Manganese in PDB 2oeu: Full-Length Hammerhead Ribozyme with Mn(II) Bound

The structure of Full-Length Hammerhead Ribozyme with Mn(II) Bound, PDB code: 2oeu was solved by M.Martick, W.G.Scott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.80 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	50.312, 68.981, 60.443, 90.00, 112.62, 90.00
R / Rfree (%)	16.6 / 22.1

The structure of Full-Length Hammerhead Ribozyme with Mn(II) Bound also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Manganese atom in the Full-Length Hammerhead Ribozyme with Mn(II) Bound (pdb code 2oeu). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Full-Length Hammerhead Ribozyme with Mn(II) Bound, PDB code: 2oeu:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in the Full-Length Hammerhead Ribozyme with Mn(II) Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Full-Length Hammerhead Ribozyme with Mn(II) Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:51.9 occ:1.00 O A:HOH705 1.7 45.0 1.0 OP2 A:A21 2.0 50.1 1.0 O A:HOH703 2.0 52.5 1.0 N7 A:G22 2.1 53.7 1.0 O A:HOH702 2.2 46.4 1.0 O A:HOH704 2.4 47.9 1.0 C8 A:G22 2.9 53.1 1.0 P A:A21 3.2 49.2 1.0 C5 A:G22 3.2 54.3 1.0 O5' A:A21 3.7 50.6 1.0 O6 A:G22 3.8 54.4 1.0 C6 A:G22 3.9 52.7 1.0 OP1 A:A21 3.9 47.3 1.0 N9 A:G22 4.2 53.5 1.0 O4 A:U23 4.3 59.4 1.0 C4 A:G22 4.3 53.5 1.0 O B:HOH50 4.4 46.1 1.0 O3' A:G20 4.5 45.7 1.0 OP2 A:G22 4.8 53.4 1.0 C8 A:A21 4.9 56.0 1.0 N7 A:A21 4.9 55.9 1.0 N2 A:G36 4.9 45.5 1.0 C5 A:U23 4.9 59.6 1.0 C4 A:U23 5.0 59.7 1.0

Manganese binding site 2 out of 5 in the Full-Length Hammerhead Ribozyme with Mn(II) Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Full-Length Hammerhead Ribozyme with Mn(II) Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:51.2 occ:1.00 O2B A:GTP1 2.0 66.7 1.0 O A:HOH706 2.1 47.7 1.0 O A:HOH707 2.2 46.0 1.0 O A:HOH708 2.2 43.8 1.0 O A:HOH709 2.3 62.5 1.0 N7 A:GTP1 2.4 46.3 1.0 C8 A:GTP1 3.2 46.1 1.0 PB A:GTP1 3.5 71.2 1.0 C5 A:GTP1 3.5 44.7 1.0 O6 A:GTP1 3.8 47.2 1.0 O3B A:GTP1 4.0 77.0 1.0 O2A A:GTP1 4.0 61.2 1.0 O A:HOH785 4.0 51.1 1.0 O1G A:GTP1 4.1 84.5 1.0 C6 A:GTP1 4.1 46.2 1.0 O1B A:GTP1 4.4 70.9 1.0 N9 A:GTP1 4.4 46.4 1.0 O A:HOH783 4.5 50.2 1.0 O3A A:GTP1 4.5 67.0 1.0 C4 A:GTP1 4.6 44.9 1.0 PA A:GTP1 4.7 64.3 1.0 O5' A:GTP1 4.7 62.6 1.0 PG A:GTP1 4.7 83.6 1.0

Manganese binding site 3 out of 5 in the Full-Length Hammerhead Ribozyme with Mn(II) Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Full-Length Hammerhead Ribozyme with Mn(II) Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:49.3 occ:1.00 OP2 A:A38 2.0 49.3 1.0 O A:HOH711 2.1 44.5 1.0 O A:HOH714 2.1 50.7 1.0 O A:HOH712 2.2 39.8 1.0 O A:HOH713 2.4 41.3 1.0 O A:HOH710 2.5 51.9 1.0 P A:A38 3.4 49.8 1.0 O5' A:A38 3.9 49.2 1.0 O A:HOH759 4.1 40.9 1.0 OP2 A:A37 4.3 48.4 1.0 OP1 A:A38 4.3 48.6 1.0 OP1 A:A37 4.3 46.8 1.0 N7 A:A38 4.3 43.8 1.0 N7 A:A39 4.4 38.4 1.0 C8 A:A38 4.4 43.2 1.0 O B:HOH65 4.5 47.0 1.0 O3' A:A37 4.5 47.3 1.0 N6 A:A39 4.6 36.5 1.0 P A:A37 4.6 49.0 1.0 O5' A:A37 4.7 47.9 1.0 O B:HOH62 4.7 40.2 1.0 C3' A:A37 4.7 47.4 1.0 OP2 A:A39 4.9 44.6 1.0 O B:HOH71 4.9 47.5 1.0

Manganese binding site 4 out of 5 in the Full-Length Hammerhead Ribozyme with Mn(II) Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Full-Length Hammerhead Ribozyme with Mn(II) Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:55.6 occ:1.00 N7 A:A27 2.1 49.5 1.0 O A:HOH716 2.4 50.1 1.0 O A:HOH717 2.6 47.5 1.0 O A:HOH715 2.7 47.5 1.0 C8 A:A27 2.9 47.8 1.0 C5 A:A27 3.2 47.3 1.0 N6 A:A27 3.6 47.8 1.0 OP2 A:A27 3.8 55.3 1.0 C6 A:A27 3.9 48.3 1.0 N9 A:A27 4.1 48.5 1.0 C4 A:A27 4.3 45.6 1.0 O A:HOH764 4.4 49.1 1.0 C5 A:C26 4.5 47.2 1.0 N7 A:A7 4.5 40.7 1.0 O A:HOH813 4.7 55.7 1.0 N6 A:A7 4.8 41.6 1.0 C6 A:C26 4.8 49.7 1.0 O5' A:A27 4.8 53.6 1.0 C4 A:C26 4.9 48.2 1.0 P A:A27 5.0 55.7 1.0

Manganese binding site 5 out of 5 in the Full-Length Hammerhead Ribozyme with Mn(II) Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Full-Length Hammerhead Ribozyme with Mn(II) Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:50.3 occ:0.50 O A:HOH720 2.2 29.5 0.5 O A:HOH722 2.3 34.1 0.5 O A:HOH721 2.4 40.5 0.5 O A:HOH718 2.4 32.9 0.5 O A:HOH719 2.7 34.9 0.5 N7 A:G41 4.1 40.4 1.0 C5 A:C40 4.2 41.5 1.0 N4 A:C42 4.2 39.4 1.0 O A:HOH729 4.3 49.4 1.0 OP2 A:C40 4.3 44.4 1.0 O B:HOH75 4.4 50.9 1.0 OP2 A:G41 4.5 41.5 1.0 C6 A:C40 4.6 44.1 1.0 O A:HOH759 4.8 40.9 1.0 O6 A:G41 4.8 39.8 1.0 O A:HOH809 4.8 59.4 1.0 N4 A:C43 4.9 37.1 1.0 C4 A:C40 4.9 42.0 1.0 C8 A:G41 5.0 40.0 1.0

M.Martick, T.S.Lee, D.M.York, W.G.Scott. Solvent Structure and Hammerhead Ribozyme Catalysis. Chem.Biol. V. 15 332 2008.
ISSN: ISSN 1074-5521
PubMed: 18420140
DOI: 10.1016/J.CHEMBIOL.2008.03.010