Phosphorus in PDB 1a3m: Paromomycin Binding Induces A Local Conformational Change in the A Site of 16S Rrna, uc(Nmr), 20 Structures

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 27;

Binding sites:

The binding sites of Phosphorus atom in the Paromomycin Binding Induces A Local Conformational Change in the A Site of 16S Rrna, uc(Nmr), 20 Structures (pdb code 1a3m). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 27 binding sites of Phosphorus where determined in the Paromomycin Binding Induces A Local Conformational Change in the A Site of 16S Rrna, uc(Nmr), 20 Structures, PDB code: 1a3m:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 27 in 1a3m

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Phosphorus binding site 1 out of 27 in the Paromomycin Binding Induces A Local Conformational Change in the A Site of 16S Rrna, uc(Nmr), 20 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Paromomycin Binding Induces A Local Conformational Change in the A Site of 16S Rrna, uc(Nmr), 20 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P1

b:0.0
occ:1.00
P A:G1 0.0 0.0 1.0
OP2 A:G1 1.5 0.0 1.0
OP1 A:G1 1.5 0.0 1.0
O5' A:G1 1.6 0.0 1.0
C5' A:G1 2.7 0.0 1.0
H5' A:G1 2.9 0.0 1.0
H5'' A:G1 3.0 0.0 1.0
H8 A:G1 3.4 0.0 1.0
C4' A:G1 4.0 0.0 1.0
H3' A:G1 4.0 0.0 1.0
O4' A:G1 4.4 0.0 1.0
C8 A:G1 4.4 0.0 1.0
C3' A:G1 4.6 0.0 1.0
H4' A:G1 4.8 0.0 1.0

Phosphorus binding site 2 out of 27 in 1a3m

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Phosphorus binding site 2 out of 27 in the Paromomycin Binding Induces A Local Conformational Change in the A Site of 16S Rrna, uc(Nmr), 20 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Paromomycin Binding Induces A Local Conformational Change in the A Site of 16S Rrna, uc(Nmr), 20 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:0.0
occ:1.00
P A:G2 0.0 0.0 1.0
OP1 A:G2 1.5 0.0 1.0
OP2 A:G2 1.5 0.0 1.0
O5' A:G2 1.6 0.0 1.0
O3' A:G1 1.6 0.0 1.0
C5' A:G2 2.7 0.0 1.0
C3' A:G1 2.7 0.0 1.0
H3' A:G1 2.8 0.0 1.0
H5' A:G2 2.8 0.0 1.0
H5'' A:G2 3.0 0.0 1.0
H2' A:G1 3.5 0.0 1.0
C2' A:G1 3.5 0.0 1.0
H8 A:G2 3.6 0.0 1.0
O2' A:G1 3.9 0.0 1.0
C4' A:G2 4.0 0.0 1.0
C4' A:G1 4.0 0.0 1.0
H3' A:G2 4.1 0.0 1.0
H5'' A:G1 4.2 0.0 1.0
H4' A:G1 4.2 0.0 1.0
O4' A:G2 4.3 0.0 1.0
C5' A:G1 4.6 0.0 1.0
C3' A:G2 4.6 0.0 1.0
HO2' A:G1 4.6 0.0 1.0
C8 A:G2 4.7 0.0 1.0
H4' A:G2 4.8 0.0 1.0
C1' A:G1 4.9 0.0 1.0
O5' A:G1 4.9 0.0 1.0

Phosphorus binding site 3 out of 27 in 1a3m

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Phosphorus binding site 3 out of 27 in the Paromomycin Binding Induces A Local Conformational Change in the A Site of 16S Rrna, uc(Nmr), 20 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Paromomycin Binding Induces A Local Conformational Change in the A Site of 16S Rrna, uc(Nmr), 20 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:0.0
occ:1.00
P A:C3 0.0 0.0 1.0
OP2 A:C3 1.5 0.0 1.0
OP1 A:C3 1.5 0.0 1.0
O5' A:C3 1.6 0.0 1.0
O3' A:G2 1.6 0.0 1.0
C5' A:C3 2.7 0.0 1.0
C3' A:G2 2.7 0.0 1.0
H3' A:G2 2.8 0.0 1.0
H5' A:C3 2.9 0.0 1.0
H5'' A:C3 3.0 0.0 1.0
H2' A:G2 3.4 0.0 1.0
C2' A:G2 3.5 0.0 1.0
H6 A:C3 3.7 0.0 1.0
O2' A:G2 3.8 0.0 1.0
C4' A:G2 4.0 0.0 1.0
C4' A:C3 4.0 0.0 1.0
H3' A:C3 4.1 0.0 1.0
H5'' A:G2 4.2 0.0 1.0
HO2' A:G2 4.2 0.0 1.0
H4' A:G2 4.2 0.0 1.0
O4' A:C3 4.4 0.0 1.0
C5' A:G2 4.6 0.0 1.0
C3' A:C3 4.6 0.0 1.0
C6 A:C3 4.7 0.0 1.0
H4' A:C3 4.8 0.0 1.0
C1' A:G2 4.9 0.0 1.0
O5' A:G2 5.0 0.0 1.0

Phosphorus binding site 4 out of 27 in 1a3m

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Phosphorus binding site 4 out of 27 in the Paromomycin Binding Induces A Local Conformational Change in the A Site of 16S Rrna, uc(Nmr), 20 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Paromomycin Binding Induces A Local Conformational Change in the A Site of 16S Rrna, uc(Nmr), 20 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:0.0
occ:1.00
P A:G4 0.0 0.0 1.0
OP1 A:G4 1.5 0.0 1.0
OP2 A:G4 1.5 0.0 1.0
O5' A:G4 1.6 0.0 1.0
O3' A:C3 1.6 0.0 1.0
C5' A:G4 2.7 0.0 1.0
C3' A:C3 2.7 0.0 1.0
H5' A:G4 2.8 0.0 1.0
H3' A:C3 2.8 0.0 1.0
H5'' A:G4 3.1 0.0 1.0
H2' A:C3 3.5 0.0 1.0
H8 A:G4 3.5 0.0 1.0
C2' A:C3 3.5 0.0 1.0
O2' A:C3 3.9 0.0 1.0
C4' A:G4 4.0 0.0 1.0
C4' A:C3 4.0 0.0 1.0
H5'' A:C3 4.1 0.0 1.0
H3' A:G4 4.2 0.0 1.0
O4' A:G4 4.2 0.0 1.0
H4' A:C3 4.2 0.0 1.0
HO2' A:C3 4.2 0.0 1.0
C5' A:C3 4.5 0.0 1.0
C8 A:G4 4.6 0.0 1.0
C3' A:G4 4.7 0.0 1.0
O5' A:C3 4.8 0.0 1.0
H4' A:G4 4.8 0.0 1.0
C1' A:C3 4.9 0.0 1.0

Phosphorus binding site 5 out of 27 in 1a3m

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Phosphorus binding site 5 out of 27 in the Paromomycin Binding Induces A Local Conformational Change in the A Site of 16S Rrna, uc(Nmr), 20 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Paromomycin Binding Induces A Local Conformational Change in the A Site of 16S Rrna, uc(Nmr), 20 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:0.0
occ:1.00
P A:U5 0.0 0.0 1.0
OP1 A:U5 1.5 0.0 1.0
OP2 A:U5 1.5 0.0 1.0
O5' A:U5 1.6 0.0 1.0
O3' A:G4 1.6 0.0 1.0
C5' A:U5 2.7 0.0 1.0
C3' A:G4 2.7 0.0 1.0
H3' A:G4 2.8 0.0 1.0
H5' A:U5 2.9 0.0 1.0
H5'' A:U5 3.0 0.0 1.0
HO2' A:G4 3.3 0.0 1.0
H2' A:G4 3.4 0.0 1.0
C2' A:G4 3.5 0.0 1.0
H6 A:U5 3.6 0.0 1.0
O2' A:G4 3.9 0.0 1.0
C4' A:G4 4.0 0.0 1.0
C4' A:U5 4.0 0.0 1.0
H5'' A:G4 4.2 0.0 1.0
H3' A:U5 4.2 0.0 1.0
H4' A:G4 4.2 0.0 1.0
O4' A:U5 4.3 0.0 1.0
C5' A:G4 4.6 0.0 1.0
C6 A:U5 4.6 0.0 1.0
C3' A:U5 4.7 0.0 1.0
H4' A:U5 4.8 0.0 1.0
C1' A:G4 4.9 0.0 1.0
O5' A:G4 5.0 0.0 1.0

Phosphorus binding site 6 out of 27 in 1a3m

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Phosphorus binding site 6 out of 27 in the Paromomycin Binding Induces A Local Conformational Change in the A Site of 16S Rrna, uc(Nmr), 20 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Paromomycin Binding Induces A Local Conformational Change in the A Site of 16S Rrna, uc(Nmr), 20 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:0.0
occ:1.00
P A:C6 0.0 0.0 1.0
OP2 A:C6 1.5 0.0 1.0
OP1 A:C6 1.5 0.0 1.0
O5' A:C6 1.6 0.0 1.0
O3' A:U5 1.6 0.0 1.0
C5' A:C6 2.7 0.0 1.0
C3' A:U5 2.7 0.0 1.0
H3' A:U5 2.8 0.0 1.0
H5' A:C6 2.8 0.0 1.0
H5'' A:C6 3.1 0.0 1.0
H2' A:U5 3.5 0.0 1.0
C2' A:U5 3.5 0.0 1.0
H6 A:C6 3.6 0.0 1.0
O2' A:U5 3.8 0.0 1.0
C4' A:C6 4.0 0.0 1.0
C4' A:U5 4.0 0.0 1.0
HO2' A:U5 4.1 0.0 1.0
H5'' A:U5 4.1 0.0 1.0
H4' A:U5 4.2 0.0 1.0
O4' A:C6 4.2 0.0 1.0
H3' A:C6 4.2 0.0 1.0
C5' A:U5 4.6 0.0 1.0
C3' A:C6 4.7 0.0 1.0
C6 A:C6 4.7 0.0 1.0
H4' A:C6 4.8 0.0 1.0
C1' A:U5 4.9 0.0 1.0

Phosphorus binding site 7 out of 27 in 1a3m

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Phosphorus binding site 7 out of 27 in the Paromomycin Binding Induces A Local Conformational Change in the A Site of 16S Rrna, uc(Nmr), 20 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Paromomycin Binding Induces A Local Conformational Change in the A Site of 16S Rrna, uc(Nmr), 20 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:0.0
occ:1.00
P A:A7 0.0 0.0 1.0
OP2 A:A7 1.5 0.0 1.0
OP1 A:A7 1.5 0.0 1.0
O5' A:A7 1.6 0.0 1.0
O3' A:C6 1.6 0.0 1.0
C5' A:A7 2.7 0.0 1.0
C3' A:C6 2.7 0.0 1.0
H5' A:A7 2.8 0.0 1.0
H3' A:C6 2.8 0.0 1.0
H5'' A:A7 3.0 0.0 1.0
H2' A:C6 3.4 0.0 1.0
C2' A:C6 3.5 0.0 1.0
H8 A:A7 3.8 0.0 1.0
O2' A:C6 3.8 0.0 1.0
C4' A:A7 4.0 0.0 1.0
C4' A:C6 4.0 0.0 1.0
H5'' A:C6 4.2 0.0 1.0
H3' A:A7 4.2 0.0 1.0
HO2' A:C6 4.2 0.0 1.0
O4' A:A7 4.2 0.0 1.0
H4' A:C6 4.2 0.0 1.0
C5' A:C6 4.6 0.0 1.0
C3' A:A7 4.7 0.0 1.0
H4' A:A7 4.8 0.0 1.0
C1' A:C6 4.9 0.0 1.0
C8 A:A7 4.9 0.0 1.0
O5' A:C6 5.0 0.0 1.0

Phosphorus binding site 8 out of 27 in 1a3m

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Phosphorus binding site 8 out of 27 in the Paromomycin Binding Induces A Local Conformational Change in the A Site of 16S Rrna, uc(Nmr), 20 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Paromomycin Binding Induces A Local Conformational Change in the A Site of 16S Rrna, uc(Nmr), 20 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:0.0
occ:1.00
P A:C8 0.0 0.0 1.0
OP2 A:C8 1.5 0.0 1.0
OP1 A:C8 1.5 0.0 1.0
O5' A:C8 1.6 0.0 1.0
O3' A:A7 1.6 0.0 1.0
C3' A:A7 2.7 0.0 1.0
C5' A:C8 2.7 0.0 1.0
H3' A:A7 2.8 0.0 1.0
H5' A:C8 2.9 0.0 1.0
H5'' A:C8 3.0 0.0 1.0
H2' A:A7 3.5 0.0 1.0
C2' A:A7 3.5 0.0 1.0
H6 A:C8 3.6 0.0 1.0
O2' A:A7 3.9 0.0 1.0
C4' A:A7 4.0 0.0 1.0
C4' A:C8 4.0 0.0 1.0
H3' A:C8 4.0 0.0 1.0
H5'' A:A7 4.1 0.0 1.0
HO2' A:A7 4.2 0.0 1.0
H4' A:A7 4.2 0.0 1.0
O4' A:C8 4.4 0.0 1.0
C5' A:A7 4.5 0.0 1.0
C3' A:C8 4.6 0.0 1.0
C6 A:C8 4.7 0.0 1.0
H4' A:C8 4.8 0.0 1.0
C1' A:A7 4.9 0.0 1.0
O5' A:A7 4.9 0.0 1.0

Phosphorus binding site 9 out of 27 in 1a3m

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Phosphorus binding site 9 out of 27 in the Paromomycin Binding Induces A Local Conformational Change in the A Site of 16S Rrna, uc(Nmr), 20 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Paromomycin Binding Induces A Local Conformational Change in the A Site of 16S Rrna, uc(Nmr), 20 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:0.0
occ:1.00
P A:A9 0.0 0.0 1.0
OP1 A:A9 1.5 0.0 1.0
OP2 A:A9 1.5 0.0 1.0
O5' A:A9 1.6 0.0 1.0
O3' A:C8 1.6 0.0 1.0
C5' A:A9 2.7 0.0 1.0
C3' A:C8 2.7 0.0 1.0
H3' A:C8 2.8 0.0 1.0
H5' A:A9 2.8 0.0 1.0
H5'' A:A9 3.1 0.0 1.0
H2' A:C8 3.5 0.0 1.0
C2' A:C8 3.6 0.0 1.0
H8 A:A9 3.6 0.0 1.0
C4' A:C8 4.0 0.0 1.0
O2' A:C8 4.0 0.0 1.0
C4' A:A9 4.0 0.0 1.0
H5'' A:C8 4.1 0.0 1.0
H3' A:A9 4.2 0.0 1.0
O4' A:A9 4.2 0.0 1.0
H4' A:C8 4.2 0.0 1.0
C5' A:C8 4.4 0.0 1.0
O5' A:C8 4.6 0.0 1.0
C8 A:A9 4.6 0.0 1.0
C3' A:A9 4.7 0.0 1.0
HO2' A:C8 4.8 0.0 1.0
H4' A:A9 4.8 0.0 1.0
C1' A:C8 4.9 0.0 1.0

Phosphorus binding site 10 out of 27 in 1a3m

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Phosphorus binding site 10 out of 27 in the Paromomycin Binding Induces A Local Conformational Change in the A Site of 16S Rrna, uc(Nmr), 20 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Paromomycin Binding Induces A Local Conformational Change in the A Site of 16S Rrna, uc(Nmr), 20 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:0.0
occ:1.00
P A:C10 0.0 0.0 1.0
OP2 A:C10 1.5 0.0 1.0
OP1 A:C10 1.5 0.0 1.0
O5' A:C10 1.6 0.0 1.0
O3' A:A9 1.6 0.0 1.0
C5' A:C10 2.7 0.0 1.0
C3' A:A9 2.7 0.0 1.0
H3' A:A9 2.8 0.0 1.0
H5' A:C10 2.8 0.0 1.0
H5'' A:C10 3.0 0.0 1.0
H2' A:A9 3.4 0.0 1.0
C2' A:A9 3.5 0.0 1.0
H6 A:C10 3.6 0.0 1.0
O2' A:A9 3.8 0.0 1.0
C4' A:C10 4.0 0.0 1.0
C4' A:A9 4.0 0.0 1.0
HO2' A:A9 4.2 0.0 1.0
H3' A:C10 4.2 0.0 1.0
H4' A:A9 4.2 0.0 1.0
H5'' A:A9 4.2 0.0 1.0
O4' A:C10 4.3 0.0 1.0
C5' A:A9 4.6 0.0 1.0
C6 A:C10 4.6 0.0 1.0
C3' A:C10 4.7 0.0 1.0
H4' A:C10 4.8 0.0 1.0
C1' A:A9 4.9 0.0 1.0

Reference:

D.Fourmy, S.Yoshizawa, J.D.Puglisi. Paromomycin Binding Induces A Local Conformational Change in the A-Site of 16 S Rrna. J.Mol.Biol. V. 277 333 1998.
ISSN: ISSN 0022-2836
PubMed: 9514734
DOI: 10.1006/JMBI.1997.1551
Page generated: Fri Sep 25 12:08:56 2020

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