Manganese in PDB 2xi7: 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: 2xi7 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)	47.29 / 2.20
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	124.590, 124.590, 294.710, 90.00, 90.00, 120.00
R / Rfree (%)	18.8 / 22.1

The binding sites of Manganese atom in the N-Terminal Endonuclease Domain of La Crosse Virus L-Protein (pdb code 2xi7). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the N-Terminal Endonuclease Domain of La Crosse Virus L-Protein, PDB code: 2xi7:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 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:21.0 occ:1.00 O11 A:XI71186 2.0 21.9 1.0 OD2 A:ASP79 2.0 22.0 1.0 OD2 A:ASP92 2.2 24.0 1.0 O A:TYR93 2.2 21.4 1.0 O8 A:XI71186 2.2 24.7 1.0 NE2 A:HIS34 2.3 18.8 1.0 C10 A:XI71186 2.8 29.9 1.0 C9 A:XI71186 2.9 29.3 1.0 CG A:ASP79 3.1 23.7 1.0 CG A:ASP92 3.1 25.8 1.0 CE1 A:HIS34 3.2 20.0 1.0 CD2 A:HIS34 3.2 19.0 1.0 C A:TYR93 3.4 21.6 1.0 OD1 A:ASP79 3.4 25.2 1.0 N A:TYR93 3.5 22.3 1.0 OD1 A:ASP92 3.6 24.5 1.0 MN A:MN1185 3.8 35.3 1.0 CA A:TYR93 3.9 22.2 1.0 O10 A:XI71186 4.0 31.0 1.0 CB A:TYR93 4.1 21.9 1.0 C8 A:XI71186 4.3 33.8 1.0 CB A:ASP92 4.3 23.5 1.0 C A:ASP92 4.3 23.2 1.0 ND1 A:HIS34 4.3 19.1 1.0 CG A:HIS34 4.4 21.2 1.0 O A:HOH2113 4.4 21.8 1.0 CB A:ASP79 4.4 24.5 1.0 CE A:LYS94 4.4 27.7 1.0 O A:HOH2056 4.5 41.1 1.0 N A:LYS94 4.5 20.9 1.0 NZ A:LYS94 4.5 27.3 1.0 CA A:ASP92 4.5 22.9 1.0 CD A:LYS94 4.6 26.6 1.0 O A:HOH2114 4.8 24.4 1.0 CG A:TYR93 4.8 21.8 1.0 CD2 A:TYR93 4.9 20.2 1.0 CA A:LYS94 4.9 21.9 1.0

Manganese binding site 2 out of 8 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 A:Mn1185 b:35.3 occ:1.00 OD1 A:ASP79 2.1 25.2 1.0 O8 A:XI71186 2.1 24.7 1.0 O14 A:XI71186 2.1 35.6 1.0 OD1 A:ASP52 2.2 32.1 1.0 O A:HOH2113 2.2 21.8 1.0 O A:HOH2114 2.3 24.4 1.0 C7 A:XI71186 3.1 41.4 1.0 CG A:ASP79 3.1 23.7 1.0 CG A:ASP52 3.2 34.9 1.0 C9 A:XI71186 3.2 29.3 1.0 OD2 A:ASP52 3.5 38.4 1.0 C8 A:XI71186 3.5 33.8 1.0 OD2 A:ASP79 3.6 22.0 1.0 MN A:MN1184 3.8 21.0 1.0 OD1 A:ASP92 4.1 24.5 1.0 OD1 A:ASN51 4.2 42.5 1.0 CE1 A:HIS34 4.2 20.0 1.0 C10 A:XI71186 4.4 29.9 1.0 CB A:ASP79 4.4 24.5 1.0 O A:THR77 4.4 27.1 1.0 NE2 A:HIS34 4.4 18.8 1.0 C1 A:XI71186 4.4 50.4 1.0 CA A:ASP79 4.5 24.3 1.0 CB A:ASP52 4.5 36.5 1.0 N A:ASP79 4.5 23.7 1.0 N A:ASP52 4.6 37.4 1.0 OD2 A:ASP92 4.7 24.0 1.0 O11 A:XI71186 4.7 21.9 1.0 CA A:ASP52 4.7 36.7 1.0 O A:HOH2056 4.8 41.1 1.0 CG A:ASP92 4.8 25.8 1.0 CG A:ASN51 4.8 42.1 1.0 ND2 A:ASN51 4.9 47.4 1.0

Manganese binding site 3 out of 8 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 B:Mn1184 b:30.8 occ:1.00 O8 B:XI71186 2.1 24.3 1.0 O B:HOH2129 2.1 20.5 1.0 OD1 B:ASP52 2.1 30.1 1.0 O14 B:XI71186 2.1 37.7 1.0 OD1 B:ASP79 2.2 17.5 1.0 O B:HOH2130 2.4 22.3 1.0 C9 B:XI71186 3.1 31.3 1.0 C7 B:XI71186 3.1 40.6 1.0 CG B:ASP79 3.2 18.9 1.0 CG B:ASP52 3.2 32.0 1.0 C8 B:XI71186 3.4 34.9 1.0 OD2 B:ASP79 3.6 19.4 1.0 OD2 B:ASP52 3.6 38.2 1.0 MN B:MN1185 3.8 20.9 1.0 O B:HOH2131 3.9 44.9 1.0 OD1 B:ASN51 4.1 35.1 1.0 OD1 B:ASP92 4.1 21.1 1.0 C10 B:XI71186 4.3 30.9 1.0 CE1 B:HIS34 4.3 17.6 1.0 CB B:ASP79 4.4 19.2 1.0 NE2 B:HIS34 4.4 17.4 1.0 O B:THR77 4.4 26.7 1.0 C1 B:XI71186 4.4 48.4 1.0 N B:ASP52 4.4 29.6 1.0 CB B:ASP52 4.5 30.3 1.0 CA B:ASP79 4.5 20.2 1.0 N B:ASP79 4.5 20.3 1.0 O B:HOH2059 4.6 38.7 1.0 OD2 B:ASP92 4.6 18.9 1.0 O11 B:XI71186 4.6 28.1 1.0 CA B:ASP52 4.6 29.9 1.0 CG B:ASP92 4.7 21.8 1.0 CG B:ASN51 4.9 32.6 1.0

Manganese binding site 4 out of 8 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 B:Mn1185 b:20.9 occ:1.00 O11 B:XI71186 1.9 28.1 1.0 OD2 B:ASP79 2.0 19.4 1.0 OD2 B:ASP92 2.2 18.9 1.0 O B:TYR93 2.2 19.9 1.0 O8 B:XI71186 2.3 24.3 1.0 NE2 B:HIS34 2.3 17.4 1.0 C10 B:XI71186 2.8 30.9 1.0 C9 B:XI71186 2.9 31.3 1.0 CG B:ASP92 3.1 21.8 1.0 CG B:ASP79 3.1 18.9 1.0 CD2 B:HIS34 3.2 17.1 1.0 C B:TYR93 3.3 20.1 1.0 CE1 B:HIS34 3.3 17.6 1.0 N B:TYR93 3.5 19.4 1.0 OD1 B:ASP79 3.6 17.5 1.0 OD1 B:ASP92 3.7 21.1 1.0 MN B:MN1184 3.8 30.8 1.0 CA B:TYR93 3.8 19.5 1.0 O10 B:XI71186 4.0 33.0 1.0 CB B:TYR93 4.1 19.0 1.0 CB B:ASP92 4.2 20.8 1.0 C B:ASP92 4.3 19.4 1.0 C8 B:XI71186 4.3 34.9 1.0 NZ B:LYS94 4.3 29.7 1.0 O B:HOH2130 4.4 22.3 1.0 CG B:HIS34 4.4 19.1 1.0 ND1 B:HIS34 4.4 18.4 1.0 CB B:ASP79 4.4 19.2 1.0 O B:HOH2129 4.4 20.5 1.0 N B:LYS94 4.5 21.0 1.0 CA B:ASP92 4.5 19.6 1.0 CD B:LYS94 4.6 25.0 1.0 O B:HOH2059 4.6 38.7 1.0 CG B:TYR93 4.7 18.4 1.0 CE B:LYS94 4.7 25.6 1.0 CD2 B:TYR93 4.8 16.1 1.0 CA B:LYS94 4.9 21.4 1.0

Manganese binding site 5 out of 8 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 5 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:21.6 occ:1.00 O11 C:XI71186 2.0 30.0 1.0 OD2 C:ASP79 2.1 20.8 1.0 O8 C:XI71186 2.1 24.5 1.0 OD1 C:ASP92 2.2 18.2 1.0 O C:TYR93 2.2 19.9 1.0 NE2 C:HIS34 2.3 16.6 1.0 C10 C:XI71186 2.7 32.0 1.0 C9 C:XI71186 2.8 31.5 1.0 CG C:ASP92 3.1 25.2 1.0 CG C:ASP79 3.1 20.7 1.0 CD2 C:HIS34 3.3 18.4 1.0 CE1 C:HIS34 3.3 18.9 1.0 C C:TYR93 3.3 21.1 1.0 OD1 C:ASP79 3.5 18.0 1.0 N C:TYR93 3.5 20.4 1.0 OD2 C:ASP92 3.6 24.4 1.0 MN C:MN1185 3.8 34.7 1.0 CA C:TYR93 3.8 20.4 1.0 O10 C:XI71186 3.9 33.4 1.0 CB C:TYR93 4.1 20.1 1.0 C8 C:XI71186 4.1 35.5 1.0 CB C:ASP92 4.3 22.5 1.0 C C:ASP92 4.3 20.7 1.0 O C:HOH2100 4.4 25.4 1.0 NZ C:LYS94 4.4 32.9 1.0 ND1 C:HIS34 4.4 16.2 1.0 CG C:HIS34 4.4 17.9 1.0 CD C:LYS94 4.5 29.3 1.0 N C:LYS94 4.5 22.4 1.0 O C:HOH2104 4.5 42.9 1.0 CB C:ASP79 4.5 20.9 1.0 CA C:ASP92 4.6 21.9 1.0 O C:HOH2101 4.7 28.0 1.0 CG C:TYR93 4.7 18.9 1.0 CE C:LYS94 4.8 32.1 1.0 CD2 C:TYR93 4.8 19.7 1.0 CA C:LYS94 4.9 23.1 1.0 CG C:LYS94 5.0 25.8 1.0

Manganese binding site 6 out of 8 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 6 of N-Terminal Endonuclease Domain of La Crosse Virus L-Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1185 b:34.7 occ:1.00 O8 C:XI71186 2.1 24.5 1.0 O14 C:XI71186 2.2 39.7 1.0 OD1 C:ASP52 2.2 29.5 1.0 OD1 C:ASP79 2.2 18.0 1.0 O C:HOH2101 2.3 28.0 1.0 O C:HOH2100 2.3 25.4 1.0 C7 C:XI71186 3.0 43.0 1.0 C9 C:XI71186 3.0 31.5 1.0 CG C:ASP52 3.2 30.7 1.0 CG C:ASP79 3.2 20.7 1.0 C8 C:XI71186 3.3 35.5 1.0 OD2 C:ASP52 3.5 31.7 1.0 OD2 C:ASP79 3.7 20.8 1.0 MN C:MN1184 3.8 21.6 1.0 OD1 C:ASN51 4.0 35.3 1.0 OD2 C:ASP92 4.0 24.4 1.0 O C:HOH2049 4.1 40.5 1.0 CE1 C:HIS34 4.3 18.9 1.0 C10 C:XI71186 4.3 32.0 1.0 C1 C:XI71186 4.3 52.2 1.0 O C:THR77 4.3 24.1 1.0 O C:HOH2104 4.4 42.9 1.0 O C:HOH2032 4.4 47.4 1.0 NE2 C:HIS34 4.4 16.6 1.0 CB C:ASP79 4.5 20.9 1.0 N C:ASP79 4.5 21.4 1.0 CB C:ASP52 4.6 30.9 1.0 CA C:ASP79 4.6 21.8 1.0 OD1 C:ASP92 4.6 18.2 1.0 N C:ASP52 4.6 30.0 1.0 CG C:ASP92 4.7 25.2 1.0 CA C:ASP52 4.8 31.0 1.0 O11 C:XI71186 4.8 30.0 1.0 CG C:ASN51 4.8 34.0 1.0 C2 C:XI71186 5.0 56.7 1.0

Manganese binding site 7 out of 8 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 7 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:25.1 occ:1.00 OD2 D:ASP92 2.1 25.9 1.0 OD2 D:ASP79 2.1 24.3 1.0 O11 D:XI71186 2.1 36.5 1.0 O D:TYR93 2.1 23.5 1.0 O8 D:XI71186 2.3 26.8 1.0 NE2 D:HIS34 2.3 23.9 1.0 C10 D:XI71186 2.8 37.0 1.0 C9 D:XI71186 2.9 38.1 1.0 CG D:ASP92 3.1 27.7 1.0 CG D:ASP79 3.2 24.4 1.0 CD2 D:HIS34 3.2 24.1 1.0 C D:TYR93 3.3 25.9 1.0 CE1 D:HIS34 3.3 24.1 1.0 N D:TYR93 3.5 23.4 1.0 OD1 D:ASP79 3.5 24.0 1.0 OD1 D:ASP92 3.7 26.6 1.0 MN D:MN1185 3.8 36.3 1.0 CA D:TYR93 3.9 24.1 1.0 O10 D:XI71186 4.0 40.6 1.0 CB D:TYR93 4.2 24.2 1.0 O D:HOH2049 4.2 47.2 1.0 CB D:ASP92 4.2 23.6 1.0 C D:ASP92 4.2 23.1 1.0 C8 D:XI71186 4.3 38.6 1.0 O D:HOH2093 4.4 24.1 1.0 CG D:HIS34 4.4 23.8 1.0 ND1 D:HIS34 4.4 20.4 1.0 CD D:LYS94 4.4 27.3 1.0 N D:LYS94 4.4 27.8 1.0 NZ D:LYS94 4.5 27.5 1.0 CB D:ASP79 4.5 24.8 1.0 CA D:ASP92 4.5 24.2 1.0 O D:HOH2092 4.6 28.5 1.0 CE D:LYS94 4.6 30.2 1.0 CG D:TYR93 4.8 24.3 1.0 CD2 D:TYR93 4.8 24.4 1.0 CA D:LYS94 4.9 28.8 1.0

Manganese binding site 8 out of 8 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 8 of N-Terminal Endonuclease Domain of La Crosse Virus L-Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1185 b:36.3 occ:1.00 O8 D:XI71186 2.1 26.8 1.0 OD1 D:ASP52 2.1 33.5 1.0 O D:HOH2092 2.1 28.5 1.0 OD1 D:ASP79 2.1 24.0 1.0 O14 D:XI71186 2.2 40.4 1.0 O D:HOH2093 2.3 24.1 1.0 C7 D:XI71186 3.1 45.7 1.0 C9 D:XI71186 3.1 38.1 1.0 CG D:ASP52 3.1 37.4 1.0 CG D:ASP79 3.2 24.4 1.0 C8 D:XI71186 3.4 38.6 1.0 OD2 D:ASP52 3.5 41.5 1.0 OD2 D:ASP79 3.6 24.3 1.0 O D:HOH2041 3.8 40.9 1.0 MN D:MN1184 3.8 25.1 1.0 OD1 D:ASP92 4.1 26.6 1.0 OD1 D:ASN51 4.2 46.7 1.0 CE1 D:HIS34 4.2 24.1 1.0 O D:THR77 4.3 27.8 1.0 C10 D:XI71186 4.4 37.0 1.0 NE2 D:HIS34 4.4 23.9 1.0 CB D:ASP79 4.4 24.8 1.0 C1 D:XI71186 4.4 54.3 1.0 O D:HOH2049 4.5 47.2 1.0 CA D:ASP79 4.5 25.0 1.0 N D:ASP79 4.5 25.0 1.0 CB D:ASP52 4.5 36.0 1.0 N D:ASP52 4.6 36.4 1.0 OD2 D:ASP92 4.6 25.9 1.0 CA D:ASP52 4.7 36.0 1.0 CG D:ASP92 4.7 27.7 1.0 O11 D:XI71186 4.8 36.5 1.0 C D:PRO78 4.9 25.1 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