Calcium in PDB 7c45: The Crystal Structure of Trypanosoma Brucei Rnase D Complex with Rna U12

Protein crystallography data

The structure of The Crystal Structure of Trypanosoma Brucei Rnase D Complex with Rna U12, PDB code: 7c45 was solved by Y.Q.Gao, J.H.Gan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.84 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.449, 65.843, 99.914, 90, 90, 90
R / Rfree (%) 19.3 / 22.1

Other elements in 7c45:

The structure of The Crystal Structure of Trypanosoma Brucei Rnase D Complex with Rna U12 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The Crystal Structure of Trypanosoma Brucei Rnase D Complex with Rna U12 (pdb code 7c45). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the The Crystal Structure of Trypanosoma Brucei Rnase D Complex with Rna U12, PDB code: 7c45:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7c45

Go back to Calcium Binding Sites List in 7c45
Calcium binding site 1 out of 2 in the The Crystal Structure of Trypanosoma Brucei Rnase D Complex with Rna U12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of Trypanosoma Brucei Rnase D Complex with Rna U12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:18.9
occ:1.00
OD2 A:ASP80 2.2 15.6 1.0
OP1 D:U12 2.2 25.6 1.0
OE2 A:GLU82 2.3 19.4 1.0
OD2 A:ASP230 2.4 25.0 1.0
O A:HOH666 2.5 36.5 1.0
O A:HOH606 2.9 18.3 1.0
CG A:ASP80 3.0 14.3 1.0
OD1 A:ASP80 3.1 14.2 1.0
CG A:ASP230 3.4 23.1 1.0
CD A:GLU82 3.4 19.9 1.0
P D:U12 3.6 23.2 1.0
O A:HOH518 3.8 45.2 1.0
CB A:ASP230 3.8 17.4 1.0
CA D:CA101 3.9 20.1 1.0
OE1 A:GLU82 3.9 16.2 1.0
O A:HOH517 4.0 26.4 1.0
NE2 A:GLN100 4.2 14.8 1.0
OP2 D:U12 4.2 20.2 1.0
O A:HOH637 4.3 35.3 1.0
OD1 A:ASP230 4.4 24.0 1.0
CB A:ASP80 4.4 14.3 1.0
O5' D:U12 4.4 21.1 1.0
O A:HOH577 4.4 14.9 1.0
O A:ILE81 4.6 14.3 1.0
C5' D:U12 4.6 23.5 1.0
O3' D:U11 4.6 19.8 1.0
CG A:GLU82 4.7 16.4 1.0
O A:HOH619 4.8 15.4 1.0
O A:ALA227 4.9 15.4 1.0

Calcium binding site 2 out of 2 in 7c45

Go back to Calcium Binding Sites List in 7c45
Calcium binding site 2 out of 2 in the The Crystal Structure of Trypanosoma Brucei Rnase D Complex with Rna U12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of Trypanosoma Brucei Rnase D Complex with Rna U12 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca101

b:20.1
occ:1.00
O3' D:U11 2.2 19.8 1.0
O A:HOH513 2.4 14.1 1.0
OD1 A:ASP80 2.4 14.2 1.0
O A:HOH619 2.4 15.4 1.0
OP1 D:U12 2.5 25.6 1.0
O A:HOH515 2.5 15.5 1.0
P D:U12 2.9 23.2 1.0
C3' D:U11 3.4 14.3 1.0
CG A:ASP80 3.5 14.3 1.0
O2' D:U11 3.5 22.9 1.0
C5' D:U12 3.9 23.5 1.0
O5' D:U12 3.9 21.1 1.0
CA A:CA403 3.9 18.9 1.0
C4' D:U11 3.9 21.3 1.0
C2' D:U11 4.0 26.2 1.0
OD2 A:ASP80 4.0 15.6 1.0
OD2 A:ASP145 4.1 23.2 1.0
OP2 D:U12 4.2 20.2 1.0
O A:HOH548 4.3 13.9 1.0
O A:ILE81 4.3 14.3 1.0
O A:PHE140 4.4 13.8 1.0
OD1 A:ASP145 4.4 18.1 1.0
OD2 A:ASP230 4.4 25.0 1.0
N A:ILE81 4.6 14.1 1.0
C5' D:U11 4.6 18.7 1.0
CB A:ASP80 4.6 14.3 1.0
CG A:ASP145 4.7 17.6 1.0
O D:HOH218 4.8 18.5 1.0
CA A:ASP80 4.8 14.1 1.0
O A:HOH517 4.9 26.4 1.0

Reference:

Y.Gao, H.Liu, C.Zhang, S.Su, Y.Chen, X.Chen, Y.Li, Z.Shao, Y.Zhang, Q.Shao, J.Li, Z.Huang, J.Ma, J.Gan. Structural Basis For Guide Rna Trimming By Rnase D Ribonuclease in Trypanosoma Brucei. Nucleic Acids Res. V. 49 568 2021.
ISSN: ESSN 1362-4962
PubMed: 33332555
DOI: 10.1093/NAR/GKAA1197
Page generated: Sat Apr 17 14:07:32 2021

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