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Strontium in PDB 3cc4: Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit

Protein crystallography data

The structure of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit, PDB code: 3cc4 was solved by G.Blaha, G.Gurel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.85 / 2.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.780, 299.084, 573.837, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 24.4

Other elements in 3cc4:

The structure of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit 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 Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit (pdb code 3cc4). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 108 binding sites of Strontium where determined in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit, PDB code: 3cc4:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Strontium binding site 1 out of 108 in 3cc4

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Strontium binding site 1 out of 108 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr8929

b:0.9
occ:1.00
 O A:HIS208 2.9 35.4 1.0
OP1 0:A2633 3.0 36.5 1.0
O A:PHE201 3.0 27.8 1.0
O A:HOH9022 3.1 37.4 1.0
O A:HOH9059 3.2 62.4 1.0
O A:GLY202 3.3 30.8 1.0
O A:GLY203 3.3 36.2 1.0
C A:GLY202 3.6 30.2 1.0
C A:GLY203 3.7 33.1 1.0
C A:PHE201 3.7 26.9 1.0
N A:GLY203 4.0 30.7 1.0
N A:GLY210 4.1 44.0 1.0
C A:HIS208 4.1 33.7 1.0
CA A:GLY203 4.2 30.9 1.0
N A:GLY204 4.3 33.2 1.0
CA A:GLY202 4.3 28.7 1.0
N A:GLY202 4.3 25.9 1.0
P 0:A2633 4.3 32.9 1.0
C A:PRO209 4.3 40.1 1.0
CA A:GLY210 4.5 47.8 1.0
CA A:PRO209 4.5 36.6 1.0
CA A:PHE201 4.5 26.6 1.0
O3' 0:G2632 4.6 32.4 1.0
CA A:GLY204 4.6 33.6 1.0
CD2 A:HIS208 4.7 29.6 1.0
N A:HIS208 4.8 32.4 1.0
NE2 A:HIS208 4.8 29.6 1.0
N A:PRO209 4.9 34.5 1.0
O A:PRO209 4.9 42.4 1.0

Strontium binding site 2 out of 108 in 3cc4

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Strontium binding site 2 out of 108 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr8930

b:0.8
occ:1.00
 O A:HOH9026 3.1 84.8 1.0
O 0:HOH7973 3.1 62.1 1.0
O 0:HOH6004 3.1 72.3 1.0
O A:HOH9013 3.3 58.8 1.0
OE1 A:GLU28 3.3 72.2 1.0
OD2 A:ASP26 3.6 69.4 1.0
OD1 A:ASP26 3.7 69.3 1.0
CG A:ASP26 4.1 68.0 1.0
NZ A:LYS117 4.2 51.7 1.0
CD A:GLU28 4.2 72.5 1.0
OP2 0:G1873 4.2 34.0 1.0
CG A:GLU28 4.3 70.6 1.0
MG A:MG8051 4.3 82.0 1.0
O 0:HOH3156 4.4 47.8 1.0
O A:HOH9002 4.4 54.9 1.0

Strontium binding site 3 out of 108 in 3cc4

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Strontium binding site 3 out of 108 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr8977

b:0.9
occ:1.00
 OE1 A:GLU28 3.4 72.2 1.0
OE2 A:GLU28 3.5 72.5 1.0
OP1 0:G2249 3.8 88.0 1.0
CD A:GLU28 3.9 72.5 1.0
NZ A:LYS31 4.5 94.5 1.0
OP2 0:G2250 4.7 0.6 1.0
O A:HOH9013 4.8 58.8 1.0
O A:ASP114 4.8 53.7 1.0

Strontium binding site 4 out of 108 in 3cc4

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Strontium binding site 4 out of 108 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr8950

b:0.4
occ:1.00
 OG B:SER245 3.0 37.5 1.0
OD1 B:ASN243 3.0 41.6 1.0
O 0:HOH3284 3.2 35.4 1.0
O 0:HOH9983 3.2 49.8 1.0
O 0:HOH3019 3.5 82.7 1.0
O 0:HOH4838 3.8 38.3 1.0
CB B:SER245 3.9 33.0 1.0
CG B:ASN243 4.0 39.7 1.0
O B:HOH8993 4.0 40.4 1.0
ND2 B:ASN243 4.3 40.4 1.0
N6 0:A631 4.7 21.0 1.0
O 0:HOH9040 4.7 29.8 1.0
N1 0:A631 4.7 24.1 1.0
N B:SER245 4.9 33.4 1.0
OP2 0:G2075 4.9 39.5 1.0

Strontium binding site 5 out of 108 in 3cc4

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Strontium binding site 5 out of 108 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr8987

b:0.0
occ:1.00
 O B:PHE26 3.3 47.8 1.0
OP1 0:C2672 3.6 41.1 1.0
O B:HOH9021 3.8 64.3 1.0
NH2 B:ARG310 3.8 49.3 1.0
N B:PHE26 3.9 43.8 1.0
C5' 0:C2672 4.0 37.1 1.0
CB B:ARG25 4.0 42.8 1.0
CA B:ARG25 4.2 43.5 1.0
C B:ARG25 4.2 44.0 1.0
C B:PHE26 4.3 46.5 1.0
O B:GLU163 4.3 55.5 1.0
CZ2 B:TRP29 4.4 45.6 1.0
P 0:C2672 4.5 41.4 1.0
O5' 0:C2672 4.5 37.6 1.0
CA B:PHE26 4.6 44.6 1.0
CD B:ARG25 4.7 42.3 1.0
NH1 B:ARG141 4.7 49.1 1.0
OP2 0:U2673 4.8 40.5 1.0
O3' 0:C2672 4.9 39.0 1.0
CG B:ARG25 4.9 43.1 1.0
O B:ARG25 4.9 45.6 1.0
CB B:PHE26 4.9 43.2 1.0
OP2 0:C2672 5.0 43.2 1.0
OP1 0:U2673 5.0 39.8 1.0

Strontium binding site 6 out of 108 in 3cc4

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Strontium binding site 6 out of 108 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Sr9005

b:0.0
occ:1.00
 O F:HOH985 3.2 84.3 1.0
O 0:HOH5163 3.3 57.4 1.0
O F:HOH6403 3.4 59.0 1.0
NE2 F:GLN80 4.0 55.4 1.0
CG1 F:VAL91 4.2 60.5 1.0
OD1 F:ASP81 4.5 70.2 1.0
N F:GLY92 4.7 53.9 1.0
OP2 0:A262 4.8 44.7 1.0

Strontium binding site 7 out of 108 in 3cc4

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Strontium binding site 7 out of 108 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Sr8972

b:0.5
occ:1.00
 O3' 0:A1133 2.7 43.1 1.0
O2' 0:A1133 3.0 39.2 1.0
O H:TYR157 3.0 60.8 1.0
O H:PRO162 3.0 57.5 1.0
O H:ILE160 3.0 56.1 1.0
OP1 0:G1134 3.3 42.9 1.0
O H:THR161 3.5 55.1 1.0
P 0:G1134 3.7 43.5 1.0
C3' 0:A1133 3.7 41.4 1.0
C H:PRO162 3.7 56.9 1.0
C2' 0:A1133 3.8 41.0 1.0
C H:THR161 3.9 54.7 1.0
C4' 0:A1133 4.1 40.8 1.0
C H:ILE160 4.1 55.0 1.0
C H:TYR157 4.2 59.6 1.0
C5' 0:G1134 4.3 44.2 1.0
O2' 0:G2520 4.3 42.9 1.0
N H:PRO162 4.3 54.6 1.0
N H:SER163 4.4 58.9 1.0
CA H:PRO162 4.4 55.1 1.0
O5' 0:G1134 4.5 44.2 1.0
CA H:THR161 4.6 54.0 1.0
CA H:SER163 4.6 60.5 1.0
CA H:ASN158 4.7 59.2 1.0
O 0:HOH4046 4.8 48.7 1.0
N H:THR161 4.8 54.5 1.0
OP2 0:G1134 4.9 42.3 1.0
N H:ASN158 4.9 59.2 1.0
C H:ASN158 4.9 59.4 1.0
C1' 0:A1133 5.0 42.2 1.0
O H:ASN158 5.0 60.1 1.0

Strontium binding site 8 out of 108 in 3cc4

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Strontium binding site 8 out of 108 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Sr8912

b:84.4
occ:1.00
 O R:GLN61 2.9 39.9 1.0
OD1 R:ASN63 3.2 37.7 1.0
NA 0:NA8575 3.7 94.1 1.0
C R:GLN61 4.1 38.9 1.0
CG R:ASN63 4.3 36.4 1.0
OP1 0:C2087 4.5 39.1 1.0
N R:ASN63 4.7 34.2 1.0
CA R:GLN61 4.8 40.5 1.0
OP1 0:G13 4.8 47.2 1.0
ND2 R:ASN63 4.9 38.3 1.0
OP1 0:G1370 5.0 28.6 1.0

Strontium binding site 9 out of 108 in 3cc4

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Strontium binding site 9 out of 108 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 9 of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Sr8961

b:0.7
occ:1.00
 O 0:HOH5074 3.0 70.6 1.0
O 0:HOH5378 3.1 60.9 1.0
OD2 S:ASP59 3.2 58.4 1.0
OD1 S:ASP59 3.4 61.0 1.0
CG S:ASP59 3.7 57.2 1.0
OP2 0:G1444 3.9 47.3 1.0
O 0:HOH7961 4.5 41.4 1.0
N7 0:G1444 4.5 45.1 1.0
O 2:HOH7875 4.6 75.5 1.0
C8 0:G1444 5.0 44.9 1.0

Strontium binding site 10 out of 108 in 3cc4

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Strontium binding site 10 out of 108 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 10 of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Sr8913

b:85.4
occ:1.00
 O 1:LYS10 2.8 31.3 1.0
OP1 0:U862 2.8 28.8 1.0
OD1 1:ASN12 2.9 30.0 1.0
O 0:HOH4943 3.0 36.1 1.0
O 0:HOH9182 3.1 49.5 1.0
O 1:HOH8989 3.6 68.3 1.0
OP2 0:U862 3.7 28.6 1.0
P 0:U862 3.7 29.0 1.0
O 0:HOH9446 3.7 34.5 1.0
C 1:LYS10 3.8 29.8 1.0
CG 1:ASN12 4.0 29.9 1.0
CB 1:LYS10 4.1 31.5 1.0
CA 1:LYS10 4.1 30.2 1.0
O 0:HOH7545 4.3 45.9 1.0
OP1 0:C778 4.3 27.5 1.0
OG1 1:THR13 4.4 30.2 1.0
O 1:HOH8994 4.5 42.9 1.0
ND2 1:ASN12 4.5 30.9 1.0
O3' 0:A861 4.6 29.6 1.0
N 1:ASN12 4.6 28.3 1.0
O 0:HOH5579 4.8 40.8 1.0
CG 1:LYS10 4.8 33.5 1.0
O 0:HOH6167 4.8 44.0 1.0
O5' 0:U862 4.9 29.4 1.0
N 1:LYS11 5.0 29.4 1.0

Reference:

G.Blaha, G.Gurel, S.J.Schroeder, P.B.Moore, T.A.Steitz. Mutations Outside the Anisomycin-Binding Site Can Make Ribosomes Drug-Resistant. J.Mol.Biol. V. 379 505 2008.
ISSN: ISSN 0022-2836
PubMed: 18455733
DOI: 10.1016/J.JMB.2008.03.075
Page generated: Thu Oct 10 21:31:22 2024

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