Manganese 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:

Zinc

(Zn)

6 atoms

The binding sites of Manganese 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 Manganese atom.
In total 6 binding sites of Manganese where determined in the The Crystal Structure of Trypanosoma Brucei Rnase D : Gmp Complex, PDB code: 7c4c:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese 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 Manganese with other atoms in the Mn 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:Mn407 b:39.5 occ:1.00 O2P A:5GP413 2.1 59.2 1.0 OE1 A:GLU82 2.1 44.7 1.0 OD2 A:ASP230 2.2 54.9 1.0 OD2 A:ASP80 2.2 32.0 1.0 O A:HOH521 2.7 25.6 1.0 CG A:ASP230 3.1 49.6 1.0 P A:5GP413 3.2 59.5 1.0 CD A:GLU82 3.2 42.9 1.0 CG A:ASP80 3.4 34.7 1.0 O1P A:5GP413 3.4 62.1 1.0 CB A:ASP230 3.7 33.7 1.0 OE2 A:GLU82 3.7 42.6 1.0 O5' A:5GP413 3.8 57.4 1.0 OD1 A:ASP80 3.8 40.9 1.0 MN A:MN408 3.9 41.2 1.0 NE2 A:GLN100 4.0 24.7 1.0 O A:ILE81 4.1 29.8 1.0 OD1 A:ASP230 4.2 53.4 1.0 C5' A:5GP413 4.3 50.9 1.0 CG A:GLU82 4.4 35.1 1.0 O3P A:5GP413 4.5 61.4 1.0 CB A:ASP80 4.6 30.9 1.0 CE1 A:TYR226 4.7 35.8 1.0 O A:HOH503 4.8 51.8 1.0 C A:ILE81 4.9 21.7 1.0 OH A:TYR226 4.9 38.1 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn408 b:41.2 occ:1.00 OD1 A:ASP80 2.1 40.9 1.0 O A:HOH501 2.1 28.6 1.0 O2P A:5GP413 2.2 59.2 1.0 O A:HOH503 2.2 51.8 1.0 O3P A:5GP413 2.5 61.4 1.0 P A:5GP413 2.8 59.5 1.0 CG A:ASP80 3.1 34.7 1.0 OD2 A:ASP80 3.4 32.0 1.0 OD2 A:ASP145 3.4 40.7 1.0 MN A:MN407 3.9 39.5 1.0 O5' A:5GP413 3.9 57.4 1.0 O1P A:5GP413 4.0 62.1 1.0 C5' A:5GP413 4.0 50.9 1.0 OD1 A:ASP145 4.1 38.8 1.0 O A:HOH529 4.1 22.1 1.0 CG A:ASP145 4.2 39.3 1.0 O A:ILE81 4.3 29.8 1.0 CB A:ASP80 4.4 30.9 1.0 O A:PHE140 4.5 20.8 1.0 N A:ILE81 4.5 20.7 1.0 OD2 A:ASP230 4.8 54.9 1.0 CA A:ASP80 4.8 26.8 1.0 O A:HOH519 4.8 24.2 1.0 O A:ASP141 5.0 24.4 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn409 b:53.4 occ:1.00 OE1 A:GLU325 2.1 50.5 1.0 N7 A:5GP414 2.3 70.6 1.0 CD A:GLU325 2.7 49.1 1.0 OE2 A:GLU325 2.7 52.4 1.0 C8 A:5GP414 3.0 72.2 1.0 C5 A:5GP414 3.4 70.4 1.0 NZ A:LYS335 3.7 55.0 1.0 O6 A:5GP414 3.8 58.0 1.0 C6 A:5GP414 4.0 65.2 1.0 CG A:GLU325 4.2 42.7 1.0 N9 A:5GP414 4.2 75.9 1.0 C4 A:5GP414 4.4 72.4 1.0 CE1 A:HIS328 4.4 48.5 1.0 CB A:GLU325 4.8 44.4 1.0 SG A:CYS323 4.8 37.9 1.0 CE A:LYS335 4.9 54.8 1.0 CD2 A:PHE334 4.9 46.4 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn410 b:91.5 occ:1.00 N7 A:5GP413 2.7 44.5 1.0 NE2 A:GLN203 3.3 75.1 1.0 O6 A:5GP413 3.5 49.6 1.0 C8 A:5GP413 3.7 46.1 1.0 C5 A:5GP413 3.7 48.8 1.0 CE A:MSE206 4.0 83.6 1.0 C6 A:5GP413 4.1 50.2 1.0 OE1 A:GLN203 4.1 73.6 1.0 CD A:GLN203 4.1 72.1 1.0 O1P A:5GP413 4.6 62.1 1.0 N9 A:5GP413 4.9 48.4 1.0 C4 A:5GP413 4.9 50.8 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn411 b:85.2 occ:1.00 CE1 A:HIS337 3.0 34.2 1.0 NZ A:LYS336 3.3 40.8 1.0 O A:ALA330 3.4 34.7 1.0 CD A:LYS336 3.5 34.2 1.0 NE2 A:HIS337 3.6 38.0 1.0 C A:ALA330 3.6 34.0 1.0 N A:ARG331 3.8 34.6 1.0 CE A:LYS336 3.9 40.0 1.0 CB A:ALA330 3.9 27.6 1.0 CA A:ARG331 3.9 36.1 1.0 ND1 A:HIS337 4.2 32.8 1.0 CA A:ALA330 4.4 32.6 1.0 CG A:LYS336 4.5 34.0 1.0 CB A:ARG331 4.8 32.2 1.0 C A:ARG331 4.9 39.4 1.0 CD2 A:HIS337 4.9 28.4 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn412 b:120.8 occ:1.00 N7 A:5GP416 2.8 76.5 1.0 C8 A:5GP416 3.8 78.5 1.0 C5 A:5GP416 3.8 76.4 1.0 O6 A:5GP416 3.8 71.6 1.0 C6 A:5GP416 4.3 74.0 1.0 CE1 A:HIS305 4.4 30.6 1.0 CE A:LYS312 4.5 34.1 1.0 CD2 A:PHE311 4.9 72.0 1.0 N9 A:5GP416 5.0 77.0 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