Magnesium in PDB 301d: Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mg(II)-Soaked

The structure of Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mg(II)-Soaked, PDB code: 301d was solved by W.G.Scott, J.B.Murray, J.R.P.Arnold, B.L.Stoddard, A.Klug, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 3.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	65.900, 65.900, 136.770, 90.00, 90.00, 120.00
R / Rfree (%)	25.8 / 29.7

The binding sites of Magnesium atom in the Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mg(II)-Soaked (pdb code 301d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mg(II)-Soaked, PDB code: 301d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mg(II)-Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mg(II)-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg42 b:31.2 occ:0.50 N4 B:C12 4.3 67.5 1.0 MG B:MG46 4.5 31.2 0.5

Magnesium binding site 2 out of 5 in the Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mg(II)-Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mg(II)-Soaked within 5.0Å range:

Magnesium binding site 3 out of 5 in the Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mg(II)-Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mg(II)-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg44 b:31.3 occ:0.50 N4 A:C30 3.6 61.5 1.0 O4 A:U21 4.2 62.6 1.0 OP1 A:G80 4.4 54.6 1.0 C5' A:U70 4.6 30.1 1.0 N6 B:A11 4.6 58.0 1.0 OP1 A:U70 4.8 49.2 1.0 N4 B:C170 4.8 75.5 1.0 C4 A:C30 4.9 60.4 1.0 C4 A:U21 5.0 57.7 1.0

Magnesium binding site 4 out of 5 in the Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mg(II)-Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mg(II)-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg45 b:29.3 occ:0.50 N2 A:G50 3.8 67.4 1.0 N1 A:G50 3.9 55.0 1.0 O4' B:U161 4.2 50.5 1.0 C2 A:G50 4.3 55.7 1.0 C4' B:U161 4.5 55.3 1.0 C2 A:A60 4.6 48.7 1.0 O2' B:G162 4.7 43.8 1.0 C1' B:U161 4.9 51.2 1.0 O2' B:U161 4.9 64.5 1.0 C6 A:G50 4.9 48.5 1.0 N3 A:A60 5.0 40.0 1.0 O6 A:G50 5.0 53.9 1.0

Magnesium binding site 5 out of 5 in the Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mg(II)-Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mg(II)-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg46 b:31.2 occ:0.50 OP2 B:A11 2.4 85.7 1.0 P B:A11 3.9 89.9 1.0 MG B:MG42 4.5 31.2 0.5 O5' B:C170 4.5 66.2 1.0 N7 B:A11 4.5 65.0 1.0 C5' B:C170 4.5 70.2 1.0 O3' B:C170 4.6 86.1 1.0 C3' B:C170 4.6 78.4 1.0 O5' B:A11 4.7 86.9 1.0 OP1 B:A11 4.8 88.3 1.0 C8 B:A11 4.8 63.4 1.0

W.G.Scott, J.B.Murray, J.R.Arnold, B.L.Stoddard, A.Klug. Capturing the Structure of A Catalytic Rna Intermediate: the Hammerhead Ribozyme. Science V. 274 2065 1996.
ISSN: ISSN 0036-8075
PubMed: 8953035
DOI: 10.1126/SCIENCE.274.5295.2065