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Calcium in PDB 7uo1: E.Coli Rnasep Holoenzyme with MG2+

Enzymatic activity of E.Coli Rnasep Holoenzyme with MG2+

All present enzymatic activity of E.Coli Rnasep Holoenzyme with MG2+:
3.1.26.5;

Calcium Binding Sites:

The binding sites of Calcium atom in the E.Coli Rnasep Holoenzyme with MG2+ (pdb code 7uo1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the E.Coli Rnasep Holoenzyme with MG2+, PDB code: 7uo1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 7uo1

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Calcium binding site 1 out of 10 in the E.Coli Rnasep Holoenzyme with MG2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of E.Coli Rnasep Holoenzyme with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:37.1
occ:1.00
 OP2 B:A352 2.3 43.2 1.0
OP1 B:A67 2.3 27.1 1.0
OP1 B:A351 2.3 30.7 0.0
OP1 C:G1 2.3 26.5 1.0
O3' C:U0 2.3 39.6 1.0
P C:G1 2.8 38.2 1.0
O3' B:G350 2.9 29.8 0.0
P B:A351 3.1 31.0 0.0
H4' B:A351 3.3 30.6 0.0
H5'' B:A67 3.4 33.0 1.0
P B:A352 3.4 30.0 1.0
OP1 B:A352 3.5 41.0 1.0
P B:A67 3.5 34.5 1.0
H4' C:U0 3.6 40.5 1.0
C3' C:U0 3.7 31.9 1.0
OP2 C:G1 3.8 36.3 1.0
O5' C:G1 3.9 21.1 1.0
HO2' C:U0 3.9 39.1 1.0
OP2 B:A67 4.0 26.6 1.0
H5' B:A67 4.0 31.5 1.0
C5' B:A67 4.0 32.5 1.0
OP2 B:A351 4.0 30.1 0.0
O2' C:U0 4.1 42.1 1.0
H5'' C:U0 4.1 38.8 1.0
C4' C:U0 4.1 38.5 1.0
H2' B:A66 4.2 20.0 1.0
C4' B:A351 4.2 31.2 0.0
C3' B:G350 4.3 29.0 0.0
H5'' B:G350 4.3 29.3 0.0
H4' B:G350 4.3 28.3 0.0
H3' C:U0 4.3 37.8 1.0
O5' B:A67 4.3 38.4 1.0
O5' B:A352 4.3 28.7 1.0
O5' B:A351 4.3 30.9 0.0
H5' B:A351 4.4 30.8 0.0
C2' C:U0 4.5 32.7 1.0
C5' B:A351 4.6 31.5 0.0
O3' B:A351 4.6 32.0 0.0
C5' C:U0 4.7 31.7 1.0
C4' B:G350 4.7 28.6 0.0
O2' B:A66 4.7 41.1 1.0
H3' B:G350 4.8 29.0 0.0
O3' B:A66 4.8 30.7 1.0
C2' B:A66 4.8 24.4 1.0
O2' B:G350 4.9 28.8 0.0
H2' C:U0 4.9 38.3 1.0
C5' B:G350 5.0 28.9 0.0
OP2 B:G68 5.0 27.7 1.0

Calcium binding site 2 out of 10 in 7uo1

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Calcium binding site 2 out of 10 in the E.Coli Rnasep Holoenzyme with MG2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of E.Coli Rnasep Holoenzyme with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:108.7
occ:1.00
 OP1 B:C355 4.1 38.4 1.0
H4' B:G63 4.3 18.4 1.0
H5'' B:G63 4.7 22.6 1.0

Calcium binding site 3 out of 10 in 7uo1

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Calcium binding site 3 out of 10 in the E.Coli Rnasep Holoenzyme with MG2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of E.Coli Rnasep Holoenzyme with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:45.0
occ:1.00
 OP1 B:G250 2.3 38.6 1.0
OP1 C:C75 2.3 63.9 1.0
P B:G250 2.9 40.4 1.0
P C:C75 2.9 57.9 1.0
OP2 C:C75 2.9 53.3 1.0
OP2 B:G250 2.9 41.3 1.0
O5' C:C75 3.0 64.9 1.0
O5' B:G250 3.2 53.0 1.0
H5'' B:G250 3.4 38.8 1.0
C5' B:G250 3.8 50.1 1.0
H5' C:C75 3.8 61.4 1.0
H5'' C:A74 3.8 51.1 1.0
C5' C:C75 3.9 60.7 1.0
H5'' C:C75 4.0 60.6 1.0
H5' B:G250 4.1 39.2 1.0
O3' B:A249 4.4 0.0 1.0
O3' C:A74 4.5 54.9 1.0
OP1 B:A249 4.6 28.4 1.0
H4' C:A74 4.6 51.5 1.0
C5' C:A74 4.7 47.5 1.0
H5' C:A74 4.8 50.1 1.0
H8 B:G250 4.9 36.9 1.0
H5'' B:A249 5.0 27.6 1.0

Calcium binding site 4 out of 10 in 7uo1

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Calcium binding site 4 out of 10 in the E.Coli Rnasep Holoenzyme with MG2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of E.Coli Rnasep Holoenzyme with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:93.0
occ:1.00
 OP1 B:C14 4.3 88.8 1.0
OP2 B:C14 4.5 88.3 1.0
O3' B:A13 4.7 84.9 1.0

Calcium binding site 5 out of 10 in 7uo1

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Calcium binding site 5 out of 10 in the E.Coli Rnasep Holoenzyme with MG2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of E.Coli Rnasep Holoenzyme with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca405

b:102.4
occ:1.00
 OP1 B:G176 2.3 91.0 1.0
OP2 B:G176 2.8 91.1 1.0
P B:G176 3.1 89.4 1.0
H4' B:G175 3.5 73.2 1.0
H5' B:G185 3.7 106.2 1.0
O5' B:G176 4.0 92.0 1.0
O2' B:G175 4.1 76.7 1.0
HO2' B:G175 4.1 73.5 1.0
OP1 B:U186 4.4 105.6 1.0
C4' B:G175 4.5 70.3 1.0
O3' B:G175 4.5 69.9 1.0
C5' B:G185 4.6 108.6 1.0
O3' B:G185 4.6 109.4 1.0
OP2 B:U186 4.6 103.7 1.0
O4' B:G176 4.7 88.1 1.0
H4' B:G176 4.7 88.5 1.0
H5'' B:G185 4.7 106.1 1.0
P B:U186 4.7 109.7 1.0
C3' B:G175 4.9 70.3 1.0

Calcium binding site 6 out of 10 in 7uo1

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Calcium binding site 6 out of 10 in the E.Coli Rnasep Holoenzyme with MG2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of E.Coli Rnasep Holoenzyme with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca406

b:89.8
occ:1.00
 OP2 B:C197 2.8 74.1 1.0
H5' B:C226 3.8 110.2 1.0
P B:C197 4.2 77.2 1.0
H5'' B:C226 4.3 110.1 1.0
H5' B:C197 4.3 77.5 1.0
C5' B:C226 4.5 108.3 1.0
O3' B:G196 4.5 76.2 1.0
H3' B:C226 4.5 110.1 1.0
O3' B:C226 4.7 110.8 1.0
H5'' B:C197 4.7 77.9 1.0
C5' B:C197 4.9 80.1 1.0

Calcium binding site 7 out of 10 in 7uo1

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Calcium binding site 7 out of 10 in the E.Coli Rnasep Holoenzyme with MG2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of E.Coli Rnasep Holoenzyme with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca407

b:69.5
occ:1.00
 O2 B:C122 2.4 87.8 1.0
O6 B:G125 3.3 80.6 1.0
H1' B:C122 3.4 90.3 1.0
C2 B:C122 3.6 90.5 1.0
O2' B:C122 3.6 91.9 1.0
C6 B:G125 3.7 78.1 1.0
H2' B:C122 3.9 89.9 1.0
H41 B:C228 4.0 107.1 1.0
HO2' B:C122 4.0 90.5 1.0
C1' B:C122 4.0 88.7 1.0
C2' B:C122 4.0 89.3 1.0
OP1 B:A124 4.1 97.6 1.0
N1 B:G125 4.3 79.9 1.0
N1 B:C122 4.3 91.9 1.0
C5 B:G125 4.3 74.7 1.0
H1 B:G125 4.3 81.5 1.0
N3 B:C122 4.5 94.3 1.0
N7 B:G125 4.7 74.3 1.0
N4 B:C228 4.7 110.1 1.0
H5'' B:A124 4.9 90.7 1.0
H5' B:C123 4.9 108.0 1.0
O4 B:U126 4.9 82.4 1.0
H5 B:U126 5.0 76.8 1.0

Calcium binding site 8 out of 10 in 7uo1

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Calcium binding site 8 out of 10 in the E.Coli Rnasep Holoenzyme with MG2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of E.Coli Rnasep Holoenzyme with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca408

b:78.9
occ:1.00
 O2 B:C301 3.1 47.8 1.0
OP2 B:A330 3.2 22.8 1.0
H3 B:U331 3.4 41.0 1.0
N3 B:C301 3.4 46.4 1.0
C2 B:C301 3.5 48.9 1.0
H5'' B:A330 3.9 30.2 1.0
O4 B:U331 4.1 51.4 1.0
N3 B:U331 4.2 47.6 1.0
O6 B:G300 4.2 52.1 1.0
C4 B:C301 4.4 43.2 1.0
H2' B:C301 4.4 41.3 1.0
P B:A330 4.4 45.9 1.0
N1 B:C301 4.5 48.8 1.0
H42 B:C301 4.6 40.2 1.0
OP1 B:A330 4.6 45.0 1.0
C4 B:U331 4.6 43.4 1.0
C5' B:A330 4.7 18.7 1.0
N7 B:G300 4.8 53.5 1.0
N4 B:C301 4.9 33.9 1.0
H5' B:A330 4.9 32.0 1.0
OP2 B:U299 5.0 54.3 1.0

Calcium binding site 9 out of 10 in 7uo1

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Calcium binding site 9 out of 10 in the E.Coli Rnasep Holoenzyme with MG2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of E.Coli Rnasep Holoenzyme with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca409

b:60.5
occ:1.00
 H62 C:A-1 2.2 44.7 1.0
H6 B:U331 2.2 39.9 1.0
N1 C:A-1 2.5 44.0 1.0
H1' B:U331 2.6 39.6 1.0
N1 B:A330 2.7 44.1 1.0
N6 C:A-1 2.7 50.7 1.0
C6 B:U331 2.9 37.1 1.0
H2 B:A330 2.9 31.8 1.0
C6 C:A-1 3.0 46.0 1.0
C2 B:A330 3.0 31.6 1.0
N3 B:A333 3.1 42.2 1.0
H1' B:A333 3.2 36.8 1.0
C1' B:U331 3.4 36.2 1.0
H61 C:A-1 3.4 44.3 1.0
N1 B:U331 3.5 26.1 1.0
C6 B:A330 3.5 37.8 1.0
C2 C:A-1 3.6 45.6 1.0
H2 B:A333 3.7 36.5 1.0
C2 B:A333 3.7 36.2 1.0
H61 B:A330 3.8 34.9 1.0
H2 C:A-1 3.8 44.1 1.0
C5 B:U331 3.8 39.9 1.0
O4' B:U331 3.9 31.2 1.0
H5 B:U331 3.9 39.7 1.0
C4 B:A333 4.0 41.1 1.0
N6 B:A330 4.0 42.9 1.0
N3 B:A330 4.0 25.0 1.0
C1' B:A333 4.1 33.5 1.0
HO2' B:U331 4.2 40.0 1.0
C5 C:A-1 4.2 43.4 1.0
N9 B:A333 4.3 30.4 1.0
HO2' B:A333 4.4 35.8 1.0
C5 B:A330 4.5 31.9 1.0
H5'' B:G332 4.5 43.4 1.0
C4 B:A330 4.6 27.2 1.0
C2' B:U331 4.6 40.4 1.0
C2 B:U331 4.7 40.0 1.0
N3 C:A-1 4.7 39.0 1.0
H62 B:A330 4.7 33.6 1.0
O2' B:A333 4.8 35.3 1.0
O2' B:U331 4.8 42.0 1.0
N1 B:A333 4.9 36.9 1.0
O3' B:U331 4.9 43.8 1.0
C4 C:A-1 4.9 34.9 1.0
C4' B:U331 4.9 35.6 1.0
H4' B:U331 5.0 38.5 1.0
C2' B:A333 5.0 31.6 1.0
O4' B:A333 5.0 38.1 1.0

Calcium binding site 10 out of 10 in 7uo1

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Calcium binding site 10 out of 10 in the E.Coli Rnasep Holoenzyme with MG2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of E.Coli Rnasep Holoenzyme with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca410

b:144.3
occ:1.00
 OP1 B:C123 2.7 108.9 1.0
O4' B:C123 2.8 110.8 1.0
N1 B:C123 3.0 110.2 1.0
C2 B:C123 3.0 110.1 1.0
OP2 B:C123 3.1 110.9 1.0
C1' B:C123 3.3 109.4 1.0
O2 B:C123 3.3 105.6 1.0
H1' B:C123 3.4 108.8 1.0
P B:C123 3.4 112.1 1.0
C6 B:C123 3.5 109.3 1.0
N3 B:C123 3.6 111.4 1.0
H6 B:C123 3.9 108.7 1.0
H5'' B:C123 4.0 107.6 1.0
C5 B:C123 4.1 109.2 1.0
C4 B:C123 4.1 110.6 1.0
C4' B:C123 4.1 109.4 1.0
O5' B:C123 4.2 108.2 1.0
C5' B:C123 4.3 106.3 1.0
H4' B:C123 4.6 109.0 1.0
C2' B:C123 4.7 109.7 1.0
H5 B:C123 4.7 108.7 1.0
O3' B:C122 4.8 91.9 1.0
H4' B:C122 4.9 90.5 1.0
H3' B:C123 4.9 108.8 1.0
C3' B:C123 4.9 110.7 1.0

Reference:

J.Zhu, W.Huang, J.Zhao, L.Huynh, D.J.Taylor, M.E.Harris. Structural and Mechanistic Basis For Recognition of Alternative Trna Precursor Substrates By Bacterial Ribonuclease P. Nat Commun V. 13 5120 2022.
ISSN: ESSN 2041-1723
PubMed: 36045135
DOI: 10.1038/S41467-022-32843-7
Page generated: Tue Apr 4 18:58:10 2023

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