Atomistry » Sodium » PDB 3c7o-3cpw » 3cme
Atomistry »
  Sodium »
    PDB 3c7o-3cpw »
      3cme »

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

Protein crystallography data

The structure of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cme 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) 49.82 / 2.95
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 210.786, 297.778, 572.588, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 25.5

Other elements in 3cme:

The structure of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Strontium (Sr) 108 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 Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 3cme). 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 Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cme:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 75 in 3cme

Go back to Sodium Binding Sites List in 3cme
Sodium binding site 1 out of 75 in the The Structure of Ca 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 Ca 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:31.8
occ:1.00
 O C:LYS96 2.7 42.4 1.0
OD1 C:ASP45 2.8 39.3 1.0
O C:HOH8509 3.0 46.0 1.0
O C:THR94 3.3 41.5 1.0
C C:LYS96 3.3 42.8 1.0
O C:HOH8623 3.4 62.5 1.0
CG C:ASP45 3.6 41.1 1.0
OD2 C:ASP45 3.7 41.6 1.0
N C:ASP97 3.8 41.8 1.0
CA C:ASP97 3.9 40.6 1.0
N C:LYS96 4.0 43.4 1.0
C C:GLU95 4.0 42.9 1.0
O C:GLU95 4.1 42.9 1.0
CA C:LYS96 4.2 43.4 1.0
C C:THR94 4.4 40.7 1.0
CA C:GLU95 4.5 43.6 1.0
CB C:ASP97 4.8 39.2 1.0
N C:ARG98 4.9 41.2 1.0
C C:ASP97 4.9 41.1 1.0
N C:GLU95 5.0 42.1 1.0
CB C:ASP45 5.0 41.3 1.0

Sodium binding site 2 out of 75 in 3cme

Go back to Sodium Binding Sites List in 3cme
Sodium binding site 2 out of 75 in the The Structure of Ca 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 Ca 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
H:Na8518

b:69.6
occ:1.00
 N4 0:C2287 3.2 75.8 1.0
NH1 H:ARG117 3.3 60.4 1.0
N3 0:C2287 3.6 76.1 1.0
C4 0:C2287 3.9 75.9 1.0
O6 0:G2286 4.0 55.6 1.0
CD H:ARG117 4.1 59.5 1.0
O H:HOH8999 4.2 31.9 1.0
O 0:HOH5666 4.3 35.5 1.0
N H:ASP114 4.3 78.5 1.0
CZ H:ARG117 4.4 61.0 1.0
NE H:ARG117 4.7 61.1 1.0
C2 0:G2288 4.7 64.8 1.0
N3 0:G2288 4.8 64.7 1.0
C2 0:C2287 4.8 75.5 1.0
C6 0:G2286 4.9 53.5 1.0
C4 0:G2288 5.0 64.5 1.0
N1 0:G2288 5.0 64.3 1.0

Sodium binding site 3 out of 75 in 3cme

Go back to Sodium Binding Sites List in 3cme
Sodium binding site 3 out of 75 in the The Structure of Ca 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 Ca 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:31.5
occ:1.00
 O J:TYR69 2.7 50.9 1.0
O 0:HOH3397 2.9 50.3 1.0
O J:ILE63 2.9 46.5 1.0
O J:VAL61 2.9 46.1 1.0
O 0:HOH6622 2.9 24.1 1.0
OP1 0:A2677 3.1 61.5 1.0
O J:ARG60 3.4 43.1 1.0
C J:VAL61 3.6 46.0 1.0
C J:TYR69 3.8 50.4 1.0
N J:TYR71 3.9 53.0 1.0
CA J:VAL61 4.0 44.5 1.0
C J:ILE63 4.1 46.4 1.0
CB J:TYR71 4.2 50.4 1.0
CL J:CL8821 4.3 64.2 1.0
C J:ARG60 4.4 41.5 1.0
CB J:TYR69 4.5 47.3 1.0
CD2 J:TYR69 4.5 46.0 1.0
N J:ASP62 4.6 47.9 1.0
CA J:PHE70 4.6 55.7 1.0
N J:ILE63 4.6 48.2 1.0
C J:PHE70 4.6 54.5 1.0
P 0:A2677 4.6 61.1 1.0
N J:PHE70 4.6 53.4 1.0
CA J:TYR71 4.6 50.9 1.0
N J:VAL61 4.7 43.2 1.0
C J:ASP62 4.7 49.4 1.0
CA J:TYR69 4.7 48.4 1.0
CA J:ILE63 4.9 46.7 1.0
CG J:TYR69 5.0 46.5 1.0

Sodium binding site 4 out of 75 in 3cme

Go back to Sodium Binding Sites List in 3cme
Sodium binding site 4 out of 75 in the The Structure of Ca 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 Ca 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:33.6
occ:1.00
 O M:PRO110 2.7 36.5 1.0
OG M:SER106 2.8 30.6 1.0
O M:LEU112 2.9 39.3 1.0
O M:SER106 3.0 37.3 1.0
O M:PHE109 3.1 31.2 1.0
C M:PRO110 3.3 35.9 1.0
CA M:PRO110 3.5 34.7 1.0
O M:HOH8929 3.5 23.9 1.0
O M:HOH8859 3.6 40.8 1.0
C M:PHE109 3.8 31.9 1.0
C M:LEU112 3.9 37.4 1.0
C M:SER106 3.9 36.9 1.0
N M:PRO110 4.0 32.8 1.0
CB M:SER106 4.1 34.9 1.0
N M:ASN111 4.3 36.8 1.0
N M:LEU112 4.3 38.0 1.0
CA M:SER106 4.4 35.3 1.0
CL M:CL8818 4.6 46.8 1.0
C M:ASN111 4.6 38.5 1.0
CA M:LEU112 4.7 38.2 1.0
OD1 M:ASP157 4.8 43.4 1.0
N M:ARG113 4.8 36.7 1.0
CB M:PRO110 4.9 34.3 1.0
CE1 M:PHE160 4.9 44.1 1.0
CA M:ASN111 4.9 39.2 1.0
N M:ARG107 5.0 37.7 1.0
CA M:ARG113 5.0 35.2 1.0

Sodium binding site 5 out of 75 in 3cme

Go back to Sodium Binding Sites List in 3cme
Sodium binding site 5 out of 75 in the The Structure of Ca 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 Ca 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:66.4
occ:1.00
 O Q:GLY22 2.7 52.4 1.0
OG Q:SER24 2.7 54.2 1.0
O Q:ASP20 2.8 59.1 1.0
O Q:HOH1795 2.9 33.9 1.0
OG Q:SER46 3.0 50.4 1.0
O Q:HOH5427 3.1 11.8 1.0
O Q:HOH7505 3.2 87.7 1.0
O Q:THR23 3.4 53.5 1.0
CB Q:SER46 3.7 48.0 1.0
CA Q:SER24 3.7 51.8 1.0
CB Q:SER24 3.7 52.7 1.0
C Q:THR23 3.7 54.0 1.0
C Q:ASP20 3.8 60.3 1.0
N Q:SER24 3.9 52.4 1.0
C Q:GLY22 3.9 53.2 1.0
O Q:ARG21 4.1 54.2 1.0
OD1 Q:ASN16 4.3 57.1 1.0
NH2 Q:ARG28 4.3 51.5 1.0
OD1 Q:ASP44 4.4 54.0 1.0
C Q:ARG21 4.4 54.5 1.0
CA Q:ASP20 4.5 62.2 1.0
OD2 Q:ASP44 4.7 53.3 1.0
CA Q:THR23 4.7 54.2 1.0
N Q:THR23 4.8 53.2 1.0
N Q:ARG21 4.8 58.5 1.0
OP1 0:C2366 4.8 45.5 1.0
N Q:GLY22 4.8 54.1 1.0
CB Q:ASP20 4.8 65.3 1.0
CA Q:GLY22 4.9 53.5 1.0
CG Q:ASP44 5.0 52.5 1.0
CG Q:ASN16 5.0 57.6 1.0

Sodium binding site 6 out of 75 in 3cme

Go back to Sodium Binding Sites List in 3cme
Sodium binding site 6 out of 75 in the The Structure of Ca 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 Ca 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:25.2
occ:1.00
 O R:SER70 2.8 39.4 1.0
O R:VAL72 2.9 44.3 1.0
O R:HOH8933 3.0 64.7 1.0
NA 0:NA8533 3.1 64.9 1.0
O 0:HOH6777 3.1 67.0 1.0
O 0:HOH4650 3.1 96.2 1.0
C R:VAL72 3.7 44.4 1.0
O R:HOH8987 3.7 59.9 1.0
CA R:ASP73 3.9 46.3 1.0
C R:SER70 4.0 38.9 1.0
OD1 R:ASP73 4.1 58.0 1.0
N R:ASP73 4.1 45.6 1.0
C R:LYS71 4.2 42.1 1.0
O R:LYS71 4.2 44.0 1.0
CB R:ASP73 4.2 50.0 1.0
N R:VAL72 4.5 43.3 1.0
O R:HOH8923 4.5 42.5 1.0
CA R:LYS71 4.5 40.9 1.0
OP1 0:G2660 4.6 48.3 1.0
CG R:ASP73 4.7 55.3 1.0
N R:LYS71 4.8 39.7 1.0
CA R:VAL72 4.8 43.7 1.0

Sodium binding site 7 out of 75 in 3cme

Go back to Sodium Binding Sites List in 3cme
Sodium binding site 7 out of 75 in the The Structure of Ca 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 Ca 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:80.5
occ:1.00
 OE2 S:GLU61 3.0 59.1 1.0
NE2 S:HIS7 3.1 59.4 1.0
O S:HOH8524 3.1 65.8 1.0
CE1 S:HIS7 3.4 60.3 1.0
CD S:GLU61 4.0 56.4 1.0
OE1 S:GLU61 4.2 57.2 1.0
CD2 S:HIS7 4.3 59.3 1.0
ND1 S:HIS7 4.6 59.5 1.0

Sodium binding site 8 out of 75 in 3cme

Go back to Sodium Binding Sites List in 3cme
Sodium binding site 8 out of 75 in the The Structure of Ca 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 Ca 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
0:Na8501

b:0.8
occ:1.00
 O 0:HOH5852 3.0 29.6 1.0
O 0:HOH4651 3.0 54.0 1.0
O 0:HOH2993 3.1 14.5 1.0
O 0:HOH6569 3.1 55.0 1.0
O 0:HOH4110 3.3 70.0 1.0
N2 0:G1071 3.3 30.0 1.0
O 0:HOH4077 3.6 38.7 1.0
N6 0:A1070 3.9 19.7 1.0
O6 0:G1072 4.1 30.2 1.0
O 0:HOH4434 4.3 19.6 1.0
C2 0:G1071 4.4 30.0 1.0
N7 0:G1072 4.7 28.5 1.0
OP2 0:C1069 4.9 27.9 1.0

Sodium binding site 9 out of 75 in 3cme

Go back to Sodium Binding Sites List in 3cme
Sodium binding site 9 out of 75 in the The Structure of Ca 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 Ca 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
0:Na8502

b:60.5
occ:1.00
 O 0:HOH9593 3.0 15.4 1.0
N7 0:G1121 3.1 30.2 1.0
O2' 0:G1119 3.1 41.0 1.0
O 0:HOH5431 3.2 20.8 1.0
O4 0:U1122 3.3 30.7 1.0
O 0:HOH5055 3.4 35.1 1.0
O6 0:G1121 3.4 25.6 1.0
OP2 0:U1120 3.5 38.4 1.0
O3' 0:G1119 3.6 38.6 1.0
O 0:HOH6550 3.8 93.1 1.0
C5 0:G1121 3.8 28.4 1.0
C4 0:U1122 3.9 30.3 1.0
C6 0:G1121 4.0 27.1 1.0
C5 0:U1122 4.0 29.9 1.0
C8 0:G1121 4.2 31.1 1.0
P 0:U1120 4.2 40.2 1.0
C2' 0:G1119 4.3 38.6 1.0
C3' 0:G1119 4.5 39.7 1.0
C1' 0:G1119 4.7 35.4 1.0
N6 0:A1242 4.8 28.0 1.0
MG 0:MG8018 4.9 3.9 1.0
CL J:CL8816 4.9 80.7 1.0

Sodium binding site 10 out of 75 in 3cme

Go back to Sodium Binding Sites List in 3cme
Sodium binding site 10 out of 75 in the The Structure of Ca 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 Ca 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
0:Na8504

b:31.7
occ:1.00
 N3 0:A630 2.7 36.9 1.0
O2' 0:A631 2.8 38.6 1.0
O2' 0:A630 3.0 32.4 1.0
O 0:HOH4978 3.0 25.3 1.0
O 0:HOH5585 3.1 56.4 1.0
O 0:HOH6648 3.2 23.8 1.0
OP2 0:A2074 3.5 40.0 1.0
C2 0:A630 3.5 36.9 1.0
C2' 0:A631 3.6 37.3 1.0
C1' 0:A630 3.6 36.8 1.0
C4 0:A630 3.7 37.5 1.0
OP1 0:A632 3.8 40.5 1.0
C3' 0:A631 3.8 36.4 1.0
C2' 0:A630 3.9 34.5 1.0
O3' 0:A631 4.0 37.0 1.0
N9 0:A630 4.1 38.1 1.0
O3' 0:A630 4.1 32.5 1.0
N2 0:G2070 4.2 33.7 1.0
P 0:A632 4.4 41.6 1.0
O 0:HOH3323 4.4 21.9 1.0
C3' 0:A630 4.6 32.6 1.0
OP2 0:A632 4.8 41.1 1.0
N1 0:A629 4.8 33.4 1.0
N1 0:A630 4.8 36.8 1.0
O4' 0:A630 4.9 36.3 1.0
C2 0:G2070 5.0 33.5 1.0
C2 0:1MA628 5.0 42.1 1.0
P 0:A2074 5.0 40.1 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: Mon Oct 7 07:18:37 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy