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Strontium in PDB 3cd6: Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin

Protein crystallography data

The structure of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin, PDB code: 3cd6 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) 49.95 / 2.75
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 212.805, 299.997, 576.002, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24.1

Other elements in 3cd6:

The structure of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin 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 - 107;

Binding sites:

The binding sites of Strontium atom in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin (pdb code 3cd6). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 107 binding sites of Strontium where determined in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin, PDB code: 3cd6:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Strontium binding site 1 out of 107 in 3cd6

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Strontium binding site 1 out of 107 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


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Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr8929

b:0.1
occ:1.00
 OP1 0:A2633 2.9 42.3 1.0
O A:HIS208 2.9 45.4 1.0
O A:PHE201 3.0 37.3 1.0
O A:HOH8974 3.1 54.5 1.0
O A:GLY203 3.1 42.7 1.0
O A:HOH9014 3.2 81.4 1.0
O A:GLY202 3.4 38.3 1.0
C A:GLY203 3.7 39.7 1.0
C A:GLY202 3.7 36.7 1.0
C A:PHE201 3.8 35.9 1.0
N A:GLY210 3.8 52.5 1.0
N A:GLY203 4.1 36.7 1.0
C A:HIS208 4.1 45.1 1.0
CA A:GLY203 4.2 37.0 1.0
P 0:A2633 4.2 38.4 1.0
N A:GLY204 4.4 40.4 1.0
CA A:GLY202 4.4 35.8 1.0
N A:GLY202 4.4 35.5 1.0
C A:PRO209 4.5 51.3 1.0
CA A:GLY210 4.5 54.6 1.0
CA A:PRO209 4.5 48.4 1.0
O3' 0:G2632 4.5 40.0 1.0
CA A:PHE201 4.6 36.7 1.0
CA A:GLY204 4.7 41.1 1.0
NE2 A:HIS208 4.7 43.8 1.0
CD2 A:HIS208 4.8 45.1 1.0
N A:HIS208 4.8 43.3 1.0
N A:PRO209 4.9 46.4 1.0
O A:ARG206 4.9 45.6 1.0
O A:HOH9002 5.0 0.8 1.0

Strontium binding site 2 out of 107 in 3cd6

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Strontium binding site 2 out of 107 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr8930

b:0.6
occ:1.00
 O A:HOH8980 3.1 0.3 1.0
O 0:HOH3013 3.1 80.2 1.0
OE1 A:GLU28 3.3 88.4 1.0
O 0:HOH5983 3.4 65.1 1.0
OD2 A:ASP26 3.5 81.0 1.0
MG A:MG8051 3.5 81.8 1.0
O 0:HOH7951 3.7 83.3 1.0
OP2 0:G1873 3.8 44.7 1.0
OD1 A:ASP26 3.9 80.2 1.0
CG A:ASP26 4.1 79.7 1.0
CD A:GLU28 4.3 88.3 1.0
O A:HOH8967 4.3 65.4 1.0
CG A:GLU28 4.5 86.2 1.0
NZ A:LYS117 4.6 68.0 1.0

Strontium binding site 3 out of 107 in 3cd6

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Strontium binding site 3 out of 107 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr8950

b:0.2
occ:1.00
 OD1 B:ASN243 3.0 44.0 1.0
OG B:SER245 3.0 32.8 1.0
O 0:HOH3272 3.1 27.0 1.0
O 0:HOH9974 3.2 74.8 1.0
O 0:HOH3010 3.3 74.8 1.0
O 0:HOH4831 3.8 60.7 1.0
CG B:ASN243 3.9 42.6 1.0
CB B:SER245 4.0 31.5 1.0
ND2 B:ASN243 4.1 43.1 1.0
O B:HOH8954 4.3 44.8 1.0
N6 0:A631 4.6 29.7 1.0
N1 0:A631 4.6 30.5 1.0
O 0:HOH9040 4.8 31.6 1.0

Strontium binding site 4 out of 107 in 3cd6

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Strontium binding site 4 out of 107 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Sr9005

b:0.6
occ:1.00
 O F:HOH985 3.1 88.8 1.0
O 0:HOH5162 3.3 62.6 1.0
O F:HOH6403 3.8 48.5 1.0
CG1 F:VAL91 4.3 69.6 1.0
OD1 F:ASP81 4.4 87.3 1.0
N F:GLY92 4.6 64.6 1.0
OP2 0:A261 4.8 53.7 1.0
OP2 0:A262 5.0 53.7 1.0

Strontium binding site 5 out of 107 in 3cd6

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Strontium binding site 5 out of 107 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Sr8986

b:0.0
occ:1.00
 OE2 J:GLU28 3.3 75.8 1.0
O 0:HOH9562 3.3 62.5 1.0
O 0:HOH3788 3.4 68.0 1.0
OP1 0:C1103 3.6 42.9 1.0
CG J:GLU28 4.1 67.0 1.0
CD J:GLU28 4.1 72.4 1.0
O 0:HOH7925 4.1 71.4 1.0
O3' 0:C1102 4.2 39.4 1.0
P 0:C1103 4.5 42.7 1.0
C5' 0:C1103 4.5 38.6 1.0
OP2 0:U1109 4.9 45.9 1.0

Strontium binding site 6 out of 107 in 3cd6

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Strontium binding site 6 out of 107 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Sr8912

b:72.8
occ:1.00
 O R:GLN61 2.8 43.1 1.0
OD1 R:ASN63 3.2 39.3 1.0
NA 0:NA8575 3.7 89.5 1.0
C R:GLN61 4.0 42.5 1.0
CG R:ASN63 4.4 39.9 1.0
N R:ASN63 4.7 35.8 1.0
CA R:GLN61 4.8 43.9 1.0
OP1 0:C2087 4.8 39.3 1.0
OP1 0:G1370 4.8 30.7 1.0
OP1 0:G13 4.9 51.2 1.0
OP1 0:U1368 5.0 33.7 1.0
ND2 R:ASN63 5.0 40.5 1.0

Strontium binding site 7 out of 107 in 3cd6

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Strontium binding site 7 out of 107 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Sr8961

b:0.1
occ:1.00
 OD2 S:ASP59 3.1 68.9 1.0
O S:HOH4349 3.5 63.3 1.0
OD1 S:ASP59 3.5 68.8 1.0
O 0:HOH7940 3.6 57.2 1.0
CG S:ASP59 3.7 67.2 1.0
OP2 0:G1444 4.3 51.9 1.0
N7 0:G1444 4.4 51.5 1.0
O 2:HOH3944 4.5 68.6 1.0
MG 0:MG8060 4.6 69.8 1.0
O S:HOH2485 4.6 72.7 1.0
O6 0:G1445 4.9 48.3 1.0

Strontium binding site 8 out of 107 in 3cd6

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Strontium binding site 8 out of 107 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Sr8913

b:79.7
occ:1.00
 O 1:LYS10 2.8 34.5 1.0
OD1 1:ASN12 2.9 34.3 1.0
OP1 0:U862 2.9 31.4 1.0
O 0:HOH4935 2.9 82.5 1.0
O 0:HOH9179 3.1 49.1 1.0
O 1:HOH8994 3.5 72.2 1.0
CG 1:ASN12 3.8 34.4 1.0
C 1:LYS10 3.8 31.5 1.0
O 0:HOH9435 3.8 29.9 1.0
P 0:U862 3.9 31.1 1.0
OP2 0:U862 4.0 32.2 1.0
CA 1:LYS10 4.2 31.9 1.0
ND2 1:ASN12 4.3 34.9 1.0
OP1 0:C778 4.3 28.8 1.0
CB 1:LYS10 4.3 32.4 1.0
O 1:HOH9012 4.3 58.1 1.0
O 0:HOH6144 4.4 44.1 1.0
N 1:ASN12 4.4 30.5 1.0
O 1:HOH9000 4.5 47.3 1.0
OG1 1:THR13 4.6 37.4 1.0
O3' 0:A861 4.7 33.0 1.0
N 1:LYS11 4.8 31.6 1.0
CB 1:ASN12 4.9 31.0 1.0
O 0:HOH5569 4.9 39.9 1.0

Strontium binding site 9 out of 107 in 3cd6

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Strontium binding site 9 out of 107 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 9 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Sr8952

b:73.2
occ:1.00
 O 1:ASP47 2.8 35.5 1.0
O 1:HOH8968 3.1 40.5 1.0
O 0:HOH9107 3.1 62.9 1.0
C 1:ASP47 3.5 35.6 1.0
O 0:HOH3255 3.5 0.5 1.0
O 0:HOH5782 3.6 41.7 1.0
O 0:HOH9315 3.6 98.7 1.0
OD1 1:ASP47 3.7 57.0 1.0
O 0:HOH3918 3.8 60.0 1.0
CB 1:ASP47 3.9 44.2 1.0
OP2 0:G180 4.2 29.1 1.0
O4 0:U1473 4.2 36.6 1.0
CA 1:ASP47 4.2 38.0 1.0
CG 1:ASP47 4.3 52.4 1.0
N 1:TYR48 4.4 32.9 1.0
N 1:ASP47 4.4 35.9 1.0
CA 1:TYR48 4.5 31.8 1.0
O 0:HOH3033 4.7 36.6 1.0
O 0:HOH5504 4.8 40.1 1.0
OP1 0:G180 4.8 26.8 1.0

Strontium binding site 10 out of 107 in 3cd6

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Strontium binding site 10 out of 107 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 10 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Sr8932

b:1.0
occ:1.00
 O 3:GLY45 3.1 0.1 1.0
O 3:GLY47 3.2 0.7 1.0
O M:HOH8941 3.3 92.4 1.0
O 0:HOH7942 3.4 91.7 1.0
OD2 3:ASP49 3.5 0.5 1.0
O 0:HOH3997 3.7 0.5 1.0
O M:HOH8865 3.8 83.9 1.0
C 3:GLY45 4.3 0.2 1.0
CG 3:ASP49 4.3 0.0 1.0
C 3:GLY47 4.4 0.8 1.0
O 3:HOH9012 4.5 76.8 1.0
N 3:GLY47 4.5 0.9 1.0
OD1 3:ASP49 4.5 0.2 1.0
OP1 0:G2121 4.7 62.2 1.0
O5' 0:G2121 4.9 58.5 1.0
N 3:GLY45 4.9 0.3 1.0
C5' 0:G2121 4.9 56.1 1.0
CA 3:GLY47 5.0 0.1 1.0
C 3:ILE46 5.0 0.5 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 23:42:40 2024

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