Manganese in PDB 3llm: Crystal Structure Analysis of A Rna Helicase

The structure of Crystal Structure Analysis of A Rna Helicase, PDB code: 3llm was solved by P.Schutz, T.Karlberg, R.Collins, C.H.Arrowsmith, H.Berglund, C.Bountra, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, A.Johansson, I.Johansson, A.Kallas, P.Kraulis, T.Kotenyova, A.Kotzsch, N.Markova, M.Moche, T.K.Nielsen, P.Nordlund, T.Nyman, C.Persson, A.K.Roos, M.I.Siponen, L.Svensson, A.G.Thorsell, L.Tresaugues, S.Van Den Berg, E.Wahlberg, J.Weigelt, M.Welin, M.Wisniewska, H.M.Schuler, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	98.51 / 2.80
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.700, 113.700, 141.650, 90.00, 90.00, 120.00
R / Rfree (%)	21.1 / 23.8

The structure of Crystal Structure Analysis of A Rna Helicase also contains other interesting chemical elements:

Arsenic

(As)

1 atom

The binding sites of Manganese atom in the Crystal Structure Analysis of A Rna Helicase (pdb code 3llm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure Analysis of A Rna Helicase, PDB code: 3llm:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure Analysis of A Rna Helicase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure Analysis of A Rna Helicase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1 b:62.3 occ:1.00 O A:HOH19 1.6 43.9 1.0 O A:HOH21 2.0 42.2 1.0 O3B A:ADP565 2.0 58.0 1.0 OE2 A:GLU512 2.2 52.4 1.0 OG1 A:THR418 2.2 52.6 1.0 O A:HOH20 2.3 51.4 1.0 CD A:GLU512 3.0 54.9 1.0 PB A:ADP565 3.2 58.1 1.0 CB A:THR418 3.2 54.1 1.0 OE1 A:GLU512 3.3 58.4 1.0 O1B A:ADP565 3.3 55.8 1.0 O1A A:ADP565 3.8 58.0 1.0 N A:THR418 4.0 55.0 1.0 OD2 A:ASP511 4.0 56.1 1.0 O A:HOH25 4.0 46.7 1.0 OD1 A:ASP511 4.0 57.5 1.0 CA A:THR418 4.1 54.3 1.0 O2B A:ADP565 4.2 58.2 1.0 NZ A:LYS417 4.3 62.0 1.0 CG2 A:THR418 4.3 53.1 1.0 O3A A:ADP565 4.3 56.6 1.0 CG A:GLU512 4.4 54.4 1.0 CG A:ASP511 4.4 54.1 1.0 CE A:LYS417 4.5 60.5 1.0 PA A:ADP565 4.6 58.2 1.0 CB A:LYS417 4.7 57.3 1.0

Manganese binding site 2 out of 2 in the Crystal Structure Analysis of A Rna Helicase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure Analysis of A Rna Helicase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2 b:56.4 occ:1.00 O B:HOH17 1.8 44.5 1.0 O B:HOH18 2.0 45.6 1.0 OE2 B:GLU512 2.0 56.1 1.0 OG1 B:THR418 2.0 53.1 1.0 O1B B:ADP1 2.1 58.1 1.0 O B:HOH23 2.2 45.1 1.0 CD B:GLU512 3.0 57.5 1.0 CB B:THR418 3.3 53.6 1.0 PB B:ADP1 3.3 58.4 1.0 OE1 B:GLU512 3.4 57.9 1.0 O3B B:ADP1 3.6 55.7 1.0 OD2 B:ASP511 3.7 56.7 1.0 O2A B:ADP1 3.8 57.5 1.0 N B:THR418 4.0 54.3 1.0 OD1 B:ASP511 4.1 56.6 1.0 CA B:THR418 4.1 53.6 1.0 O B:HOH26 4.2 50.2 1.0 O2B B:ADP1 4.3 56.5 1.0 CG B:ASP511 4.3 54.0 1.0 CG2 B:THR418 4.3 51.2 1.0 O3A B:ADP1 4.4 57.5 1.0 CG B:GLU512 4.4 55.6 1.0 CE B:LYS417 4.5 60.2 1.0 PA B:ADP1 4.6 59.5 1.0 CB B:LYS417 4.6 57.2 1.0 NZ B:LYS417 4.9 61.5 1.0

P.Schutz, E.Wahlberg, T.Karlberg, M.Hammarstrom, R.Collins, A.Flores, H.Schuler. Crystal Structure of Human Rna Helicase A (DHX9): Structural Basis For Unselective Nucleotide Base Binding in A Dead-Box Variant Protein. J.Mol.Biol. V. 400 768 2010.
ISSN: ISSN 0022-2836
PubMed: 20510246
DOI: 10.1016/J.JMB.2010.05.046