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Sodium in PDB 3e3y: Q138F Hincii Bound to Gttaac and Cocrystallized with 5 Mm CA2+

Enzymatic activity of Q138F Hincii Bound to Gttaac and Cocrystallized with 5 Mm CA2+

All present enzymatic activity of Q138F Hincii Bound to Gttaac and Cocrystallized with 5 Mm CA2+:
3.1.21.4;

Protein crystallography data

The structure of Q138F Hincii Bound to Gttaac and Cocrystallized with 5 Mm CA2+, PDB code: 3e3y was solved by N.C.Horton, A.C.Babic, E.J.Little, V.M.Manohar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.06 / 2.13
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.480, 91.640, 65.780, 90.00, 104.92, 90.00
R / Rfree (%) 18 / 23.4

Other elements in 3e3y:

The structure of Q138F Hincii Bound to Gttaac and Cocrystallized with 5 Mm CA2+ also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Q138F Hincii Bound to Gttaac and Cocrystallized with 5 Mm CA2+ (pdb code 3e3y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Q138F Hincii Bound to Gttaac and Cocrystallized with 5 Mm CA2+, PDB code: 3e3y:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3e3y

Go back to Sodium Binding Sites List in 3e3y
Sodium binding site 1 out of 3 in the Q138F Hincii Bound to Gttaac and Cocrystallized with 5 Mm CA2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Q138F Hincii Bound to Gttaac and Cocrystallized with 5 Mm CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na260

b:30.5
occ:1.00
O A:ILE142 2.5 16.4 1.0
OD1 A:ASP127 2.6 29.1 1.0
OP2 F:DA8 2.6 24.9 1.0
O A:HOH459 2.7 24.1 1.0
O A:HOH297 2.8 20.0 1.0
O A:HOH337 3.5 23.4 1.0
P F:DA8 3.6 18.8 1.0
C A:ILE142 3.6 20.8 1.0
O F:HOH394 3.6 31.4 1.0
O3' F:DT7 3.7 19.9 1.0
CG A:ASP127 3.8 26.2 1.0
NZ A:LYS129 3.8 22.7 1.0
O5' F:DT7 3.9 20.1 1.0
C3' F:DT7 4.0 20.8 1.0
OP1 F:DA8 4.1 19.6 1.0
O A:HOH309 4.1 26.9 1.0
CA A:ILE143 4.2 16.9 1.0
C5' F:DT7 4.3 20.3 1.0
N A:ILE143 4.3 17.9 1.0
OD2 A:ASP127 4.3 22.3 1.0
CE A:LYS129 4.4 23.5 1.0
O A:THR112 4.4 20.4 1.0
OP1 F:DT7 4.6 15.9 1.0
CB A:ILE143 4.6 19.8 1.0
P F:DT7 4.6 19.3 1.0
CA A:ILE142 4.6 14.5 1.0
C4' F:DT7 4.7 20.7 1.0
O A:ASN141 4.8 22.7 1.0
OP2 F:DT7 4.8 19.9 1.0
OE1 A:GLN207 4.8 16.4 1.0
CG1 A:ILE143 4.9 19.3 1.0
CB A:ASP127 4.9 24.1 1.0
O5' F:DA8 4.9 19.1 1.0

Sodium binding site 2 out of 3 in 3e3y

Go back to Sodium Binding Sites List in 3e3y
Sodium binding site 2 out of 3 in the Q138F Hincii Bound to Gttaac and Cocrystallized with 5 Mm CA2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Q138F Hincii Bound to Gttaac and Cocrystallized with 5 Mm CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na260

b:33.4
occ:1.00
O B:ILE142 2.6 23.4 1.0
OP2 E:DA8 2.7 27.8 1.0
O E:HOH17 2.7 22.3 1.0
OD2 B:ASP127 2.7 30.9 1.0
O B:HOH302 2.8 21.2 1.0
O B:HOH306 3.5 22.8 1.0
P E:DA8 3.5 26.0 1.0
O3' E:DT7 3.6 25.4 1.0
C B:ILE142 3.7 24.0 1.0
CG B:ASP127 3.8 33.4 1.0
O5' E:DT7 3.9 24.7 1.0
O B:HOH304 3.9 29.4 1.0
NZ B:LYS129 3.9 32.1 1.0
C3' E:DT7 3.9 27.8 1.0
OP1 E:DA8 4.1 29.7 1.0
CA B:ILE143 4.2 23.2 1.0
C5' E:DT7 4.3 21.9 1.0
O B:THR112 4.3 26.3 1.0
OD1 B:ASP127 4.3 32.8 1.0
N B:ILE143 4.4 21.4 1.0
OP1 E:DT7 4.5 19.6 1.0
P E:DT7 4.6 20.9 1.0
CB B:ILE143 4.6 21.7 1.0
CA B:ILE142 4.6 21.3 1.0
C4' E:DT7 4.7 25.4 1.0
O B:ASN141 4.7 24.0 1.0
OP2 E:DT7 4.7 22.8 1.0
OE1 B:GLN207 4.8 19.1 1.0
CG1 B:ILE143 4.8 24.3 1.0
O5' E:DA8 4.9 29.8 1.0

Sodium binding site 3 out of 3 in 3e3y

Go back to Sodium Binding Sites List in 3e3y
Sodium binding site 3 out of 3 in the Q138F Hincii Bound to Gttaac and Cocrystallized with 5 Mm CA2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Q138F Hincii Bound to Gttaac and Cocrystallized with 5 Mm CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na15

b:40.0
occ:1.00
O A:HOH366 2.4 43.3 1.0
OP1 F:DA8 2.6 19.6 1.0
OD2 A:ASP114 2.7 27.0 1.0
O A:HOH309 2.7 26.9 1.0
O A:HOH367 2.9 41.1 1.0
O3' F:DT7 3.0 19.9 1.0
P F:DA8 3.4 18.8 1.0
CG A:ASP114 3.6 29.1 1.0
O A:HOH410 3.8 29.0 1.0
O A:ASP111 3.8 22.3 1.0
OD1 A:ASP114 4.1 23.5 1.0
C5' F:DA8 4.2 22.7 1.0
C3' F:DT7 4.2 20.8 1.0
O5' F:DA8 4.2 19.1 1.0
O A:ALA113 4.2 21.8 1.0
CA A:CA259 4.2 25.5 1.0
C A:ALA113 4.3 23.6 1.0
N A:ASP114 4.4 24.3 1.0
C4' F:DT7 4.4 20.7 1.0
CA A:ASP114 4.5 24.0 1.0
CB A:ASP114 4.7 25.2 1.0
OP2 F:DA8 4.7 24.9 1.0
O A:HOH440 4.8 24.7 1.0
O A:THR112 4.8 20.4 1.0
C2' F:DT7 4.8 18.5 1.0
O A:HOH433 4.9 39.0 1.0
C A:ASP111 4.9 24.8 1.0

Reference:

A.C.Babic, E.J.Little, V.M.Manohar, J.Bitinaite, N.C.Horton. Dna Distortion and Specificity in A Sequence-Specific Endonuclease. J.Mol.Biol. V. 383 186 2008.
ISSN: ISSN 0022-2836
PubMed: 18762194
DOI: 10.1016/J.JMB.2008.08.032
Page generated: Tue Dec 15 06:09:22 2020

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