Nickel in PDB 4pei: DBR1 in Complex with Synthetic Branched Rna Analog

The structure of DBR1 in Complex with Synthetic Branched Rna Analog, PDB code: 4pei 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)	46.37 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.037, 142.479, 214.665, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 22.9

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

Nickel binding site 1 out of 5 in the DBR1 in Complex with Synthetic Branched Rna Analog


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of DBR1 in Complex with Synthetic Branched Rna Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:30.6 occ:1.00 NE2 A:HIS180 2.1 17.2 1.0 OD1 A:ASN90 2.2 19.0 1.0 O1P Q:G46510 2.3 26.8 0.7 OD2 A:ASP45 2.3 22.4 1.0 ND1 A:HIS230 2.4 21.5 1.0 O A:HOH550 2.4 28.0 1.0 CE1 A:HIS180 3.1 16.1 1.0 CE1 A:HIS230 3.1 24.0 1.0 CG A:ASP45 3.1 21.1 1.0 CD2 A:HIS180 3.2 14.1 1.0 OD1 A:ASP45 3.2 21.4 1.0 CG A:ASN90 3.3 19.6 1.0 CG A:HIS230 3.5 21.0 1.0 P Q:G46510 3.6 43.6 0.7 CA A:HIS230 3.8 22.4 1.0 ND2 A:ASN90 3.9 23.9 1.0 O A:HIS230 4.0 31.8 1.0 CB A:HIS230 4.0 18.8 1.0 ND1 A:HIS180 4.2 12.4 1.0 CG A:HIS180 4.3 11.0 1.0 NE2 A:HIS230 4.3 25.1 1.0 O5' Q:G46510 4.3 42.6 0.7 C A:HIS230 4.4 27.4 1.0 S2P Q:G46510 4.4 46.2 0.7 CD2 A:HIS91 4.4 30.2 1.0 OG A:SER14 4.4 27.5 1.0 N A:ASN90 4.4 14.6 1.0 CD2 A:HIS230 4.5 24.0 1.0 CB A:ASP45 4.6 17.0 1.0 CB A:ASN90 4.6 18.4 1.0 N A:HIS230 4.7 24.8 1.0 O3P Q:G46510 4.8 38.1 0.7 NE2 A:HIS91 4.9 27.9 1.0

Nickel binding site 2 out of 5 in the DBR1 in Complex with Synthetic Branched Rna Analog


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of DBR1 in Complex with Synthetic Branched Rna Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni401 b:23.9 occ:1.00 NE2 B:HIS180 2.0 14.5 1.0 OD1 B:ASN90 2.1 21.0 1.0 OD2 B:ASP45 2.2 23.0 1.0 O1P R:G46510 2.3 19.2 0.7 ND1 B:HIS230 2.3 21.4 1.0 O B:HOH511 2.3 25.2 1.0 CE1 B:HIS180 3.0 18.1 1.0 CE1 B:HIS230 3.0 22.5 1.0 CG B:ASP45 3.0 18.2 1.0 CD2 B:HIS180 3.1 12.2 1.0 OD1 B:ASP45 3.1 16.1 1.0 CG B:ASN90 3.2 16.5 1.0 CG B:HIS230 3.4 18.8 1.0 P R:G46510 3.5 45.2 0.7 ND2 B:ASN90 3.8 22.0 1.0 CA B:HIS230 3.9 18.8 1.0 CB B:HIS230 3.9 17.1 1.0 S2P R:G46510 4.0 44.4 0.7 ND1 B:HIS180 4.1 19.4 1.0 NE2 B:HIS230 4.2 24.2 1.0 CG B:HIS180 4.2 15.4 1.0 O B:HIS230 4.2 24.9 1.0 O5' R:G46510 4.4 35.7 0.7 CB B:ASP45 4.4 15.9 1.0 CD2 B:HIS230 4.4 27.0 1.0 CB B:ASN90 4.5 19.3 1.0 N B:ASN90 4.5 15.5 1.0 C B:HIS230 4.6 27.4 1.0 C5' R:G46510 4.7 31.4 0.7 CD2 B:HIS91 4.7 23.9 1.0 O3P R:G46510 4.7 35.2 0.7 O B:GLY229 4.9 28.1 1.0 N B:HIS230 5.0 18.2 1.0

Nickel binding site 3 out of 5 in the DBR1 in Complex with Synthetic Branched Rna Analog


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of DBR1 in Complex with Synthetic Branched Rna Analog within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni401 b:18.4 occ:1.00 OD1 C:ASN90 2.0 16.7 1.0 OP2 X:A503 2.1 21.4 1.0 O C:HOH825 2.1 14.7 1.0 OD2 C:ASP45 2.2 17.8 1.0 NE2 C:HIS180 2.2 15.6 1.0 ND1 C:HIS230 2.2 19.7 1.0 CG C:ASP45 3.0 17.9 1.0 CE1 C:HIS230 3.0 16.6 1.0 CG C:ASN90 3.0 15.9 1.0 CE1 C:HIS180 3.1 19.4 1.0 OD1 C:ASP45 3.1 13.3 1.0 CD2 C:HIS180 3.2 16.4 1.0 CG C:HIS230 3.4 16.7 1.0 P X:A503 3.4 28.4 1.0 ND2 C:ASN90 3.5 17.0 1.0 CA C:HIS230 3.8 16.7 1.0 CB C:HIS230 3.9 17.0 1.0 OP1 X:A503 4.0 25.1 1.0 O C:HOH707 4.0 34.5 1.0 O C:HIS230 4.1 18.0 1.0 NE2 C:HIS230 4.2 19.7 1.0 ND1 C:HIS180 4.2 15.6 1.0 O5' X:A503 4.2 27.5 1.0 CG C:HIS180 4.3 14.5 1.0 CB C:ASN90 4.3 17.6 1.0 N C:ASN90 4.3 13.7 1.0 CB C:ASP45 4.4 17.8 1.0 CD2 C:HIS230 4.4 19.6 1.0 C C:HIS230 4.5 15.4 1.0 O3' X:C502 4.5 26.3 0.9 C5' X:A503 4.6 28.0 1.0 CA C:ASN90 4.9 14.6 1.0 N C:HIS230 4.9 16.0 1.0

Nickel binding site 4 out of 5 in the DBR1 in Complex with Synthetic Branched Rna Analog


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of DBR1 in Complex with Synthetic Branched Rna Analog within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni401 b:26.9 occ:1.00 OD1 D:ASN90 2.1 21.2 1.0 NE2 D:HIS180 2.2 18.0 1.0 O D:HOH800 2.2 25.6 1.0 OD2 D:ASP45 2.3 20.9 1.0 ND1 D:HIS230 2.4 25.0 1.0 O1P T:G46510 2.4 25.0 0.7 CG D:ASP45 3.1 21.7 1.0 CD2 D:HIS180 3.1 14.7 1.0 CE1 D:HIS230 3.2 26.6 1.0 CG D:ASN90 3.2 20.2 1.0 CE1 D:HIS180 3.2 18.1 1.0 OD1 D:ASP45 3.3 16.9 1.0 CG D:HIS230 3.5 23.0 1.0 CA D:HIS230 3.6 26.4 1.0 ND2 D:ASN90 3.7 23.7 1.0 P T:G46510 3.7 46.5 0.7 CB D:HIS230 3.9 26.5 1.0 O D:HIS230 4.1 34.4 1.0 S2P T:G46510 4.2 44.3 0.7 OG D:SER14 4.2 32.1 1.0 ND1 D:HIS180 4.3 15.6 1.0 CG D:HIS180 4.3 18.2 1.0 NE2 D:HIS230 4.4 25.8 1.0 C D:HIS230 4.4 28.4 1.0 N D:ASN90 4.4 15.0 1.0 CB D:ASP45 4.5 18.8 1.0 N D:HIS230 4.5 26.9 1.0 CB D:ASN90 4.5 18.1 1.0 CD2 D:HIS230 4.5 21.0 1.0 O5' T:G46510 4.7 52.8 0.7 O3P T:G46510 4.9 45.3 0.7 ND1 D:HIS91 4.9 35.9 1.0

Nickel binding site 5 out of 5 in the DBR1 in Complex with Synthetic Branched Rna Analog


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of DBR1 in Complex with Synthetic Branched Rna Analog within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni401 b:21.9 occ:1.00 NE2 E:HIS180 2.1 16.8 1.0 ND1 E:HIS230 2.2 18.2 1.0 OD1 E:ASN90 2.2 20.6 1.0 OP2 Z:A503 2.2 21.6 0.8 O E:HOH777 2.2 26.2 1.0 OD2 E:ASP45 2.2 19.8 1.0 CE1 E:HIS230 2.8 21.9 1.0 CE1 E:HIS180 3.0 12.4 1.0 CG E:ASP45 3.1 16.0 1.0 CD2 E:HIS180 3.2 12.9 1.0 OD1 E:ASP45 3.3 16.3 1.0 CG E:ASN90 3.3 20.7 1.0 CG E:HIS230 3.4 17.3 1.0 P Z:A503 3.5 29.8 0.8 ND2 E:ASN90 3.8 21.8 1.0 CA E:HIS230 3.8 20.1 1.0 CB E:HIS230 3.9 22.2 1.0 NE2 E:HIS230 4.0 21.7 1.0 O E:HIS230 4.1 25.9 1.0 OP1 Z:A503 4.1 21.3 0.8 ND1 E:HIS180 4.2 16.1 1.0 O5' Z:A503 4.2 33.0 0.8 CG E:HIS180 4.3 13.0 1.0 CD2 E:HIS230 4.3 22.9 1.0 OG E:SER14 4.4 33.8 1.0 C E:HIS230 4.4 23.9 1.0 CB E:ASP45 4.5 17.3 1.0 C5' Z:A503 4.5 31.7 0.8 N E:ASN90 4.6 16.1 1.0 CB E:ASN90 4.6 14.1 1.0 O3' Z:C502 4.7 29.5 0.7 CD2 E:HIS91 4.7 21.8 0.5 N E:HIS230 4.9 19.9 1.0 CE1 E:HIS16 4.9 25.4 0.5 O E:GLY229 5.0 25.8 1.0 NE2 E:HIS16 5.0 28.9 0.5

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