Zinc 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:

Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the The Crystal Structure of Trypanosoma Brucei Rnase D Complex with Rna U12, PDB code: 7c45:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7c45

Go back to Zinc Binding Sites List in 7c45
Zinc 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 Zinc with other atoms in the Zn 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:Zn401

b:16.7
occ:1.00
NE2 A:HIS305 2.2 16.3 1.0
SG A:CYS297 2.3 16.7 1.0
SG A:CYS310 2.3 16.9 1.0
SG A:CYS300 2.4 16.9 1.0
CB A:CYS297 3.1 18.4 1.0
CB A:CYS310 3.1 16.7 1.0
CD2 A:HIS305 3.1 16.1 1.0
CE1 A:HIS305 3.1 16.3 1.0
CB A:CYS300 3.3 17.3 1.0
N A:CYS300 3.8 17.4 1.0
CA A:CYS310 3.9 16.6 1.0
CA A:CYS300 4.1 17.5 1.0
ND1 A:HIS305 4.2 16.1 1.0
CG A:HIS305 4.3 16.0 1.0
O D:HOH215 4.3 30.8 1.0
O A:HOH676 4.4 26.9 1.0
O4 D:U6 4.5 16.4 1.0
CA A:CYS297 4.5 16.6 1.0
CB A:PHE299 4.6 17.4 1.0
C A:CYS300 4.8 17.5 1.0
C A:PHE299 4.8 17.6 1.0
N A:GLY301 4.8 17.4 1.0
C A:CYS310 4.8 16.8 1.0
O A:THR306 4.9 16.2 1.0
N A:CYS310 5.0 16.5 1.0

Zinc binding site 2 out of 2 in 7c45

Go back to Zinc Binding Sites List in 7c45
Zinc 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 Zinc with other atoms in the Zn 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
A:Zn402

b:19.7
occ:1.00
NE2 A:HIS328 2.1 19.3 1.0
SG A:CYS323 2.3 20.6 1.0
SG A:CYS333 2.3 19.8 1.0
SG A:CYS320 2.4 19.1 1.0
CE1 A:HIS328 3.0 19.6 1.0
CB A:CYS333 3.0 19.0 1.0
CD2 A:HIS328 3.1 18.8 1.0
CB A:CYS320 3.1 19.1 1.0
CB A:CYS323 3.3 21.3 1.0
N A:CYS323 3.7 20.6 1.0
CA A:CYS333 3.9 18.8 1.0
CA A:CYS323 4.1 21.1 1.0
ND1 A:HIS328 4.1 19.2 1.0
CG A:HIS328 4.2 18.7 1.0
O A:HOH664 4.4 39.8 1.0
O4 D:U4 4.5 19.6 1.0
CB A:PHE322 4.5 19.9 1.0
O D:HOH203 4.5 24.5 1.0
CA A:CYS320 4.6 18.8 1.0
C A:CYS323 4.7 21.2 1.0
N A:GLY324 4.8 20.7 1.0
C A:PHE322 4.8 21.3 1.0
C A:CYS333 4.8 19.2 1.0
CG A:LYS335 4.9 21.8 1.0
O A:THR329 4.9 17.8 1.0
CD2 A:PHE322 5.0 21.1 1.0
N A:CYS333 5.0 18.2 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 17:46:43 2021

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy