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Calcium in PDB 1tw8: Hincii Bound to CA2+ and Cognate Dna Gtcgac

Enzymatic activity of Hincii Bound to CA2+ and Cognate Dna Gtcgac

All present enzymatic activity of Hincii Bound to CA2+ and Cognate Dna Gtcgac:
3.1.21.4;

Protein crystallography data

The structure of Hincii Bound to CA2+ and Cognate Dna Gtcgac, PDB code: 1tw8 was solved by C.Etzkorn, N.C.Horton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.80
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.945, 177.180, 254.890, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 28.6

Other elements in 1tw8:

The structure of Hincii Bound to CA2+ and Cognate Dna Gtcgac also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Hincii Bound to CA2+ and Cognate Dna Gtcgac (pdb code 1tw8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Hincii Bound to CA2+ and Cognate Dna Gtcgac, PDB code: 1tw8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1tw8

Go back to Calcium Binding Sites List in 1tw8
Calcium binding site 1 out of 6 in the Hincii Bound to CA2+ and Cognate Dna Gtcgac


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Hincii Bound to CA2+ and Cognate Dna Gtcgac within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca805

b:72.1
occ:1.00
 O F:HOH841 2.3 42.0 1.0
N4 F:DC2 2.9 18.6 1.0
O B:HOH1059 2.9 31.1 1.0
O6 F:DG1 3.0 28.2 1.0
O6 E:DG12 3.5 36.9 1.0
O B:HOH1060 3.8 48.1 1.0
C6 F:DG1 4.0 24.0 1.0
C4 F:DC2 4.1 24.7 1.0
O F:HOH823 4.3 26.4 1.0
C6 E:DG12 4.4 35.2 1.0
O F:HOH842 4.4 34.3 1.0
N3 F:DC2 4.6 17.7 1.0
N7 F:DG1 4.7 35.3 1.0
C5 F:DG1 4.7 21.3 1.0
N7 E:DG12 4.8 26.3 1.0
C5 E:DG12 4.9 23.3 1.0

Calcium binding site 2 out of 6 in 1tw8

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Calcium binding site 2 out of 6 in the Hincii Bound to CA2+ and Cognate Dna Gtcgac


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Hincii Bound to CA2+ and Cognate Dna Gtcgac within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca806

b:31.8
occ:0.50
 O6 H:DG1 2.0 43.6 1.0
O H:HOH43 2.8 44.5 1.0
C6 H:DG1 3.1 31.2 1.0
C5 H:DG1 3.8 29.4 1.0
N7 H:DG1 3.9 39.1 1.0
N4 H:DC2 3.9 58.3 1.0
N1 H:DG1 4.2 24.5 1.0

Calcium binding site 3 out of 6 in 1tw8

Go back to Calcium Binding Sites List in 1tw8
Calcium binding site 3 out of 6 in the Hincii Bound to CA2+ and Cognate Dna Gtcgac


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Hincii Bound to CA2+ and Cognate Dna Gtcgac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca801

b:19.4
occ:1.00
 OD1 A:ASP127 2.2 12.9 1.0
O F:HOH806 2.2 38.5 1.0
O A:HOH1058 2.2 24.4 1.0
OP1 F:DG8 2.2 25.3 1.0
OD1 A:ASP114 2.3 30.3 1.0
O A:VAL128 2.4 29.2 1.0
CG A:ASP114 3.1 44.1 1.0
OD2 A:ASP114 3.1 38.9 1.0
P F:DG8 3.3 37.4 1.0
CG A:ASP127 3.3 23.6 1.0
C A:VAL128 3.4 24.9 1.0
N A:VAL128 3.6 24.9 1.0
O5' F:DG8 3.7 35.7 1.0
OP2 F:DG8 3.9 8.5 1.0
OD2 A:ASP127 3.9 24.9 1.0
CA A:VAL128 4.1 27.2 1.0
C A:ASP127 4.1 29.0 1.0
CD A:LYS129 4.2 40.4 1.0
NZ A:LYS129 4.2 32.3 1.0
O A:HOH1061 4.2 42.6 1.0
CA A:ASP127 4.4 27.3 1.0
CE A:LYS129 4.4 47.0 1.0
C5' F:DG8 4.5 40.2 1.0
CB A:ASP127 4.5 29.9 1.0
N A:LYS129 4.5 25.6 1.0
CB A:ASP114 4.5 33.1 1.0
OP2 F:DA9 4.5 18.7 1.0
O A:HOH1020 4.5 39.2 1.0
O3' F:DC7 4.7 31.9 1.0
CG1 A:VAL128 4.7 25.0 1.0
CA A:LYS129 4.8 19.1 1.0
CB A:VAL128 4.9 31.3 1.0
O A:ASP127 4.9 17.4 1.0
C3' F:DG8 4.9 34.7 1.0

Calcium binding site 4 out of 6 in 1tw8

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Calcium binding site 4 out of 6 in the Hincii Bound to CA2+ and Cognate Dna Gtcgac


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Hincii Bound to CA2+ and Cognate Dna Gtcgac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca802

b:37.1
occ:1.00
 O B:HOH1006 2.1 5.3 1.0
OP1 E:DG8 2.2 30.3 1.0
OD2 B:ASP127 2.3 19.5 1.0
OD1 B:ASP114 2.3 32.6 1.0
O B:VAL128 2.4 18.3 1.0
O E:HOH244 2.6 35.2 1.0
P E:DG8 3.2 33.4 1.0
CG B:ASP114 3.2 33.8 1.0
CG B:ASP127 3.5 28.5 1.0
OD2 B:ASP114 3.5 35.5 1.0
C B:VAL128 3.5 23.1 1.0
O5' E:DG8 3.5 36.9 1.0
N B:VAL128 3.7 16.8 1.0
OP2 E:DG8 3.7 8.7 1.0
OD1 B:ASP127 4.1 25.0 1.0
CA B:VAL128 4.1 20.6 1.0
C B:ASP127 4.2 21.9 1.0
OP2 E:DA9 4.3 29.9 1.0
C5' E:DG8 4.3 44.5 1.0
O B:HOH1058 4.3 38.9 1.0
O B:HOH1056 4.4 46.1 1.0
O B:HOH1020 4.5 19.6 1.0
O B:HOH1055 4.5 14.6 1.0
CA B:ASP127 4.5 13.2 1.0
CB B:ASP127 4.6 17.9 1.0
CB B:ASP114 4.6 18.1 1.0
O3' E:DC7 4.6 38.5 1.0
CD B:LYS129 4.6 19.7 1.0
N B:LYS129 4.6 28.4 1.0
NZ B:LYS129 4.6 21.0 1.0
CB B:VAL128 4.7 22.6 1.0
C3' E:DG8 4.7 41.7 1.0
CE B:LYS129 4.8 19.7 1.0
O B:ASP127 4.9 19.8 1.0
CA B:LYS129 5.0 21.6 1.0
O E:HOH615 5.0 31.5 1.0

Calcium binding site 5 out of 6 in 1tw8

Go back to Calcium Binding Sites List in 1tw8
Calcium binding site 5 out of 6 in the Hincii Bound to CA2+ and Cognate Dna Gtcgac


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Hincii Bound to CA2+ and Cognate Dna Gtcgac within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca803

b:49.0
occ:1.00
 O C:HOH971 2.1 31.0 1.0
OD1 C:ASP127 2.2 53.3 1.0
OP1 H:DG8 2.3 64.8 1.0
OD2 C:ASP114 2.4 68.3 1.0
O C:VAL128 2.4 62.9 1.0
P H:DG8 3.1 62.0 1.0
CG C:ASP127 3.3 62.4 1.0
CG C:ASP114 3.4 76.3 1.0
OP2 H:DG8 3.4 34.5 1.0
O5' H:DG8 3.4 56.1 1.0
C C:VAL128 3.4 54.4 1.0
N C:VAL128 3.4 54.4 1.0
O C:HOH970 3.6 26.1 1.0
OD1 C:ASP114 3.7 79.1 1.0
C C:ASP127 3.9 61.2 1.0
CA C:VAL128 4.0 53.4 1.0
CD C:LYS129 4.0 45.5 1.0
OD2 C:ASP127 4.0 55.9 1.0
CA C:ASP127 4.2 64.7 1.0
CB C:ASP127 4.3 63.2 1.0
OP2 H:DA9 4.5 37.8 1.0
N C:LYS129 4.5 53.3 1.0
O C:HOH999 4.5 58.0 1.0
NZ C:LYS129 4.5 50.9 1.0
O3' H:DC7 4.6 64.6 1.0
CB C:VAL128 4.6 48.5 1.0
O C:ASP127 4.6 63.4 1.0
CB C:ASP114 4.7 72.5 1.0
O C:HOH972 4.8 57.9 1.0
C5' H:DG8 4.8 63.0 1.0
CA C:LYS129 4.9 55.7 1.0
CE C:LYS129 4.9 56.7 1.0

Calcium binding site 6 out of 6 in 1tw8

Go back to Calcium Binding Sites List in 1tw8
Calcium binding site 6 out of 6 in the Hincii Bound to CA2+ and Cognate Dna Gtcgac


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Hincii Bound to CA2+ and Cognate Dna Gtcgac within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca804

b:43.4
occ:1.00
 OD2 D:ASP127 2.2 40.9 1.0
O D:VAL128 2.3 75.4 1.0
OP1 G:DG8 2.3 71.7 1.0
O D:HOH922 2.3 22.2 1.0
OD2 D:ASP114 2.5 54.4 1.0
OD1 D:ASP114 3.1 76.1 1.0
CG D:ASP114 3.2 63.0 1.0
P G:DG8 3.2 68.7 1.0
OP2 G:DG8 3.3 61.2 1.0
CG D:ASP127 3.4 42.1 1.0
C D:VAL128 3.4 66.3 1.0
N D:VAL128 3.8 51.5 1.0
O5' G:DG8 3.8 67.4 1.0
OD1 D:ASP127 3.9 34.5 1.0
CD D:LYS129 4.0 63.6 1.0
O D:HOH979 4.0 39.1 1.0
CA D:VAL128 4.1 57.6 1.0
NZ D:LYS129 4.2 78.5 1.0
C D:ASP127 4.3 48.6 1.0
CE D:LYS129 4.4 68.3 1.0
N D:LYS129 4.4 67.9 1.0
OP2 G:DA9 4.5 56.0 1.0
O D:HOH956 4.5 38.0 1.0
C5' G:DG8 4.6 72.0 1.0
CB D:ASP127 4.6 45.6 1.0
CB D:ASP114 4.6 56.8 1.0
O3' G:DC7 4.6 57.2 1.0
CA D:ASP127 4.6 50.1 1.0
CA D:LYS129 4.7 64.1 1.0
CB D:VAL128 4.7 53.7 1.0
C3' G:DG8 4.8 64.2 1.0
NA D:NA904 4.9 62.4 1.0
CG D:LYS129 4.9 62.2 1.0
O D:ASP127 5.0 46.4 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
Page generated: Thu Jul 11 23:12:59 2024

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