Atomistry » Calcium » PDB 6ok8-6p8w » 6ozf
Atomistry »
  Calcium »
    PDB 6ok8-6p8w »
      6ozf »

Calcium in PDB 6ozf: Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine

Enzymatic activity of Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine

All present enzymatic activity of Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine:
3.1.21.7;

Protein crystallography data

The structure of Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine, PDB code: 6ozf 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) 28.09 / 1.80
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.129, 75.578, 106.397, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 19.8

Other elements in 6ozf:

The structure of Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine (pdb code 6ozf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine, PDB code: 6ozf:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6ozf

Go back to Calcium Binding Sites List in 6ozf
Calcium binding site 1 out of 4 in the Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER 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 Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:18.8
occ:1.00
 OP1 C:DG7 2.3 23.9 1.0
OD1 A:ASP43 2.4 22.1 0.5
O C:HOH227 2.4 25.3 1.0
O A:HOH496 2.4 23.4 1.0
O A:HOH419 2.4 21.9 1.0
OD1 A:ASP43 2.5 26.8 0.5
ND1 A:HIS214 2.6 21.0 1.0
OD2 A:ASP43 2.8 27.6 0.5
OD2 A:ASP43 2.9 27.2 0.5
CG A:ASP43 2.9 24.2 0.5
CG A:ASP43 3.0 22.8 0.5
CE1 A:HIS214 3.4 24.9 1.0
P C:DG7 3.6 19.8 1.0
CG A:HIS214 3.6 21.3 1.0
CB A:HIS214 3.9 13.8 1.0
O5' C:DG7 4.1 17.2 1.0
O A:LEU44 4.2 21.7 1.0
OP2 C:DG7 4.2 22.0 1.0
C5' C:DG7 4.3 17.4 1.0
ND2 A:ASN110 4.3 28.7 0.6
O A:HOH476 4.3 49.0 1.0
O C:HOH210 4.3 31.8 1.0
CB A:ASP43 4.4 16.7 0.5
O A:HOH474 4.5 41.9 1.0
CA A:HIS214 4.5 16.4 1.0
CB A:ASP43 4.5 15.5 0.5
O C:HOH201 4.6 29.8 1.0
NA A:NA302 4.6 28.9 1.0
OG1 A:THR217 4.6 27.6 1.0
NE2 A:HIS214 4.6 19.7 1.0
O3' C:A6 4.7 16.2 1.0
CD2 A:HIS214 4.7 21.8 1.0
O C:HOH206 4.7 31.9 1.0
NE2 A:GLN218 4.9 29.1 1.0
OP2 C:DA8 5.0 29.6 1.0

Calcium binding site 2 out of 4 in 6ozf

Go back to Calcium Binding Sites List in 6ozf
Calcium binding site 2 out of 4 in the Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER 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 Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:19.3
occ:1.00
 OP1 D:DG7 2.3 22.1 1.0
O B:HOH415 2.3 26.3 1.0
OD1 B:ASP43 2.4 28.7 1.0
O B:HOH519 2.4 21.1 1.0
O D:HOH226 2.5 22.5 1.0
ND1 B:HIS214 2.5 19.4 1.0
OD2 B:ASP43 3.1 40.0 1.0
CG B:ASP43 3.1 30.8 1.0
CE1 B:HIS214 3.4 23.6 1.0
P D:DG7 3.5 22.6 1.0
CG B:HIS214 3.6 20.9 1.0
CB B:HIS214 3.9 21.1 1.0
ND2 B:ASN110 4.1 31.3 0.7
O5' D:DG7 4.1 19.8 1.0
OP2 D:DG7 4.2 23.9 1.0
OD1 B:ASN110 4.2 31.6 0.3
O B:HOH443 4.3 48.0 1.0
O B:LEU44 4.3 23.9 1.0
C5' D:DG7 4.4 28.3 1.0
NA B:NA306 4.4 36.8 1.0
CA B:HIS214 4.5 21.8 1.0
NE2 B:HIS214 4.5 23.0 1.0
CB B:ASP43 4.6 17.8 1.0
O D:HOH206 4.6 33.0 1.0
O B:HOH537 4.6 30.9 1.0
CD2 B:HIS214 4.7 21.1 1.0
O3' D:A6 4.7 20.8 1.0
NZ B:LYS139 4.8 46.4 1.0
OP2 D:DA8 4.9 37.0 1.0
OE1 B:GLN218 4.9 41.2 1.0

Calcium binding site 3 out of 4 in 6ozf

Go back to Calcium Binding Sites List in 6ozf
Calcium binding site 3 out of 4 in the Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER 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 Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca101

b:21.9
occ:1.00
 O6 C:DG7 2.3 24.6 1.0
OP2 C:DT3 2.4 24.6 1.0
O C:HOH220 2.4 18.7 1.0
O C:HOH222 2.4 17.3 1.0
O C:HOH212 2.5 29.1 1.0
O C:HOH216 3.0 56.4 1.0
C6 C:DG7 3.5 25.0 1.0
P C:DT3 3.8 32.3 1.0
N7 C:A6 4.1 18.1 1.0
OP1 C:DI5 4.2 19.6 1.0
C5 C:DG7 4.3 23.3 1.0
O3' C:DA2 4.3 30.6 1.0
N7 C:DG7 4.3 22.8 1.0
N6 C:DA8 4.3 21.7 1.0
N1 C:DA8 4.4 26.1 1.0
O C:HOH223 4.5 34.3 1.0
N1 C:DG7 4.6 28.0 1.0
C3' C:DA2 4.6 33.9 1.0
OP2 C:A6 4.7 15.4 1.0
O5' C:DT3 4.7 31.4 1.0
C5' C:DT3 4.8 40.5 1.0
C6 C:DA8 4.8 27.9 1.0
OP1 C:DT3 4.8 43.6 1.0
N6 C:A6 4.8 27.5 1.0
OP2 C:DI5 4.9 16.3 1.0
C8 C:A6 4.9 20.7 1.0

Calcium binding site 4 out of 4 in 6ozf

Go back to Calcium Binding Sites List in 6ozf
Calcium binding site 4 out of 4 in the Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER 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 Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca101

b:25.0
occ:1.00
 O D:HOH222 2.2 35.1 1.0
O6 D:DG7 2.3 27.8 1.0
O D:HOH215 2.3 21.6 1.0
O D:HOH218 2.3 17.3 1.0
O D:HOH210 2.4 20.2 1.0
OP2 D:DT3 2.5 29.6 1.0
O D:HOH219 2.9 36.5 1.0
C6 D:DG7 3.4 27.2 1.0
P D:DT3 4.0 34.9 1.0
OP1 D:DI5 4.0 21.7 1.0
N6 D:DA8 4.1 27.5 1.0
N7 D:A6 4.2 18.4 1.0
C5 D:DG7 4.2 21.4 1.0
N7 D:DG7 4.2 20.4 1.0
O D:HOH220 4.3 46.9 1.0
N1 D:DA8 4.5 30.9 1.0
O3' D:DA2 4.5 36.1 1.0
N1 D:DG7 4.5 28.4 1.0
OP2 D:DI5 4.7 19.8 1.0
C6 D:DA8 4.7 31.3 1.0
OG B:SER140 4.7 18.2 1.0
OP2 D:A6 4.8 16.6 1.0
C3' D:DA2 4.8 46.6 1.0
O5' D:DT3 4.8 37.3 1.0
P D:DI5 4.9 19.6 1.0
C8 D:A6 4.9 16.9 1.0
C5' D:DT3 4.9 31.3 1.0
OP1 D:DT3 4.9 32.9 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 12:40:02 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy