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Calcium in PDB 6ozh: Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V in Complex with A 24MER Dna Containing An Inosine Followed By A Ribo-Adenosine

Protein crystallography data

The structure of Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V in Complex with A 24MER Dna Containing An Inosine Followed By A Ribo-Adenosine, PDB code: 6ozh was solved by N.L.Samara, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.22 / 3.03
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.245, 121.975, 79.921, 90.00, 98.75, 90.00
R / Rfree (%) 23.3 / 26.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V in Complex with A 24MER Dna Containing An Inosine Followed By A Ribo-Adenosine (pdb code 6ozh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V in Complex with A 24MER Dna Containing An Inosine Followed By A Ribo-Adenosine, PDB code: 6ozh:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6ozh

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Calcium binding site 1 out of 8 in the Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V in Complex with A 24MER Dna Containing An Inosine Followed By A Ribo-Adenosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V in Complex with A 24MER Dna Containing An Inosine Followed By A Ribo-Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:46.2
occ:1.00
 OD2 A:ASP234 2.4 38.1 1.0
OP1 E:DT12 2.4 45.8 1.0
OD2 A:ASP43 2.5 45.5 1.0
CG A:ASP43 3.3 43.8 1.0
C5' E:DT12 3.5 45.7 1.0
OD1 A:ASP43 3.5 45.0 1.0
O5' E:DT12 3.5 44.7 1.0
P E:DT12 3.5 44.5 1.0
CG A:ASP234 3.5 41.0 1.0
O A:VAL44 3.8 47.8 1.0
OP2 E:DA13 4.0 52.2 1.0
OG A:SER45 4.1 48.5 1.0
OP1 E:DA13 4.3 56.5 1.0
OD1 A:ASP234 4.3 44.5 1.0
CA E:CA101 4.3 52.1 1.0
P E:DA13 4.4 54.4 1.0
CB A:ASP234 4.4 41.3 1.0
O3' E:DT12 4.5 49.7 1.0
OP2 E:DT12 4.5 43.6 1.0
C4' E:DT12 4.5 45.9 1.0
OD2 A:ASP117 4.6 37.0 1.0
C3' E:DT12 4.6 47.6 1.0
C A:VAL44 4.6 47.3 1.0
O3' E:A11 4.6 44.2 1.0
CA A:ASP234 4.7 43.2 1.0
CB A:ASP43 4.8 42.9 1.0
CA A:SER45 4.8 49.9 1.0
CD A:ARG238 4.9 46.3 1.0
CG A:ARG238 5.0 48.4 1.0

Calcium binding site 2 out of 8 in 6ozh

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Calcium binding site 2 out of 8 in the Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V in Complex with A 24MER Dna Containing An Inosine Followed By A Ribo-Adenosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V in Complex with A 24MER Dna Containing An Inosine Followed By A Ribo-Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:43.5
occ:1.00
 OD1 B:ASP234 2.3 54.4 1.0
OP1 F:DT12 2.4 49.0 1.0
OD2 B:ASP43 2.5 44.8 1.0
CG B:ASP234 2.8 49.1 1.0
OD2 B:ASP234 3.4 47.1 1.0
CG B:ASP43 3.4 43.1 1.0
NH2 B:ARG238 3.5 54.5 1.0
P F:DT12 3.5 48.7 1.0
OD1 B:ASP43 3.6 42.2 1.0
CB B:ASP234 3.7 44.7 1.0
O5' F:DT12 3.8 48.2 1.0
OD2 B:ASP117 4.1 45.7 1.0
OP2 F:DT12 4.1 48.8 1.0
C5' F:DT12 4.2 48.3 1.0
CA B:ASP234 4.4 42.9 1.0
OP2 F:DA13 4.5 50.9 1.0
CZ B:ARG238 4.6 50.5 1.0
O B:VAL44 4.6 46.0 1.0
CB B:ASP43 4.7 42.7 1.0
CA F:CA101 4.7 52.6 1.0
O3' F:A11 4.8 49.6 1.0
OG B:SER45 5.0 51.5 1.0

Calcium binding site 3 out of 8 in 6ozh

Go back to Calcium Binding Sites List in 6ozh
Calcium binding site 3 out of 8 in the Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V in Complex with A 24MER Dna Containing An Inosine Followed By A Ribo-Adenosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V in Complex with A 24MER Dna Containing An Inosine Followed By A Ribo-Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:54.3
occ:1.00
 OD1 C:ASP234 2.4 43.8 1.0
OP1 G:DT12 2.4 52.8 1.0
OD2 C:ASP43 2.5 54.7 1.0
CG C:ASP43 3.3 54.2 1.0
O5' G:DT12 3.4 56.8 1.0
OD1 C:ASP43 3.5 56.9 1.0
P G:DT12 3.5 55.0 1.0
C5' G:DT12 3.5 57.4 1.0
CG C:ASP234 3.6 46.3 1.0
NH2 C:ARG238 3.8 51.8 1.0
O C:VAL44 3.9 60.9 1.0
OP1 G:DA13 3.9 64.9 1.0
OP2 G:DA13 3.9 62.4 1.0
P G:DA13 4.2 64.0 1.0
OG C:SER45 4.3 60.3 1.0
O3' G:DT12 4.3 60.4 1.0
OD2 C:ASP234 4.3 47.8 1.0
OP2 G:DT12 4.4 55.8 1.0
CB C:ASP234 4.5 45.8 1.0
C3' G:DT12 4.5 60.5 1.0
C4' G:DT12 4.6 60.0 1.0
CA G:CA101 4.6 59.6 1.0
O3' G:A11 4.7 56.0 1.0
C C:VAL44 4.7 61.0 1.0
CA C:ASP234 4.8 47.8 1.0
CB C:ASP43 4.8 53.1 1.0
OD2 C:ASP117 4.8 53.0 1.0
CZ C:ARG238 4.8 54.8 1.0
CA C:SER45 5.0 62.1 1.0

Calcium binding site 4 out of 8 in 6ozh

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Calcium binding site 4 out of 8 in the Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V in Complex with A 24MER Dna Containing An Inosine Followed By A Ribo-Adenosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V in Complex with A 24MER Dna Containing An Inosine Followed By A Ribo-Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:48.8
occ:1.00
 OD1 D:ASP234 2.3 41.9 1.0
OD2 D:ASP43 2.5 49.1 1.0
OP1 H:DT12 2.5 47.7 1.0
CG D:ASP43 3.3 47.7 1.0
CG D:ASP234 3.4 42.6 1.0
OD1 D:ASP43 3.4 48.0 1.0
P H:DT12 3.7 51.1 1.0
NH2 D:ARG238 3.7 48.8 1.0
O5' H:DT12 3.7 50.8 1.0
C5' H:DT12 3.8 48.7 1.0
O D:VAL44 4.0 48.9 1.0
OP1 H:DA13 4.1 55.1 1.0
CA H:CA101 4.2 62.9 1.0
OD2 D:ASP234 4.2 44.2 1.0
OP2 H:DA13 4.2 56.7 1.0
CB D:ASP234 4.3 43.0 1.0
OD1 D:ASP117 4.5 53.2 1.0
P H:DA13 4.5 56.1 1.0
CA D:ASP234 4.6 43.9 1.0
OP2 H:DT12 4.6 66.9 1.0
O3' H:DT12 4.7 46.8 1.0
CZ D:ARG238 4.7 49.8 1.0
CB D:ASP43 4.7 45.1 1.0
O3' H:A11 4.8 52.2 1.0
C D:VAL44 4.9 49.9 1.0
C4' H:DT12 4.9 49.9 1.0
C3' H:DT12 4.9 49.8 1.0

Calcium binding site 5 out of 8 in 6ozh

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Calcium binding site 5 out of 8 in the Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V in Complex with A 24MER Dna Containing An Inosine Followed By A Ribo-Adenosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V in Complex with A 24MER Dna Containing An Inosine Followed By A Ribo-Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca101

b:52.1
occ:1.00
 OD1 A:ASP43 2.4 45.0 1.0
O3' E:A11 2.5 44.2 1.0
OP1 E:DT12 2.9 45.8 1.0
O2' E:A11 3.2 44.6 1.0
OD2 A:ASP117 3.2 37.0 1.0
P E:DT12 3.3 44.5 1.0
OE2 A:GLU91 3.5 43.1 1.0
C3' E:A11 3.6 43.3 1.0
CG A:ASP43 3.6 43.8 1.0
CB A:ASP117 3.6 38.5 1.0
C5' E:DT12 3.7 45.7 1.0
O A:VAL44 3.7 47.8 1.0
CG A:ASP117 3.8 37.4 1.0
C2' E:A11 4.0 43.5 1.0
O5' E:DT12 4.0 44.7 1.0
N A:VAL44 4.0 44.2 1.0
C4' E:A11 4.1 43.0 1.0
OD2 A:ASP43 4.3 45.5 1.0
CD A:GLU91 4.3 43.1 1.0
CA A:CA301 4.3 46.2 1.0
OE1 A:GLU91 4.4 41.0 1.0
OP2 E:DT12 4.5 43.6 1.0
C A:VAL44 4.7 47.3 1.0
CA A:ASP43 4.7 42.4 1.0
CB A:ASP43 4.7 42.9 1.0
CA A:VAL44 4.8 46.0 1.0
C A:ASP43 4.9 44.1 1.0
CE2 A:TYR46 5.0 53.3 1.0
C5' E:A11 5.0 42.6 1.0
OD1 A:ASP117 5.0 37.5 1.0

Calcium binding site 6 out of 8 in 6ozh

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Calcium binding site 6 out of 8 in the Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V in Complex with A 24MER Dna Containing An Inosine Followed By A Ribo-Adenosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V in Complex with A 24MER Dna Containing An Inosine Followed By A Ribo-Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca101

b:52.6
occ:1.00
 OD1 B:ASP43 2.5 42.2 1.0
O3' F:A11 2.5 49.6 1.0
OP1 F:DT12 2.8 49.0 1.0
OE2 B:GLU91 3.1 42.1 1.0
P F:DT12 3.3 48.7 1.0
OD2 B:ASP117 3.3 45.7 1.0
O2' F:A11 3.5 51.9 1.0
C3' F:A11 3.7 50.6 1.0
CB B:ASP117 3.7 43.0 1.0
O B:VAL44 3.7 46.0 1.0
CG B:ASP43 3.7 43.1 1.0
C5' F:DT12 3.8 48.3 1.0
CG B:ASP117 3.9 42.7 1.0
N B:VAL44 4.0 43.5 1.0
CD B:GLU91 4.0 43.3 1.0
O5' F:DT12 4.0 48.2 1.0
OE1 B:GLU91 4.1 41.5 1.0
C2' F:A11 4.1 50.9 1.0
C4' F:A11 4.2 53.5 1.0
OD2 B:ASP43 4.4 44.8 1.0
OP2 F:DT12 4.5 48.8 1.0
C B:VAL44 4.6 46.7 1.0
CA B:ASP43 4.7 42.3 1.0
CA B:VAL44 4.7 45.3 1.0
CA B:CA301 4.7 43.5 1.0
CB B:ASP43 4.8 42.7 1.0
CE2 B:TYR46 4.8 47.1 1.0
CB B:VAL44 4.9 45.1 1.0
C B:ASP43 4.9 44.8 1.0
OH B:TYR46 4.9 45.4 1.0

Calcium binding site 7 out of 8 in 6ozh

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Calcium binding site 7 out of 8 in the Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V in Complex with A 24MER Dna Containing An Inosine Followed By A Ribo-Adenosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V in Complex with A 24MER Dna Containing An Inosine Followed By A Ribo-Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca101

b:59.6
occ:1.00
 OD1 C:ASP43 2.5 56.9 1.0
O3' G:A11 2.5 56.0 1.0
OP1 G:DT12 2.9 52.8 1.0
OE2 C:GLU91 3.1 60.0 1.0
P G:DT12 3.3 55.0 1.0
O2' G:A11 3.4 60.2 1.0
OD2 C:ASP117 3.5 53.0 1.0
CB C:ASP117 3.6 55.1 1.0
C3' G:A11 3.6 58.6 1.0
CG C:ASP43 3.7 54.2 1.0
C5' G:DT12 3.8 57.4 1.0
CG C:ASP117 3.8 53.4 1.0
CD C:GLU91 3.9 62.0 1.0
OE1 C:GLU91 3.9 60.6 1.0
O C:VAL44 4.0 60.9 1.0
C2' G:A11 4.1 60.8 1.0
O5' G:DT12 4.1 56.8 1.0
N C:VAL44 4.1 57.1 1.0
C4' G:A11 4.1 59.5 1.0
OD2 C:ASP43 4.5 54.7 1.0
CA C:CA301 4.6 54.3 1.0
OP2 G:DT12 4.6 55.8 1.0
CA C:ASP43 4.6 53.6 1.0
CB C:ASP43 4.7 53.1 1.0
OD1 C:ASP117 4.8 52.9 1.0
C C:VAL44 4.9 61.0 1.0
CA C:VAL44 4.9 58.4 1.0
C C:ASP43 4.9 55.4 1.0
C5' G:A11 5.0 59.1 1.0

Calcium binding site 8 out of 8 in 6ozh

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Calcium binding site 8 out of 8 in the Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V in Complex with A 24MER Dna Containing An Inosine Followed By A Ribo-Adenosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Ciona Intestinalis (Ci) Endonuclease V in Complex with A 24MER Dna Containing An Inosine Followed By A Ribo-Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca101

b:62.9
occ:1.00
 O3' H:A11 2.5 52.2 1.0
OD1 D:ASP43 2.5 48.0 1.0
OP1 H:DT12 2.8 47.7 1.0
P H:DT12 3.2 51.1 1.0
OE2 D:GLU91 3.2 49.3 1.0
O2' H:A11 3.3 53.4 1.0
OD1 D:ASP117 3.4 53.2 1.0
C5' H:DT12 3.5 48.7 1.0
C3' H:A11 3.6 55.8 1.0
CG D:ASP43 3.7 47.7 1.0
O D:VAL44 3.8 48.9 1.0
O5' H:DT12 3.8 50.8 1.0
CB D:ASP117 3.9 51.4 1.0
C2' H:A11 4.0 56.0 1.0
CG D:ASP117 4.0 52.4 1.0
N D:VAL44 4.2 48.0 1.0
CD D:GLU91 4.2 51.5 1.0
CA D:CA301 4.2 48.8 1.0
C4' H:A11 4.2 58.2 1.0
OD2 D:ASP43 4.3 49.1 1.0
OE1 D:GLU91 4.4 55.0 1.0
OP2 H:DT12 4.5 66.9 1.0
CE2 D:TYR46 4.7 50.2 1.0
C D:VAL44 4.7 49.9 1.0
CB D:ASP43 4.8 45.1 1.0
CA D:ASP43 4.8 42.9 1.0
C4' H:DT12 4.8 49.9 1.0
CA D:VAL44 4.9 47.7 1.0
OH D:TYR46 4.9 47.1 1.0

Reference:

J.Wu, N.L.Samara, I.Kuraoka, W.Yang. Evolution of Inosine-Specific Endonuclease V From Bacterial Dnase to Eukaryotic Rnase. Mol.Cell V. 76 44 2019.
ISSN: ISSN 1097-2765
PubMed: 31444105
DOI: 10.1016/J.MOLCEL.2019.06.046
Page generated: Tue Jul 16 12:40:39 2024

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