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Sodium in PDB 3ow2: Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit

Protein crystallography data

The structure of Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit, PDB code: 3ow2 was solved by Z.F.Kanyo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.853, 298.000, 574.985, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 3ow2:

The structure of Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit also contains other interesting chemical elements:

Fluorine (F) 1 atom
Strontium (Sr) 98 atoms
Magnesium (Mg) 61 atoms
Potassium (K) 1 atom
Cadmium (Cd) 4 atoms
Chlorine (Cl) 13 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 26;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit (pdb code 3ow2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 26 binding sites of Sodium where determined in the Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit, PDB code: 3ow2:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 26 in 3ow2

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Sodium binding site 1 out of 26 in the Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit


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Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8057

b:46.4
occ:1.00
 N3 0:A630 2.8 27.8 1.0
O2' 0:A631 2.9 28.3 1.0
O2' 0:A630 3.0 24.3 1.0
OP2 0:A2074 3.3 30.8 1.0
C2' 0:A631 3.5 26.6 1.0
C2 0:A630 3.6 26.9 1.0
C1' 0:A630 3.8 27.2 1.0
C4 0:A630 3.9 28.0 1.0
C3' 0:A631 3.9 25.0 1.0
C2' 0:A630 4.0 26.6 1.0
N2 0:G2070 4.0 23.7 1.0
O3' 0:A631 4.1 25.4 1.0
OP1 0:A632 4.2 25.7 1.0
N9 0:A630 4.2 27.9 1.0
OP2 0:G2072 4.3 41.8 1.0
O3' 0:A630 4.3 25.1 1.0
P 0:A632 4.6 25.5 1.0
N1 0:A629 4.6 27.3 1.0
C2 0:G2070 4.7 24.5 1.0
P 0:A2074 4.8 30.4 1.0
C3' 0:A630 4.9 25.1 1.0
N1 0:A630 4.9 26.7 1.0
OP2 0:A632 5.0 25.4 1.0
C1' 0:A631 5.0 26.8 1.0
C2 0:A629 5.0 27.6 1.0

Sodium binding site 2 out of 26 in 3ow2

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Sodium binding site 2 out of 26 in the Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit


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Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8058

b:62.8
occ:1.00
 O2' 0:C40 3.0 47.9 1.0
O2 0:C443 3.1 51.2 1.0
O2 0:C40 3.1 50.0 1.0
N1 0:A442 3.2 53.1 1.0
O4' 0:G41 3.2 39.4 1.0
C2 0:A442 3.5 54.0 1.0
C2' 0:C40 3.7 48.1 1.0
C1' 0:C40 4.0 47.9 1.0
C2 0:C443 4.0 50.2 1.0
C1' 0:G41 4.1 37.5 1.0
C4' 0:G41 4.2 38.9 1.0
N2 0:G39 4.2 43.1 1.0
C2 0:C40 4.2 49.5 1.0
C6 0:A442 4.3 53.3 1.0
C5' 0:G41 4.4 40.9 1.0
C1' 0:C443 4.5 49.8 1.0
N9 0:G41 4.6 37.3 1.0
N6 0:A442 4.6 53.0 1.0
N1 0:C40 4.6 48.5 1.0
N1 0:C443 4.7 49.7 1.0
N3 0:A442 4.8 54.0 1.0
N3 0:C443 4.8 49.9 1.0
C2 0:G39 5.0 42.7 1.0

Sodium binding site 3 out of 26 in 3ow2

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Sodium binding site 3 out of 26 in the Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit


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Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8059

b:39.0
occ:1.00
 O2 0:U1724 2.5 59.2 1.0
O2 0:C1394 2.6 38.5 1.0
O4 0:U1432 2.7 42.3 1.0
O6 0:G1433 3.4 41.4 1.0
O2' 0:C1394 3.5 33.7 1.0
C2 0:C1394 3.6 35.5 1.0
C2 0:U1724 3.7 57.1 1.0
C2' 0:C1394 3.8 34.5 1.0
SR 0:SR8130 3.8 0.8 1.0
O2' 0:U1724 3.9 52.2 1.0
C4 0:U1432 3.9 38.6 1.0
C1' 0:C1394 4.1 35.0 1.0
C1' 0:U1724 4.1 51.8 1.0
C6 0:G1433 4.1 38.5 1.0
N1 0:C1394 4.3 35.8 1.0
C2' 0:U1724 4.3 50.4 1.0
N1 0:U1724 4.4 54.5 1.0
N3 0:U1432 4.5 37.5 1.0
N3 0:C1394 4.6 34.7 1.0
N1 0:G1433 4.6 37.7 1.0
N3 0:U1724 4.6 57.1 1.0
O2' 0:C1725 4.9 31.6 1.0

Sodium binding site 4 out of 26 in 3ow2

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Sodium binding site 4 out of 26 in the Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8060

b:46.1
occ:1.00
 O6 0:G2579 2.9 30.2 1.0
O4' 0:A2577 3.0 34.9 1.0
N7 0:G2579 3.1 29.3 1.0
N3 0:A2577 3.1 30.6 1.0
N7 0:G2578 3.2 27.9 1.0
O6 0:G2578 3.4 32.2 1.0
C6 0:G2579 3.5 29.5 1.0
C5 0:G2579 3.6 29.8 1.0
C5 0:G2578 3.6 28.7 1.0
C1' 0:A2577 3.7 33.1 1.0
C6 0:G2578 3.8 29.4 1.0
C4' 0:A2577 3.9 34.4 1.0
C2 0:A2577 3.9 29.8 1.0
C4 0:A2577 4.0 31.0 1.0
C8 0:G2578 4.1 27.4 1.0
N9 0:A2577 4.2 31.0 1.0
C8 0:G2579 4.2 30.3 1.0
N4 0:C2556 4.7 25.5 1.0
C4 0:G2578 4.7 29.0 1.0
O3' 0:A2577 4.8 33.6 1.0
N1 0:G2579 4.8 29.7 1.0
C3' 0:A2577 4.8 34.0 1.0
C5' 0:A2577 4.9 33.6 1.0
C4 0:G2579 4.9 29.9 1.0
N3 0:U2554 4.9 27.2 1.0
N1 0:G2578 4.9 29.8 1.0
N9 0:G2578 4.9 28.7 1.0
C2' 0:A2577 5.0 33.7 1.0

Sodium binding site 5 out of 26 in 3ow2

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Sodium binding site 5 out of 26 in the Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8061

b:56.7
occ:1.00
 O2' 0:U2607 2.9 28.6 1.0
O2 0:U2607 3.0 35.8 1.0
OP1 0:U2541 3.2 27.9 1.0
CZ3 B:TRP242 3.9 21.8 1.0
OP2 0:C2608 4.0 27.3 1.0
C2 0:U2607 4.0 33.8 1.0
P 0:U2541 4.2 30.2 1.0
C2' 0:U2607 4.2 28.3 1.0
OP2 0:U2541 4.3 31.1 1.0
CH2 B:TRP242 4.3 22.1 1.0
C1' 0:U2607 4.4 30.2 1.0
O3' 0:U2607 4.5 27.3 1.0
OP1 0:U2610 4.6 27.8 1.0
N1 0:U2607 4.6 32.4 1.0
O3' 0:G2540 4.7 30.7 1.0
O2 0:U2539 4.7 60.8 1.0
P 0:C2608 4.8 26.4 1.0
O2' 0:U2539 4.8 46.4 1.0
CE3 B:TRP242 4.8 22.6 1.0
N3 0:U2607 4.9 35.0 1.0
C3' 0:U2607 5.0 27.8 1.0

Sodium binding site 6 out of 26 in 3ow2

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Sodium binding site 6 out of 26 in the Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8062

b:39.8
occ:1.00
 O3' 0:G1416 2.7 29.2 1.0
O 1:TRP42 2.7 35.7 1.0
O 1:ASN45 2.9 41.7 1.0
OP1 0:G1417 3.1 30.8 1.0
O2' 0:G1416 3.4 28.3 1.0
P 0:G1417 3.6 28.7 1.0
C3' 0:G1416 3.7 27.6 1.0
C 1:TRP42 3.9 35.2 1.0
C 1:ASN45 4.0 41.6 1.0
C4' 0:G1416 4.0 26.9 1.0
C2' 0:G1416 4.2 27.8 1.0
CA 1:ASP46 4.2 43.1 1.0
O 1:ARG43 4.2 39.9 1.0
C5' 0:G1417 4.3 28.0 1.0
OP1 0:C1686 4.4 28.8 1.0
O5' 0:G1417 4.5 28.8 1.0
CB 1:ASP46 4.6 45.4 1.0
N 1:ASP46 4.6 42.1 1.0
CA 1:ARG43 4.7 36.3 1.0
C 1:ARG43 4.7 38.4 1.0
OP2 0:G1417 4.7 27.1 1.0
OP2 0:C1687 4.7 30.1 1.0
N 1:ARG43 4.8 36.1 1.0
OP1 0:C1687 4.8 28.6 1.0
OD2 1:ASP46 4.8 51.3 1.0
C5' 0:G1416 4.9 26.4 1.0
CA 1:TRP42 4.9 34.2 1.0

Sodium binding site 7 out of 26 in 3ow2

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Sodium binding site 7 out of 26 in the Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8063

b:48.8
occ:1.00
 N7 0:G2544 2.9 30.2 1.0
O4 0:U2545 3.2 32.0 1.0
O6 0:G2544 3.5 29.5 1.0
C5 0:G2544 3.8 28.0 1.0
O4 0:U2610 3.8 31.4 1.0
C8 0:G2544 3.9 28.6 1.0
C6 0:G2544 4.0 28.3 1.0
C4 0:U2545 4.0 29.5 1.0
C4 0:U2610 4.3 26.3 1.0
N7 0:G2543 4.5 30.2 1.0
C5 0:U2545 4.5 29.0 1.0
C5 0:U2610 4.6 26.9 1.0
OP2 0:G2544 4.6 30.3 1.0
N3 0:U2545 5.0 28.5 1.0

Sodium binding site 8 out of 26 in 3ow2

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Sodium binding site 8 out of 26 in the Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8064

b:61.2
occ:1.00
 O2' 0:G885 2.8 28.6 1.0
O4' 0:G2113 3.0 24.8 1.0
N3 0:A2112 3.1 26.5 1.0
O2' 0:A2112 3.1 24.6 1.0
N4 0:C2475 3.3 30.5 1.0
C1' 0:G2113 3.5 25.0 1.0
C2' 0:A2112 3.5 22.4 1.0
N3 0:C2475 3.7 28.0 1.0
C1' 0:A2112 3.7 22.3 1.0
N9 0:G2113 3.7 24.0 1.0
O2 0:C2476 3.8 25.7 1.0
C2 0:A2112 3.9 25.8 1.0
C4 0:C2475 4.0 29.1 1.0
C4 0:A2112 4.0 24.3 1.0
O3' 0:G885 4.0 30.6 1.0
C8 0:G2113 4.1 24.3 1.0
C2' 0:G885 4.1 27.1 1.0
N9 0:A2112 4.3 23.7 1.0
N2 0:G2111 4.3 24.7 1.0
C4' 0:G2113 4.4 23.0 1.0
OP2 0:A886 4.5 34.9 1.0
C4 0:G2113 4.5 23.8 1.0
C2 0:C2476 4.5 27.4 1.0
C3' 0:G885 4.7 27.9 1.0
P 0:A886 4.7 32.3 1.0
C1' 0:G885 4.8 26.0 1.0
C5' 0:G2113 4.8 20.8 1.0
N7 0:G2113 4.9 24.1 1.0
C2 0:C2475 4.9 28.2 1.0
OP1 0:A886 4.9 31.5 1.0
C2' 0:G2113 5.0 24.3 1.0
N3 0:C2476 5.0 26.7 1.0

Sodium binding site 9 out of 26 in 3ow2

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Sodium binding site 9 out of 26 in the Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8065

b:48.6
occ:1.00
 O4' 0:C141 3.1 50.3 1.0
O6 0:G142 3.1 43.4 1.0
O2 0:C141 3.2 52.4 1.0
N7 0:G142 3.3 42.0 1.0
N2 0:G140 3.5 61.4 1.0
C4' 0:C141 3.8 48.9 1.0
C6 0:G142 3.9 43.0 1.0
OP2 0:C141 3.9 54.4 1.0
C5 0:G142 3.9 42.3 1.0
C2 0:G140 3.9 60.6 1.0
C2 0:C141 4.0 52.8 1.0
C5' 0:C141 4.2 51.1 1.0
C1' 0:C141 4.2 50.4 1.0
N3 0:G140 4.2 60.1 1.0
C8 0:G142 4.5 42.2 1.0
N1 0:C141 4.5 52.0 1.0
N4 0:C143 4.6 38.1 1.0
N1 0:G140 4.7 60.0 1.0
O5' 0:C141 4.8 54.0 1.0
N4 0:C136 4.8 33.0 1.0
N3 0:C141 4.9 53.2 1.0
P 0:C141 5.0 56.1 1.0

Sodium binding site 10 out of 26 in 3ow2

Go back to Sodium Binding Sites List in 3ow2
Sodium binding site 10 out of 26 in the Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8066

b:42.7
occ:1.00
 O6 0:G1896 2.8 44.2 1.0
O4' 0:C1894 2.9 46.7 1.0
N7 0:G1896 3.0 45.0 1.0
O2 0:C1894 3.0 47.0 1.0
N7 0:A1895 3.3 53.9 1.0
C6 0:G1896 3.5 44.7 1.0
C5 0:G1896 3.5 45.2 1.0
O4 0:U1897 3.5 42.3 1.0
C2 0:C1894 3.6 45.3 1.0
C1' 0:C1894 3.7 46.6 1.0
C5 0:A1895 3.7 53.8 1.0
N6 0:A1895 3.8 54.6 1.0
C4' 0:C1894 3.9 46.6 1.0
N1 0:C1894 4.0 45.7 1.0
C6 0:A1895 4.0 54.2 1.0
C8 0:A1895 4.0 53.1 1.0
N6 0:A1942 4.0 37.9 1.0
C8 0:G1896 4.2 44.7 1.0
C4 0:U1897 4.3 39.9 1.0
SR 0:SR8141 4.4 0.5 1.0
N3 0:C1894 4.6 44.9 1.0
C4 0:A1895 4.6 53.3 1.0
C5' 0:C1894 4.7 45.3 1.0
N9 0:A1895 4.8 52.8 1.0
N1 0:G1896 4.8 44.6 1.0
C4 0:G1896 4.9 44.9 1.0
C5 0:U1897 4.9 39.1 1.0
C3' 0:C1894 5.0 47.6 1.0
N3 0:U1897 5.0 38.2 1.0

Reference:

Z.F.Kanyo, N/A. N/A N/A.
Page generated: Tue Dec 15 06:20:38 2020

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