Atomistry » Calcium » PDB 6oly-6p8x » 6ozf
Atomistry »
  Calcium »
    PDB 6oly-6p8x »
      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: Wed Jul 9 16:40:16 2025

Last articles

Ca in 7KNV
Ca in 7KLF
Ca in 7KLE
Ca in 7KMQ
Ca in 7KIQ
Ca in 7KL5
Ca in 7KIR
Ca in 7KBU
Ca in 7KHV
Ca in 7KIO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy