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

Go back to Calcium Binding Sites List in 6ozh
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

Go back to Calcium Binding Sites List in 6ozh
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

Go back to Calcium Binding Sites List in 6ozh
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

Go back to Calcium Binding Sites List in 6ozh
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

Go back to Calcium Binding Sites List in 6ozh
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

Go back to Calcium Binding Sites List in 6ozh
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

Go back to Calcium Binding Sites List in 6ozh
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: Sat Dec 12 07:24:40 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy