Atomistry » Calcium » PDB 7ucy-7uwv » 7uo1
Atomistry »
  Calcium »
    PDB 7ucy-7uwv »
      7uo1 »

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

Go back to Calcium Binding Sites List in 7uo1
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

Go back to Calcium Binding Sites List in 7uo1
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

Go back to Calcium Binding Sites List in 7uo1
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

Go back to Calcium Binding Sites List in 7uo1
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

Go back to Calcium Binding Sites List in 7uo1
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

Go back to Calcium Binding Sites List in 7uo1
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

Go back to Calcium Binding Sites List in 7uo1
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

Go back to Calcium Binding Sites List in 7uo1
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

Go back to Calcium Binding Sites List in 7uo1
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

Go back to Calcium Binding Sites List in 7uo1
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: Thu Jul 10 01:45:51 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy