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Calcium in PDB 7e8o: Crystal Structure of Proteinaceous Rnase P(Prorp) From Planctomycetes Bacterium GWF2_40_8 Complexed with Escherichia Coli Histidine Pre- Trna

Enzymatic activity of Crystal Structure of Proteinaceous Rnase P(Prorp) From Planctomycetes Bacterium GWF2_40_8 Complexed with Escherichia Coli Histidine Pre- Trna

All present enzymatic activity of Crystal Structure of Proteinaceous Rnase P(Prorp) From Planctomycetes Bacterium GWF2_40_8 Complexed with Escherichia Coli Histidine Pre- Trna:
3.1.26.5;

Protein crystallography data

The structure of Crystal Structure of Proteinaceous Rnase P(Prorp) From Planctomycetes Bacterium GWF2_40_8 Complexed with Escherichia Coli Histidine Pre- Trna, PDB code: 7e8o was solved by Y.Y.Li, J.H.Gan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.46 / 2.80
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 146.277, 146.277, 143.369, 90, 90, 90
R / Rfree (%) 23 / 28.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Proteinaceous Rnase P(Prorp) From Planctomycetes Bacterium GWF2_40_8 Complexed with Escherichia Coli Histidine Pre- Trna (pdb code 7e8o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Proteinaceous Rnase P(Prorp) From Planctomycetes Bacterium GWF2_40_8 Complexed with Escherichia Coli Histidine Pre- Trna, PDB code: 7e8o:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 7e8o

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Calcium binding site 1 out of 5 in the Crystal Structure of Proteinaceous Rnase P(Prorp) From Planctomycetes Bacterium GWF2_40_8 Complexed with Escherichia Coli Histidine Pre- Trna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Proteinaceous Rnase P(Prorp) From Planctomycetes Bacterium GWF2_40_8 Complexed with Escherichia Coli Histidine Pre- Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:77.0
occ:1.00
 O A:ARG146 2.2 32.7 1.0
OD2 A:ASP151 2.2 38.7 1.0
O A:ILE149 2.5 15.6 1.0
CG A:ASP151 3.3 40.0 1.0
OD1 A:ASP173 3.4 40.9 1.0
C A:ARG146 3.4 29.8 1.0
C A:ILE149 3.6 18.4 1.0
OD2 A:ASP173 3.6 41.5 1.0
CB A:ASP151 3.8 35.5 1.0
CG A:ASP173 3.9 41.5 1.0
N A:ILE149 4.0 15.9 1.0
N A:ASP151 4.2 32.0 1.0
CA A:GLU147 4.2 33.7 1.0
N A:GLU147 4.3 27.4 1.0
N A:GLY148 4.3 27.5 1.0
CA A:ARG146 4.4 21.0 1.0
OD1 A:ASP151 4.4 45.0 1.0
CA A:ILE149 4.5 21.3 1.0
CB A:ARG146 4.5 23.6 1.0
N A:ILE150 4.6 26.1 1.0
OD2 A:ASP155 4.6 56.2 1.0
CA A:GLY175 4.6 27.4 1.0
CA A:ILE150 4.6 28.4 1.0
CA A:ASP151 4.7 31.4 1.0
C A:GLU147 4.7 27.0 1.0
C A:ILE150 4.7 30.3 1.0
N A:GLY175 4.8 32.6 1.0
C A:GLY148 4.9 27.0 1.0
CG2 A:ILE149 5.0 27.1 1.0

Calcium binding site 2 out of 5 in 7e8o

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Calcium binding site 2 out of 5 in the Crystal Structure of Proteinaceous Rnase P(Prorp) From Planctomycetes Bacterium GWF2_40_8 Complexed with Escherichia Coli Histidine Pre- Trna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Proteinaceous Rnase P(Prorp) From Planctomycetes Bacterium GWF2_40_8 Complexed with Escherichia Coli Histidine Pre- Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:59.0
occ:1.00
 OD2 B:ASP151 2.6 73.2 1.0
CG B:ASP151 3.1 70.4 1.0
OD1 B:ASP151 3.3 79.2 1.0
NH2 A:ARG108 3.8 57.0 1.0
CA B:CA302 4.2 115.9 1.0
CB B:ASP151 4.2 46.0 1.0
CB B:SER152 4.9 54.6 1.0
CZ A:ARG108 4.9 57.5 1.0
OD2 B:ASP173 4.9 50.3 1.0

Calcium binding site 3 out of 5 in 7e8o

Go back to Calcium Binding Sites List in 7e8o
Calcium binding site 3 out of 5 in the Crystal Structure of Proteinaceous Rnase P(Prorp) From Planctomycetes Bacterium GWF2_40_8 Complexed with Escherichia Coli Histidine Pre- Trna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Proteinaceous Rnase P(Prorp) From Planctomycetes Bacterium GWF2_40_8 Complexed with Escherichia Coli Histidine Pre- Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:115.9
occ:1.00
 OD2 B:ASP151 2.3 73.2 1.0
O B:ARG146 2.4 41.9 1.0
CG B:ASP151 3.4 70.4 1.0
OD2 B:ASP173 3.4 50.3 1.0
C B:ARG146 3.5 37.8 1.0
O B:ILE149 3.6 48.6 1.0
OD1 B:ASP173 3.8 50.3 1.0
CB B:ASP151 4.0 46.0 1.0
CG B:ASP173 4.0 44.7 1.0
CA B:GLU147 4.1 39.1 1.0
CA B:CA301 4.2 59.0 1.0
N B:GLU147 4.2 36.8 1.0
OD1 B:ASP151 4.3 79.2 1.0
CB B:ARG146 4.5 27.6 1.0
CA B:ARG146 4.5 32.7 1.0
N B:GLY148 4.7 41.2 1.0
C B:ILE149 4.8 45.5 1.0
C B:GLU147 4.9 41.1 1.0

Calcium binding site 4 out of 5 in 7e8o

Go back to Calcium Binding Sites List in 7e8o
Calcium binding site 4 out of 5 in the Crystal Structure of Proteinaceous Rnase P(Prorp) From Planctomycetes Bacterium GWF2_40_8 Complexed with Escherichia Coli Histidine Pre- Trna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Proteinaceous Rnase P(Prorp) From Planctomycetes Bacterium GWF2_40_8 Complexed with Escherichia Coli Histidine Pre- Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:86.7
occ:1.00
 OD2 C:ASP151 2.7 73.1 1.0
OD1 C:ASP151 2.9 80.8 1.0
OD2 C:ASP173 2.9 85.5 1.0
CG C:ASP151 3.2 76.3 1.0
OD2 C:ASP155 3.8 91.8 1.0
OD1 C:ASP155 4.1 92.5 1.0
CG C:ASP173 4.2 83.5 1.0
CG C:ASP155 4.4 89.7 1.0
NH2 D:ARG108 4.4 89.8 1.0
OG C:SER152 4.5 82.3 1.0
CB C:SER152 4.6 76.7 1.0
CB C:ASP151 4.7 70.4 1.0
CB C:ASP173 4.9 78.1 1.0

Calcium binding site 5 out of 5 in 7e8o

Go back to Calcium Binding Sites List in 7e8o
Calcium binding site 5 out of 5 in the Crystal Structure of Proteinaceous Rnase P(Prorp) From Planctomycetes Bacterium GWF2_40_8 Complexed with Escherichia Coli Histidine Pre- Trna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Proteinaceous Rnase P(Prorp) From Planctomycetes Bacterium GWF2_40_8 Complexed with Escherichia Coli Histidine Pre- Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:92.2
occ:1.00
 O D:ARG146 2.4 72.6 1.0
O D:ILE149 2.4 67.9 1.0
OD2 D:ASP151 2.9 70.4 1.0
CG D:ASP151 3.3 69.2 1.0
OD2 D:ASP173 3.5 60.3 1.0
C D:ARG146 3.6 71.3 1.0
C D:ILE149 3.6 62.3 1.0
CB D:ASP151 3.8 67.6 1.0
OD1 D:ASP173 3.9 63.0 1.0
OD1 D:ASP151 4.0 68.6 1.0
N D:ILE149 4.1 68.9 1.0
CG D:ASP173 4.1 57.5 1.0
N D:ASP151 4.2 61.6 1.0
CA D:GLU147 4.2 71.5 1.0
N D:GLY148 4.4 72.5 1.0
N D:GLU147 4.4 68.1 1.0
CA D:ILE149 4.5 68.8 1.0
OD2 D:ASP155 4.5 84.7 1.0
N D:ILE150 4.6 53.4 1.0
CA D:ARG146 4.6 75.1 1.0
C D:GLU147 4.7 71.2 1.0
CA D:ASP151 4.7 63.2 1.0
CA D:ILE150 4.7 53.5 1.0
C D:ILE150 4.7 61.9 1.0
CG2 D:ILE149 4.8 74.9 1.0
CB D:ARG146 4.9 70.9 1.0

Reference:

Y.Li, S.Su, Y.Gao, G.Lu, H.Liu, X.Chen, Z.Shao, Y.Zhang, Q.Shao, X.Zhao, J.Yang, C.Cao, J.Lin, J.Ma, J.Gan. Crystal Structures and Insights Into Precursor Trna 5'-End Processing By Prokaryotic Minimal Protein-Only Rnase P. Nat Commun V. 13 2290 2022.
ISSN: ESSN 2041-1723
PubMed: 35484139
DOI: 10.1038/S41467-022-30072-6
Page generated: Fri Jul 19 00:19:38 2024

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