Zinc in PDB 7c4c: The Crystal Structure of Trypanosoma Brucei Rnase D : Gmp Complex

The structure of The Crystal Structure of Trypanosoma Brucei Rnase D : Gmp Complex, PDB code: 7c4c 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)	30.00 / 2.27
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.169, 75.001, 101.409, 90, 90, 90
R / Rfree (%)	19.2 / 23.9

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

Manganese

(Mn)

6 atoms

The binding sites of Zinc atom in the The Crystal Structure of Trypanosoma Brucei Rnase D : Gmp Complex (pdb code 7c4c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the The Crystal Structure of Trypanosoma Brucei Rnase D : Gmp Complex, PDB code: 7c4c:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the The Crystal Structure of Trypanosoma Brucei Rnase D : Gmp Complex


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 : Gmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:34.2 occ:1.00 NE2 A:HIS328 2.2 46.0 1.0 SG A:CYS333 2.2 28.8 1.0 SG A:CYS320 2.2 31.4 1.0 SG A:CYS323 2.3 37.9 1.0 CB A:CYS333 2.9 32.1 1.0 CD2 A:HIS328 3.0 45.8 1.0 CB A:CYS320 3.1 33.1 1.0 CE1 A:HIS328 3.3 48.5 1.0 CB A:CYS323 3.3 38.1 1.0 O6 A:5GP414 3.7 58.0 1.0 N A:CYS323 3.8 38.3 1.0 CA A:CYS333 3.8 31.2 1.0 CA A:CYS323 4.1 40.5 1.0 CG A:HIS328 4.2 46.8 1.0 ND1 A:HIS328 4.3 50.1 1.0 CA A:CYS320 4.5 35.1 1.0 C6 A:5GP414 4.7 65.2 1.0 C A:CYS333 4.7 31.1 1.0 C A:CYS323 4.8 43.2 1.0 C A:PHE322 4.8 38.6 1.0 CB A:PHE322 4.8 27.3 1.0 N A:PHE334 4.8 30.3 1.0 O A:THR329 4.9 39.8 1.0 N A:CYS333 4.9 37.6 1.0 N A:GLY324 5.0 42.4 1.0

Zinc binding site 2 out of 6 in the The Crystal Structure of Trypanosoma Brucei Rnase D : Gmp Complex


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 : Gmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:26.6 occ:1.00 NE2 A:HIS305 2.1 34.4 1.0 SG A:CYS300 2.2 28.0 1.0 SG A:CYS310 2.3 25.1 1.0 SG A:CYS297 2.3 26.5 1.0 CB A:CYS310 3.0 26.9 1.0 CE1 A:HIS305 3.0 30.6 1.0 CB A:CYS297 3.1 25.4 1.0 CD2 A:HIS305 3.1 35.7 1.0 CB A:CYS300 3.2 26.9 1.0 N A:CYS300 3.7 31.4 1.0 CA A:CYS310 3.9 34.3 1.0 CA A:CYS300 4.0 30.1 1.0 ND1 A:HIS305 4.1 28.9 1.0 CG A:HIS305 4.2 28.4 1.0 O6 A:5GP416 4.5 71.6 1.0 CA A:CYS297 4.6 22.7 1.0 CB A:PHE299 4.7 23.8 1.0 C A:CYS300 4.8 27.4 1.0 C A:PHE299 4.8 30.2 1.0 N A:GLY301 4.8 25.5 1.0 C A:CYS310 4.9 41.6 1.0 N A:CYS310 4.9 29.0 1.0 O A:THR306 5.0 28.2 1.0

Zinc binding site 3 out of 6 in the The Crystal Structure of Trypanosoma Brucei Rnase D : Gmp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of Trypanosoma Brucei Rnase D : Gmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:78.9 occ:1.00 NZ A:LYS65 2.0 81.9 1.0 NE2 A:HIS61 2.4 40.6 1.0 OD1 A:ASP125 2.7 54.6 1.0 CE A:LYS65 2.9 75.7 1.0 OD2 A:ASP125 3.0 57.1 1.0 CE1 A:HIS61 3.1 46.3 1.0 CG A:ASP125 3.2 51.4 1.0 CD2 A:HIS61 3.5 40.2 1.0 CD A:LYS65 4.3 67.0 1.0 ND1 A:HIS61 4.3 50.9 1.0 CG A:HIS61 4.5 41.6 1.0 CB A:ASP125 4.7 41.8 1.0 CG A:LYS65 4.8 56.0 1.0

Zinc binding site 4 out of 6 in the The Crystal Structure of Trypanosoma Brucei Rnase D : Gmp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of Trypanosoma Brucei Rnase D : Gmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:45.0 occ:1.00 OE2 A:GLU197 2.2 48.0 1.0 NE2 A:HIS233 2.3 34.8 1.0 O A:HOH539 2.3 18.8 1.0 CE1 A:HIS233 3.0 37.8 1.0 CD A:GLU197 3.2 46.4 1.0 CD2 A:HIS233 3.3 30.2 1.0 OE1 A:GLU197 3.5 44.6 1.0 ND1 A:HIS233 4.1 36.8 1.0 CA A:GLY229 4.2 25.1 1.0 CD2 A:LEU51 4.3 39.6 1.0 CG A:HIS233 4.3 33.1 1.0 O A:GLY229 4.5 26.4 1.0 CG A:GLU197 4.5 44.1 1.0 C A:GLY229 4.7 23.2 1.0

Zinc binding site 5 out of 6 in the The Crystal Structure of Trypanosoma Brucei Rnase D : Gmp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Crystal Structure of Trypanosoma Brucei Rnase D : Gmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:64.4 occ:1.00 SG A:CYS374 2.3 62.9 1.0 SG A:CYS365 2.5 67.7 1.0 SG A:CYS362 2.7 76.7 1.0 NE2 A:HIS369 2.7 72.8 1.0 CB A:CYS374 3.0 67.2 1.0 CE1 A:HIS369 3.3 73.3 1.0 CB A:CYS362 3.4 80.3 1.0 CB A:CYS365 3.7 67.3 1.0 CD2 A:HIS369 3.8 71.7 1.0 CA A:CYS374 3.9 71.5 1.0 N A:CYS365 4.0 74.2 1.0 CB A:HIS364 4.4 96.4 1.0 ND1 A:HIS369 4.4 73.2 1.0 CA A:CYS365 4.5 66.9 1.0 CG A:HIS369 4.7 73.0 1.0 C A:HIS364 4.8 82.8 1.0 CA A:HIS364 4.8 89.1 1.0 N A:GLY367 4.9 59.3 1.0 N A:CYS374 4.9 79.8 1.0 C A:CYS374 4.9 66.6 1.0 CD A:LYS376 4.9 58.5 1.0 CA A:CYS362 4.9 81.8 1.0 N A:HIS364 4.9 88.9 1.0

Zinc binding site 6 out of 6 in the The Crystal Structure of Trypanosoma Brucei Rnase D : Gmp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Crystal Structure of Trypanosoma Brucei Rnase D : Gmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:125.3 occ:1.00 SG A:CYS343 2.3 165.7 1.0 SG A:CYS356 2.3 105.7 1.0 SG A:CYS346 2.7 103.8 1.0 CD2 A:HIS351 2.9 89.4 1.0 NE2 A:HIS351 3.0 90.1 1.0 CB A:CYS356 3.3 101.4 1.0 CB A:CYS346 3.6 107.6 1.0 CB A:CYS343 3.6 157.4 1.0 CA A:CYS356 4.0 98.3 1.0 CG A:HIS351 4.2 89.6 1.0 N A:CYS346 4.2 94.7 1.0 O A:THR352 4.2 121.2 1.0 CE1 A:HIS351 4.3 89.2 1.0 CA A:CYS346 4.5 109.1 1.0 C A:LYS345 4.7 92.0 1.0 ND1 A:HIS351 4.9 89.3 1.0 N A:LYS345 4.9 100.8 1.0 N A:CYS356 4.9 95.5 1.0 CA A:CYS343 4.9 143.3 1.0 O A:HIS351 5.0 102.5 1.0 O A:CYS356 5.0 103.5 1.0

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