Manganese in PDB 4dwr: Rna Ligase Rtcb/MN2+ Complex

The structure of Rna Ligase Rtcb/MN2+ Complex, PDB code: 4dwr was solved by S.Xia, M.Englert, D.Soll, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.74 / 1.48
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	114.081, 84.899, 124.200, 90.00, 115.65, 90.00
R / Rfree (%)	14.2 / 17.8

The binding sites of Manganese atom in the Rna Ligase Rtcb/MN2+ Complex (pdb code 4dwr). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Rna Ligase Rtcb/MN2+ Complex, PDB code: 4dwr:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Rna Ligase Rtcb/MN2+ Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Rna Ligase Rtcb/MN2+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn602 b:28.0 occ:1.00 O1 B:SO4607 1.9 45.9 0.8 OD2 B:ASP95 2.0 25.1 1.0 NE2 B:HIS203 2.0 25.8 1.0 SG B:CYS98 2.2 23.3 1.0 CE1 B:HIS203 3.0 31.9 1.0 S B:SO4607 3.0 48.3 0.8 CG B:ASP95 3.0 20.7 1.0 CB B:CYS98 3.0 20.5 1.0 CD2 B:HIS203 3.0 22.1 1.0 O2 B:SO4607 3.2 51.8 0.8 O B:HOH967 3.5 36.5 1.0 O4 B:SO4607 3.5 49.6 0.8 CB B:ASP95 3.6 20.7 1.0 O B:HOH756 3.9 35.7 1.0 MN B:MN603 3.9 30.6 1.0 OD1 B:ASP95 4.0 21.6 1.0 CA B:CYS98 4.1 17.6 1.0 ND1 B:HIS203 4.1 31.8 1.0 CG B:HIS203 4.2 22.1 1.0 O B:HOH960 4.2 22.2 1.0 O3 B:SO4607 4.2 48.3 0.8 N B:GLY236 4.5 18.8 1.0 CA B:GLY236 4.6 19.8 1.0 C B:THR235 4.7 18.0 1.0 NE2 B:HIS234 5.0 21.8 1.0 O B:ASN202 5.0 28.8 1.0 N B:CYS98 5.0 18.9 1.0

Manganese binding site 2 out of 6 in the Rna Ligase Rtcb/MN2+ Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Rna Ligase Rtcb/MN2+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn603 b:30.6 occ:1.00 NE2 B:HIS329 2.2 30.0 1.0 O B:HOH970 2.2 42.8 1.0 O B:HOH756 2.2 35.7 1.0 NE2 B:HIS234 2.2 21.8 1.0 O B:HOH967 2.3 36.5 1.0 SG B:CYS98 2.6 23.3 1.0 CE1 B:HIS329 3.0 34.7 1.0 CE1 B:HIS234 3.1 23.1 1.0 CD2 B:HIS329 3.2 28.3 1.0 CD2 B:HIS234 3.3 22.0 1.0 CB B:CYS98 3.6 20.5 1.0 NE2 B:HIS404 3.6 22.7 0.5 CE1 B:HIS404 3.9 24.8 0.5 MN B:MN602 3.9 28.0 1.0 O1 B:SO4607 4.1 45.9 0.8 ND1 B:HIS329 4.1 31.0 1.0 ND1 B:HIS234 4.3 21.8 1.0 CG B:HIS329 4.3 26.0 1.0 O B:HOH920 4.4 43.1 1.0 O B:ASN202 4.4 28.8 1.0 CG B:HIS234 4.4 18.0 1.0 O B:HOH1149 4.5 43.1 1.0 CD2 B:HIS404 4.6 23.3 0.5 C B:CYS98 4.6 18.5 1.0 CA B:CYS98 4.6 17.6 1.0 O4 B:SO4607 4.7 49.6 0.8 O B:HOH1038 4.7 95.9 1.0 N B:GLY99 4.8 17.5 1.0 NE2 B:HIS203 4.8 25.8 1.0 CD2 B:HIS203 4.8 22.1 1.0 ND1 B:HIS404 4.9 22.9 0.5 ND1 B:HIS404 4.9 18.0 0.5

Manganese binding site 3 out of 6 in the Rna Ligase Rtcb/MN2+ Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Rna Ligase Rtcb/MN2+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:28.6 occ:1.00 O2 A:SO4608 1.9 33.2 0.8 NE2 A:HIS203 2.0 25.9 1.0 OD2 A:ASP95 2.0 23.4 1.0 SG A:CYS98 2.3 24.9 1.0 CE1 A:HIS203 2.9 32.0 1.0 CG A:ASP95 3.0 22.9 1.0 CB A:CYS98 3.0 19.0 1.0 CD2 A:HIS203 3.1 25.3 1.0 S A:SO4608 3.1 42.9 0.8 O3 A:SO4608 3.4 41.0 0.8 CB A:ASP95 3.5 18.9 1.0 O A:HOH764 3.6 31.6 1.0 O1 A:SO4608 3.7 43.3 0.8 O A:HOH1219 3.7 50.7 1.0 ND1 A:HIS203 4.0 33.0 1.0 MN A:MN603 4.1 28.9 1.0 CA A:CYS98 4.1 18.3 1.0 OD1 A:ASP95 4.1 24.0 1.0 CG A:HIS203 4.2 22.3 1.0 O A:HOH816 4.2 31.8 1.0 O A:HOH710 4.2 22.2 1.0 O4 A:SO4608 4.2 45.5 0.8 N A:GLY236 4.5 18.9 1.0 CA A:GLY236 4.5 19.6 1.0 O A:HOH1012 4.6 0.9 1.0 O4 A:SO4605 4.6 44.8 1.0 C A:THR235 4.8 19.0 1.0 O A:HOH1038 4.8 58.8 1.0 O A:ASP95 5.0 18.3 1.0

Manganese binding site 4 out of 6 in the Rna Ligase Rtcb/MN2+ Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Rna Ligase Rtcb/MN2+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn603 b:28.9 occ:1.00 CE1 A:HIS329 2.2 23.6 1.0 NE2 A:HIS234 2.3 22.0 1.0 O A:HOH816 2.3 31.8 1.0 O A:HOH764 2.3 31.6 1.0 O A:HOH778 2.4 41.1 1.0 SG A:CYS98 2.5 24.9 1.0 NE2 A:HIS329 2.9 31.9 1.0 CE1 A:HIS234 3.1 24.1 1.0 ND1 A:HIS329 3.3 29.1 1.0 CD2 A:HIS234 3.4 21.6 1.0 CB A:CYS98 3.6 19.0 1.0 O1 A:SO4608 4.0 43.3 0.8 MN A:MN602 4.1 28.6 1.0 CD2 A:HIS329 4.1 23.6 1.0 O3 A:SO4608 4.3 41.0 0.8 ND1 A:HIS234 4.3 24.0 1.0 CG A:HIS329 4.3 24.4 1.0 O A:ASN202 4.4 30.8 1.0 CG A:HIS234 4.4 21.0 1.0 C A:CYS98 4.6 16.9 1.0 S A:SO4608 4.6 42.9 0.8 O A:HOH865 4.6 34.8 1.0 O A:HOH1086 4.6 49.4 1.0 CA A:CYS98 4.6 18.3 1.0 O2 A:SO4608 4.7 33.2 0.8 N A:GLY99 4.7 17.8 1.0 ND1 A:HIS404 4.8 30.1 1.0 CD2 A:HIS203 4.9 25.3 1.0 NE2 A:HIS203 4.9 25.9 1.0 O A:CYS98 5.0 18.3 1.0

Manganese binding site 5 out of 6 in the Rna Ligase Rtcb/MN2+ Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Rna Ligase Rtcb/MN2+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn602 b:26.1 occ:1.00 NE2 C:HIS329 2.2 23.8 1.0 O C:HOH709 2.2 30.5 1.0 O C:HOH748 2.3 28.2 1.0 O C:HOH912 2.3 28.6 1.0 NE2 C:HIS234 2.3 21.0 1.0 SG C:CYS98 2.5 24.1 1.0 CE1 C:HIS329 3.1 28.2 1.0 CE1 C:HIS234 3.1 22.1 1.0 CD2 C:HIS329 3.3 23.6 1.0 CD2 C:HIS234 3.3 20.3 1.0 CB C:CYS98 3.6 22.5 1.0 MN C:MN603 4.1 28.2 1.0 O4 C:SO4608 4.1 46.2 0.8 ND1 C:HIS329 4.2 23.6 1.0 ND1 C:HIS234 4.3 23.0 1.0 CG C:HIS329 4.3 22.5 1.0 O C:ASN202 4.4 26.2 1.0 O3 C:SO4608 4.4 41.9 0.8 CG C:HIS234 4.4 21.1 1.0 O C:HOH807 4.5 27.7 1.0 C C:CYS98 4.5 18.4 1.0 O C:HOH840 4.5 31.1 1.0 CA C:CYS98 4.6 19.4 1.0 N C:GLY99 4.6 19.0 1.0 ND1 C:HIS404 4.7 23.0 1.0 S C:SO4608 4.7 46.2 0.8 O1 C:SO4608 4.7 34.7 0.8 O C:HOH1058 4.8 52.7 1.0 O C:CYS98 4.9 21.3 1.0 CD2 C:HIS203 5.0 23.0 1.0

Manganese binding site 6 out of 6 in the Rna Ligase Rtcb/MN2+ Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Rna Ligase Rtcb/MN2+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn603 b:28.2 occ:1.00 O1 C:SO4608 1.9 34.7 0.8 OD2 C:ASP95 1.9 26.2 1.0 NE2 C:HIS203 2.1 23.4 1.0 SG C:CYS98 2.2 24.1 1.0 CG C:ASP95 3.0 21.4 1.0 CB C:CYS98 3.0 22.5 1.0 CE1 C:HIS203 3.0 26.0 1.0 S C:SO4608 3.1 46.2 0.8 CD2 C:HIS203 3.2 23.0 1.0 O3 C:SO4608 3.4 41.9 0.8 CB C:ASP95 3.5 21.9 1.0 O C:HOH912 3.7 28.6 1.0 O4 C:SO4608 3.7 46.2 0.8 O C:HOH996 3.8 44.2 1.0 CA C:CYS98 4.0 19.4 1.0 OD1 C:ASP95 4.0 28.6 1.0 MN C:MN602 4.1 26.1 1.0 O C:HOH748 4.1 28.2 1.0 ND1 C:HIS203 4.2 28.9 1.0 O C:HOH982 4.2 26.0 1.0 O2 C:SO4608 4.2 44.5 0.8 CG C:HIS203 4.3 21.9 1.0 N C:GLY236 4.3 22.0 1.0 CA C:GLY236 4.5 23.9 1.0 O C:HOH971 4.6 52.1 1.0 C C:THR235 4.6 20.8 1.0 O3 C:SO4605 4.8 29.4 0.8 O C:ASP95 4.9 21.2 1.0 N C:CYS98 4.9 21.7 1.0 CA C:ASP95 5.0 19.7 1.0 CA C:THR235 5.0 20.6 1.0

M.Englert, S.Xia, C.Okada, A.Nakamura, V.Tanavde, M.Yao, S.H.Eom, W.H.Konigsberg, D.Soll, J.Wang. Structural and Mechanistic Insights Into Guanylylation of Rna-Splicing Ligase Rtcb Joining Rna Between 3'-Terminal Phosphate and 5'-Oh. Proc.Natl.Acad.Sci.Usa V. 109 15235 2012.
ISSN: ISSN 0027-8424
PubMed: 22949672
DOI: 10.1073/PNAS.1213795109