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Sodium in PDB 1tx3: Hincii Bound to Cognate Dna

Enzymatic activity of Hincii Bound to Cognate Dna

All present enzymatic activity of Hincii Bound to Cognate Dna:
3.1.21.4;

Protein crystallography data

The structure of Hincii Bound to Cognate Dna, PDB code: 1tx3 was solved by N.C.Horton, L.F.Dorner, J.J.Perona, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.50
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.120, 177.670, 256.360, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 27.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Hincii Bound to Cognate Dna (pdb code 1tx3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Hincii Bound to Cognate Dna, PDB code: 1tx3:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 1tx3

Go back to Sodium Binding Sites List in 1tx3
Sodium binding site 1 out of 4 in the Hincii Bound to Cognate Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hincii Bound to Cognate Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na801

b:23.2
occ:1.00
 O A:HOH921 2.1 15.2 1.0
O A:HOH920 2.4 26.7 1.0
O A:ILE142 2.5 10.8 1.0
OP2 F:DG8 2.6 5.2 1.0
OD2 A:ASP127 2.8 24.9 1.0
O A:HOH943 3.5 18.7 1.0
NZ A:LYS129 3.5 18.1 1.0
C A:ILE142 3.6 15.9 1.0
O5' F:DC7 3.7 17.2 1.0
C3' F:DC7 3.9 30.8 1.0
P F:DG8 3.9 18.9 1.0
CG A:ASP127 3.9 30.6 1.0
CA A:ILE143 4.0 14.1 1.0
O F:HOH196 4.1 18.9 1.0
OP1 F:DC7 4.1 17.1 1.0
N A:ILE143 4.2 17.6 1.0
O3' F:DC7 4.3 20.9 1.0
P F:DC7 4.3 13.8 1.0
O A:THR112 4.4 18.8 1.0
CB A:ILE143 4.5 17.8 1.0
OD1 A:ASP127 4.5 44.4 1.0
CE A:LYS129 4.5 14.1 1.0
OP2 F:DC7 4.6 16.5 1.0
C5' F:DC7 4.6 25.0 1.0
O A:HOH849 4.6 41.5 1.0
OE1 A:GLN207 4.6 6.9 1.0
C2' F:DC7 4.6 39.8 1.0
OP1 F:DG8 4.7 11.0 1.0
CA A:ILE142 4.7 9.1 1.0
CG1 A:ILE143 4.8 6.4 1.0
C4' F:DC7 4.8 29.6 1.0
CE1 A:TYR168 4.8 14.4 1.0
CB A:ASP127 5.0 21.8 1.0

Sodium binding site 2 out of 4 in 1tx3

Go back to Sodium Binding Sites List in 1tx3
Sodium binding site 2 out of 4 in the Hincii Bound to Cognate Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hincii Bound to Cognate Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na802

b:12.5
occ:1.00
 O E:HOH508 2.1 15.5 1.0
OP2 E:DG8 2.1 1.0 1.0
O B:HOH1056 2.3 15.4 1.0
OD1 B:ASP127 2.5 35.2 1.0
O B:ILE142 2.6 9.5 1.0
P E:DG8 3.5 23.5 1.0
C B:ILE142 3.6 15.5 1.0
CG B:ASP127 3.6 23.3 1.0
C3' E:DC7 3.7 21.2 1.0
O E:HOH251 3.8 27.6 1.0
O B:HOH917 3.8 35.3 1.0
O5' E:DC7 3.9 17.1 1.0
O3' E:DC7 4.0 14.5 1.0
NZ B:LYS129 4.1 46.4 1.0
CE B:LYS129 4.2 5.0 1.0
OD2 B:ASP127 4.2 34.7 1.0
CA B:ILE143 4.3 13.7 1.0
N B:ILE143 4.3 16.3 1.0
OP1 E:DG8 4.3 15.4 1.0
C2' E:DC7 4.3 43.0 1.0
O B:HOH1043 4.5 27.7 1.0
CA B:ILE142 4.5 14.2 1.0
O B:THR112 4.6 24.3 1.0
O5' E:DG8 4.6 11.5 1.0
O B:ASN141 4.6 14.1 1.0
P E:DC7 4.7 15.1 1.0
CB B:ILE143 4.7 16.1 1.0
CB B:ASP127 4.7 16.7 1.0
C5' E:DC7 4.8 15.2 1.0
OP2 E:DC7 4.8 15.1 1.0
OP1 E:DC7 4.8 14.6 1.0
C4' E:DC7 4.8 19.7 1.0
OE1 B:GLN207 4.8 13.7 1.0
O E:HOH776 4.9 29.8 1.0

Sodium binding site 3 out of 4 in 1tx3

Go back to Sodium Binding Sites List in 1tx3
Sodium binding site 3 out of 4 in the Hincii Bound to Cognate Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Hincii Bound to Cognate Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na803

b:47.4
occ:1.00
 OP2 H:DG8 2.4 20.5 1.0
O C:ILE142 2.4 29.5 1.0
O C:HOH832 2.7 53.3 1.0
OD2 C:ASP127 2.8 74.3 1.0
O C:HOH809 3.2 45.4 1.0
NZ C:LYS129 3.6 42.0 1.0
C C:ILE142 3.6 29.8 1.0
CG2 C:ILE143 3.7 53.3 1.0
CG C:ASP127 3.7 68.8 1.0
C3' H:DC7 3.7 49.5 1.0
P H:DG8 3.8 37.8 1.0
O5' H:DC7 4.0 27.1 1.0
OD1 C:ASP127 4.0 69.8 1.0
O3' H:DC7 4.1 46.7 1.0
C2' H:DC7 4.2 51.4 1.0
CA C:ILE143 4.2 37.3 1.0
N C:ILE143 4.3 35.6 1.0
O C:THR112 4.5 33.5 1.0
O C:ASN141 4.6 39.7 1.0
CB C:ILE143 4.6 41.8 1.0
CA C:ILE142 4.6 35.4 1.0
OP1 H:DG8 4.6 34.7 1.0
CE C:LYS129 4.7 45.0 1.0
OP2 H:DC7 4.7 37.6 1.0
P H:DC7 4.7 42.4 1.0
O5' H:DG8 4.8 39.2 1.0
OP1 H:DC7 4.8 29.9 1.0
C5' H:DC7 4.8 35.6 1.0
CE1 C:TYR168 4.8 45.6 1.0
CB C:ASP127 4.9 57.1 1.0
C4' H:DC7 4.9 42.5 1.0

Sodium binding site 4 out of 4 in 1tx3

Go back to Sodium Binding Sites List in 1tx3
Sodium binding site 4 out of 4 in the Hincii Bound to Cognate Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Hincii Bound to Cognate Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na804

b:21.5
occ:1.00
 OP2 G:DG8 2.4 22.2 1.0
O D:HOH861 2.4 15.2 1.0
O G:HOH511 2.5 16.0 1.0
O D:ILE142 2.5 26.9 1.0
OD1 D:ASP127 2.7 31.7 1.0
NZ D:LYS129 3.3 35.2 1.0
O D:HOH813 3.5 24.6 1.0
C D:ILE142 3.5 27.7 1.0
C3' G:DC7 3.7 32.7 1.0
P G:DG8 3.7 32.2 1.0
CG D:ASP127 3.8 39.6 1.0
O5' G:DC7 4.0 29.5 1.0
O3' G:DC7 4.1 32.6 1.0
O D:HOH812 4.2 36.1 1.0
CG2 D:ILE143 4.2 52.5 1.0
CE D:LYS129 4.2 28.0 1.0
C2' G:DC7 4.3 34.6 1.0
N D:ILE143 4.3 29.2 1.0
OD2 D:ASP127 4.3 33.4 1.0
O D:THR112 4.4 29.1 1.0
CA D:ILE143 4.4 31.1 1.0
CA D:ILE142 4.5 24.0 1.0
OP1 G:DG8 4.5 28.8 1.0
OP1 G:DC7 4.6 12.6 1.0
OP2 G:DC7 4.6 24.1 1.0
P G:DC7 4.6 27.7 1.0
OE1 D:GLN207 4.8 23.1 1.0
C5' G:DC7 4.8 32.4 1.0
O5' G:DG8 4.9 25.9 1.0
C4' G:DC7 4.9 22.8 1.0
CB D:ILE143 4.9 38.2 1.0
CB D:ASP127 5.0 33.4 1.0
O D:ASN141 5.0 25.0 1.0

Reference:

C.Etzkorn, N.C.Horton. CA2+ Binding in the Active Site of Hincii: Implications For the Catalytic Mechanism Biochemistry V. 43 13256 2004.
ISSN: ISSN 0006-2960
PubMed: 15491133
DOI: 10.1021/BI0490082
Page generated: Sun Oct 6 22:42:03 2024

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