Manganese in PDB 4dwq: Rna Ligase Rtcb-Gmp/Mn(2+) Complex

The structure of Rna Ligase Rtcb-Gmp/Mn(2+) Complex, PDB code: 4dwq was solved by C.Okada, S.Xia, M.Englert, M.Yao, D.Soll, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	101.29 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.296, 137.756, 148.408, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 19.3

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

Manganese binding site 1 out of 2 in the Rna Ligase Rtcb-Gmp/Mn(2+) 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-Gmp/Mn(2+) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:26.7 occ:0.30 NE2 A:HIS329 2.2 46.3 1.0 SG A:CYS98 2.4 46.6 1.0 O2P A:5GP501 2.4 67.2 1.0 O A:HOH807 2.4 50.7 1.0 NE2 A:HIS234 2.5 27.6 1.0 CB A:CYS98 2.8 16.5 1.0 CE1 A:HIS234 3.1 23.3 1.0 CD2 A:HIS329 3.1 44.1 1.0 CE1 A:HIS329 3.2 89.3 1.0 CD2 A:HIS234 3.7 34.7 1.0 P A:5GP501 3.9 54.4 1.0 CA A:CYS98 3.9 22.0 1.0 C A:CYS98 4.1 27.4 1.0 ND2 A:ASN202 4.3 38.0 1.0 ND1 A:HIS329 4.3 55.5 1.0 CG A:HIS329 4.3 28.0 1.0 OD1 A:ASN202 4.4 36.9 1.0 ND1 A:HIS234 4.4 27.1 1.0 N A:GLY99 4.4 24.2 1.0 C5' A:5GP501 4.5 37.6 1.0 O5' A:5GP501 4.5 52.6 1.0 NE2 A:HIS203 4.6 23.3 1.0 ND2 A:ASN330 4.6 28.2 1.0 O A:CYS98 4.6 21.3 1.0 CG A:ASN202 4.7 35.8 1.0 OD2 A:ASP95 4.7 67.7 1.0 CG A:HIS234 4.7 25.8 1.0 CD2 A:HIS203 4.7 22.9 1.0 O3P A:5GP501 4.8 55.6 1.0 CD2 A:HIS404 4.9 22.3 1.0 NE2 A:HIS404 5.0 41.3 1.0

Manganese binding site 2 out of 2 in the Rna Ligase Rtcb-Gmp/Mn(2+) 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-Gmp/Mn(2+) Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:26.4 occ:0.25 SG B:CYS98 1.9 43.4 1.0 NE2 B:HIS329 2.1 56.8 1.0 NE2 B:HIS234 2.5 35.5 1.0 O2P B:5GP501 2.8 59.9 1.0 CB B:CYS98 2.9 24.3 1.0 CD2 B:HIS329 3.1 64.8 1.0 CE1 B:HIS329 3.1 0.3 1.0 CE1 B:HIS234 3.2 34.8 1.0 CD2 B:HIS234 3.5 34.6 1.0 CA B:CYS98 3.9 17.4 1.0 C B:CYS98 3.9 19.7 1.0 N B:GLY99 4.2 15.1 1.0 ND1 B:HIS329 4.3 44.7 1.0 CG B:HIS329 4.3 26.8 1.0 P B:5GP501 4.3 0.0 1.0 O B:CYS98 4.4 16.0 1.0 ND1 B:HIS234 4.4 39.2 1.0 NE2 B:HIS203 4.4 30.7 1.0 C5' B:5GP501 4.5 44.2 1.0 CG B:HIS234 4.6 26.0 1.0 CD2 B:HIS203 4.7 25.9 1.0 ND2 B:ASN330 4.8 27.4 1.0 O5' B:5GP501 4.8 79.5 1.0 OD2 B:ASP95 4.9 49.0 1.0 CD2 B:HIS404 4.9 22.2 1.0 CA B:GLY99 5.0 12.9 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