Manganese in PDB 2xi5: N-Terminal Endonuclease Domain of La Crosse Virus L-Protein

The structure of N-Terminal Endonuclease Domain of La Crosse Virus L-Protein, PDB code: 2xi5 was solved by J.Reguera, F.Weber, S.Cusack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.16 / 2.20
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	124.200, 124.200, 294.320, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 22.4

The binding sites of Manganese atom in the N-Terminal Endonuclease Domain of La Crosse Virus L-Protein (pdb code 2xi5). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the N-Terminal Endonuclease Domain of La Crosse Virus L-Protein, PDB code: 2xi5:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the N-Terminal Endonuclease Domain of La Crosse Virus L-Protein


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of N-Terminal Endonuclease Domain of La Crosse Virus L-Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1184 b:31.1 occ:1.00 OD2 A:ASP79 2.3 24.2 1.0 O A:TYR93 2.3 19.7 1.0 O A:HOH2110 2.3 19.4 1.0 OD1 A:ASP92 2.3 24.5 1.0 NE2 A:HIS34 2.4 19.9 1.0 O A:HOH2111 2.7 26.3 1.0 CG A:ASP79 3.2 21.7 1.0 CG A:ASP92 3.2 23.9 1.0 CD2 A:HIS34 3.3 19.6 1.0 C A:TYR93 3.4 18.4 1.0 CE1 A:HIS34 3.4 19.6 1.0 OD1 A:ASP79 3.4 19.0 1.0 N A:TYR93 3.5 18.2 1.0 OD2 A:ASP92 3.7 28.4 1.0 CA A:TYR93 3.8 18.2 1.0 CB A:TYR93 4.1 18.2 1.0 NZ A:LYS94 4.1 21.5 1.0 O A:HOH2060 4.1 26.4 1.0 C A:ASP92 4.3 18.9 1.0 CB A:ASP92 4.4 20.0 1.0 CG A:HIS34 4.5 19.0 1.0 N A:LYS94 4.5 19.1 1.0 ND1 A:HIS34 4.5 19.1 1.0 CA A:ASP92 4.5 19.8 1.0 CB A:ASP79 4.6 22.6 1.0 CD A:LYS94 4.8 25.8 1.0 CG A:TYR93 4.8 18.4 1.0 O A:HOH2054 4.8 34.9 1.0 CA A:LYS94 5.0 19.5 1.0 CE A:LYS94 5.0 25.4 1.0

Manganese binding site 2 out of 4 in the N-Terminal Endonuclease Domain of La Crosse Virus L-Protein


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of N-Terminal Endonuclease Domain of La Crosse Virus L-Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1184 b:30.8 occ:1.00 OD2 B:ASP79 2.2 22.6 1.0 O B:TYR93 2.3 20.1 1.0 OD1 B:ASP92 2.4 24.4 1.0 NE2 B:HIS34 2.4 19.1 1.0 O B:HOH2130 2.5 22.4 1.0 O B:HOH2129 2.6 25.4 1.0 CG B:ASP79 3.3 21.9 1.0 CG B:ASP92 3.3 21.1 1.0 C B:TYR93 3.3 19.2 1.0 CE1 B:HIS34 3.4 17.7 1.0 CD2 B:HIS34 3.4 18.6 1.0 N B:TYR93 3.4 17.3 1.0 OD1 B:ASP79 3.6 22.4 1.0 OD2 B:ASP92 3.7 23.4 1.0 CA B:TYR93 3.8 18.7 1.0 NZ B:LYS94 4.0 21.9 1.0 O B:HOH2061 4.0 26.9 1.0 CB B:TYR93 4.1 18.8 1.0 C B:ASP92 4.2 17.9 1.0 O B:HOH2015 4.3 42.5 1.0 CB B:ASP92 4.5 18.6 1.0 CA B:ASP92 4.5 18.4 1.0 N B:LYS94 4.5 20.4 1.0 ND1 B:HIS34 4.5 18.6 1.0 CG B:HIS34 4.6 18.1 1.0 CB B:ASP79 4.6 20.1 1.0 CD B:LYS94 4.6 25.4 1.0 CG B:TYR93 4.8 18.4 1.0 CG B:LYS94 4.8 22.5 1.0 CE B:LYS94 4.9 27.8 1.0 CA B:LYS94 4.9 20.4 1.0 CD2 B:TYR93 5.0 18.8 1.0

Manganese binding site 3 out of 4 in the N-Terminal Endonuclease Domain of La Crosse Virus L-Protein


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of N-Terminal Endonuclease Domain of La Crosse Virus L-Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1184 b:34.1 occ:1.00 O C:TYR93 2.2 27.9 1.0 OD2 C:ASP79 2.2 23.3 1.0 O C:HOH2098 2.3 24.4 1.0 OD1 C:ASP92 2.4 32.5 1.0 NE2 C:HIS34 2.4 26.3 1.0 O C:HOH2097 2.6 30.7 1.0 CG C:ASP79 3.2 24.8 1.0 C C:TYR93 3.3 28.0 1.0 CG C:ASP92 3.3 29.8 1.0 CD2 C:HIS34 3.3 26.6 1.0 N C:TYR93 3.4 26.7 1.0 CE1 C:HIS34 3.4 25.0 1.0 OD1 C:ASP79 3.6 24.5 1.0 OD2 C:ASP92 3.7 30.9 1.0 CA C:TYR93 3.8 26.9 1.0 NZ C:LYS94 3.8 27.4 1.0 O C:HOH2052 4.1 25.5 1.0 CB C:TYR93 4.2 27.8 1.0 C C:ASP92 4.2 26.4 1.0 O C:HOH2014 4.3 44.0 1.0 N C:LYS94 4.4 28.5 1.0 CB C:ASP92 4.4 27.6 1.0 CA C:ASP92 4.5 27.0 1.0 CG C:HIS34 4.5 25.6 1.0 ND1 C:HIS34 4.5 26.8 1.0 CB C:ASP79 4.6 25.3 1.0 CD C:LYS94 4.6 31.4 1.0 CE C:LYS94 4.7 31.6 1.0 CG C:TYR93 4.9 28.0 1.0 CA C:LYS94 4.9 29.2 1.0 O C:HOH2046 5.0 43.2 1.0 CD2 C:TYR93 5.0 29.4 1.0 CG C:LYS94 5.0 30.0 1.0

Manganese binding site 4 out of 4 in the N-Terminal Endonuclease Domain of La Crosse Virus L-Protein


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of N-Terminal Endonuclease Domain of La Crosse Virus L-Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1184 b:28.1 occ:1.00 OD2 D:ASP79 2.2 20.3 1.0 O D:TYR93 2.2 19.6 1.0 O D:HOH2125 2.3 20.6 1.0 OD1 D:ASP92 2.3 25.1 1.0 O D:HOH2126 2.4 21.2 1.0 NE2 D:HIS34 2.5 19.1 1.0 CG D:ASP92 3.2 25.0 1.0 CG D:ASP79 3.2 22.8 1.0 C D:TYR93 3.3 19.4 1.0 CD2 D:HIS34 3.4 21.1 1.0 CE1 D:HIS34 3.5 17.2 1.0 N D:TYR93 3.5 20.9 1.0 OD1 D:ASP79 3.6 18.5 1.0 OD2 D:ASP92 3.7 28.6 1.0 CA D:TYR93 3.8 19.9 1.0 O D:HOH2066 4.0 23.4 1.0 NZ D:LYS94 4.1 18.6 1.0 CB D:TYR93 4.1 20.3 1.0 C D:ASP92 4.2 21.8 1.0 CB D:ASP92 4.4 21.8 1.0 CA D:ASP92 4.4 22.0 1.0 N D:LYS94 4.5 19.1 1.0 CG D:HIS34 4.6 19.9 1.0 CB D:ASP79 4.6 23.8 1.0 ND1 D:HIS34 4.6 18.6 1.0 CD D:LYS94 4.7 21.8 1.0 CG D:TYR93 4.8 21.1 1.0 CA D:LYS94 4.9 19.7 1.0 CG D:LYS94 4.9 20.7 1.0 CD2 D:TYR93 4.9 22.5 1.0 CE D:LYS94 5.0 23.5 1.0

J.Reguera, F.Weber, S.Cusack. Bunyaviridae Rna Polymerases (L-Protein) Have An N-Terminal, Influenza-Like Endonuclease Domain, Essential For Viral Cap- Dependent Transcription. Plos Pathog. V. 6 1101 2010.
ISSN: ISSN 1553-7366
PubMed: 20862319
DOI: 10.1371/JOURNAL.PPAT.1001101