Manganese in PDB 300d: Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mn(II)-Soaked

The structure of Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mn(II)-Soaked, PDB code: 300d 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 (°)	64.550, 64.550, 135.870, 90.00, 90.00, 120.00
R / Rfree (%)	21.7 / 26.2

The binding sites of Manganese atom in the Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mn(II)-Soaked (pdb code 300d). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mn(II)-Soaked, PDB code: 300d:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mn(II)-Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mn(II)-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn42 b:51.5 occ:1.00 N7 A:G101 2.2 38.8 1.0 OP1 A:A90 2.3 53.6 1.0 C8 A:G101 2.9 37.5 1.0 C5 A:G101 3.5 35.0 1.0 P A:A90 3.8 51.3 1.0 O2' A:G80 3.9 48.6 1.0 O6 A:G101 4.2 32.2 1.0 N9 A:G101 4.2 38.5 1.0 C6 A:G101 4.2 36.0 1.0 N2 B:G120 4.4 24.9 1.0 OP2 A:G101 4.4 56.5 1.0 C4 A:G101 4.4 35.1 1.0 C5' A:A90 4.5 53.9 1.0 O3' A:G80 4.6 51.0 1.0 OP2 A:A90 4.6 49.1 1.0 O5' A:A90 4.6 50.4 1.0 N7 A:G102 4.7 32.0 1.0

Manganese binding site 2 out of 6 in the Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mn(II)-Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mn(II)-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn43 b:27.7 occ:0.25 N4 B:C170 3.1 35.4 1.0 OP2 A:U70 3.2 24.5 1.0 OP1 A:U70 3.6 24.4 1.0 N6 B:A11 3.7 55.0 1.0 P A:U70 3.9 22.0 1.0 C4 B:C170 4.3 44.3 1.0 N4 A:C30 4.4 46.0 1.0 O5' A:U70 4.5 8.8 1.0 O4 A:U21 4.8 32.5 1.0 C5 B:C170 4.8 45.4 1.0 C6 B:A11 4.9 46.4 1.0

Manganese binding site 3 out of 6 in the Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mn(II)-Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mn(II)-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn44 b:25.2 occ:0.25 N7 A:G50 3.1 41.7 1.0 N6 A:A60 3.8 48.7 1.0 C8 A:G50 3.9 36.7 1.0 C5 A:G50 4.2 44.6 1.0 O6 A:G50 4.3 54.9 1.0 MN A:MN46 4.4 40.0 0.2 O2' A:U40 4.6 29.6 1.0 C6 A:G50 4.7 51.3 1.0

Manganese binding site 4 out of 6 in the Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mn(II)-Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mn(II)-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn45 b:38.8 occ:0.50 N1 A:G50 3.4 55.5 1.0 O6 A:G50 4.0 54.9 1.0 N2 A:G50 4.1 69.3 1.0 C6 A:G50 4.2 51.3 1.0 C2 A:G50 4.3 58.7 1.0 C2 A:A60 4.6 34.5 1.0 N1 A:A60 4.8 36.1 1.0

Manganese binding site 5 out of 6 in the Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mn(II)-Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mn(II)-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn46 b:40.0 occ:0.25 MN A:MN44 4.4 25.2 0.2 N6 A:A60 4.8 48.7 1.0

Manganese binding site 6 out of 6 in the Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mn(II)-Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Capturing the Structure of A Catalytic Rna Intermediate: Rna Hammerhead Ribozyme, Mn(II)-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn47 b:33.5 occ:0.50 N4 B:C12 3.0 55.1 1.0 C4 B:C12 3.8 47.6 1.0 C5 B:C12 3.8 46.9 1.0 N4 B:C13 4.9 44.4 1.0 N6 B:A11 5.0 55.0 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