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

Protein crystallography data

The structure of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cma 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) 49.79 / 2.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.316, 297.905, 573.138, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 24.5

Other elements in 3cma:

The structure of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui 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 The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 3cma). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 75 binding sites of Sodium where determined in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cma:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 75 in 3cma

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Sodium binding site 1 out of 75 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of Cca 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:Na8552

b:69.7
occ:1.00
 O B:GLN230 2.8 26.5 1.0
O 0:HOH5967 3.0 86.7 1.0
OP1 0:U837 3.0 27.1 1.0
O 0:HOH5465 3.0 54.5 1.0
O 0:HOH5779 3.2 77.4 1.0
OP2 0:U837 3.6 21.7 1.0
O 0:HOH7649 3.6 81.2 1.0
P 0:U837 3.7 24.1 1.0
CA B:GLY231 3.9 30.3 1.0
O B:HOH8997 3.9 30.3 1.0
C B:GLN230 3.9 28.5 1.0
OP2 0:C838 4.1 22.4 1.0
O B:HOH9139 4.2 94.2 1.0
N B:GLY231 4.4 30.1 1.0
CZ3 B:TRP232 4.5 26.0 1.0
O5' 0:U837 4.6 21.3 1.0
CH2 B:TRP232 4.8 25.6 1.0
O B:HOH9045 4.9 72.0 1.0

Sodium binding site 2 out of 75 in 3cma

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Sodium binding site 2 out of 75 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of Cca 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
C:Na8503

b:22.2
occ:1.00
 OD1 C:ASP45 2.7 35.6 1.0
O C:LYS96 2.7 40.6 1.0
O C:THR94 3.0 37.4 1.0
O C:HOH8508 3.1 31.2 1.0
CG C:ASP45 3.4 36.9 1.0
C C:LYS96 3.5 39.0 1.0
OD2 C:ASP45 3.5 37.0 1.0
O C:GLU95 3.7 37.3 1.0
C C:GLU95 3.8 37.7 1.0
O C:HOH8625 3.9 38.8 1.0
N C:LYS96 4.1 38.1 1.0
N C:ASP97 4.1 37.7 1.0
CA C:ASP97 4.1 35.7 1.0
C C:THR94 4.2 36.0 1.0
CA C:GLU95 4.3 38.8 1.0
CA C:LYS96 4.4 38.3 1.0
N C:GLU95 4.7 37.3 1.0
O C:HOH8592 4.8 55.4 1.0
CB C:ASP45 4.8 34.8 1.0

Sodium binding site 3 out of 75 in 3cma

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Sodium binding site 3 out of 75 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of Cca 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
D:Na8543

b:60.5
occ:1.00
 N4 9:C40 3.6 79.5 1.0
CB D:ARG51 3.7 89.2 1.0
N3 9:C40 3.8 79.8 1.0
CG D:ARG51 4.0 90.7 1.0
CG D:PRO68 4.1 99.2 1.0
C4 9:C40 4.2 79.8 1.0
CD D:PRO68 4.5 99.6 1.0
CE D:LYS53 4.5 0.9 1.0
CG D:LYS53 4.9 0.9 1.0
CD D:ARG51 4.9 91.4 1.0
C2 9:C40 4.9 80.1 1.0

Sodium binding site 4 out of 75 in 3cma

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Sodium binding site 4 out of 75 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Structure of Cca 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
J:Na8538

b:31.6
occ:1.00
 O J:TYR69 2.8 50.6 1.0
O J:ILE63 2.9 41.3 1.0
O J:HOH4949 2.9 31.3 1.0
O J:VAL61 2.9 39.3 1.0
O J:HOH603 3.0 51.3 1.0
O J:ARG60 3.1 35.6 1.0
OP1 0:A2677 3.4 52.5 1.0
C J:VAL61 3.6 38.3 1.0
C J:TYR69 3.8 48.8 1.0
CA J:VAL61 3.8 36.9 1.0
C J:ILE63 4.0 40.4 1.0
N J:TYR71 4.0 48.9 1.0
C J:ARG60 4.2 35.0 1.0
CB J:TYR71 4.3 46.2 1.0
CL J:CL8821 4.3 61.5 1.0
CB J:TYR69 4.4 44.7 1.0
CD2 J:TYR69 4.5 44.0 1.0
N J:VAL61 4.5 36.6 1.0
N J:ILE63 4.5 42.1 1.0
N J:ASP62 4.6 39.5 1.0
CA J:PHE70 4.6 53.2 1.0
N J:PHE70 4.6 51.3 1.0
C J:PHE70 4.6 51.5 1.0
CA J:TYR69 4.6 46.2 1.0
C J:ASP62 4.7 42.3 1.0
CA J:TYR71 4.8 46.0 1.0
CA J:ILE63 4.8 41.3 1.0
P 0:A2677 4.9 52.5 1.0
CG J:TYR69 4.9 44.3 1.0
N J:GLY64 4.9 38.7 1.0
CA J:GLY64 5.0 37.7 1.0
N J:TYR69 5.0 43.1 1.0

Sodium binding site 5 out of 75 in 3cma

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Sodium binding site 5 out of 75 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Structure of Cca 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:Na8568

b:30.8
occ:1.00
 O 0:HOH4110 3.0 43.9 1.0
O L:HOH8832 3.0 0.1 1.0
O4 0:U903 3.0 22.4 1.0
O L:HOH8854 3.1 38.0 1.0
O L:HIS18 3.1 25.4 1.0
CA L:HIS18 3.3 26.8 1.0
O6 0:G902 3.3 17.9 1.0
N4 0:C762 3.4 14.5 1.0
C L:HIS18 3.4 26.2 1.0
O 0:HOH4120 3.7 4.1 1.0
CB L:ARG21 3.8 28.8 1.0
C4 0:U903 3.9 22.0 1.0
N L:ARG21 3.9 30.6 1.0
O L:SER17 4.0 28.1 1.0
CB L:HIS18 4.0 28.0 1.0
N3 0:U903 4.0 23.6 1.0
O L:ARG21 4.2 30.8 1.0
CA L:ARG21 4.3 29.8 1.0
C4 0:C762 4.3 12.8 1.0
N L:LYS19 4.4 26.7 1.0
N L:HIS18 4.4 25.5 1.0
C6 0:G902 4.4 18.6 1.0
N L:ASN20 4.5 29.2 1.0
C L:ARG21 4.6 30.2 1.0
CG L:ARG21 4.6 28.4 1.0
C L:SER17 4.6 26.5 1.0
CD L:ARG21 4.8 30.0 1.0
C L:ASN20 4.9 31.8 1.0
N3 0:C762 4.9 12.1 1.0

Sodium binding site 6 out of 75 in 3cma

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Sodium binding site 6 out of 75 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Structure of Cca 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
M:Na8539

b:33.8
occ:1.00
 O M:LEU112 2.7 37.9 1.0
OG M:SER106 2.7 27.1 1.0
O M:SER106 2.9 34.8 1.0
O M:PHE109 3.0 29.0 1.0
O M:HOH8936 3.0 42.0 1.0
O M:PRO110 3.1 33.1 1.0
C M:PRO110 3.3 32.6 1.0
CA M:PRO110 3.4 31.7 1.0
C M:PHE109 3.6 29.6 1.0
C M:SER106 3.8 33.6 1.0
N M:PRO110 3.8 30.5 1.0
C M:LEU112 3.9 35.2 1.0
CB M:SER106 4.0 31.4 1.0
CA M:SER106 4.1 31.6 1.0
N M:LEU112 4.2 33.9 1.0
N M:ASN111 4.2 34.2 1.0
CA M:LEU112 4.6 34.4 1.0
C M:ASN111 4.6 34.2 1.0
O M:HOH8862 4.6 29.9 1.0
CL M:CL8818 4.8 33.4 1.0
CB M:PRO110 4.8 30.8 1.0
N M:ARG113 4.8 33.7 1.0
N M:ARG107 4.8 34.2 1.0
OD1 M:ASP157 4.9 44.2 1.0
CA M:PHE109 4.9 28.7 1.0
CA M:ASN111 4.9 34.8 1.0
CE1 M:PHE160 5.0 34.7 1.0
CA M:ARG113 5.0 32.1 1.0

Sodium binding site 7 out of 75 in 3cma

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Sodium binding site 7 out of 75 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Structure of Cca 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
Q:Na8540

b:48.5
occ:1.00
 O Q:GLY22 2.6 46.5 1.0
O Q:ASP20 2.7 57.8 1.0
OG Q:SER24 2.9 45.6 1.0
O Q:HOH1795 3.0 36.7 1.0
O Q:HOH5427 3.1 25.9 1.0
OG Q:SER46 3.1 40.4 1.0
CA Q:SER24 3.6 43.8 1.0
N Q:SER24 3.7 45.0 1.0
C Q:ASP20 3.7 59.1 1.0
CB Q:SER24 3.8 44.0 1.0
C Q:THR23 3.8 46.2 1.0
C Q:GLY22 3.8 47.0 1.0
O Q:THR23 3.8 46.9 1.0
CB Q:SER46 3.8 39.4 1.0
O Q:HOH7505 4.1 55.4 1.0
O Q:ARG21 4.1 54.4 1.0
C Q:ARG21 4.3 53.0 1.0
OD1 Q:ASN16 4.4 50.4 1.0
NH2 Q:ARG28 4.5 50.4 1.0
CA Q:ASP20 4.5 61.8 1.0
OD1 Q:ASP44 4.6 46.5 1.0
CA Q:THR23 4.6 46.7 1.0
N Q:GLY22 4.6 51.2 1.0
N Q:THR23 4.7 46.8 1.0
N Q:ARG21 4.7 57.0 1.0
CA Q:GLY22 4.8 48.2 1.0
OP1 0:C2366 4.8 38.3 1.0
CB Q:ASP20 4.8 66.0 1.0
OD2 Q:ASP44 4.9 46.4 1.0
CA Q:ARG21 4.9 54.8 1.0

Sodium binding site 8 out of 75 in 3cma

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Sodium binding site 8 out of 75 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of The Structure of Cca 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:Na8533

b:42.4
occ:1.00
 O R:VAL72 2.7 36.4 1.0
O R:HOH8919 2.9 29.0 1.0
NA R:NA8532 3.1 29.6 1.0
O R:SER70 3.2 36.1 1.0
OP1 0:G2660 3.3 41.3 1.0
O 0:HOH4647 3.3 1.0 1.0
O3' 0:U2659 3.3 39.7 1.0
O 0:HOH4992 3.5 39.4 1.0
P 0:G2660 3.8 41.1 1.0
O R:TRP75 3.9 35.9 1.0
C R:VAL72 3.9 38.2 1.0
C R:SER70 4.1 34.1 1.0
O R:HOH8930 4.2 98.1 1.0
O R:HOH8986 4.3 68.5 1.0
O R:LYS69 4.3 34.9 1.0
C5' 0:U2659 4.3 34.5 1.0
CA R:SER70 4.4 34.5 1.0
C3' 0:U2659 4.4 35.9 1.0
C4' 0:U2659 4.4 35.2 1.0
OP2 0:G2660 4.5 36.5 1.0
CA R:ASP73 4.7 43.2 1.0
N R:VAL72 4.7 36.4 1.0
O R:HOH8966 4.7 78.2 1.0
N R:ASP73 4.8 41.2 1.0
CA R:VAL72 4.9 36.8 1.0

Sodium binding site 9 out of 75 in 3cma

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Sodium binding site 9 out of 75 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of The Structure of Cca 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:Na8532

b:29.6
occ:1.00
 O R:SER70 2.9 36.1 1.0
NA R:NA8533 3.1 42.4 1.0
O R:HOH8966 3.1 78.2 1.0
O R:HOH8986 3.2 68.5 1.0
O R:VAL72 3.2 36.4 1.0
O R:HOH8930 3.3 98.1 1.0
C R:VAL72 3.8 38.2 1.0
CA R:ASP73 3.9 43.2 1.0
OD1 R:ASP73 4.0 56.3 1.0
O 0:HOH4647 4.0 1.0 1.0
O R:HOH8921 4.0 39.8 1.0
O R:LYS71 4.1 37.4 1.0
C R:LYS71 4.1 35.8 1.0
C R:SER70 4.1 34.1 1.0
N R:ASP73 4.1 41.2 1.0
CB R:ASP73 4.2 46.9 1.0
OP1 0:G2660 4.4 41.3 1.0
CA R:LYS71 4.4 34.2 1.0
N R:VAL72 4.5 36.4 1.0
CG R:ASP73 4.6 53.2 1.0
N R:LYS71 4.8 33.1 1.0
CA R:VAL72 4.8 36.8 1.0

Sodium binding site 10 out of 75 in 3cma

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Sodium binding site 10 out of 75 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of The Structure of Cca 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
S:Na8510

b:59.0
occ:1.00
 O S:HOH2519 3.4 31.1 1.0
NE2 S:HIS7 3.9 50.0 1.0
CE1 S:HIS7 4.0 50.0 1.0
OE2 S:GLU61 4.2 53.1 1.0
CD2 S:HIS7 4.9 50.0 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: Tue Dec 15 06:07:16 2020

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