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Calcium in PDB 1m5k: Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation

Protein crystallography data

The structure of Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation, PDB code: 1m5k was solved by P.B.Rupert, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.07 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 256.300, 44.100, 102.400, 90.00, 109.00, 90.00
R / Rfree (%) 22.9 / 28.4

Other elements in 1m5k:

The structure of Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation also contains other interesting chemical elements:

Iodine (I) 2 atoms
Chlorine (Cl) 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 - 33;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation (pdb code 1m5k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 33 binding sites of Calcium where determined in the Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation, PDB code: 1m5k:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 33 in 1m5k

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Calcium binding site 1 out of 33 in the Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca93

b:85.9
occ:1.00
OP2 B:A22 2.7 89.9 1.0
OP2 B:A59 2.9 73.5 1.0
O5' B:A22 3.0 95.9 1.0
P B:A22 3.5 97.8 1.0
O4 B:U60 3.8 80.8 1.0
C5' B:A22 4.1 95.9 1.0
P B:A59 4.3 88.7 1.0
C3' B:G21 4.4 0.5 1.0
O3' B:G21 4.5 0.6 1.0
N7 B:A59 4.6 65.2 1.0
C4' B:U58 4.6 72.6 1.0
OP1 B:A22 4.6 93.7 1.0
C4 B:U60 4.6 72.6 1.0
C5' B:U58 4.7 62.8 1.0
C5 B:U60 4.8 70.2 1.0
C2' B:G21 4.9 92.7 1.0
O3' B:U58 5.0 82.3 1.0

Calcium binding site 2 out of 33 in 1m5k

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Calcium binding site 2 out of 33 in the Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca93

b:81.9
occ:1.00
OP2 E:A59 2.4 73.6 1.0
OP2 E:A22 2.6 84.2 1.0
O5' E:A22 3.4 82.5 1.0
P E:A22 3.6 79.3 1.0
P E:A59 3.8 74.1 1.0
O4 E:U60 3.8 84.5 1.0
C5' E:A22 4.4 80.0 1.0
N7 E:A59 4.4 65.4 1.0
C4' E:U58 4.5 73.4 1.0
OP1 E:A59 4.5 74.1 1.0
C5' E:U58 4.5 75.0 1.0
C3' E:G21 4.5 83.2 1.0
O3' E:G21 4.6 85.7 1.0
C4 E:U60 4.7 85.4 1.0
O3' E:U58 4.7 62.9 1.0
OP1 E:A22 4.7 95.2 1.0
O5' E:A59 4.7 67.7 1.0
C8 E:A59 4.8 66.7 1.0
C5 E:U60 4.8 87.8 1.0
C3' E:U58 5.0 60.6 1.0

Calcium binding site 3 out of 33 in 1m5k

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Calcium binding site 3 out of 33 in the Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca22

b:0.9
occ:1.00
OP2 D:C21 2.8 71.4 1.0
P D:C21 4.0 91.2 1.0
OP1 D:C21 4.5 82.1 1.0
O5' D:C21 4.8 92.4 1.0

Calcium binding site 4 out of 33 in 1m5k

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Calcium binding site 4 out of 33 in the Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca22

b:88.4
occ:1.00
OP2 A:C21 3.1 87.3 1.0
OP2 A:C20 4.1 71.0 1.0
OP1 A:C20 4.4 81.1 1.0
P A:C20 4.6 77.3 1.0
P A:C21 4.6 94.4 1.0
O5' A:C20 4.6 87.0 1.0

Calcium binding site 5 out of 33 in 1m5k

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Calcium binding site 5 out of 33 in the Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca94

b:93.7
occ:1.00
OP1 E:U38 2.2 47.7 1.0
OP1 E:G39 2.5 52.2 1.0
P E:U38 3.7 43.6 1.0
P E:G39 4.0 52.6 1.0
C3' E:U38 4.2 42.1 1.0
C5' E:U38 4.3 48.7 1.0
C5' E:G39 4.3 44.9 1.0
O5' E:U38 4.3 51.9 1.0
O3' E:U37 4.3 43.2 1.0
O3' E:U38 4.6 51.1 1.0
O5' E:G39 4.6 56.5 1.0
C4' E:U38 4.8 49.8 1.0
OP2 E:U38 4.8 49.8 1.0

Calcium binding site 6 out of 33 in 1m5k

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Calcium binding site 6 out of 33 in the Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca95

b:0.2
occ:1.00
OP2 E:U43 4.0 73.2 1.0
OD1 F:ASP92 4.2 44.9 1.0
OD2 F:ASP92 4.3 42.0 1.0
C5 E:C42 4.3 30.3 1.0
OP2 E:C42 4.5 48.7 1.0
C6 E:C42 4.6 42.5 1.0
CG F:ASP92 4.7 35.2 1.0
OP1 E:U43 4.7 59.9 1.0
P E:U43 4.8 71.9 1.0
O E:HOH258 4.9 62.6 1.0
O5' E:C42 4.9 46.6 1.0
C4 E:C42 4.9 39.4 1.0

Calcium binding site 7 out of 33 in 1m5k

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Calcium binding site 7 out of 33 in the Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca94

b:95.6
occ:1.00
OP2 B:C42 4.1 59.3 1.0
C5 B:C42 4.2 37.0 1.0
OP1 B:U43 4.4 89.5 1.0
C6 B:C42 4.5 42.8 1.0
O5' B:C42 4.8 59.2 1.0
OD1 C:ASP92 5.0 54.5 1.0
C4 B:C42 5.0 40.7 1.0

Calcium binding site 8 out of 33 in 1m5k

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Calcium binding site 8 out of 33 in the Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca95

b:0.1
occ:1.00
OP1 B:U38 2.4 70.4 1.0
OP1 B:G39 2.7 55.0 1.0
P B:U38 3.9 56.7 1.0
P B:G39 4.1 57.2 1.0
C3' B:U38 4.2 48.5 1.0
O3' B:U38 4.5 50.2 1.0
C5' B:U38 4.5 50.9 1.0
O5' B:U38 4.5 61.5 1.0
O3' B:U37 4.7 46.0 1.0
C5' B:G39 4.8 54.2 1.0
O5' B:G39 4.9 62.5 1.0
OP2 B:U38 4.9 71.7 1.0
C4' B:U38 4.9 52.6 1.0

Calcium binding site 9 out of 33 in 1m5k

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Calcium binding site 9 out of 33 in the Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca96

b:86.9
occ:1.00
OP1 E:A59 2.4 74.1 1.0
P E:A59 3.9 74.1 1.0
OP2 E:A20 4.2 64.9 1.0
O5' E:A59 4.4 67.7 1.0
OP2 E:U60 4.6 62.0 1.0
C5' E:A59 4.7 67.2 1.0
O3' E:U58 4.7 62.9 1.0
N7 E:G21 4.8 77.2 1.0
OP2 E:A59 4.8 73.6 1.0

Calcium binding site 10 out of 33 in 1m5k

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Calcium binding site 10 out of 33 in the Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca96

b:0.8
occ:1.00
O B:HOH240 2.4 98.0 1.0
OP1 B:A59 2.4 96.8 1.0
P B:A59 3.8 88.7 1.0
OP2 B:A20 4.1 94.7 1.0
N7 B:G21 4.3 83.8 1.0
OP2 B:A59 4.3 73.5 1.0
OP2 B:U60 4.5 97.2 1.0
O6 B:G21 4.6 79.6 1.0
O3' B:U58 4.6 82.3 1.0
O5' B:A59 4.8 89.1 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: 11298439
DOI: 10.1126/SCIENCE.1076093
Page generated: Sat Dec 12 03:06:29 2020

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