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Calcium in PDB 3o3g: T. Maritima Rnase H2 in Complex with Nucleic Acid Substrate and Calcium Ions

Enzymatic activity of T. Maritima Rnase H2 in Complex with Nucleic Acid Substrate and Calcium Ions

All present enzymatic activity of T. Maritima Rnase H2 in Complex with Nucleic Acid Substrate and Calcium Ions:
3.1.26.4;

Protein crystallography data

The structure of T. Maritima Rnase H2 in Complex with Nucleic Acid Substrate and Calcium Ions, PDB code: 3o3g was solved by M.P.Rychlik, H.Chon, S.M.Cerritelli, P.Klimek, R.J.Crouch, M.Nowotny, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.75 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 106.122, 47.347, 79.012, 90.00, 132.81, 90.00
R / Rfree (%) 17.1 / 24.5

Calcium Binding Sites:

The binding sites of Calcium atom in the T. Maritima Rnase H2 in Complex with Nucleic Acid Substrate and Calcium Ions (pdb code 3o3g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the T. Maritima Rnase H2 in Complex with Nucleic Acid Substrate and Calcium Ions, PDB code: 3o3g:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 3o3g

Go back to Calcium Binding Sites List in 3o3g
Calcium binding site 1 out of 5 in the T. Maritima Rnase H2 in Complex with Nucleic Acid Substrate and Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of T. Maritima Rnase H2 in Complex with Nucleic Acid Substrate and Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:30.6
occ:1.00
 OP1 D:C6 2.4 26.4 1.0
OD1 A:ASP18 2.4 25.1 1.0
OP2 D:DT7 2.5 26.8 1.0
O A:GLU19 2.5 20.8 1.0
O A:HOH229 2.6 41.8 1.0
O A:HOH230 2.6 29.4 1.0
CG A:ASP18 3.2 27.2 1.0
OD2 A:ASP18 3.3 28.7 1.0
P D:C6 3.6 24.8 1.0
C A:GLU19 3.6 22.9 1.0
P D:DT7 3.8 22.9 1.0
C5' D:C6 3.9 24.9 1.0
O5' D:C6 4.0 26.7 1.0
CA A:CA224 4.1 40.2 1.0
CB A:SER134 4.1 29.1 1.0
N A:GLU19 4.2 22.7 1.0
OP1 D:DT7 4.4 21.0 1.0
OP2 D:C6 4.5 28.7 1.0
OD2 A:ASP107 4.5 47.5 1.0
CA A:GLU19 4.5 22.0 1.0
OD2 A:ASP124 4.5 50.1 1.0
OE2 A:GLU19 4.6 29.7 1.0
N A:ALA20 4.6 15.6 1.0
O3' D:C6 4.6 23.9 1.0
CB A:ASP18 4.6 17.8 1.0
CA A:ALA20 4.6 18.7 1.0
CA A:SER134 4.6 29.6 1.0
O D:HOH230 4.7 35.4 1.0
O A:HOH266 4.8 49.9 1.0
O3' D:DC5 4.8 24.0 1.0
O5' D:DT7 4.8 25.9 1.0
C4' D:C6 4.9 22.2 1.0
C A:ASP18 5.0 26.1 1.0

Calcium binding site 2 out of 5 in 3o3g

Go back to Calcium Binding Sites List in 3o3g
Calcium binding site 2 out of 5 in the T. Maritima Rnase H2 in Complex with Nucleic Acid Substrate and Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of T. Maritima Rnase H2 in Complex with Nucleic Acid Substrate and Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca224

b:40.2
occ:1.00
 OE2 A:GLU19 2.5 29.7 1.0
OD2 A:ASP18 2.5 28.7 1.0
OP1 D:C6 2.6 26.4 1.0
OD2 A:ASP107 2.6 47.5 1.0
O3' D:DC5 2.7 24.0 1.0
O A:HOH238 3.2 57.8 1.0
P D:C6 3.3 24.8 1.0
CG A:ASP107 3.3 48.7 1.0
CD A:GLU19 3.3 35.4 1.0
OE1 A:GLU19 3.5 50.7 1.0
CG A:ASP18 3.7 27.2 1.0
CB A:ASP107 3.7 35.9 1.0
O A:ASP107 3.8 42.2 1.0
C3' D:DC5 4.0 44.0 1.0
CA A:CA1 4.1 30.6 1.0
OD1 A:ASP107 4.1 48.5 1.0
N A:GLU19 4.1 22.7 1.0
C A:ASP107 4.2 43.0 1.0
C4' D:DC5 4.2 41.6 1.0
C5' D:C6 4.3 24.9 1.0
O5' D:C6 4.3 26.7 1.0
OD1 A:ASP18 4.3 25.1 1.0
OP2 D:C6 4.4 28.7 1.0
C5' D:DC5 4.4 48.4 1.0
O A:GLU19 4.4 20.8 1.0
O D:HOH182 4.5 48.0 1.0
CA A:ASP107 4.6 34.0 1.0
CG A:GLU19 4.6 29.1 1.0
C2' D:DC5 4.7 38.0 1.0
CA A:ASP18 4.8 19.2 1.0
CB A:ASP18 4.8 17.8 1.0
N A:GLY108 4.8 48.3 1.0
NH2 A:ARG22 5.0 49.3 1.0
C A:ASP18 5.0 26.1 1.0
CA A:GLU19 5.0 22.0 1.0

Calcium binding site 3 out of 5 in 3o3g

Go back to Calcium Binding Sites List in 3o3g
Calcium binding site 3 out of 5 in the T. Maritima Rnase H2 in Complex with Nucleic Acid Substrate and Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of T. Maritima Rnase H2 in Complex with Nucleic Acid Substrate and Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca225

b:69.2
occ:1.00
 O D:HOH182 2.7 48.0 1.0
O A:HOH266 2.8 49.9 1.0
OP2 D:C6 3.0 28.7 1.0
OD2 A:ASP124 3.1 50.1 1.0
OD1 A:ASP124 3.2 56.3 1.0
CG A:ASP124 3.5 60.8 1.0
O A:HOH278 4.2 60.9 1.0
NZ A:LYS47 4.2 37.5 1.0
P D:C6 4.3 24.8 1.0
CG A:LYS122 4.5 49.0 1.0
CA A:LYS122 4.5 36.2 1.0
OP2 D:DC5 4.5 52.5 1.0
OP1 D:DC5 4.6 50.4 1.0
O5' D:DC5 4.6 52.9 1.0
OD2 A:ASP107 4.7 47.5 1.0
CD A:LYS47 4.7 51.0 1.0
O A:HOH229 4.7 41.8 1.0
P D:DC5 4.8 59.1 1.0
O3' D:DC5 4.8 24.0 1.0
OP1 D:C6 4.8 26.4 1.0
OD1 A:ASP107 4.9 48.5 1.0
CE A:LYS47 4.9 44.1 1.0
OD1 A:ASP45 5.0 63.3 1.0

Calcium binding site 4 out of 5 in 3o3g

Go back to Calcium Binding Sites List in 3o3g
Calcium binding site 4 out of 5 in the T. Maritima Rnase H2 in Complex with Nucleic Acid Substrate and Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of T. Maritima Rnase H2 in Complex with Nucleic Acid Substrate and Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca226

b:38.5
occ:1.00
 ND2 A:ASN216 3.0 17.0 1.0
CB A:ASN216 3.6 25.1 1.0
CG A:ASN216 3.8 27.1 1.0
NE A:ARG213 4.1 47.1 1.0
O A:HOH303 4.2 38.7 1.0
CD A:ARG213 4.3 42.3 1.0
CA A:ARG213 4.7 26.8 1.0
O A:ARG213 4.9 24.4 1.0
OD1 A:ASN216 4.9 23.2 1.0

Calcium binding site 5 out of 5 in 3o3g

Go back to Calcium Binding Sites List in 3o3g
Calcium binding site 5 out of 5 in the T. Maritima Rnase H2 in Complex with Nucleic Acid Substrate and Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of T. Maritima Rnase H2 in Complex with Nucleic Acid Substrate and Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca13

b:43.8
occ:1.00
 O A:HOH239 2.6 35.9 1.0
O A:HOH235 2.6 42.1 1.0
O A:HOH233 2.7 38.3 1.0
O D:HOH129 2.7 41.9 1.0
O C:HOH234 2.7 41.7 1.0
O D:HOH236 2.8 38.4 1.0
O A:HOH312 3.1 28.9 1.0
O D:HOH76 4.3 29.8 1.0
O D:HOH193 4.5 38.4 1.0
O4' C:DA6 4.6 32.8 1.0
O A:HOH320 4.7 34.4 1.0
O D:HOH91 4.7 26.5 1.0
CB A:LYS166 4.7 30.2 1.0
CE A:LYS166 4.8 46.9 1.0
N2 D:DG8 4.8 23.2 1.0
O A:HOH234 4.9 14.4 1.0
O4' D:DA9 4.9 28.2 1.0
C1' C:DA6 5.0 29.8 1.0
C4' C:DA6 5.0 33.1 1.0
C4' D:DA9 5.0 26.1 1.0

Reference:

M.P.Rychlik, H.Chon, S.M.Cerritelli, P.Klimek, R.J.Crouch, M.Nowotny. Crystal Structures of Rnase H2 in Complex with Nucleic Acid Reveal the Mechanism of Rna-Dna Junction Recognition and Cleavage. Mol.Cell V. 40 658 2010.
ISSN: ISSN 1097-2765
PubMed: 21095591
DOI: 10.1016/J.MOLCEL.2010.11.001
Page generated: Sat Jul 13 15:12:18 2024

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