Manganese in PDB 4peh: DBR1 in Complex with Synthetic Linear Rna

The structure of DBR1 in Complex with Synthetic Linear Rna, PDB code: 4peh was solved by E.J.Montemayor, A.Katolik, N.E.Clark, A.B.Taylor, J.P.Schuermann, D.J.Combs, R.Johnsson, S.P.Holloway, S.W.Stevens, M.J.Damha, P.J.Hart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.03 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.021, 141.936, 212.942, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 24.7

The binding sites of Manganese atom in the DBR1 in Complex with Synthetic Linear Rna (pdb code 4peh). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the DBR1 in Complex with Synthetic Linear Rna, PDB code: 4peh:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in the DBR1 in Complex with Synthetic Linear Rna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of DBR1 in Complex with Synthetic Linear Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:28.2 occ:1.00 OD1 A:ASN90 2.1 25.4 1.0 OD2 A:ASP45 2.1 30.6 1.0 NE2 A:HIS180 2.2 25.2 1.0 O1P V:A2P501 2.2 33.1 1.0 O V:HOH701 2.4 28.9 1.0 ND1 A:HIS230 2.4 30.8 1.0 CG A:ASP45 3.0 27.9 1.0 CG A:ASN90 3.1 28.4 1.0 CE1 A:HIS230 3.2 31.8 1.0 CD2 A:HIS180 3.2 23.0 1.0 CE1 A:HIS180 3.2 27.1 1.0 OD1 A:ASP45 3.3 28.6 1.0 P1 V:A2P501 3.3 36.1 1.0 O3P V:A2P501 3.4 32.6 1.0 ND2 A:ASN90 3.5 27.9 1.0 CG A:HIS230 3.6 32.5 1.0 CA A:HIS230 3.9 40.3 1.0 CB A:HIS230 4.0 33.3 1.0 O2P V:A2P501 4.2 41.6 1.0 O A:HIS230 4.3 40.2 1.0 ND1 A:HIS180 4.3 22.9 1.0 CG A:HIS180 4.3 28.3 1.0 OG A:SER14 4.4 33.6 1.0 NE2 A:HIS230 4.4 29.3 1.0 CB A:ASP45 4.4 25.7 1.0 N A:ASN90 4.4 25.7 1.0 CD2 A:HIS91 4.4 34.2 1.0 CB A:ASN90 4.5 26.8 1.0 O2' V:A2P501 4.6 40.1 1.0 CD2 A:HIS230 4.6 34.1 1.0 C A:HIS230 4.6 36.2 1.0 NE2 A:HIS91 4.9 32.7 1.0 CE1 A:HIS16 4.9 34.4 1.0 CA A:ASN90 5.0 26.1 1.0 N A:HIS230 5.0 41.1 1.0

Manganese binding site 2 out of 5 in the DBR1 in Complex with Synthetic Linear Rna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of DBR1 in Complex with Synthetic Linear Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:29.8 occ:1.00 O2P W:A2P501 2.1 34.3 1.0 ND1 B:HIS230 2.1 27.5 1.0 OD2 B:ASP45 2.2 33.9 1.0 OD1 B:ASN90 2.3 30.2 1.0 NE2 B:HIS180 2.3 29.1 1.0 O W:HOH701 2.8 40.1 1.0 CE1 B:HIS230 2.9 27.5 1.0 CG B:ASP45 3.0 29.9 1.0 CE1 B:HIS180 3.1 25.9 1.0 OD1 B:ASP45 3.1 29.0 1.0 P1 W:A2P501 3.2 45.7 1.0 CG B:ASN90 3.3 25.1 1.0 CG B:HIS230 3.3 25.3 1.0 CD2 B:HIS180 3.4 28.2 1.0 O1P W:A2P501 3.4 37.6 1.0 ND2 B:ASN90 3.6 27.9 1.0 O3P W:A2P501 3.8 52.1 1.0 CB B:HIS230 3.8 27.2 1.0 CA B:HIS230 3.8 38.9 1.0 NE2 B:HIS230 4.1 36.4 1.0 OG B:SER14 4.2 37.2 1.0 CD2 B:HIS230 4.3 30.3 1.0 ND1 B:HIS180 4.3 31.9 1.0 O B:HIS230 4.4 38.9 1.0 CB B:ASP45 4.4 25.2 1.0 CG B:HIS180 4.4 31.6 1.0 O2' W:A2P501 4.5 34.9 1.0 N B:ASN90 4.6 25.9 1.0 CD2 B:HIS91 4.6 33.0 1.0 CB B:ASN90 4.6 29.3 1.0 C B:HIS230 4.6 37.4 1.0 N B:HIS230 4.7 40.4 1.0

Manganese binding site 3 out of 5 in the DBR1 in Complex with Synthetic Linear Rna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of DBR1 in Complex with Synthetic Linear Rna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn401 b:26.6 occ:1.00 O C:HOH725 2.0 28.9 1.0 OD1 C:ASN90 2.1 20.9 1.0 O2P X:A2P501 2.2 32.5 1.0 OD2 C:ASP45 2.2 24.2 1.0 NE2 C:HIS180 2.2 24.4 1.0 ND1 C:HIS230 2.4 27.2 1.0 CG C:ASP45 3.0 25.8 1.0 CE1 C:HIS230 3.0 28.6 1.0 CE1 C:HIS180 3.1 27.7 1.0 CG C:ASN90 3.1 22.0 1.0 OD1 C:ASP45 3.1 22.9 1.0 CD2 C:HIS180 3.3 23.9 1.0 P1 X:A2P501 3.3 30.4 1.0 O3P X:A2P501 3.5 29.6 1.0 ND2 C:ASN90 3.6 25.0 1.0 CG C:HIS230 3.6 27.7 1.0 CA C:HIS230 3.9 30.4 1.0 O1P X:A2P501 4.0 37.5 1.0 CB C:HIS230 4.1 29.8 1.0 O C:HIS230 4.1 25.4 1.0 NE2 C:HIS230 4.2 27.3 1.0 ND1 C:HIS180 4.3 22.1 1.0 OG C:SER14 4.3 32.3 1.0 CG C:HIS180 4.4 26.9 1.0 CB C:ASP45 4.4 28.4 1.0 CB C:ASN90 4.5 18.6 1.0 CD2 C:HIS91 4.5 31.3 1.0 N C:ASN90 4.5 23.5 1.0 C C:HIS230 4.5 26.4 1.0 CD2 C:HIS230 4.5 24.7 1.0 O2' X:A2P501 4.6 34.6 1.0 N C:HIS230 4.8 32.0 1.0 NE2 C:HIS91 4.9 27.0 1.0 NE2 C:HIS16 4.9 33.4 1.0

Manganese binding site 4 out of 5 in the DBR1 in Complex with Synthetic Linear Rna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of DBR1 in Complex with Synthetic Linear Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn401 b:33.5 occ:1.00 O D:HOH691 2.0 37.2 1.0 OD1 D:ASN90 2.1 29.1 1.0 O1P Y:A2P501 2.2 39.1 1.0 OD2 D:ASP45 2.2 32.8 1.0 NE2 D:HIS180 2.2 28.6 1.0 ND1 D:HIS230 2.5 37.0 1.0 CG D:ASN90 3.0 33.8 1.0 CG D:ASP45 3.0 28.7 1.0 CE1 D:HIS180 3.2 31.0 1.0 OD1 D:ASP45 3.2 33.7 1.0 CD2 D:HIS180 3.2 29.7 1.0 P1 Y:A2P501 3.3 43.6 1.0 CE1 D:HIS230 3.3 35.3 1.0 ND2 D:ASN90 3.3 37.3 1.0 O3P Y:A2P501 3.4 34.4 1.0 CG D:HIS230 3.6 38.6 1.0 CA D:HIS230 3.9 40.7 1.0 O2P Y:A2P501 4.0 49.5 1.0 CB D:HIS230 4.1 37.7 1.0 O D:HIS230 4.3 45.1 1.0 N D:ASN90 4.3 28.4 1.0 ND1 D:HIS180 4.3 35.8 1.0 CB D:ASN90 4.3 29.4 1.0 OG D:SER14 4.4 36.8 1.0 CG D:HIS180 4.4 34.9 1.0 CB D:ASP45 4.4 29.2 1.0 CD2 D:HIS91 4.4 36.7 1.0 NE2 D:HIS230 4.5 38.5 1.0 O2' Y:A2P501 4.5 47.2 1.0 C D:HIS230 4.6 45.9 1.0 CD2 D:HIS230 4.7 40.0 1.0 N D:HIS230 4.8 39.2 1.0 CA D:ASN90 4.9 29.7 1.0 NE2 D:HIS91 5.0 38.8 1.0

Manganese binding site 5 out of 5 in the DBR1 in Complex with Synthetic Linear Rna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of DBR1 in Complex with Synthetic Linear Rna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn401 b:24.0 occ:1.00 O2P Z:A2P501 2.1 31.7 1.0 OD1 E:ASN90 2.2 18.2 1.0 OD2 E:ASP45 2.2 23.1 1.0 O Z:HOH703 2.2 30.4 1.0 NE2 E:HIS180 2.2 24.2 1.0 ND1 E:HIS230 2.3 24.1 1.0 CG E:ASP45 3.0 25.2 1.0 CE1 E:HIS230 3.1 34.6 1.0 OD1 E:ASP45 3.2 22.8 1.0 CG E:ASN90 3.2 28.9 1.0 CD2 E:HIS180 3.2 22.4 1.0 CE1 E:HIS180 3.2 25.8 1.0 P1 Z:A2P501 3.4 39.0 1.0 CG E:HIS230 3.5 31.5 1.0 ND2 E:ASN90 3.6 31.0 1.0 O3P Z:A2P501 3.6 32.5 1.0 CA E:HIS230 3.9 31.5 1.0 CB E:HIS230 3.9 30.7 1.0 O1P Z:A2P501 4.0 39.6 1.0 OG E:SER14 4.2 36.6 1.0 O E:HIS230 4.2 40.4 1.0 NE2 E:HIS230 4.3 33.1 1.0 ND1 E:HIS180 4.3 26.4 1.0 CG E:HIS180 4.4 26.5 1.0 CB E:ASP45 4.4 25.8 1.0 CD2 E:HIS91 4.4 39.0 1.0 N E:ASN90 4.5 18.8 1.0 CD2 E:HIS230 4.5 33.8 1.0 CB E:ASN90 4.5 21.5 1.0 C E:HIS230 4.6 38.7 1.0 O2' Z:A2P501 4.6 44.8 1.0 N E:HIS230 4.8 32.7 1.0 NE2 E:HIS16 4.9 40.8 1.0 NE2 E:HIS91 4.9 37.0 1.0

E.J.Montemayor, A.Katolik, N.E.Clark, A.B.Taylor, J.P.Schuermann, D.J.Combs, R.Johnsson, S.P.Holloway, S.W.Stevens, M.J.Damha, P.J.Hart. Structural Basis of Lariat Rna Recognition By the Intron Debranching Enzyme DBR1. Nucleic Acids Res. V. 42 10845 2014.
ISSN: ESSN 1362-4962
PubMed: 25123664
DOI: 10.1093/NAR/GKU725