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Sodium in PDB 2q16: Structure of the E. Coli Inosine Triphosphate Pyrophosphatase Rgdb in Complex with Itp

Enzymatic activity of Structure of the E. Coli Inosine Triphosphate Pyrophosphatase Rgdb in Complex with Itp

All present enzymatic activity of Structure of the E. Coli Inosine Triphosphate Pyrophosphatase Rgdb in Complex with Itp:
3.6.1.19;

Protein crystallography data

The structure of Structure of the E. Coli Inosine Triphosphate Pyrophosphatase Rgdb in Complex with Itp, PDB code: 2q16 was solved by A.U.Singer, R.Lam, M.Proudfoot, T.Skarina, A.Savchenko, A.F.Yakunin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.98 / 1.95
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 120.646, 120.646, 66.562, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 20.8

Other elements in 2q16:

The structure of Structure of the E. Coli Inosine Triphosphate Pyrophosphatase Rgdb in Complex with Itp also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the E. Coli Inosine Triphosphate Pyrophosphatase Rgdb in Complex with Itp (pdb code 2q16). 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 E. Coli Inosine Triphosphate Pyrophosphatase Rgdb in Complex with Itp, PDB code: 2q16:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 2q16

Go back to Sodium Binding Sites List in 2q16
Sodium binding site 1 out of 5 in the Structure of the E. Coli Inosine Triphosphate Pyrophosphatase Rgdb in Complex with Itp


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 E. Coli Inosine Triphosphate Pyrophosphatase Rgdb in Complex with Itp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:27.2
occ:1.00
 O A:HOH6268 2.7 23.9 1.0
O2' A:ITT6246 2.7 17.1 1.0
OD1 A:ASP95 2.8 27.7 1.0
OD1 A:ASN10 2.9 32.8 1.0
C2' A:ITT6246 3.4 15.1 1.0
CG A:ASP95 3.6 27.1 1.0
OD2 A:ASP95 3.6 26.8 1.0
O A:HOH6291 3.7 47.8 1.0
CD1 A:PHE154 3.7 25.5 1.0
C3' A:ITT6246 3.8 18.2 1.0
O A:HOH6323 3.8 19.4 1.0
CG A:ASN10 3.9 27.9 1.0
CE1 A:PHE154 4.0 25.4 1.0
O1B A:ITT6246 4.0 28.9 1.0
O A:HOH6289 4.1 30.6 1.0
ND2 A:ASN10 4.3 25.9 1.0
CA A:GLY155 4.3 22.2 1.0
O3' A:ITT6246 4.3 18.2 1.0
N A:GLY155 4.5 23.5 1.0
O A:HOH6303 4.8 30.6 1.0
CG A:PHE154 4.9 25.0 1.0
C1' A:ITT6246 4.9 17.0 1.0
CB A:ASP95 5.0 25.9 1.0

Sodium binding site 2 out of 5 in 2q16

Go back to Sodium Binding Sites List in 2q16
Sodium binding site 2 out of 5 in the Structure of the E. Coli Inosine Triphosphate Pyrophosphatase Rgdb in Complex with Itp


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 E. Coli Inosine Triphosphate Pyrophosphatase Rgdb in Complex with Itp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:29.2
occ:1.00
 O A:ILE83 2.8 26.8 1.0
O A:HOH6372 2.9 27.9 1.0
O1A A:ITT6246 3.0 22.4 1.0
N A:ALA86 3.1 22.1 1.0
O A:HOH6371 3.2 29.9 1.0
O5' A:ITT6246 3.4 20.1 1.0
N A:SER85 3.4 23.1 1.0
CB A:ALA86 3.4 23.0 1.0
C A:ILE83 3.6 26.3 1.0
PA A:ITT6246 3.8 20.5 1.0
C A:TYR84 3.8 24.9 1.0
CA A:ALA86 3.8 23.8 1.0
O A:HOH6455 3.9 45.4 1.0
C5' A:ITT6246 4.0 22.9 1.0
CA A:TYR84 4.0 26.7 1.0
C A:SER85 4.0 22.7 1.0
CA A:SER85 4.1 22.7 1.0
O A:HOH6288 4.1 39.6 1.0
N A:TYR84 4.2 25.7 1.0
CB A:SER85 4.3 22.0 1.0
O A:HOH6374 4.3 42.6 1.0
O A:SER70 4.6 22.5 1.0
O A:TYR84 4.6 25.3 1.0
CA A:ILE83 4.6 26.6 1.0
C4' A:ITT6246 4.6 18.2 1.0
N A:ARG87 4.7 24.7 1.0
O2A A:ITT6246 4.7 19.4 1.0
O A:GLY82 4.7 23.9 1.0
C A:ALA86 4.8 24.5 1.0
O A:HOH6319 4.8 23.9 1.0
CA A:CA200 4.9 34.8 1.0

Sodium binding site 3 out of 5 in 2q16

Go back to Sodium Binding Sites List in 2q16
Sodium binding site 3 out of 5 in the Structure of the E. Coli Inosine Triphosphate Pyrophosphatase Rgdb in Complex with Itp


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 E. Coli Inosine Triphosphate Pyrophosphatase Rgdb in Complex with Itp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:35.0
occ:1.00
 OG A:SER181 2.6 25.9 1.0
OE1 A:GLU16 2.8 28.4 1.0
O A:HOH6292 3.3 37.7 1.0
CD A:GLU16 3.5 30.6 1.0
CB A:SER181 3.5 24.8 1.0
CE A:LYS177 3.8 25.3 1.0
CA A:SER178 3.9 31.1 1.0
CB A:ARG183 3.9 25.2 1.0
CG A:LYS177 3.9 24.8 1.0
N A:GLY184 4.0 24.7 1.0
O A:LYS177 4.0 28.4 1.0
C A:LYS177 4.1 28.0 1.0
N A:SER178 4.1 29.8 1.0
OE2 A:GLU16 4.2 29.8 1.0
O A:HOH6429 4.2 38.3 1.0
CD A:LYS177 4.2 25.4 1.0
CB A:GLU16 4.2 29.7 1.0
CG A:GLU16 4.2 27.6 1.0
CG A:ARG183 4.3 26.9 1.0
CD A:ARG183 4.5 26.1 1.0
CB A:SER178 4.6 32.1 1.0
NH1 A:ARG183 4.6 26.1 1.0
C A:ARG183 4.6 25.9 1.0
CA A:ARG183 4.7 25.2 1.0
NZ A:LYS177 4.7 23.6 1.0
CA A:GLY184 4.7 24.7 1.0
CB A:LYS177 4.7 26.4 1.0
CA A:SER181 4.8 24.8 1.0
N A:ARG183 4.8 25.2 1.0
C A:SER178 4.9 30.5 1.0

Sodium binding site 4 out of 5 in 2q16

Go back to Sodium Binding Sites List in 2q16
Sodium binding site 4 out of 5 in the Structure of the E. Coli Inosine Triphosphate Pyrophosphatase Rgdb in Complex with Itp


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 E. Coli Inosine Triphosphate Pyrophosphatase Rgdb in Complex with Itp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:27.8
occ:1.00
 O B:HOH237 2.6 21.7 1.0
OD1 B:ASP95 2.7 27.6 1.0
O2' B:ITT203 2.9 18.6 1.0
ND2 B:ASN10 3.1 27.0 1.0
O B:HOH283 3.4 43.7 1.0
CG B:ASP95 3.5 27.9 1.0
C2' B:ITT203 3.5 17.9 1.0
OD2 B:ASP95 3.5 27.7 1.0
CD1 B:PHE154 3.7 23.6 1.0
C3' B:ITT203 3.9 17.9 1.0
NA B:NA202 3.9 27.0 1.0
O1B B:ITT203 4.1 28.8 1.0
CG B:ASN10 4.1 28.6 1.0
CE1 B:PHE154 4.1 24.5 1.0
O B:HOH306 4.2 36.5 1.0
CA B:GLY155 4.3 22.7 1.0
O3' B:ITT203 4.4 19.4 1.0
OD1 B:ASN10 4.4 28.9 1.0
N B:GLY155 4.4 23.0 1.0
O B:HOH252 4.7 35.2 1.0
CB B:ASP95 4.9 27.3 1.0
CG B:PHE154 4.9 25.6 1.0

Sodium binding site 5 out of 5 in 2q16

Go back to Sodium Binding Sites List in 2q16
Sodium binding site 5 out of 5 in the Structure of the E. Coli Inosine Triphosphate Pyrophosphatase Rgdb in Complex with Itp


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 E. Coli Inosine Triphosphate Pyrophosphatase Rgdb in Complex with Itp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:27.0
occ:1.00
 O B:HOH227 2.8 17.4 1.0
O3' B:ITT203 2.8 19.4 1.0
ND2 B:ASN98 3.0 21.9 1.0
OD1 B:ASP95 3.1 27.6 1.0
O2' B:ITT203 3.1 18.6 1.0
CE2 B:TYR156 3.7 23.2 1.0
C3' B:ITT203 3.8 17.9 1.0
CA B:ASP95 3.8 27.2 1.0
CB B:ASN98 3.8 22.5 1.0
CG B:ASN98 3.9 21.9 1.0
NA B:NA201 3.9 27.8 1.0
CG B:ASP95 4.0 27.9 1.0
C2' B:ITT203 4.0 17.9 1.0
CA B:GLY155 4.1 22.7 1.0
CZ B:TYR156 4.1 22.6 1.0
O B:SER85 4.2 24.4 1.0
OH B:TYR156 4.3 23.3 1.0
CD2 B:TYR156 4.3 24.0 1.0
CB B:ASP95 4.3 27.3 1.0
O B:HOH252 4.4 35.2 1.0
N B:ASP95 4.4 27.0 1.0
O B:HOH237 4.5 21.7 1.0
CA B:ALA86 4.6 25.1 1.0
O B:THR94 4.6 26.8 1.0
O B:ASP95 4.6 26.3 1.0
O B:ALA86 4.7 25.4 1.0
C B:ASP95 4.7 26.8 1.0
C B:GLY155 4.7 22.7 1.0
C B:THR94 4.8 28.0 1.0
C1' B:ITT203 4.8 17.7 1.0
C B:SER85 4.9 24.2 1.0
OD2 B:ASP95 4.9 27.7 1.0
CE1 B:TYR156 4.9 21.1 1.0

Reference:

A.Savchenko, M.Proudfoot, T.Skarina, A.Singer, O.Litvinova, R.Sanishvili, G.Brown, N.Chirgadze, A.F.Yakunin. Molecular Basis of the Antimutagenic Activity of the House-Cleaning Inosine Triphosphate Pyrophosphatase Rdgb From Escherichia Coli. J.Mol.Biol. V. 374 1091 2007.
ISSN: ISSN 0022-2836
PubMed: 17976651
DOI: 10.1016/J.JMB.2007.10.012
Page generated: Mon Oct 7 03:45:54 2024

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