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Strontium in PDB 3cme: The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cme was solved by M.Simonovic, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.82 / 2.95
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 210.786, 297.778, 572.588, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 25.5

Other elements in 3cme:

The structure of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Magnesium (Mg) 93 atoms
Potassium (K) 2 atoms
Cadmium (Cd) 5 atoms
Chlorine (Cl) 22 atoms
Sodium (Na) 75 atoms

Strontium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 108;

Binding sites:

The binding sites of Strontium atom in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 3cme). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 108 binding sites of Strontium where determined in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cme:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Strontium binding site 1 out of 108 in 3cme

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Strontium binding site 1 out of 108 in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr8929

b:0.4
occ:1.00
 O A:HIS208 2.7 41.1 1.0
O A:PHE201 2.8 33.4 1.0
O A:GLY203 3.0 53.0 1.0
O A:GLY202 3.1 36.3 1.0
O A:HOH9077 3.2 95.4 1.0
OP1 0:A2633 3.3 41.4 1.0
O A:HOH9036 3.4 0.4 1.0
C A:HIS208 3.6 40.1 1.0
C A:GLY203 3.8 50.2 1.0
C A:GLY202 3.8 37.9 1.0
C A:PHE201 3.8 31.8 1.0
N A:HIS208 3.9 40.6 1.0
CA A:PRO209 4.2 40.8 1.0
N A:PRO209 4.3 39.7 1.0
CD2 A:HIS208 4.3 42.1 1.0
CA A:HIS208 4.4 40.7 1.0
N A:GLY210 4.4 41.5 1.0
C A:PRO209 4.4 42.2 1.0
O A:HOH9065 4.4 0.5 1.0
N A:GLY204 4.5 52.0 1.0
N A:GLY203 4.5 40.6 1.0
NE2 A:HIS208 4.5 43.5 1.0
O A:VAL192 4.5 34.6 1.0
CA A:GLY204 4.5 52.8 1.0
CA A:GLY203 4.6 45.9 1.0
CA A:GLY202 4.6 35.8 1.0
CA A:PHE201 4.6 31.4 1.0
N A:GLY202 4.7 33.2 1.0
CG A:HIS208 4.7 41.5 1.0
P 0:A2633 4.7 39.4 1.0
O A:ARG206 4.7 44.0 1.0
C A:GLN207 4.8 40.2 1.0
O A:GLY204 4.9 54.1 1.0
CA A:GLN207 4.9 40.1 1.0
CE1 A:HIS208 5.0 42.5 1.0

Strontium binding site 2 out of 108 in 3cme

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Strontium binding site 2 out of 108 in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr8930

b:78.5
occ:1.00
 O 0:HOH4577 3.0 0.3 1.0
O A:HOH9042 3.1 0.1 1.0
OE1 A:GLU28 3.1 75.2 1.0
O 0:HOH6792 3.1 82.6 1.0
O 0:HOH9698 3.5 0.5 1.0
CD A:GLU28 4.1 73.8 1.0
NZ A:LYS117 4.2 36.4 1.0
CG A:GLU28 4.2 71.6 1.0
O 0:HOH4026 4.3 43.9 1.0
OD2 A:ASP26 4.4 68.3 1.0
OP2 0:G1873 4.6 36.5 1.0
O A:ASP114 4.8 44.9 1.0

Strontium binding site 3 out of 108 in 3cme

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Strontium binding site 3 out of 108 in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr8977

b:95.4
occ:1.00
 OE1 A:GLU28 3.0 75.2 1.0
OE2 A:GLU28 3.3 74.8 1.0
CD A:GLU28 3.5 73.8 1.0
OP1 0:G2249 4.2 71.5 1.0
NZ A:LYS31 4.2 96.1 1.0
O A:ASP114 4.7 44.9 1.0
CG A:GLU28 5.0 71.6 1.0

Strontium binding site 4 out of 108 in 3cme

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Strontium binding site 4 out of 108 in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr8950

b:98.7
occ:1.00
 OD1 B:ASN243 2.9 48.2 1.0
OG B:SER245 3.0 34.4 1.0
O 0:HOH5665 3.5 55.0 1.0
O 0:HOH4155 3.8 48.8 1.0
CB B:SER245 3.8 34.3 1.0
O 0:HOH3079 3.9 55.8 1.0
O 0:HOH3866 4.0 82.1 1.0
CG B:ASN243 4.1 47.4 1.0
N B:SER245 4.7 33.2 1.0
ND2 B:ASN243 4.8 49.9 1.0
N6 0:A631 4.9 37.9 1.0
CA B:SER245 4.9 34.4 1.0
O 0:HOH3899 4.9 82.2 1.0
N1 0:A631 4.9 37.6 1.0

Strontium binding site 5 out of 108 in 3cme

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Strontium binding site 5 out of 108 in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr8987

b:1.0
occ:1.00
 NH2 B:ARG310 3.0 45.0 1.0
OP1 0:C2672 3.1 37.6 1.0
CA B:ARG25 3.4 33.0 1.0
N B:PHE26 3.5 33.9 1.0
O B:GLU163 3.6 46.4 1.0
C B:ARG25 3.7 33.0 1.0
CD B:ARG25 3.8 31.3 1.0
CB B:ARG25 3.8 32.2 1.0
CZ B:ARG310 3.8 43.8 1.0
O B:PRO24 4.2 34.8 1.0
NH1 B:ARG310 4.3 43.8 1.0
P 0:C2672 4.3 39.2 1.0
O B:PHE26 4.3 40.1 1.0
O B:HOH9030 4.3 72.9 1.0
N B:GLU163 4.4 44.4 1.0
CG B:ARG25 4.4 32.1 1.0
CZ2 B:TRP29 4.5 52.0 1.0
NE B:ARG310 4.6 43.5 1.0
CA B:PHE26 4.6 35.7 1.0
N B:ARG25 4.6 33.4 1.0
C B:GLU163 4.6 46.0 1.0
NH1 B:ARG25 4.6 33.6 1.0
O B:ARG25 4.7 32.7 1.0
CB B:PHE26 4.8 33.2 1.0
O5' 0:C2672 4.8 34.7 1.0
C B:PRO24 4.8 34.4 1.0
C5' 0:C2672 4.9 35.3 1.0
CA B:GLU163 4.9 44.7 1.0
C B:PHE26 4.9 38.6 1.0
OP2 0:C2672 4.9 39.6 1.0
CB B:GLU163 4.9 43.4 1.0
NE B:ARG25 5.0 33.0 1.0

Strontium binding site 6 out of 108 in 3cme

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Strontium binding site 6 out of 108 in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Sr9005

b:98.9
occ:1.00
 O F:HOH985 3.1 66.5 1.0
O 0:HOH5981 3.5 65.2 1.0
CG1 F:VAL91 3.8 63.9 1.0
OP2 0:A262 4.1 53.0 1.0
OP2 0:A261 4.4 59.2 1.0
NE2 F:GLN80 4.6 71.5 1.0
N F:GLY92 4.6 64.2 1.0

Strontium binding site 7 out of 108 in 3cme

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Strontium binding site 7 out of 108 in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Sr8907

b:48.5
occ:1.00
 O H:ASP13 2.7 41.8 1.0
O6 0:G1055 2.8 35.2 1.0
O 0:HOH5711 3.0 33.7 1.0
O 0:HOH7185 3.1 35.1 1.0
O 0:HOH4718 3.1 81.8 1.0
O 0:HOH3486 3.1 66.8 1.0
O 0:HOH4943 3.9 95.5 1.0
C H:ASP13 3.9 44.1 1.0
C6 0:G1055 4.0 33.5 1.0
OD1 H:ASP13 4.2 48.7 1.0
O 0:HOH4189 4.4 13.3 1.0
CB H:ASP13 4.4 46.4 1.0
CG H:LYS14 4.4 40.1 1.0
N7 0:G1055 4.5 34.0 1.0
N7 0:G1054 4.5 40.9 1.0
O 0:HOH3444 4.6 23.6 1.0
OP2 0:G1054 4.6 37.0 1.0
C5 0:G1055 4.6 32.9 1.0
CG H:ASP13 4.7 48.0 1.0
CA H:ASP13 4.8 44.8 1.0
N H:LYS14 4.9 43.8 1.0
CA H:LYS14 4.9 42.0 1.0

Strontium binding site 8 out of 108 in 3cme

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Strontium binding site 8 out of 108 in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Sr8972

b:0.7
occ:1.00
 O H:TYR157 2.9 55.9 1.0
O H:PRO162 3.0 53.3 1.0
O3' 0:A1133 3.0 44.5 1.0
O H:ILE160 3.2 45.7 1.0
O H:THR161 3.3 44.2 1.0
O2' 0:A1133 3.4 43.7 1.0
C H:PRO162 3.5 51.2 1.0
C H:THR161 3.5 44.9 1.0
OP1 0:G1134 3.5 47.5 1.0
C H:ILE160 3.8 45.9 1.0
N H:PRO162 3.8 46.1 1.0
P 0:G1134 3.9 47.5 1.0
C3' 0:A1133 4.0 43.2 1.0
N H:SER163 4.1 54.5 1.0
C H:TYR157 4.1 55.5 1.0
CA H:THR161 4.1 42.8 1.0
CA H:PRO162 4.1 47.7 1.0
C4' 0:A1133 4.2 42.6 1.0
N H:THR161 4.2 44.3 1.0
CG1 H:ILE160 4.3 45.4 1.0
CA H:SER163 4.3 57.2 1.0
C2' 0:A1133 4.3 43.0 1.0
O2' 0:G2520 4.7 39.3 1.0
CD H:PRO162 4.7 45.8 1.0
N H:ILE160 4.8 48.5 1.0
CA H:ILE160 4.8 46.1 1.0
CA H:TYR157 4.9 55.9 1.0
C5' 0:G1134 4.9 44.8 1.0
O5' 0:G1134 4.9 45.0 1.0
CB H:TYR157 5.0 54.7 1.0
OP2 0:G1134 5.0 46.8 1.0

Strontium binding site 9 out of 108 in 3cme

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Strontium binding site 9 out of 108 in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 9 of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Sr8969

b:0.1
occ:1.00
 OP1 0:A1296 3.0 33.2 1.0
O 0:HOH5759 3.2 78.2 1.0
O L:GLY14 3.2 26.9 1.0
NH2 L:ARG21 3.3 42.0 1.0
O2' 0:A1040 3.6 29.4 1.0
O3' 0:A1040 3.6 33.5 1.0
C L:GLY14 3.7 25.5 1.0
O3' 0:G1295 3.9 32.9 1.0
P 0:A1296 4.1 33.7 1.0
CA L:GLY14 4.1 24.8 1.0
OP1 0:U1041 4.3 36.3 1.0
NZ L:LYS3 4.3 20.6 1.0
O 0:HOH7427 4.4 31.9 1.0
OP1 0:A1040 4.5 31.1 1.0
C3' 0:A1040 4.5 30.4 1.0
N L:GLY15 4.5 25.4 1.0
CZ L:ARG21 4.6 42.8 1.0
C4' 0:A1040 4.6 29.9 1.0
C2' 0:A1040 4.6 30.1 1.0
P 0:U1041 4.7 35.8 1.0
O 0:HOH3135 4.7 82.1 1.0
OP1 0:G755 4.8 26.2 1.0
CA L:GLY15 4.9 26.0 1.0
C5' 0:U1041 5.0 29.8 1.0
OP2 0:A1296 5.0 32.0 1.0

Strontium binding site 10 out of 108 in 3cme

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Strontium binding site 10 out of 108 in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 10 of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Sr8912

b:64.6
occ:1.00
 O R:GLN61 2.7 36.5 1.0
OD1 R:ASN63 3.1 38.8 1.0
NA 0:NA8575 3.4 45.0 1.0
C R:GLN61 3.9 36.9 1.0
CG R:ASN63 4.3 37.3 1.0
N R:ASN63 4.5 36.4 1.0
CA R:GLN61 4.7 39.0 1.0
OP1 0:C2087 4.8 40.9 1.0
O R:LYS60 4.8 37.4 1.0
OP1 0:G13 4.9 46.0 1.0
ND2 R:ASN63 4.9 38.8 1.0
N R:HIS62 4.9 35.7 1.0
CA R:HIS62 5.0 36.6 1.0

Reference:

M.Simonovic, T.A.Steitz. Peptidyl-Cca Deacylation on the Ribosome Promoted By Induced Fit and the O3'-Hydroxyl Group of A76 of the Unacylated A-Site Trna. Rna V. 14 2372 2008.
ISSN: ISSN 1355-8382
PubMed: 18818369
DOI: 10.1261/RNA.1118908
Page generated: Fri Oct 11 00:46:12 2024

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