Sodium in PDB 3zp8: High-Resolution Full-Length Hammerhead Ribozyme

The structure of High-Resolution Full-Length Hammerhead Ribozyme, PDB code: 3zp8 was solved by M.Anderson, E.Schultz, M.Martick, W.G.Scott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.390 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	50.820, 68.530, 58.900, 90.00, 112.35, 90.00
R / Rfree (%)	18.67 / 21.57

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Sodium atom in the High-Resolution Full-Length Hammerhead Ribozyme (pdb code 3zp8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 16 binding sites of Sodium where determined in the High-Resolution Full-Length Hammerhead Ribozyme, PDB code: 3zp8:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 16 in the High-Resolution Full-Length Hammerhead Ribozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High-Resolution Full-Length Hammerhead Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1044 b:24.7 occ:1.00 OP2 A:A21 2.4 26.2 1.0 O A:HOH2130 2.4 36.7 1.0 O A:HOH2122 2.4 30.7 1.0 N7 A:G22 2.6 23.8 1.0 O A:HOH2120 2.6 35.3 1.0 O A:HOH2121 2.6 40.9 1.0 C8 A:G22 3.5 26.0 1.0 P A:A21 3.5 23.3 1.0 C5 A:G22 3.6 23.0 1.0 O6 A:G22 3.7 24.8 1.0 O5' A:A21 3.8 26.1 1.0 C6 A:G22 4.0 24.4 1.0 O A:HOH2117 4.3 33.9 1.0 OP1 A:A21 4.3 20.8 1.0 O A:HOH2131 4.4 34.2 1.0 O A:HOH2009 4.4 36.2 1.0 O4 A:U23 4.4 28.1 1.0 N9 A:G22 4.7 28.2 1.0 OP2 A:G22 4.7 34.1 1.0 C4 A:G22 4.7 27.2 1.0 O3' A:G20 4.8 20.8 1.0 O A:HOH2119 4.8 40.4 1.0 C8 A:A21 4.8 19.9 1.0 N7 A:A21 4.9 24.4 1.0

Sodium binding site 2 out of 16 in the High-Resolution Full-Length Hammerhead Ribozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High-Resolution Full-Length Hammerhead Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1045 b:20.2 occ:1.00 O2' A:U19 2.3 19.0 1.0 O A:HOH2113 2.5 34.0 1.0 O2 A:U19 2.5 23.5 1.0 C2 A:U19 3.4 21.3 1.0 C2' A:U19 3.5 16.3 1.0 C1' A:U19 3.6 15.2 1.0 N1 A:U19 4.0 20.5 1.0 O3' A:U19 4.3 19.2 1.0 N3 A:U19 4.5 22.2 1.0 C3' A:U19 4.5 15.7 1.0 O A:HOH2118 4.6 29.3 1.0 O A:HOH2112 4.9 40.9 1.0 O4' A:U19 5.0 19.5 1.0

Sodium binding site 3 out of 16 in the High-Resolution Full-Length Hammerhead Ribozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of High-Resolution Full-Length Hammerhead Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1046 b:29.1 occ:1.00 O A:HOH2108 2.3 29.2 1.0 O A:HOH2184 2.6 29.6 1.0 O2' A:A18 2.7 18.3 1.0 O3' A:A18 2.9 16.6 1.0 C3' A:A18 3.6 16.3 1.0 C2' A:A18 3.7 15.9 1.0 O A:HOH2111 3.7 42.2 1.0 OP1 A:U19 3.8 17.4 1.0 C4' A:A18 4.0 16.6 1.0 P A:U19 4.0 17.7 1.0 O A:HOH2183 4.3 44.7 1.0 C5' A:G20 4.4 19.9 1.0 N1 A:A37 4.4 19.8 1.0 C2 A:A37 4.5 21.5 1.0 N3 A:A38 4.6 22.8 1.0 O A:HOH2125 4.8 40.0 0.5 C1' A:A18 4.8 15.1 1.0 O4' A:A18 4.9 18.1 1.0 C2 A:A38 4.9 19.3 1.0 C4' A:G20 5.0 16.4 1.0 OP2 A:U19 5.0 16.8 1.0

Sodium binding site 4 out of 16 in the High-Resolution Full-Length Hammerhead Ribozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of High-Resolution Full-Length Hammerhead Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1047 b:39.2 occ:0.50 O A:HOH2091 2.3 43.5 1.0 O4 A:U19 2.5 28.8 1.0 C4 A:U19 3.6 21.5 1.0 O2' A:C15 4.0 31.7 1.0 O A:HOH2098 4.1 32.9 1.0 N3 A:U19 4.1 22.2 1.0 O A:HOH2092 4.3 45.4 1.0 O A:HOH2093 4.3 43.5 1.0 C2' A:C15 4.4 27.8 1.0 O A:HOH2014 4.5 63.2 1.0 C5 A:U19 4.7 24.6 1.0 C6 A:C15 4.9 24.2 1.0

Sodium binding site 5 out of 16 in the High-Resolution Full-Length Hammerhead Ribozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of High-Resolution Full-Length Hammerhead Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1048 b:51.4 occ:1.00 OP1 A:A18 2.8 20.7 1.0 O A:HOH2099 2.9 34.5 1.0 O A:HOH2107 3.1 34.9 1.0 OP2 A:U19 3.4 16.8 1.0 O4 A:U16 3.6 24.0 1.0 O A:HOH2111 3.7 42.2 1.0 C5' A:A18 3.8 21.0 1.0 P A:A18 3.9 21.2 1.0 O5' A:A18 4.1 18.6 1.0 C4 A:U16 4.3 18.8 1.0 NA A:NA1052 4.3 28.9 1.0 N3 A:U16 4.5 22.3 1.0 P A:U19 4.7 17.7 1.0 OP2 A:A18 4.9 22.9 1.0 O A:HOH2097 4.9 28.4 1.0

Sodium binding site 6 out of 16 in the High-Resolution Full-Length Hammerhead Ribozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of High-Resolution Full-Length Hammerhead Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1049 b:39.0 occ:1.00 O A:HOH2068 2.3 38.2 1.0 O A:HOH2069 2.3 26.9 1.0 O2 A:U9 2.4 23.0 1.0 O A:HOH2067 2.5 39.5 1.0 O A:HOH2153 2.5 35.1 1.0 C2 A:U9 3.6 18.9 1.0 N6 A:A31 4.0 23.2 1.0 O A:HOH2010 4.0 33.3 1.0 C1' A:U9 4.0 30.1 1.0 O2' A:U9 4.1 31.2 1.0 N1 A:U9 4.3 21.5 1.0 C2' A:U9 4.3 28.4 1.0 C2 B:A12 4.5 24.1 1.0 N1 A:A28 4.6 25.7 1.0 N3 A:U9 4.6 20.1 1.0 O4' A:A10 4.7 29.9 1.0 O A:HOH2055 4.8 25.2 1.0 C6 A:A31 4.9 21.1 1.0 C2 A:A28 4.9 22.9 1.0 C1' A:A10 5.0 29.1 1.0 O2 B:U13 5.0 28.0 1.0

Sodium binding site 7 out of 16 in the High-Resolution Full-Length Hammerhead Ribozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of High-Resolution Full-Length Hammerhead Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1050 b:42.0 occ:1.00 O A:HOH2142 2.4 37.4 1.0 O A:HOH2137 2.4 43.0 1.0 O A:HOH2139 2.4 39.8 1.0 N7 A:A27 2.5 25.1 1.0 O A:HOH2056 2.5 30.6 1.0 O A:HOH2208 2.8 47.4 1.0 C8 A:A27 3.3 24.1 1.0 C5 A:A27 3.6 21.5 1.0 OP2 A:A27 3.9 33.8 1.0 N6 A:A27 4.0 28.6 1.0 O A:HOH2050 4.2 44.5 1.0 C6 A:A27 4.2 20.7 1.0 N7 A:A7 4.5 20.1 1.0 N9 A:A27 4.6 24.0 1.0 C5 A:C26 4.7 27.7 1.0 C4 A:A27 4.7 22.5 1.0 OP2 A:C26 4.7 33.0 1.0 N6 A:A7 4.8 21.7 1.0 O5' A:A27 5.0 29.5 1.0

Sodium binding site 8 out of 16 in the High-Resolution Full-Length Hammerhead Ribozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of High-Resolution Full-Length Hammerhead Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1051 b:38.0 occ:1.00 O A:HOH2176 2.2 34.1 1.0 OP2 A:A38 2.3 36.7 1.0 O A:HOH2181 2.3 39.1 1.0 O A:HOH2182 2.4 48.2 1.0 O A:HOH2178 2.6 43.1 1.0 O A:HOH2209 2.6 46.8 1.0 P A:A38 3.6 36.8 1.0 O A:HOH2177 3.7 41.2 1.0 O5' A:A38 4.0 34.8 1.0 O A:HOH2193 4.1 44.0 1.0 O B:HOH2016 4.1 36.8 1.0 N7 A:A38 4.3 26.9 1.0 C8 A:A38 4.4 27.5 1.0 OP1 A:A38 4.5 40.0 1.0 OP2 A:A37 4.5 37.2 1.0 N7 A:A39 4.5 26.8 1.0 O5' A:A37 4.6 35.9 1.0 OP1 A:A37 4.6 40.0 1.0 N6 A:A39 4.7 21.1 1.0 O3' A:A37 4.7 41.4 1.0 P A:A37 4.8 36.9 1.0 O A:HOH2187 4.8 26.5 1.0 C3' A:A37 4.9 35.1 1.0

Sodium binding site 9 out of 16 in the High-Resolution Full-Length Hammerhead Ribozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of High-Resolution Full-Length Hammerhead Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1052 b:28.9 occ:1.00 O A:HOH2098 2.3 32.9 1.0 O A:HOH2097 2.3 28.4 1.0 O A:HOH2099 2.4 34.5 1.0 O4 A:U16 2.4 24.0 1.0 O A:HOH2210 2.7 30.9 1.0 C4 A:U16 3.4 18.8 1.0 C5 A:U16 3.7 26.5 1.0 O A:HOH2107 4.1 34.9 1.0 NA A:NA1048 4.3 51.4 1.0 O A:HOH2093 4.5 43.5 1.0 N3 A:U16 4.6 22.3 1.0 O A:HOH2094 4.8 32.1 1.0

Sodium binding site 10 out of 16 in the High-Resolution Full-Length Hammerhead Ribozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of High-Resolution Full-Length Hammerhead Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1053 b:30.3 occ:1.00 O A:HOH2167 2.2 29.1 1.0 O6 A:G36 2.4 28.4 1.0 O A:HOH2175 2.5 28.4 1.0 O A:HOH2172 2.6 33.8 1.0 C6 A:G36 3.5 26.4 1.0 C5 B:OMC6 3.6 26.1 1.0 C6 B:OMC6 3.9 25.6 1.0 O A:HOH2033 4.0 48.6 1.0 N7 A:G36 4.0 33.4 1.0 C5 A:G36 4.1 28.9 1.0 O A:HOH2168 4.1 34.4 1.0 OP2 A:C35 4.2 38.8 1.0 C4 B:OMC6 4.3 23.9 1.0 OP2 B:OMC6 4.5 27.5 1.0 C5 A:C35 4.6 33.1 1.0 O A:HOH2170 4.6 29.9 1.0 N1 A:G36 4.6 25.3 1.0 CM2 B:OMC6 4.6 26.1 1.0 N4 B:OMC6 4.7 32.7 1.0 N1 B:OMC6 4.8 21.0 1.0 OP2 A:A34 4.8 38.2 1.0 C2' B:OMC6 5.0 21.9 1.0 O2' B:OMC6 5.0 24.9 1.0

M.Anderson, E.Schultz, M.Martick, W.G.Scott. Active-Site Monovalent Cations Revealed in A 1.55 A Resolution Hammerhead Ribozyme Structure J.Mol.Biol. V. 425 3790 2013.
ISSN: ISSN 0022-2836
PubMed: 23711504
DOI: 10.1016/J.JMB.2013.05.017