Magnesium in PDB 4pr6: A Second Look at the Hdv Ribozyme Structure and Dynamics.

The structure of A Second Look at the Hdv Ribozyme Structure and Dynamics., PDB code: 4pr6 was solved by G.J.Kapral, S.Jain, J.Noeske, J.A.Doudna, D.C.Richardson, J.S.Richardson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.58 / 2.30
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	109.350, 109.350, 190.680, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 24.1

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Magnesium atom in the A Second Look at the Hdv Ribozyme Structure and Dynamics. (pdb code 4pr6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 17 binding sites of Magnesium where determined in the A Second Look at the Hdv Ribozyme Structure and Dynamics., PDB code: 4pr6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 17 in the A Second Look at the Hdv Ribozyme Structure and Dynamics.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A Second Look at the Hdv Ribozyme Structure and Dynamics. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:85.7 occ:1.00 H41 B:C172 4.0 0.9 1.0 O6 B:G110 4.3 88.9 1.0 H42 B:C172 4.4 0.9 1.0 N4 B:C172 4.5 96.6 1.0

Magnesium binding site 2 out of 17 in the A Second Look at the Hdv Ribozyme Structure and Dynamics.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A Second Look at the Hdv Ribozyme Structure and Dynamics. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:92.6 occ:1.00 N7 B:G170 2.3 97.7 1.0 O6 B:G170 3.2 75.3 1.0 C5 B:G170 3.2 97.1 1.0 C8 B:G170 3.4 88.4 1.0 C6 B:G170 3.5 92.3 1.0 N7 B:G169 3.5 91.5 1.0 O6 B:G169 3.6 99.2 1.0 H8 B:G170 3.6 0.1 1.0 C5 B:G169 3.6 93.7 1.0 C6 B:G169 3.7 95.4 1.0 C8 B:G169 4.3 0.8 1.0 C4 B:G170 4.4 92.8 1.0 C4 B:G169 4.5 1.0 1.0 N9 B:G170 4.5 98.8 1.0 N1 B:G169 4.5 94.8 1.0 H62 B:A171 4.7 0.8 1.0 H8 B:G169 4.8 0.9 1.0 H42 B:C113 4.8 99.1 1.0 N9 B:G169 4.9 98.3 1.0 N1 B:G170 4.9 96.9 1.0 H1 B:G169 4.9 0.8 1.0 H42 B:C114 4.9 1.0 1.0

Magnesium binding site 3 out of 17 in the A Second Look at the Hdv Ribozyme Structure and Dynamics.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A Second Look at the Hdv Ribozyme Structure and Dynamics. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:77.4 occ:1.00 OP2 B:A153 2.7 58.7 1.0 O2' B:C152 2.8 57.8 1.0 HO2' B:C152 3.0 69.3 1.0 O B:HOH501 3.1 45.5 1.0 HZ2 A:LYS88 3.3 0.6 1.0 O3' B:C152 3.3 53.2 1.0 O B:HOH506 3.4 59.0 1.0 HG1 A:THR89 3.4 79.1 1.0 HZ1 A:LYS88 3.4 0.6 1.0 P B:A153 3.6 58.3 1.0 H8 B:A153 3.7 63.1 1.0 H1' B:C152 3.7 62.6 1.0 OG1 A:THR89 3.7 66.0 1.0 NZ A:LYS88 3.8 93.8 1.0 HB2 A:LYS88 3.8 69.5 1.0 C2' B:C152 3.9 50.1 1.0 HB A:THR89 4.0 84.0 1.0 N7 B:A153 4.1 45.0 1.0 C3' B:C152 4.2 45.1 1.0 C8 B:A153 4.2 52.5 1.0 C1' B:C152 4.3 52.2 1.0 HZ3 A:LYS88 4.4 0.6 1.0 O2 B:C152 4.4 41.9 1.0 CB A:THR89 4.4 70.0 1.0 HE3 A:LYS88 4.5 72.9 1.0 O5' B:A153 4.6 51.3 1.0 H3' B:C152 4.6 54.1 1.0 H2' B:C152 4.7 60.1 1.0 CB A:LYS88 4.7 57.9 1.0 OP1 B:A153 4.8 60.5 1.0 H41 B:C154 4.8 50.5 1.0 CE A:LYS88 4.8 60.8 1.0 H A:THR89 4.9 71.7 1.0 HB3 A:LYS88 5.0 69.5 1.0

Magnesium binding site 4 out of 17 in the A Second Look at the Hdv Ribozyme Structure and Dynamics.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of A Second Look at the Hdv Ribozyme Structure and Dynamics. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:80.4 occ:1.00 O B:HOH509 2.2 77.3 1.0 O6 B:G138 3.2 0.2 1.0 H41 B:C121 3.6 0.6 1.0 H42 B:C122 3.9 0.9 1.0 O B:HOH518 3.9 72.9 1.0 H41 B:C122 4.0 0.9 1.0 H42 B:C121 4.1 0.6 1.0 HO2' B:C163 4.2 0.1 1.0 N4 B:C121 4.2 88.8 1.0 OP1 B:G164 4.3 93.3 1.0 N4 B:C122 4.3 0.6 1.0 OP2 B:G164 4.3 78.7 1.0 C6 B:G138 4.4 0.3 1.0 O6 B:G139 4.4 92.6 1.0 O6 B:G101 4.7 87.0 1.0 O2' B:C163 4.7 0.1 1.0 P B:G164 4.8 78.7 1.0 N7 B:G138 4.9 0.2 1.0 OP2 B:G162 5.0 58.7 1.0

Magnesium binding site 5 out of 17 in the A Second Look at the Hdv Ribozyme Structure and Dynamics.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of A Second Look at the Hdv Ribozyme Structure and Dynamics. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:87.1 occ:1.00 O6 B:G105 3.7 0.3 1.0 H41 B:C104 3.8 0.7 1.0 N7 B:G105 4.1 0.1 1.0 N4 B:C104 4.1 0.6 1.0 H5 B:C104 4.2 0.4 1.0 H42 B:C104 4.5 0.7 1.0 C4 B:C104 4.5 0.9 1.0 C5 B:C104 4.5 0.2 1.0 C6 B:G105 4.5 0.3 1.0 C5 B:G105 4.7 0.4 1.0 O6 B:G106 4.8 90.5 1.0

Magnesium binding site 6 out of 17 in the A Second Look at the Hdv Ribozyme Structure and Dynamics.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of A Second Look at the Hdv Ribozyme Structure and Dynamics. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg406 b:0.2 occ:1.00 OP2 B:C118 2.5 80.3 1.0 H5'' B:G117 2.5 0.6 1.0 OP1 B:G117 3.0 0.7 1.0 O5' B:G117 3.2 0.7 1.0 C5' B:G117 3.3 0.7 1.0 H3' B:G117 3.4 0.2 1.0 P B:C118 3.4 0.1 1.0 O3' B:G117 3.6 0.2 1.0 P B:G117 3.6 0.3 1.0 C3' B:G117 3.8 0.5 1.0 OP1 B:C118 3.9 0.5 1.0 H5' B:G117 4.0 0.6 1.0 C4' B:G117 4.1 0.6 1.0 OP2 B:G117 4.3 86.6 1.0 H4' B:G117 4.6 0.1 1.0 O5' B:C118 4.8 0.2 1.0

Magnesium binding site 7 out of 17 in the A Second Look at the Hdv Ribozyme Structure and Dynamics.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of A Second Look at the Hdv Ribozyme Structure and Dynamics. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg407 b:94.4 occ:1.00 OP2 B:C119 2.6 85.0 1.0 H6 B:C119 3.2 0.8 1.0 H5 B:C119 3.2 0.9 1.0 O5' B:C119 3.3 86.0 1.0 P B:C119 3.5 94.5 1.0 H3' B:C119 3.5 0.5 1.0 C6 B:C119 3.5 84.9 1.0 C5 B:C119 3.6 84.9 1.0 H5 B:U120 3.6 0.3 1.0 OP2 B:U120 3.9 0.0 1.0 OP1 B:C119 4.3 0.6 1.0 H3' B:C118 4.4 0.1 1.0 C3' B:C119 4.5 0.4 1.0 C5 B:U120 4.5 0.9 1.0 N1 B:C119 4.6 83.4 1.0 C5' B:C119 4.6 96.8 1.0 C4 B:C119 4.6 87.2 1.0 H6 B:U120 4.7 0.9 1.0 O3' B:C118 4.8 1.0 1.0 H2' B:C118 4.8 0.1 1.0 H5'' B:C119 4.9 0.2 1.0 C4' B:C119 5.0 95.9 1.0 C3' B:C118 5.0 1.0 1.0

Magnesium binding site 8 out of 17 in the A Second Look at the Hdv Ribozyme Structure and Dynamics.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of A Second Look at the Hdv Ribozyme Structure and Dynamics. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg408 b:94.7 occ:1.00 HO2' B:G110 2.7 0.8 1.0 O2' B:G110 3.2 85.6 1.0 H5' B:G111 3.8 0.9 1.0 H4' B:G110 4.2 0.5 1.0 O3' B:G110 4.5 0.3 1.0 C2' B:G110 4.6 0.1 1.0 C5' B:G111 4.7 0.7 1.0 H5'' B:G111 4.8 0.9 1.0 C3' B:G110 4.9 0.7 1.0 C4' B:G110 5.0 0.6 1.0

Magnesium binding site 9 out of 17 in the A Second Look at the Hdv Ribozyme Structure and Dynamics.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of A Second Look at the Hdv Ribozyme Structure and Dynamics. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg409 b:0.9 occ:1.00 H5'' B:G135 2.3 0.0 1.0 OP2 B:C136 2.6 0.4 1.0 O3' B:G135 2.9 0.4 1.0 P B:C136 3.0 0.8 1.0 C5' B:G135 3.1 0.8 1.0 H3' B:G135 3.2 0.6 1.0 O5' B:G135 3.4 1.0 1.0 OP1 B:C136 3.4 0.3 1.0 C3' B:G135 3.4 0.2 1.0 OP1 B:G135 3.5 0.4 1.0 C4' B:G135 3.7 0.1 1.0 H5' B:G135 3.9 0.0 1.0 P B:G135 4.0 0.1 1.0 H4' B:G135 4.1 0.9 1.0 O5' B:C136 4.6 0.2 1.0 OP2 B:G135 4.8 0.8 1.0 C2' B:G135 4.9 1.0 1.0 O4' B:G135 5.0 0.2 1.0

Magnesium binding site 10 out of 17 in the A Second Look at the Hdv Ribozyme Structure and Dynamics.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of A Second Look at the Hdv Ribozyme Structure and Dynamics. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg410 b:0.5 occ:0.23 C2 B:U123 0.9 0.3 0.4 N1 B:U123 1.1 1.0 0.4 O2 B:U123 1.3 0.2 0.4 C1' B:U123 1.7 0.0 0.4 H1' B:U123 1.7 0.0 0.4 N3 B:U123 2.2 0.2 0.4 OP1 B:C124 2.4 0.9 0.6 OP2 B:C124 2.5 0.4 0.6 C6 B:U123 2.5 0.0 0.4 C2' B:U123 2.6 0.7 0.4 O2' B:U123 2.7 0.8 0.4 H3 B:U123 2.8 0.1 0.4 P B:C124 2.8 0.3 0.6 O4' B:U123 2.9 0.5 0.4 H2' B:U123 2.9 0.9 0.4 H6 B:U123 3.1 0.2 0.4 C4 B:U123 3.2 0.0 0.4 C5 B:U123 3.2 0.8 0.4 HO2' B:U123 3.5 0.8 0.4 C3' B:U123 3.8 0.1 0.4 O3' B:U123 3.9 0.1 0.6 H4' B:U123 4.0 0.8 0.6 C4' B:U123 4.0 0.5 0.4 O5' B:C124 4.1 0.2 0.6 H5 B:U123 4.1 0.2 0.4 O3' B:U123 4.2 0.2 0.4 O4 B:U123 4.4 0.8 0.4 H3' B:U123 4.6 0.9 0.4 H4' B:U123 4.6 0.2 0.4 H5' B:U123 4.7 0.3 0.4 C3' B:U123 4.8 0.2 0.6 C4' B:U123 4.8 0.8 0.6 H3' B:U123 4.8 0.8 0.6 H5' B:C124 4.9 0.3 0.4 C5' B:U123 5.0 0.9 0.4

G.J.Kapral, S.Jain, J.Noeske, J.A.Doudna, D.C.Richardson, J.S.Richardson. New Tools Provide A Second Look at Hdv Ribozyme Structure, Dynamics and Cleavage. Nucleic Acids Res. 2014.
ISSN: ESSN 1362-4962
PubMed: 25326328
DOI: 10.1093/NAR/GKU992