Atomistry » Strontium » PDB 2hdf-3i5a » 3cd6
Atomistry »
  Strontium »
    PDB 2hdf-3i5a »
      3cd6 »

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

Go back to Strontium Binding Sites List in 3cd6
Strontium binding site 1 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 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

Go back to Strontium Binding Sites List in 3cd6
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

Go back to Strontium Binding Sites List in 3cd6
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

Go back to Strontium Binding Sites List in 3cd6
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

Go back to Strontium Binding Sites List in 3cd6
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

Go back to Strontium Binding Sites List in 3cd6
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

Go back to Strontium Binding Sites List in 3cd6
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

Go back to Strontium Binding Sites List in 3cd6
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

Go back to Strontium Binding Sites List in 3cd6
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

Go back to Strontium Binding Sites List in 3cd6
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy