Manganese in PDB 4isz: Rna Ligase Rtcb in Complex with Gtp Alphas and Mn(II)

The structure of Rna Ligase Rtcb in Complex with Gtp Alphas and Mn(II), PDB code: 4isz 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 / 2.30
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 (%)	16.5 / 20.5

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

Manganese binding site 1 out of 4 in the Rna Ligase Rtcb in Complex with Gtp Alphas and Mn(II)


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 in Complex with Gtp Alphas and Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:37.5 occ:0.87 O2A A:GAV501 2.2 48.9 0.7 SG A:CYS98 2.3 33.8 1.0 NE2 A:HIS329 2.4 35.7 1.0 NE2 A:HIS234 2.4 27.4 1.0 HB3 A:CYS98 2.8 31.3 1.0 O3B A:GAV501 2.9 62.8 0.7 CB A:CYS98 3.1 26.1 1.0 O A:HOH682 3.2 44.6 1.0 CE1 A:HIS234 3.2 30.7 1.0 HE1 A:HIS234 3.3 36.9 1.0 CD2 A:HIS329 3.3 34.3 1.0 PA A:GAV501 3.4 63.9 0.7 CE1 A:HIS329 3.4 49.9 1.0 HD2 A:HIS329 3.4 41.2 1.0 O3A A:GAV501 3.4 66.9 0.7 CD2 A:HIS234 3.5 24.9 1.0 HE1 A:HIS329 3.6 59.9 1.0 MN A:MN503 3.6 37.0 0.6 PB A:GAV501 3.7 61.4 0.7 HB2 A:CYS98 3.7 31.3 1.0 HD2 A:HIS234 3.7 29.9 1.0 O2G A:GAV501 3.8 30.7 0.7 PG A:GAV501 4.0 55.8 0.7 HD2 A:HIS404 4.2 48.3 1.0 CA A:CYS98 4.2 22.4 1.0 C A:CYS98 4.2 22.3 1.0 O2B A:GAV501 4.2 42.8 0.7 HD2 A:HIS203 4.3 43.8 1.0 O5' A:GAV501 4.3 63.5 0.7 ND1 A:HIS234 4.4 27.0 1.0 HD21 A:ASN330 4.5 38.2 1.0 N A:GLY99 4.5 16.9 1.0 CG A:HIS329 4.5 36.4 1.0 HA A:CYS98 4.5 26.8 1.0 ND1 A:HIS329 4.5 38.0 1.0 H A:GLY99 4.5 20.3 1.0 O A:CYS98 4.6 19.3 1.0 CG A:HIS234 4.6 21.8 1.0 C5' A:GAV501 4.6 51.2 0.7 NE2 A:HIS203 4.7 30.6 1.0 ND2 A:ASN330 4.8 31.9 1.0 CD2 A:HIS203 4.8 36.5 1.0 CD2 A:HIS404 4.8 40.2 1.0 HD22 A:ASN330 4.9 38.2 1.0 S1A A:GAV501 4.9 71.4 0.7 NE2 A:HIS404 4.9 54.8 1.0 O3G A:GAV501 5.0 69.0 0.7

Manganese binding site 2 out of 4 in the Rna Ligase Rtcb in Complex with Gtp Alphas and Mn(II)


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 in Complex with Gtp Alphas and Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:37.0 occ:0.62 OD2 A:ASP95 2.1 36.5 1.0 NE2 A:HIS203 2.3 30.6 1.0 SG A:CYS98 2.4 33.8 1.0 O3B A:GAV501 2.5 62.8 0.7 O1G A:GAV501 2.8 53.9 0.7 HB2 A:CYS98 3.0 31.3 1.0 CG A:ASP95 3.0 22.2 1.0 PG A:GAV501 3.0 55.8 0.7 HB3 A:ASP95 3.1 31.5 1.0 CE1 A:HIS203 3.1 28.8 1.0 HE1 A:HIS203 3.1 34.6 1.0 CB A:CYS98 3.2 26.1 1.0 O2G A:GAV501 3.4 30.7 0.7 CB A:ASP95 3.4 26.2 1.0 CD2 A:HIS203 3.4 36.5 1.0 O2B A:GAV501 3.5 42.8 0.7 HB2 A:ASP95 3.5 31.5 1.0 MN A:MN502 3.6 37.5 0.9 PB A:GAV501 3.6 61.4 0.7 HD2 A:HIS203 3.7 43.8 1.0 HB3 A:CYS98 3.8 31.3 1.0 OD1 A:ASP95 4.0 24.3 1.0 HA3 A:GLY236 4.1 24.7 1.0 HA A:CYS98 4.3 26.8 1.0 ND1 A:HIS203 4.3 31.2 1.0 CA A:CYS98 4.4 22.4 1.0 O A:HOH615 4.4 22.4 1.0 CG A:HIS203 4.5 26.8 1.0 O3G A:GAV501 4.5 69.0 0.7 HD22 A:ASN330 4.5 38.2 1.0 O1B A:GAV501 4.6 61.8 0.7 HD21 A:ASN330 4.7 38.2 1.0 O2 A:SO4504 4.7 34.0 0.9 O3A A:GAV501 4.7 66.9 0.7 H A:GLY236 4.8 19.0 1.0 N A:GLY236 4.8 15.9 1.0 CA A:GLY236 4.9 20.6 1.0 NE2 A:HIS234 4.9 27.4 1.0 CA A:ASP95 4.9 23.1 1.0 ND2 A:ASN330 4.9 31.9 1.0 O A:ASP95 5.0 22.0 1.0

Manganese binding site 3 out of 4 in the Rna Ligase Rtcb in Complex with Gtp Alphas and Mn(II)


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 in Complex with Gtp Alphas and Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:40.5 occ:0.85 NE2 B:HIS329 2.0 53.6 1.0 SG B:CYS98 2.2 35.4 1.0 O2A B:GAV501 2.3 48.9 0.6 NE2 B:HIS234 2.5 31.6 1.0 HE1 B:HIS329 2.5 56.5 1.0 CE1 B:HIS329 2.6 47.0 1.0 O3B B:GAV501 2.6 62.8 0.6 HB3 B:CYS98 2.8 35.3 1.0 CB B:CYS98 3.1 29.4 1.0 O2G B:GAV501 3.3 30.7 0.6 CD2 B:HIS329 3.3 44.6 1.0 CE1 B:HIS234 3.4 30.4 1.0 CD2 B:HIS234 3.4 29.6 1.0 MN B:MN503 3.5 45.2 0.6 HE1 B:HIS234 3.5 36.5 1.0 PA B:GAV501 3.5 63.9 0.6 HD2 B:HIS234 3.6 35.6 1.0 PB B:GAV501 3.6 61.4 0.6 O3A B:GAV501 3.7 66.9 0.6 PG B:GAV501 3.7 55.8 0.6 HB2 B:CYS98 3.7 35.3 1.0 HD2 B:HIS329 3.7 53.5 1.0 ND1 B:HIS329 3.9 50.5 1.0 O2B B:GAV501 4.0 42.8 0.6 HD2 B:HIS203 4.1 43.9 1.0 C B:CYS98 4.2 31.6 1.0 CA B:CYS98 4.2 27.4 1.0 CG B:HIS329 4.2 36.4 1.0 O5' B:GAV501 4.4 63.5 0.6 O B:CYS98 4.4 31.4 1.0 NE2 B:HIS203 4.4 32.5 1.0 HA B:CYS98 4.5 32.9 1.0 ND1 B:HIS234 4.5 35.1 1.0 N B:GLY99 4.5 22.6 1.0 HD1 B:HIS329 4.5 60.5 1.0 O B:HOH728 4.5 49.6 1.0 CG B:HIS234 4.6 24.9 1.0 CD2 B:HIS203 4.6 36.6 1.0 O1G B:GAV501 4.6 53.9 0.6 C5' B:GAV501 4.7 51.2 0.6 H B:GLY99 4.7 27.1 1.0 HD21 B:ASN330 4.7 42.4 1.0 NE2 B:HIS404 4.8 60.2 1.0 O3G B:GAV501 4.8 69.0 0.6 HA2 B:GLY99 4.9 32.4 1.0 HD2 B:HIS404 4.9 55.7 1.0 O1B B:GAV501 5.0 61.8 0.6

Manganese binding site 4 out of 4 in the Rna Ligase Rtcb in Complex with Gtp Alphas and Mn(II)


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 in Complex with Gtp Alphas and Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn503 b:45.2 occ:0.57 OD2 B:ASP95 2.2 38.3 1.0 SG B:CYS98 2.2 35.4 1.0 NE2 B:HIS203 2.3 32.5 1.0 O1G B:GAV501 2.5 53.9 0.6 HB2 B:CYS98 2.7 35.3 1.0 O3B B:GAV501 2.9 62.8 0.6 O2G B:GAV501 2.9 30.7 0.6 PG B:GAV501 3.0 55.8 0.6 O B:HOH716 3.0 41.6 1.0 CB B:CYS98 3.0 29.4 1.0 HB3 B:ASP95 3.1 26.3 1.0 CE1 B:HIS203 3.1 37.8 1.0 HE1 B:HIS203 3.1 45.3 1.0 CG B:ASP95 3.1 30.6 1.0 O2B B:GAV501 3.4 42.8 0.6 CD2 B:HIS203 3.4 36.6 1.0 MN B:MN502 3.5 40.5 0.8 CB B:ASP95 3.5 21.9 1.0 HB3 B:CYS98 3.6 35.3 1.0 HB2 B:ASP95 3.7 26.3 1.0 HD2 B:HIS203 3.7 43.9 1.0 PB B:GAV501 3.7 61.4 0.6 HA3 B:GLY236 4.1 26.8 1.0 HA B:CYS98 4.1 32.9 1.0 CA B:CYS98 4.2 27.4 1.0 OD1 B:ASP95 4.2 31.9 1.0 ND1 B:HIS203 4.3 35.2 1.0 O B:HOH614 4.4 26.4 1.0 O3G B:GAV501 4.5 69.0 0.6 CG B:HIS203 4.5 32.6 1.0 O1B B:GAV501 4.6 61.8 0.6 HD22 B:ASN330 4.6 42.4 1.0 HD21 B:ASN330 4.7 42.4 1.0 N B:GLY236 4.7 26.5 1.0 O2 B:SO4504 4.7 42.0 1.0 H B:GLY236 4.7 31.9 1.0 O B:ASP95 4.8 25.1 1.0 CA B:GLY236 4.9 22.3 1.0 HA B:THR235 4.9 33.7 1.0 O2A B:GAV501 4.9 48.9 0.6 ND2 B:ASN330 4.9 35.3 1.0 H B:CYS98 5.0 34.5 1.0 CA B:ASP95 5.0 29.9 1.0 O3A B:GAV501 5.0 66.9 0.6 NE2 B:HIS234 5.0 31.6 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