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Calcium in PDB 1m5o: Transition State Stabilization By A Catalytic Rna

Protein crystallography data

The structure of Transition State Stabilization By A Catalytic Rna, PDB code: 1m5o was solved by P.B.Rupert, A.P.Massey, S.T.Sigurdsson, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 259.380, 44.220, 102.500, 90.00, 106.30, 90.00
R / Rfree (%) 22.9 / 26.4

Other elements in 1m5o:

The structure of Transition State Stabilization By A Catalytic Rna also contains other interesting chemical elements:

Vanadium (V) 2 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 37;

Binding sites:

The binding sites of Calcium atom in the Transition State Stabilization By A Catalytic Rna (pdb code 1m5o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 37 binding sites of Calcium where determined in the Transition State Stabilization By A Catalytic Rna, PDB code: 1m5o:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 37 in 1m5o

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Calcium binding site 1 out of 37 in the Transition State Stabilization By A Catalytic Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Transition State Stabilization By A Catalytic Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca22

b:0.0
occ:1.00
O A:HOH256 2.5 50.6 1.0
O3' A:C21 4.6 72.4 1.0
O2' A:C21 4.6 52.0 1.0
C2' A:C21 5.0 48.3 1.0

Calcium binding site 2 out of 37 in 1m5o

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Calcium binding site 2 out of 37 in the Transition State Stabilization By A Catalytic Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Transition State Stabilization By A Catalytic Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca30

b:0.9
occ:1.00
OP1 A:U14 3.7 72.7 1.0
OP2 A:C15 4.7 71.0 1.0
OP2 B:G2 5.0 59.6 1.0

Calcium binding site 3 out of 37 in 1m5o

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Calcium binding site 3 out of 37 in the Transition State Stabilization By A Catalytic Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Transition State Stabilization By A Catalytic Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca93

b:84.5
occ:1.00
OP1 B:U38 2.3 52.3 1.0
OP1 B:G39 2.5 39.2 1.0
P B:U38 3.7 45.1 1.0
P B:G39 3.9 41.0 1.0
C3' B:U38 4.2 29.4 1.0
C5' B:G39 4.2 40.0 1.0
O3' B:U37 4.3 40.3 1.0
O5' B:U38 4.3 46.9 1.0
C5' B:U38 4.3 45.8 1.0
O B:HOH238 4.4 39.7 1.0
O5' B:G39 4.5 42.6 1.0
O3' B:U38 4.5 45.0 1.0
C4' B:U38 4.8 43.8 1.0
OP2 B:U38 4.8 51.8 1.0

Calcium binding site 4 out of 37 in 1m5o

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Calcium binding site 4 out of 37 in the Transition State Stabilization By A Catalytic Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Transition State Stabilization By A Catalytic Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca94

b:81.8
occ:1.00
OP2 B:A41 2.6 46.4 1.0
O2' B:C40 2.6 46.5 1.0
O B:HOH206 2.9 38.7 1.0
O3' B:C40 3.2 41.2 1.0
P B:A41 3.5 39.7 1.0
C2' B:C40 3.8 37.4 1.0
N7 B:A41 3.9 36.0 1.0
O B:HOH337 4.1 60.9 1.0
C3' B:C40 4.1 31.7 1.0
C8 B:A41 4.1 29.3 1.0
OG1 C:THR89 4.1 41.6 1.0
CG2 C:THR89 4.3 44.8 1.0
O B:HOH373 4.3 50.8 1.0
C1' B:C40 4.4 34.8 1.0
O2 B:C40 4.5 35.8 1.0
O5' B:A41 4.6 38.9 1.0
OP1 B:A41 4.6 42.4 1.0
NZ C:LYS88 4.8 54.2 1.0
CE C:LYS88 4.8 65.2 1.0
CB C:LYS88 4.8 33.1 1.0
CB C:THR89 4.9 43.5 1.0

Calcium binding site 5 out of 37 in 1m5o

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Calcium binding site 5 out of 37 in the Transition State Stabilization By A Catalytic Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Transition State Stabilization By A Catalytic Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca95

b:0.9
occ:1.00
OP2 B:A24 4.0 80.7 1.0
N4 B:C25 4.7 57.0 1.0
O6 B:G54 5.0 44.6 1.0

Calcium binding site 6 out of 37 in 1m5o

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Calcium binding site 6 out of 37 in the Transition State Stabilization By A Catalytic Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Transition State Stabilization By A Catalytic Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca96

b:0.4
occ:1.00
O C:HOH325 2.5 57.5 1.0
OP1 B:U43 3.7 69.3 1.0
OP2 B:C42 4.0 47.6 1.0
C5 B:C42 4.1 33.7 1.0
C6 B:C42 4.2 38.1 1.0
OD2 C:ASP92 4.4 53.6 1.0
O5' B:C42 4.5 41.6 1.0
OD1 C:ASP92 4.5 43.7 1.0
C3' B:C42 4.8 44.8 1.0
P B:C42 4.9 38.1 1.0
P B:U43 4.9 59.5 1.0
CG C:ASP92 4.9 43.0 1.0
C4 B:C42 4.9 38.8 1.0

Calcium binding site 7 out of 37 in 1m5o

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Calcium binding site 7 out of 37 in the Transition State Stabilization By A Catalytic Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Transition State Stabilization By A Catalytic Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca97

b:82.9
occ:1.00
N4 B:C35 3.0 34.6 1.0
N4 B:C34 3.7 44.4 1.0
C5 B:C34 3.8 51.7 1.0
C5 B:C35 3.9 41.4 1.0
C4 B:C35 3.9 39.2 1.0
N6 B:A36 3.9 43.0 1.0
C4 B:C34 4.0 50.4 1.0
CE C:LYS20 4.6 96.8 1.0
O C:HOH328 4.6 52.1 1.0
C6 B:C34 4.7 52.0 1.0
C6 B:A36 4.9 43.2 1.0

Calcium binding site 8 out of 37 in 1m5o

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Calcium binding site 8 out of 37 in the Transition State Stabilization By A Catalytic Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Transition State Stabilization By A Catalytic Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca98

b:93.1
occ:1.00
O B:HOH393 2.4 85.8 1.0
OP1 B:A59 2.8 85.0 1.0
N7 B:G21 3.6 73.6 1.0
P B:A59 4.0 80.6 1.0
OP2 B:A20 4.1 95.8 1.0
OP2 B:U60 4.2 77.5 1.0
OP2 B:A59 4.4 58.0 1.0
C8 B:G21 4.4 75.3 1.0
O6 B:G21 4.5 71.2 1.0
C5 B:G21 4.6 72.9 1.0
O5' B:A59 4.9 73.0 1.0
C6 B:G21 4.9 73.5 1.0

Calcium binding site 9 out of 37 in 1m5o

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Calcium binding site 9 out of 37 in the Transition State Stabilization By A Catalytic Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Transition State Stabilization By A Catalytic Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca99

b:97.2
occ:1.00
O B:HOH283 2.5 55.4 1.0
O2' B:G1 2.9 75.7 1.0
C1' B:G1 3.9 48.2 1.0
C2' B:G1 4.0 55.5 1.0
O4' B:G2 4.1 65.2 1.0
N3 B:G1 4.1 49.0 1.0
C4' B:G2 4.8 57.8 1.0
O4' B:G1 4.8 56.2 1.0
N9 B:G1 4.9 51.4 1.0
C5' B:G2 4.9 53.5 1.0
C4 B:G1 4.9 50.5 1.0

Calcium binding site 10 out of 37 in 1m5o

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Calcium binding site 10 out of 37 in the Transition State Stabilization By A Catalytic Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Transition State Stabilization By A Catalytic Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca100

b:0.1
occ:1.00
N3 B:G83 2.5 0.9 1.0
O2' B:G83 2.6 0.4 1.0
C2' B:G83 2.9 0.1 1.0
C1' B:G83 3.1 0.8 1.0
C2 B:G83 3.4 0.3 1.0
C4 B:G83 3.4 0.2 1.0
N2 B:G83 3.5 0.0 1.0
O4' B:U84 3.5 0.9 1.0
N9 B:G83 3.6 0.4 1.0
C1' B:U84 3.8 0.4 1.0
N1 B:U84 4.3 0.4 1.0
C3' B:G83 4.5 0.3 1.0
O4' B:G83 4.5 1.0 1.0
N3 B:G71 4.5 0.1 1.0
C4' B:U84 4.5 0.5 1.0
C6 B:U84 4.6 0.4 1.0
N1 B:G83 4.7 0.7 1.0
C5 B:G83 4.7 0.5 1.0
N2 B:G71 4.7 0.0 1.0
C2 B:G71 4.8 0.4 1.0
O5' B:U84 4.8 0.9 1.0
C8 B:G83 5.0 0.1 1.0

Reference:

P.B.Rupert, A.P.Massey, S.T.Sigurdsson, A.R.Ferre-D'amare. Transition State Stabilization By A Catalytic Rna Science V. 298 1421 2002.
ISSN: ISSN 0036-8075
PubMed: 12376595
DOI: 10.1126/SCIENCE.1076093
Page generated: Wed Oct 28 07:15:28 2020

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