Manganese in PDB 4it0: Structure of the Rna Ligase Rtcb-Gmp/Mn(II) Complex

The structure of Structure of the Rna Ligase Rtcb-Gmp/Mn(II) Complex, PDB code: 4it0 was solved by K.K.Desai, C.A.Bingman, G.N.Phillips Jr., R.T.Raines, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.75 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	81.108, 138.912, 149.469, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 19.2

The binding sites of Manganese atom in the Structure of the Rna Ligase Rtcb-Gmp/Mn(II) Complex (pdb code 4it0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Structure of the Rna Ligase Rtcb-Gmp/Mn(II) Complex, PDB code: 4it0:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Structure of the Rna Ligase Rtcb-Gmp/Mn(II) Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of the Rna Ligase Rtcb-Gmp/Mn(II) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:41.7 occ:0.86 NE2 A:HIS329 2.1 48.5 1.0 SG A:CYS98 2.1 43.7 1.0 NE2 A:HIS234 2.3 35.2 1.0 O2P A:5GP503 2.4 47.1 0.7 HB3 A:CYS98 2.6 39.6 1.0 CB A:CYS98 2.9 33.0 1.0 CD2 A:HIS329 3.0 40.3 1.0 CE1 A:HIS329 3.1 45.7 1.0 CE1 A:HIS234 3.2 31.9 1.0 HD2 A:HIS329 3.2 48.4 1.0 HE1 A:HIS234 3.2 38.2 1.0 HE1 A:HIS329 3.3 54.8 1.0 CD2 A:HIS234 3.4 34.6 1.0 MN A:MN502 3.4 51.3 0.4 HD22 A:ASN202 3.5 66.7 1.0 HB2 A:CYS98 3.5 39.6 1.0 O A:HOH841 3.6 41.0 1.0 HD2 A:HIS234 3.6 41.5 1.0 P A:5GP503 3.8 60.4 0.7 H5'2 A:5GP503 4.0 49.2 0.7 CA A:CYS98 4.0 29.7 1.0 C A:CYS98 4.0 31.9 1.0 H A:GLY99 4.1 37.6 1.0 ND2 A:ASN202 4.1 55.6 1.0 HD2 A:HIS404 4.1 49.5 1.0 ND1 A:HIS329 4.2 40.4 1.0 CG A:HIS329 4.2 36.4 1.0 N A:GLY99 4.2 31.3 1.0 HD2 A:HIS203 4.2 41.1 1.0 H5'1 A:5GP503 4.3 49.2 0.7 HA A:CYS98 4.3 35.7 1.0 ND1 A:HIS234 4.3 36.8 1.0 NE2 A:HIS203 4.3 33.4 1.0 O5' A:5GP503 4.4 50.2 0.7 C5' A:5GP503 4.4 41.0 0.7 CG A:HIS234 4.5 28.0 1.0 O A:CYS98 4.5 24.3 1.0 HD21 A:ASN202 4.6 66.7 1.0 CD2 A:HIS203 4.6 34.2 1.0 OD1 A:ASN202 4.6 46.9 1.0 HD21 A:ASN330 4.7 40.5 1.0 CG A:ASN202 4.7 50.3 1.0 CD2 A:HIS404 4.8 41.3 1.0 NE2 A:HIS404 4.9 48.9 1.0 ND2 A:ASN330 4.9 33.8 1.0 HD1 A:HIS329 5.0 48.4 1.0 OD2 A:ASP95 5.0 35.5 1.0

Manganese binding site 2 out of 4 in the Structure of the Rna Ligase Rtcb-Gmp/Mn(II) Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of the Rna Ligase Rtcb-Gmp/Mn(II) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:51.3 occ:0.39 OD2 A:ASP95 2.2 35.5 1.0 SG A:CYS98 2.4 43.7 1.0 NE2 A:HIS203 2.5 33.4 1.0 HE1 A:HIS203 2.9 46.5 1.0 O A:HOH841 2.9 41.0 1.0 CE1 A:HIS203 3.0 38.7 1.0 CG A:ASP95 3.1 32.4 1.0 HB3 A:ASP95 3.2 37.9 1.0 HB2 A:CYS98 3.2 39.6 1.0 MN A:MN501 3.4 41.7 0.9 CB A:CYS98 3.4 33.0 1.0 CB A:ASP95 3.5 31.6 1.0 HB2 A:ASP95 3.5 37.9 1.0 OD1 A:ASN202 3.5 46.9 1.0 CD2 A:HIS203 3.6 34.2 1.0 HD22 A:ASN202 3.7 66.7 1.0 HB3 A:CYS98 3.9 39.6 1.0 HD2 A:HIS203 4.0 41.1 1.0 ND1 A:HIS203 4.1 33.9 1.0 OD1 A:ASP95 4.2 27.0 1.0 O A:HOH850 4.3 47.6 1.0 ND2 A:ASN202 4.3 55.6 1.0 CG A:ASN202 4.4 50.3 1.0 CG A:HIS203 4.5 30.0 1.0 HA A:CYS98 4.5 35.7 1.0 O2P A:5GP503 4.5 47.1 0.7 CA A:CYS98 4.6 29.7 1.0 HA3 A:GLY236 4.7 36.6 1.0 O2 A:SO4505 4.7 43.8 1.0 HD21 A:ASN330 4.8 40.5 1.0 HD1 A:HIS203 4.8 40.7 1.0 NE2 A:HIS234 4.8 35.2 1.0 HD22 A:ASN330 4.8 40.5 1.0 O A:HOH676 4.9 30.1 1.0 HE1 A:HIS234 5.0 38.2 1.0

Manganese binding site 3 out of 4 in the Structure of the Rna Ligase Rtcb-Gmp/Mn(II) Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of the Rna Ligase Rtcb-Gmp/Mn(II) Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:53.1 occ:0.92 NE2 B:HIS329 2.1 50.0 1.0 SG B:CYS98 2.1 45.1 1.0 NE2 B:HIS234 2.3 37.7 1.0 O B:HOH816 2.7 40.1 1.0 CE1 B:HIS329 2.8 48.2 1.0 HE1 B:HIS329 2.9 57.9 1.0 HB3 B:CYS98 3.1 37.6 1.0 CE1 B:HIS234 3.2 35.1 1.0 CD2 B:HIS329 3.2 47.0 1.0 CB B:CYS98 3.2 31.3 1.0 HD22 B:ASN202 3.3 69.1 1.0 HE1 B:HIS234 3.3 42.1 1.0 CD2 B:HIS234 3.3 34.0 1.0 HD21 B:ASN202 3.4 69.1 1.0 HE1 B:HIS404 3.5 68.1 1.0 HD2 B:HIS329 3.5 56.4 1.0 HD2 B:HIS234 3.5 40.8 1.0 MN B:MN502 3.6 48.4 0.4 ND2 B:ASN202 3.6 57.5 1.0 HB2 B:CYS98 3.8 37.6 1.0 CE1 B:HIS404 4.0 56.7 1.0 ND1 B:HIS329 4.0 50.7 1.0 HD2 B:HIS203 4.1 45.1 1.0 HE2 B:HIS404 4.1 79.2 1.0 CA B:CYS98 4.2 28.7 1.0 C B:CYS98 4.2 36.0 1.0 CG B:HIS329 4.2 41.9 1.0 NE2 B:HIS404 4.3 66.0 1.0 ND1 B:HIS234 4.3 36.3 1.0 N B:GLY99 4.4 26.7 1.0 NE2 B:HIS203 4.4 38.6 1.0 CG B:HIS234 4.4 30.3 1.0 H B:GLY99 4.5 32.1 1.0 HA B:CYS98 4.5 34.5 1.0 CD2 B:HIS203 4.6 37.5 1.0 O B:CYS98 4.7 30.8 1.0 HD1 B:HIS329 4.8 60.8 1.0 CG B:ASN202 4.8 63.6 1.0 HA2 B:GLY99 4.8 33.4 1.0 ND1 B:HIS404 4.9 51.4 1.0 HD21 B:ASN330 5.0 45.0 1.0

Manganese binding site 4 out of 4 in the Structure of the Rna Ligase Rtcb-Gmp/Mn(II) Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of the Rna Ligase Rtcb-Gmp/Mn(II) Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:48.4 occ:0.40 SG B:CYS98 2.1 45.1 1.0 O B:HOH740 2.2 43.9 1.0 OD2 B:ASP95 2.2 42.5 1.0 NE2 B:HIS203 2.3 38.6 1.0 HB2 B:CYS98 2.5 37.6 1.0 CB B:CYS98 2.9 31.3 1.0 HE1 B:HIS203 3.0 44.0 1.0 CE1 B:HIS203 3.0 36.7 1.0 CG B:ASP95 3.2 32.4 1.0 HB3 B:ASP95 3.2 37.3 1.0 HD22 B:ASN202 3.2 69.1 1.0 HB3 B:CYS98 3.5 37.6 1.0 CD2 B:HIS203 3.5 37.5 1.0 MN B:MN501 3.6 53.1 0.9 CB B:ASP95 3.6 31.1 1.0 HB2 B:ASP95 3.7 37.3 1.0 HA B:CYS98 3.8 34.5 1.0 HD2 B:HIS203 3.8 45.1 1.0 HA3 B:GLY236 3.9 31.3 1.0 CA B:CYS98 3.9 28.7 1.0 ND2 B:ASN202 4.0 57.5 1.0 OD1 B:ASP95 4.2 34.3 1.0 ND1 B:HIS203 4.3 33.8 1.0 OD1 B:ASN202 4.4 54.4 1.0 O B:HOH762 4.5 32.6 1.0 CG B:HIS203 4.5 35.2 1.0 N B:GLY236 4.5 26.3 1.0 H B:GLY236 4.5 31.6 1.0 HD21 B:ASN202 4.5 69.1 1.0 O B:HOH816 4.6 40.1 1.0 HD22 B:ASN330 4.6 45.0 1.0 CG B:ASN202 4.6 63.6 1.0 CA B:GLY236 4.7 26.1 1.0 O B:HOH866 4.7 45.2 1.0 HD21 B:ASN330 4.7 45.0 1.0 O3 B:SO4503 4.7 48.0 1.0 H B:CYS98 4.7 35.1 1.0 N B:CYS98 4.8 29.2 1.0 HA B:THR235 4.9 38.0 1.0 C B:THR235 4.9 27.0 1.0 NE2 B:HIS234 4.9 37.7 1.0 O B:ASP95 5.0 25.8 1.0 HD1 B:HIS203 5.0 40.6 1.0 ND2 B:ASN330 5.0 37.5 1.0 HA2 B:GLY236 5.0 31.3 1.0

K.K.Desai, C.A.Bingman, G.N.Phillips, R.T.Raines. Structures of the Noncanonical Rna Ligase Rtcb Reveal the Mechanism of Histidine Guanylylation. Biochemistry V. 52 2518 2013.
ISSN: ISSN 0006-2960
PubMed: 23560983
DOI: 10.1021/BI4002375