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Sodium 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:

Strontium (Sr) 107 atoms
Magnesium (Mg) 93 atoms
Potassium (K) 2 atoms
Cadmium (Cd) 5 atoms
Chlorine (Cl) 22 atoms

Sodium 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 - 75;

Binding sites:

The binding sites of Sodium 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 Sodium atom.
In total 75 binding sites of Sodium where determined in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin, PDB code: 3cd6:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 75 in 3cd6

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Sodium binding site 1 out of 75 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 Sodium with other atoms in the Na 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
B:Na8552

b:78.5
occ:1.00
 O 0:HOH4956 3.0 69.7 1.0
O B:GLN230 3.1 36.5 1.0
O 0:HOH4635 3.3 63.4 1.0
O 0:HOH6877 3.3 47.6 1.0
O 0:HOH5157 3.4 53.7 1.0
OP1 0:U837 3.6 32.2 1.0
O 0:HOH9284 3.8 79.4 1.0
OP2 0:U837 4.0 33.0 1.0
CZ3 B:TRP232 4.0 39.7 1.0
O 0:HOH7392 4.2 57.4 1.0
C B:GLN230 4.3 36.4 1.0
P 0:U837 4.3 30.3 1.0
CH2 B:TRP232 4.3 40.2 1.0
O 0:HOH6110 4.3 56.1 1.0
CA B:GLY231 4.4 39.0 1.0
N4 0:C839 4.5 32.4 1.0
OP2 0:C838 4.5 28.4 1.0
O 0:HOH3378 4.8 61.5 1.0
N B:GLY231 4.8 38.1 1.0
CE3 B:TRP232 4.8 39.8 1.0
O 0:HOH9567 4.9 49.6 1.0
O 0:HOH4501 4.9 49.0 1.0

Sodium binding site 2 out of 75 in 3cd6

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Sodium binding site 2 out of 75 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
C:Na8503

b:36.2
occ:1.00
 OD1 C:ASP45 2.8 45.6 1.0
O C:THR94 2.9 41.3 1.0
O C:LYS96 2.9 42.2 1.0
OD2 C:ASP45 3.2 44.3 1.0
CG C:ASP45 3.2 44.1 1.0
O C:HOH8507 3.2 23.2 1.0
C C:LYS96 3.7 40.4 1.0
O C:GLU95 3.8 39.8 1.0
C C:GLU95 3.9 41.0 1.0
C C:THR94 4.1 40.7 1.0
O C:HOH8617 4.1 45.7 1.0
N C:LYS96 4.2 39.6 1.0
O C:HOH8586 4.3 38.0 1.0
CA C:GLU95 4.4 42.5 1.0
N C:ASP97 4.4 40.3 1.0
CB C:ASP45 4.4 40.7 1.0
CA C:ASP97 4.6 38.5 1.0
CA C:LYS96 4.6 39.7 1.0
N C:GLU95 4.7 41.2 1.0

Sodium binding site 3 out of 75 in 3cd6

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Sodium binding site 3 out of 75 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
H:Na8518

b:69.5
occ:1.00
 O H:HOH8539 3.6 78.6 1.0
N H:ASP114 3.6 88.0 1.0
O 0:HOH7764 3.8 49.2 1.0
CD H:ARG117 4.0 56.6 1.0
NH1 H:ARG117 4.0 60.6 1.0
O6 0:G2286 4.1 69.3 1.0
CA H:ASP114 4.2 88.2 1.0
O 0:HOH4832 4.3 43.3 1.0
N4 0:C2287 4.5 72.2 1.0
NE H:ARG117 4.6 59.2 1.0
CZ H:ARG117 4.6 58.7 1.0
N3 0:C2287 4.9 70.7 1.0
CG H:ARG117 5.0 56.2 1.0

Sodium binding site 4 out of 75 in 3cd6

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Sodium binding site 4 out of 75 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
J:Na8538

b:57.0
occ:1.00
 O J:TYR69 2.7 59.6 1.0
O 0:HOH9501 2.9 79.1 1.0
O 0:HOH5802 2.9 50.7 1.0
O J:VAL61 3.0 53.3 1.0
O J:ILE63 3.0 54.0 1.0
O J:ARG60 3.0 46.3 1.0
OP1 0:A2677 3.5 58.1 1.0
C J:VAL61 3.5 51.2 1.0
CA J:VAL61 3.6 48.3 1.0
N J:TYR71 3.7 57.1 1.0
C J:TYR69 3.9 59.3 1.0
CB J:TYR71 4.0 53.1 1.0
C J:ARG60 4.0 43.9 1.0
C J:ILE63 4.2 52.9 1.0
N J:VAL61 4.3 45.5 1.0
CA J:TYR71 4.4 55.3 1.0
CD2 J:TYR69 4.4 55.7 1.0
N J:ASP62 4.5 52.8 1.0
CB J:TYR69 4.6 56.8 1.0
C J:PHE70 4.6 59.3 1.0
N J:ILE63 4.6 54.2 1.0
CA J:PHE70 4.7 61.5 1.0
N J:PHE70 4.8 60.5 1.0
O J:TYR71 4.8 55.7 1.0
CB J:VAL61 4.9 48.1 1.0
CA J:TYR69 4.9 57.9 1.0
P 0:A2677 4.9 58.5 1.0
CA J:ILE63 5.0 52.9 1.0
C J:ASP62 5.0 55.0 1.0

Sodium binding site 5 out of 75 in 3cd6

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Sodium binding site 5 out of 75 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
M:Na8539

b:38.1
occ:1.00
 O M:LEU112 2.7 38.6 1.0
O M:HOH8924 2.8 51.8 1.0
O M:SER106 2.9 42.1 1.0
OG M:SER106 2.9 38.2 1.0
O M:PHE109 3.1 39.6 1.0
O M:PRO110 3.3 40.6 1.0
C M:PRO110 3.5 39.0 1.0
CA M:PRO110 3.7 38.4 1.0
C M:SER106 3.8 41.8 1.0
C M:LEU112 3.9 37.9 1.0
C M:PHE109 4.0 39.8 1.0
CB M:SER106 4.0 39.4 1.0
OD1 M:ASP157 4.1 52.7 1.0
CA M:SER106 4.2 40.6 1.0
N M:PRO110 4.3 39.3 1.0
N M:LEU112 4.3 36.9 1.0
N M:ASN111 4.3 38.7 1.0
CL M:CL8818 4.4 40.5 1.0
CA M:LEU112 4.6 36.6 1.0
C M:ASN111 4.7 37.5 1.0
O M:HOH8857 4.7 71.9 1.0
CE1 M:PHE160 4.7 33.9 1.0
N M:ARG113 4.9 36.9 1.0
N M:ARG107 4.9 42.3 1.0
CA M:ASN111 5.0 37.8 1.0

Sodium binding site 6 out of 75 in 3cd6

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Sodium binding site 6 out of 75 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
Q:Na8540

b:74.3
occ:1.00
 O Q:ASP20 2.8 73.0 1.0
O Q:GLY22 2.9 66.2 1.0
O Q:HOH1795 3.0 54.6 1.0
OG Q:SER24 3.0 57.5 1.0
OG Q:SER46 3.0 52.6 1.0
O Q:HOH5427 3.0 87.6 1.0
O Q:ARG21 3.2 71.9 1.0
O Q:HOH7505 3.3 76.9 1.0
CA Q:SER24 3.7 60.1 1.0
C Q:ASP20 3.7 73.5 1.0
N Q:SER24 3.8 61.5 1.0
CB Q:SER46 3.8 52.0 1.0
C Q:ARG21 3.9 70.2 1.0
C Q:GLY22 3.9 66.0 1.0
CB Q:SER24 3.9 60.4 1.0
C Q:THR23 4.0 62.6 1.0
O Q:THR23 4.1 62.9 1.0
OD1 Q:ASN16 4.4 64.5 1.0
N Q:ARG21 4.5 71.9 1.0
N Q:GLY22 4.5 69.0 1.0
CA Q:ARG21 4.6 70.8 1.0
CA Q:ASP20 4.6 75.3 1.0
OD1 Q:ASP44 4.7 59.2 1.0
N Q:THR23 4.7 65.3 1.0
CA Q:GLY22 4.7 66.9 1.0
OP1 0:C2366 4.7 51.3 1.0
NH2 Q:ARG28 4.8 58.8 1.0
CA Q:THR23 4.8 63.9 1.0
O Q:HOH7164 4.9 61.5 1.0
CG Q:ASN16 5.0 64.5 1.0
CB Q:ASP20 5.0 77.5 1.0

Sodium binding site 7 out of 75 in 3cd6

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Sodium binding site 7 out of 75 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
R:Na8532

b:57.0
occ:1.00
 O R:SER70 2.8 45.4 1.0
O 0:HOH3779 2.8 90.3 1.0
O 0:HOH3105 3.1 79.8 1.0
O 0:HOH3791 3.1 0.1 1.0
O R:VAL72 3.2 52.0 1.0
O 0:HOH5967 3.4 87.3 1.0
NA 0:NA8533 3.5 70.3 1.0
OD1 R:ASP73 3.7 64.4 1.0
C R:VAL72 3.7 52.5 1.0
CA R:ASP73 3.9 55.1 1.0
C R:SER70 4.0 45.4 1.0
N R:ASP73 4.0 53.9 1.0
C R:LYS71 4.0 49.7 1.0
O 0:HOH7046 4.1 56.3 1.0
O R:LYS71 4.2 51.1 1.0
N R:VAL72 4.3 49.7 1.0
CB R:ASP73 4.3 58.4 1.0
CA R:LYS71 4.3 48.7 1.0
CG R:ASP73 4.4 62.5 1.0
N R:LYS71 4.7 46.5 1.0
CA R:VAL72 4.7 51.7 1.0
OP1 0:G2660 4.7 42.4 1.0

Sodium binding site 8 out of 75 in 3cd6

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Sodium binding site 8 out of 75 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
S:Na8510

b:47.6
occ:1.00
 NE2 S:HIS7 2.8 59.5 1.0
OE2 S:GLU61 2.9 66.8 1.0
O S:HOH2519 3.0 65.1 1.0
OE1 S:GLU61 3.1 65.9 1.0
CD S:GLU61 3.3 65.4 1.0
CE1 S:HIS7 3.5 60.9 1.0
CD2 S:HIS7 3.8 60.2 1.0
ND1 S:HIS7 4.6 60.1 1.0
CG S:HIS7 4.8 59.3 1.0
CG S:GLU61 4.8 61.5 1.0

Sodium binding site 9 out of 75 in 3cd6

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Sodium binding site 9 out of 75 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
0:Na8501

b:39.4
occ:1.00
 OP2 0:C1069 2.7 27.7 1.0
N7 0:G1072 2.8 32.9 1.0
O 0:HOH3195 2.9 42.9 1.0
O 0:HOH3226 2.9 50.5 1.0
O 0:HOH5025 3.0 73.2 1.0
O6 0:G1072 3.1 36.7 1.0
O6 0:G1087 3.2 34.5 1.0
C5 0:G1072 3.4 32.6 1.0
O 0:HOH9076 3.5 30.6 1.0
C6 0:G1072 3.6 32.1 1.0
C8 0:G1072 3.9 33.1 1.0
P 0:C1069 4.0 31.0 1.0
C6 0:G1087 4.1 32.1 1.0
O 0:HOH5382 4.2 48.3 1.0
C5' 0:C1068 4.3 41.4 1.0
O 0:HOH3561 4.4 34.7 1.0
O3' 0:C1068 4.5 32.1 1.0
C3' 0:C1068 4.5 35.7 1.0
C4 0:G1072 4.7 32.5 1.0
OP1 0:C1069 4.7 28.0 1.0
N1 0:G1087 4.8 28.9 1.0
OP2 0:C1068 4.8 45.4 1.0
O 0:HOH4310 4.8 76.2 1.0
N9 0:G1072 4.9 32.2 1.0
N1 0:G1072 4.9 31.8 1.0

Sodium binding site 10 out of 75 in 3cd6

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Sodium binding site 10 out of 75 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
0:Na8502

b:49.5
occ:1.00
 O 0:HOH7838 2.9 63.4 1.0
O2' 0:G1119 2.9 41.5 1.0
O 0:HOH4591 3.0 43.9 1.0
O3' 0:G1119 3.1 40.8 1.0
OP2 0:U1120 3.1 45.6 1.0
O6 0:G1121 3.2 36.0 1.0
N7 0:G1121 3.4 36.9 1.0
O 0:HOH4208 3.5 30.8 1.0
O4 0:U1122 3.6 43.2 1.0
P 0:U1120 3.7 45.4 1.0
O 0:HOH5728 3.7 61.3 1.0
O 0:HOH6988 3.7 74.5 1.0
C2' 0:G1119 3.8 39.6 1.0
C6 0:G1121 3.9 35.6 1.0
C3' 0:G1119 4.0 41.1 1.0
C5 0:G1121 4.0 35.4 1.0
C1' 0:G1119 4.2 37.4 1.0
MG 0:MG8018 4.4 37.5 1.0
C4 0:U1122 4.4 40.8 1.0
OP1 0:U1120 4.5 44.4 1.0
C8 0:G1121 4.6 36.6 1.0
N4 0:C1243 4.8 39.0 1.0
C5 0:U1122 4.8 40.0 1.0
N6 0:A1242 4.8 36.8 1.0
O5' 0:U1120 4.9 41.9 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: Mon Oct 7 07:07:49 2024

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