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Manganese in PDB 7ex6: Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 11

Enzymatic activity of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 11

All present enzymatic activity of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 11:
2.7.7.48;

Protein crystallography data

The structure of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 11, PDB code: 7ex6 was solved by W.Kuang, Z.Hu, P.Gong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.38 / 2.18
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.852, 41.667, 145.276, 90, 101.95, 90
R / Rfree (%) 22 / 27.7

Other elements in 7ex6:

The structure of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 11 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 11 (pdb code 7ex6). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 11, PDB code: 7ex6:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 7ex6

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Manganese binding site 1 out of 8 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 11


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 11 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn201

b:46.3
occ:1.00
 O6 A:11I203 2.0 28.0 1.0
OD1 A:ASP79 2.0 27.0 1.0
O9 A:11I203 2.1 35.5 1.0
OD1 A:ASN52 2.3 23.6 1.0
O A:HOH304 2.3 27.6 1.0
O A:HOH321 2.3 23.4 1.0
C8 A:11I203 3.0 34.9 1.0
C5 A:11I203 3.1 32.2 1.0
CG A:ASP79 3.2 25.9 1.0
CG A:ASN52 3.2 29.3 1.0
ND2 A:ASN52 3.4 33.8 1.0
C7 A:11I203 3.4 35.6 1.0
MN A:MN202 3.7 26.7 1.0
OD2 A:ASP79 3.7 28.8 1.0
OD1 A:ASN51 3.9 33.4 1.0
CE1 A:HIS34 4.1 28.4 1.0
OD1 A:ASP92 4.2 27.5 1.0
O A:HOH353 4.2 41.3 1.0
O A:THR77 4.3 28.6 1.0
CB A:ASP79 4.3 29.8 1.0
NE2 A:HIS34 4.4 30.3 1.0
C10 A:11I203 4.4 37.0 1.0
CA A:ASP79 4.4 28.1 1.0
C3 A:11I203 4.4 35.1 1.0
CB A:ASN52 4.6 25.5 1.0
N A:ASP79 4.6 26.8 1.0
O A:HOH323 4.7 31.4 1.0
O2 A:11I203 4.7 27.9 1.0
OD2 A:ASP92 4.7 25.3 1.0
C13 A:11I203 4.7 31.8 1.0
C19 A:11I203 4.8 43.4 1.0
O A:HOH348 4.8 41.2 1.0
CG A:ASP92 4.8 33.1 1.0
N A:ASN52 4.8 32.1 1.0
CA A:ASN52 4.9 29.5 1.0
C11 A:11I203 5.0 36.9 1.0

Manganese binding site 2 out of 8 in 7ex6

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Manganese binding site 2 out of 8 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 11


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 11 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn202

b:26.7
occ:1.00
 OD2 A:ASP92 2.2 25.3 1.0
OD2 A:ASP79 2.2 28.8 1.0
O2 A:11I203 2.3 27.9 1.0
O6 A:11I203 2.4 28.0 1.0
O A:TYR93 2.4 23.9 1.0
NE2 A:HIS34 2.4 30.3 1.0
CG A:ASP92 3.1 33.1 1.0
C1 A:11I203 3.1 49.5 1.0
CG A:ASP79 3.1 25.9 1.0
C5 A:11I203 3.2 32.2 1.0
C3 A:11I203 3.2 35.1 1.0
CD2 A:HIS34 3.3 24.3 1.0
OD1 A:ASP79 3.3 27.0 1.0
CE1 A:HIS34 3.4 28.4 1.0
C A:TYR93 3.5 22.1 1.0
OD1 A:ASP92 3.6 27.5 1.0
N A:TYR93 3.6 25.6 1.0
MN A:MN201 3.7 46.3 1.0
CA A:TYR93 4.0 22.8 1.0
O A:HOH348 4.2 41.2 1.0
CB A:ASP92 4.3 30.6 1.0
C A:ASP92 4.3 27.6 1.0
CB A:TYR93 4.3 29.5 1.0
O4 A:11I203 4.3 49.5 1.0
O A:HOH321 4.3 23.4 1.0
CG A:HIS34 4.4 31.2 1.0
C7 A:11I203 4.4 35.6 1.0
ND1 A:HIS34 4.4 30.9 1.0
CB A:ASP79 4.5 29.8 1.0
CA A:ASP92 4.5 26.5 1.0
CE A:LYS94 4.6 33.5 1.0
O A:HOH304 4.6 27.6 1.0
N A:LYS94 4.6 27.3 1.0
CG A:TYR93 4.9 26.6 1.0
CD2 A:TYR93 4.9 28.5 1.0

Manganese binding site 3 out of 8 in 7ex6

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Manganese binding site 3 out of 8 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 11


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 11 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn201

b:44.8
occ:1.00
 O6 B:11I203 2.1 25.1 1.0
OD1 B:ASP79 2.1 27.7 1.0
O B:HOH319 2.1 24.6 1.0
OD1 B:ASN52 2.2 25.6 1.0
O9 B:11I203 2.3 30.4 1.0
O B:HOH311 2.4 24.3 1.0
CG B:ASN52 3.2 30.2 1.0
C5 B:11I203 3.2 27.5 1.0
C8 B:11I203 3.2 31.0 1.0
CG B:ASP79 3.3 28.4 1.0
ND2 B:ASN52 3.5 30.2 1.0
C7 B:11I203 3.6 29.3 1.0
MN B:MN202 3.8 27.7 1.0
OD2 B:ASP79 3.8 25.7 1.0
NE2 B:HIS34 4.2 27.7 1.0
CE1 B:HIS34 4.2 27.1 1.0
OD1 B:ASP92 4.2 32.4 1.0
O B:HOH313 4.3 29.9 1.0
O B:THR77 4.3 26.5 1.0
CB B:ASP79 4.4 26.8 1.0
CA B:ASP79 4.5 25.0 1.0
C3 B:11I203 4.5 25.6 1.0
CB B:ASN52 4.5 29.0 1.0
C10 B:11I203 4.6 31.9 1.0
N B:ASP79 4.6 21.0 1.0
N B:ASN52 4.7 30.8 1.0
OD1 B:ASN51 4.7 40.0 1.0
O2 B:11I203 4.8 26.7 1.0
CA B:ASN52 4.8 31.1 1.0
C19 B:11I203 4.9 37.6 1.0
C20 B:11I203 5.0 35.1 1.0
C13 B:11I203 5.0 32.5 1.0

Manganese binding site 4 out of 8 in 7ex6

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Manganese binding site 4 out of 8 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 11


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 11 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn202

b:27.7
occ:1.00
 OD2 B:ASP79 2.1 25.7 1.0
C1 B:11I203 2.3 33.2 1.0
O B:TYR93 2.3 23.0 1.0
O2 B:11I203 2.4 26.7 1.0
NE2 B:HIS34 2.4 27.7 1.0
O6 B:11I203 2.5 25.1 1.0
OD2 B:ASP92 2.5 28.0 1.0
CG B:ASP79 3.1 28.4 1.0
CD2 B:HIS34 3.1 19.4 1.0
CG B:ASP92 3.2 34.1 1.0
C3 B:11I203 3.3 25.6 1.0
C5 B:11I203 3.3 27.5 1.0
OD1 B:ASP79 3.3 27.7 1.0
C B:TYR93 3.4 25.7 1.0
OD1 B:ASP92 3.5 32.4 1.0
CE1 B:HIS34 3.6 27.1 1.0
N B:TYR93 3.6 27.1 1.0
MN B:MN201 3.8 44.8 1.0
CA B:TYR93 3.9 20.9 1.0
NZ B:LYS94 4.2 28.4 1.0
CB B:TYR93 4.3 27.9 1.0
C B:ASP92 4.3 27.4 1.0
CB B:ASP92 4.3 26.1 1.0
CG B:HIS34 4.4 26.1 1.0
O4 B:11I203 4.4 32.6 1.0
CB B:ASP79 4.5 26.8 1.0
O B:HOH311 4.5 24.3 1.0
CA B:ASP92 4.5 25.7 1.0
N B:LYS94 4.6 25.1 1.0
ND1 B:HIS34 4.6 24.9 1.0
C7 B:11I203 4.6 29.3 1.0
O B:HOH319 4.6 24.6 1.0
CD2 B:TYR93 4.8 28.1 1.0
CG B:TYR93 4.9 27.5 1.0
CA B:LYS94 5.0 23.2 1.0

Manganese binding site 5 out of 8 in 7ex6

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Manganese binding site 5 out of 8 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 11


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 11 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn201

b:50.6
occ:1.00
 OD1 C:ASP79 2.0 30.7 1.0
O6 C:11I203 2.0 33.5 1.0
O9 C:11I203 2.1 38.0 1.0
OD1 C:ASN52 2.1 33.4 1.0
O C:HOH307 2.3 30.4 1.0
O C:HOH302 2.3 27.1 1.0
C8 C:11I203 3.0 34.3 1.0
C5 C:11I203 3.1 36.7 1.0
CG C:ASP79 3.2 29.3 1.0
CG C:ASN52 3.2 41.2 1.0
C7 C:11I203 3.4 34.1 1.0
ND2 C:ASN52 3.7 35.4 1.0
MN C:MN202 3.8 28.5 1.0
OD2 C:ASP79 3.8 32.2 1.0
OD1 C:ASN51 3.9 37.2 1.0
OD1 C:ASP92 4.1 35.4 1.0
O C:THR77 4.2 36.1 1.0
CA C:ASP79 4.2 31.5 1.0
CB C:ASP79 4.3 29.6 1.0
N C:ASP79 4.3 29.3 1.0
C3 C:11I203 4.4 34.6 1.0
NE2 C:HIS34 4.4 28.6 1.0
C10 C:11I203 4.4 39.0 1.0
CE1 C:HIS34 4.5 33.0 1.0
CB C:ASN52 4.5 37.6 1.0
O2 C:11I203 4.5 28.8 1.0
N C:ASN52 4.5 39.8 1.0
CA C:ASN52 4.6 38.6 1.0
C19 C:11I203 4.7 44.2 1.0
OD2 C:ASP92 4.8 32.0 1.0
C C:PRO78 4.8 37.4 1.0
CG C:ASP92 4.8 38.9 1.0
O C:HOH301 4.9 39.1 1.0
C13 C:11I203 5.0 33.1 1.0

Manganese binding site 6 out of 8 in 7ex6

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Manganese binding site 6 out of 8 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 11


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 11 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn202

b:28.5
occ:1.00
 O2 C:11I203 2.0 28.8 1.0
OD2 C:ASP79 2.2 32.2 1.0
OD2 C:ASP92 2.3 32.0 1.0
O6 C:11I203 2.3 33.5 1.0
O C:TYR93 2.4 29.2 1.0
NE2 C:HIS34 2.5 28.6 1.0
C1 C:11I203 2.7 40.1 1.0
CG C:ASP79 3.1 29.3 1.0
C3 C:11I203 3.1 34.6 1.0
CD2 C:HIS34 3.1 28.3 1.0
CG C:ASP92 3.1 38.9 1.0
C5 C:11I203 3.2 36.7 1.0
OD1 C:ASP79 3.3 30.7 1.0
C C:TYR93 3.4 27.7 1.0
N C:TYR93 3.5 31.1 1.0
OD1 C:ASP92 3.6 35.4 1.0
CE1 C:HIS34 3.6 33.0 1.0
MN C:MN201 3.8 50.6 1.0
CA C:TYR93 3.9 30.9 1.0
O4 C:11I203 4.2 39.2 1.0
C C:ASP92 4.2 31.1 1.0
CB C:TYR93 4.2 31.9 1.0
CB C:ASP92 4.2 31.3 1.0
CG C:HIS34 4.4 31.4 1.0
CB C:ASP79 4.5 29.6 1.0
C7 C:11I203 4.5 34.1 1.0
CA C:ASP92 4.5 32.0 1.0
CE C:LYS94 4.5 34.5 1.0
O C:HOH307 4.5 30.4 1.0
ND1 C:HIS34 4.6 33.6 1.0
N C:LYS94 4.6 32.0 1.0
O C:HOH302 4.7 27.1 1.0
NZ C:LYS94 4.7 37.1 1.0
CD2 C:TYR93 4.8 29.5 1.0
CG C:TYR93 4.8 29.0 1.0

Manganese binding site 7 out of 8 in 7ex6

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Manganese binding site 7 out of 8 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 11


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 11 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn201

b:46.3
occ:0.71
 OD1 D:ASP79 1.8 30.0 1.0
O6 D:11I203 2.0 26.1 1.0
O9 D:11I203 2.1 29.2 1.0
O D:HOH301 2.1 27.8 1.0
OD1 D:ASN52 2.2 27.7 1.0
O D:HOH319 2.5 24.8 1.0
CG D:ASP79 2.9 29.4 1.0
C8 D:11I203 3.0 28.5 1.0
CG D:ASN52 3.1 30.8 1.0
C5 D:11I203 3.1 30.4 1.0
ND2 D:ASN52 3.4 31.2 1.0
OD2 D:ASP79 3.5 25.7 1.0
C7 D:11I203 3.5 29.5 1.0
OD1 D:ASN51 3.5 39.8 1.0
MN D:MN202 3.8 30.4 1.0
CE1 D:HIS34 4.0 28.0 1.0
NE2 D:HIS34 4.1 29.4 1.0
CB D:ASP79 4.1 29.9 1.0
O D:HOH350 4.3 36.5 1.0
CA D:ASP79 4.3 29.4 1.0
C10 D:11I203 4.4 36.1 1.0
C3 D:11I203 4.4 27.5 1.0
OD1 D:ASP92 4.5 40.5 1.0
CB D:ASN52 4.5 28.5 1.0
O D:THR77 4.5 31.8 1.0
O D:HOH313 4.5 26.0 1.0
N D:ASP79 4.6 29.5 1.0
N D:ASN52 4.6 31.4 1.0
C13 D:11I203 4.6 32.6 1.0
O2 D:11I203 4.6 24.1 1.0
CG D:ASN51 4.7 38.3 1.0
CA D:ASN52 4.8 32.1 1.0
C19 D:11I203 4.8 31.8 1.0
C11 D:11I203 4.9 29.9 1.0

Manganese binding site 8 out of 8 in 7ex6

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Manganese binding site 8 out of 8 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 11


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 11 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn202

b:30.4
occ:1.00
 OD2 D:ASP79 2.0 25.7 1.0
O2 D:11I203 2.1 24.1 1.0
O D:TYR93 2.3 28.8 1.0
NE2 D:HIS34 2.4 29.4 1.0
O6 D:11I203 2.5 26.1 1.0
OD1 D:ASP92 2.7 40.5 1.0
C1 D:11I203 2.8 44.0 1.0
CG D:ASP79 3.1 29.4 1.0
C3 D:11I203 3.1 27.5 1.0
CD2 D:HIS34 3.2 24.9 1.0
CG D:ASP92 3.2 35.7 1.0
C5 D:11I203 3.3 30.4 1.0
OD2 D:ASP92 3.3 37.4 1.0
C D:TYR93 3.4 27.3 1.0
OD1 D:ASP79 3.4 30.0 1.0
CE1 D:HIS34 3.5 28.0 1.0
N D:TYR93 3.5 29.3 1.0
MN D:MN201 3.8 46.3 0.7
CA D:TYR93 3.9 26.2 1.0
CB D:TYR93 4.1 27.8 1.0
O4 D:11I203 4.2 38.1 1.0
C D:ASP92 4.3 30.1 1.0
CG D:HIS34 4.4 35.1 1.0
CB D:ASP79 4.4 29.9 1.0
CB D:ASP92 4.5 31.1 1.0
O D:HOH319 4.5 24.8 1.0
C7 D:11I203 4.5 29.5 1.0
ND1 D:HIS34 4.5 30.2 1.0
CA D:ASP92 4.5 32.6 1.0
N D:LYS94 4.5 28.5 1.0
CG D:TYR93 4.8 29.8 1.0
O D:HOH301 4.8 27.8 1.0
CE D:LYS94 4.8 35.6 1.0
CD2 D:TYR93 4.8 31.8 1.0
NZ D:LYS94 4.9 40.9 1.0
CA D:LYS94 5.0 22.6 1.0

Reference:

W.Kuang, H.Zhang, Y.Cai, G.Zhang, F.Deng, H.Li, Y.Zhou, M.Wang, P.Gong, Y.Guo, Z.Hu. Structural and Biochemical Basis For Development of Diketo Acid Inhibitors Targeting the Cap-Snatching Endonuclease of the Ebinur Lake Virus (Order: Bunyavirales ). J.Virol. V. 96 17321 2022.
ISSN: ESSN 1098-5514
PubMed: 35266805
DOI: 10.1128/JVI.02173-21
Page generated: Sun Oct 6 08:37:03 2024

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