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

Protein crystallography data

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

Other elements in 7c4c:

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

Manganese (Mn) 6 atoms

Zinc Binding Sites:

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 7c4c

Go back to Zinc Binding Sites List in 7c4c
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 7c4c

Go back to Zinc Binding Sites List in 7c4c
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 7c4c

Go back to Zinc Binding Sites List in 7c4c
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 7c4c

Go back to Zinc Binding Sites List in 7c4c
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 7c4c

Go back to Zinc Binding Sites List in 7c4c
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 7c4c

Go back to Zinc Binding Sites List in 7c4c
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

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 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy