ga4
Sodium binding site 5 out of 5 in the STX2 with Adenine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of STX2 with Adenine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na711

b:41.9
occ:1.00
O F:GLY61 2.3 26.1 1.0
OG F:SER53 2.4 33.0 1.0
OG F:SER60 2.4 36.9 1.0
O F:THR55 2.5 47.0 1.0
CB F:THR55 3.2 47.6 1.0
CB F:SER53 3.3 30.1 1.0
C F:THR55 3.4 46.1 1.0
C F:GLY61 3.4 24.6 1.0
CB F:SER60 3.5 34.1 1.0
N F:GLY61 3.6 27.5 1.0
CA F:THR55 3.7 45.5 1.0
O F:HOH756 3.7 35.3 1.0
N F:THR55 3.9 44.3 1.0
OG1 F:THR55 3.9 48.5 1.0
CA F:GLY61 4.1 27.1 1.0
CG2 F:THR55 4.1 48.7 1.0
C F:SER60 4.1 31.4 1.0
O F:HOH751 4.4 42.5 1.0
CA F:SER60 4.5 33.2 1.0
N F:PHE62 4.5 21.1 1.0
N F:CYS56 4.6 45.4 1.0
CA F:SER53 4.7 30.5 1.0
CA F:PHE62 4.7 18.4 1.0
O F:SER60 4.8 27.8 1.0
N F:SER54 4.8 37.1 1.0

Reference:

M.E.Fraser, M.M.Cherney, P.Marcato, G.L.Mulvey, G.D.Armstrong, M.N.James. Binding of Adenine to STX2, the Protein Toxin From Escherichia Coli O157:H7. Acta Crystallogr.,Sect.F V. 62 627 2006.
ISSN: ESSN 1744-3091
PubMed: 16820678
DOI: 10.1107/S1744309106021968
Page generated: Tue Dec 15 05:49:28 2020

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