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Manganese in PDB 7ex7: Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 16

Enzymatic activity of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 16

All present enzymatic activity of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 16:
2.7.7.48;

Protein crystallography data

The structure of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 16, PDB code: 7ex7 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) 44.94 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.272, 41.676, 145.305, 90, 102.03, 90
R / Rfree (%) 20.9 / 26.6

Other elements in 7ex7:

The structure of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 16 also contains other interesting chemical elements:

Chlorine (Cl) 5 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 16 (pdb code 7ex7). 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 16, PDB code: 7ex7:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 7ex7

Go back to Manganese Binding Sites List in 7ex7
Manganese binding site 1 out of 8 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 16


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 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn201

b:40.4
occ:0.66
 O9 A:1I6203 1.9 27.6 1.0
O6 A:1I6203 2.0 25.2 1.0
O A:HOH308 2.1 23.3 1.0
OD1 A:ASP79 2.1 22.2 1.0
O A:HOH316 2.2 23.6 1.0
OD1 A:ASN52 2.2 26.3 1.0
C8 A:1I6203 2.9 26.6 1.0
C5 A:1I6203 3.0 26.1 1.0
CG A:ASN52 3.2 25.6 1.0
CG A:ASP79 3.2 23.2 1.0
C7 A:1I6203 3.3 23.3 1.0
ND2 A:ASN52 3.5 23.4 1.0
OD2 A:ASP79 3.7 20.4 1.0
MN A:MN202 3.8 24.2 1.0
OD1 A:ASN51 4.0 28.6 1.0
OD1 A:ASP92 4.1 31.4 1.0
O A:THR77 4.1 24.6 1.0
C10 A:1I6203 4.3 27.2 1.0
CE1 A:HIS34 4.3 25.8 1.0
C3 A:1I6203 4.4 26.6 1.0
NE2 A:HIS34 4.4 27.0 1.0
O A:HOH322 4.4 23.0 1.0
CB A:ASP79 4.4 23.8 1.0
CA A:ASP79 4.5 24.4 1.0
CB A:ASN52 4.5 27.3 1.0
N A:ASP79 4.6 22.8 1.0
C13 A:1I6203 4.6 26.3 1.0
C19 A:1I6203 4.7 27.9 1.0
O2 A:1I6203 4.8 23.0 1.0
CA A:ASN52 4.8 27.3 1.0
N A:ASN52 4.9 30.1 1.0
O A:HOH320 4.9 30.8 1.0
C11 A:1I6203 4.9 22.8 1.0
CG A:ASP92 5.0 30.3 1.0

Manganese binding site 2 out of 8 in 7ex7

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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 16


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 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn202

b:24.2
occ:1.00
 OD2 A:ASP79 2.2 20.4 1.0
O A:TYR93 2.3 20.8 1.0
O6 A:1I6203 2.4 25.2 1.0
O2 A:1I6203 2.4 23.0 1.0
NE2 A:HIS34 2.4 27.0 1.0
C1 A:1I6203 2.6 34.4 1.0
OD2 A:ASP92 2.7 32.1 1.0
CD2 A:HIS34 3.2 20.3 1.0
CG A:ASP79 3.2 23.2 1.0
CG A:ASP92 3.2 30.3 1.0
C5 A:1I6203 3.2 26.1 1.0
C3 A:1I6203 3.2 26.6 1.0
OD1 A:ASP92 3.3 31.4 1.0
C A:TYR93 3.4 21.8 1.0
OD1 A:ASP79 3.5 22.2 1.0
CE1 A:HIS34 3.5 25.8 1.0
N A:TYR93 3.5 24.4 1.0
MN A:MN201 3.8 40.4 0.7
CA A:TYR93 3.9 21.4 1.0
NZ A:LYS94 4.0 32.2 1.0
CB A:TYR93 4.2 21.5 1.0
O A:HOH320 4.2 30.8 1.0
C A:ASP92 4.3 25.3 1.0
CB A:ASP92 4.3 24.2 1.0
O4 A:1I6203 4.4 28.3 1.0
O A:HOH316 4.4 23.6 1.0
CG A:HIS34 4.4 24.6 1.0
C7 A:1I6203 4.5 23.3 1.0
CB A:ASP79 4.5 23.8 1.0
ND1 A:HIS34 4.5 22.8 1.0
O A:HOH308 4.5 23.3 1.0
N A:LYS94 4.5 23.7 1.0
CA A:ASP92 4.5 23.5 1.0
CD2 A:TYR93 4.7 20.0 1.0
CD A:LYS94 4.8 28.6 1.0
CG A:TYR93 4.8 22.4 1.0
CE A:LYS94 4.9 30.1 1.0
CA A:LYS94 5.0 25.0 1.0
O9 A:1I6203 5.0 27.6 1.0

Manganese binding site 3 out of 8 in 7ex7

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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 16


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 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn201

b:44.4
occ:0.57
 O B:HOH303 1.8 25.0 1.0
O9 B:1I6203 1.9 27.7 1.0
O6 B:1I6203 2.0 26.6 1.0
OD1 B:ASP79 2.1 22.0 1.0
OD1 B:ASN52 2.3 30.8 1.0
O B:HOH324 2.6 24.6 1.0
C8 B:1I6203 2.9 26.7 1.0
C5 B:1I6203 3.0 28.4 1.0
CG B:ASP79 3.2 25.8 1.0
CG B:ASN52 3.3 29.4 1.0
C7 B:1I6203 3.3 27.8 1.0
ND2 B:ASN52 3.6 31.9 1.0
OD1 B:ASN51 3.8 31.9 1.0
MN B:MN202 3.8 28.0 1.0
OD2 B:ASP79 3.8 23.8 1.0
CE1 B:HIS34 4.0 27.1 1.0
C10 B:1I6203 4.2 30.8 1.0
NE2 B:HIS34 4.3 27.9 1.0
O B:HOH307 4.3 30.0 1.0
C13 B:1I6203 4.3 30.8 1.0
C3 B:1I6203 4.4 30.9 1.0
CB B:ASP79 4.4 28.0 1.0
O B:HOH353 4.5 37.3 1.0
CA B:ASP79 4.6 25.7 1.0
C19 B:1I6203 4.6 28.9 1.0
O B:THR77 4.6 30.7 1.0
O2 B:1I6203 4.6 23.3 1.0
CB B:ASN52 4.6 29.2 1.0
N B:ASP79 4.7 24.4 1.0
C11 B:1I6203 4.7 28.1 1.0
OD1 B:ASP92 4.7 30.8 1.0
N B:ASN52 4.8 31.5 1.0
CA B:ASN52 4.9 31.7 1.0
CG B:ASN51 5.0 33.0 1.0
C12 B:1I6203 5.0 31.5 1.0

Manganese binding site 4 out of 8 in 7ex7

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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 16


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 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn202

b:28.0
occ:1.00
 OD2 B:ASP79 2.2 23.8 1.0
O2 B:1I6203 2.2 23.3 1.0
O B:TYR93 2.3 22.6 1.0
NE2 B:HIS34 2.4 27.9 1.0
O6 B:1I6203 2.4 26.6 1.0
OD1 B:ASP92 2.6 30.8 1.0
C1 B:1I6203 2.6 34.5 1.0
CG B:ASP79 3.1 25.8 1.0
C3 B:1I6203 3.2 30.9 1.0
CD2 B:HIS34 3.2 23.1 1.0
C5 B:1I6203 3.3 28.4 1.0
OD1 B:ASP79 3.3 22.0 1.0
C B:TYR93 3.3 22.6 1.0
CG B:ASP92 3.3 32.5 1.0
CE1 B:HIS34 3.4 27.1 1.0
N B:TYR93 3.5 28.5 1.0
OD2 B:ASP92 3.6 31.4 1.0
CA B:TYR93 3.8 24.6 1.0
MN B:MN201 3.8 44.4 0.6
CB B:TYR93 4.0 25.2 1.0
C B:ASP92 4.2 25.4 1.0
O4 B:1I6203 4.3 31.3 1.0
CG B:HIS34 4.4 29.1 1.0
CB B:ASP79 4.5 28.0 1.0
N B:LYS94 4.5 21.9 1.0
ND1 B:HIS34 4.5 29.2 1.0
NZ B:LYS94 4.5 31.8 1.0
O B:HOH324 4.5 24.6 1.0
CB B:ASP92 4.5 28.1 1.0
CA B:ASP92 4.5 27.8 1.0
C7 B:1I6203 4.5 27.8 1.0
O B:HOH303 4.6 25.0 1.0
CG B:TYR93 4.8 23.3 1.0
CD2 B:TYR93 4.9 26.9 1.0
CD B:LYS94 4.9 28.1 1.0
CA B:LYS94 5.0 27.1 1.0

Manganese binding site 5 out of 8 in 7ex7

Go back to Manganese Binding Sites List in 7ex7
Manganese binding site 5 out of 8 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 16


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 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn201

b:39.9
occ:0.62
 OD1 C:ASP79 1.8 29.1 1.0
OD1 C:ASN52 2.2 31.9 1.0
O C:HOH304 2.3 25.1 1.0
O6 C:1I6203 2.3 23.1 1.0
O9 C:1I6203 2.5 26.4 1.0
O C:HOH315 2.5 25.3 1.0
CG C:ASP79 3.0 28.2 1.0
CG C:ASN52 3.2 35.0 1.0
C5 C:1I6203 3.5 27.1 1.0
C8 C:1I6203 3.5 27.2 1.0
OD1 C:ASN51 3.6 31.8 1.0
ND2 C:ASN52 3.6 30.4 1.0
OD2 C:ASP79 3.7 25.0 1.0
MN C:MN202 3.7 26.7 1.0
C7 C:1I6203 3.9 28.7 1.0
OD1 C:ASP92 4.1 28.5 1.0
CA C:ASP79 4.1 28.2 1.0
CB C:ASP79 4.1 26.1 1.0
CE1 C:HIS34 4.2 24.1 1.0
O C:THR77 4.2 26.0 1.0
N C:ASP79 4.3 28.8 1.0
O C:HOH349 4.4 29.1 1.0
NE2 C:HIS34 4.4 24.9 1.0
CB C:ASN52 4.5 32.7 1.0
N C:ASN52 4.5 33.7 1.0
CA C:ASN52 4.7 31.5 1.0
O C:HOH309 4.7 28.3 1.0
CG C:ASN51 4.7 32.1 1.0
C3 C:1I6203 4.8 27.2 1.0
O2 C:1I6203 4.8 26.0 1.0
C C:PRO78 4.8 28.2 1.0
C10 C:1I6203 4.9 26.1 1.0
O C:HOH318 4.9 25.8 1.0
CG C:ASP92 4.9 33.6 1.0
OD2 C:ASP92 4.9 29.0 1.0
C13 C:1I6203 4.9 28.5 1.0

Manganese binding site 6 out of 8 in 7ex7

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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 16


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 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn202

b:26.7
occ:1.00
 OD2 C:ASP79 2.2 25.0 1.0
O C:TYR93 2.4 25.9 1.0
C1 C:1I6203 2.4 28.9 1.0
O2 C:1I6203 2.4 26.0 1.0
NE2 C:HIS34 2.5 24.9 1.0
O6 C:1I6203 2.5 23.1 1.0
OD2 C:ASP92 2.5 29.0 1.0
CG C:ASP79 3.1 28.2 1.0
CD2 C:HIS34 3.2 21.7 1.0
CG C:ASP92 3.2 33.6 1.0
OD1 C:ASP79 3.2 29.1 1.0
C5 C:1I6203 3.4 27.1 1.0
C3 C:1I6203 3.5 27.2 1.0
CE1 C:HIS34 3.5 24.1 1.0
C C:TYR93 3.5 25.3 1.0
OD1 C:ASP92 3.5 28.5 1.0
N C:TYR93 3.6 29.9 1.0
MN C:MN201 3.7 39.9 0.6
O C:HOH318 3.9 25.8 1.0
CA C:TYR93 4.0 25.3 1.0
CB C:TYR93 4.3 30.5 1.0
C C:ASP92 4.3 25.9 1.0
CB C:ASP92 4.3 22.6 1.0
CE C:LYS94 4.4 29.7 1.0
CG C:HIS34 4.4 26.1 1.0
O C:HOH315 4.5 25.3 1.0
ND1 C:HIS34 4.5 23.4 1.0
CB C:ASP79 4.5 26.1 1.0
CA C:ASP92 4.6 24.2 1.0
O4 C:1I6203 4.6 31.8 1.0
NZ C:LYS94 4.6 28.6 1.0
N C:LYS94 4.7 27.9 1.0
C7 C:1I6203 4.7 28.7 1.0
O C:HOH304 4.7 25.1 1.0
CD C:LYS94 4.8 31.5 1.0
CD2 C:TYR93 4.9 24.5 1.0
CG C:TYR93 4.9 25.6 1.0

Manganese binding site 7 out of 8 in 7ex7

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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 16


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 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn201

b:37.8
occ:0.64
 OD1 D:ASP79 2.1 23.9 1.0
O D:HOH315 2.1 26.1 1.0
O9 D:1I6203 2.1 24.1 1.0
OD1 D:ASN52 2.2 27.6 1.0
O6 D:1I6203 2.2 22.3 1.0
O D:HOH322 2.3 19.1 1.0
CG D:ASN52 3.0 23.9 1.0
C8 D:1I6203 3.1 24.3 1.0
ND2 D:ASN52 3.2 28.5 1.0
C5 D:1I6203 3.2 23.3 1.0
CG D:ASP79 3.3 22.5 1.0
C7 D:1I6203 3.5 25.8 1.0
OD2 D:ASP79 3.9 21.7 1.0
MN D:MN202 3.9 18.9 1.0
OD1 D:ASN51 4.1 29.2 1.0
O D:THR77 4.3 23.8 1.0
OD1 D:ASP92 4.3 20.6 1.0
O D:HOH349 4.3 27.4 1.0
O D:HOH318 4.3 22.0 1.0
CB D:ASN52 4.4 22.5 1.0
CE1 D:HIS34 4.4 22.1 1.0
C10 D:1I6203 4.4 28.7 1.0
CB D:ASP79 4.4 23.6 1.0
CA D:ASP79 4.5 22.3 1.0
NE2 D:HIS34 4.5 25.5 1.0
C3 D:1I6203 4.5 20.5 1.0
N D:ASN52 4.6 28.5 1.0
N D:ASP79 4.6 19.7 1.0
CA D:ASN52 4.7 27.1 1.0
C19 D:1I6203 4.7 26.1 1.0
O2 D:1I6203 4.7 20.2 1.0
C13 D:1I6203 4.8 26.3 1.0
OD2 D:ASP92 4.9 22.8 1.0
C11 D:1I6203 5.0 25.8 1.0
CG D:ASN51 5.0 29.6 1.0

Manganese binding site 8 out of 8 in 7ex7

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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 16


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 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn202

b:18.9
occ:1.00
 O2 D:1I6203 2.1 20.2 1.0
OD2 D:ASP92 2.2 22.8 1.0
OD2 D:ASP79 2.3 21.7 1.0
O6 D:1I6203 2.4 22.3 1.0
O D:TYR93 2.4 21.6 1.0
C1 D:1I6203 2.6 33.9 1.0
NE2 D:HIS34 2.6 25.5 1.0
CG D:ASP92 3.1 24.9 1.0
C3 D:1I6203 3.2 20.5 1.0
CG D:ASP79 3.2 22.5 1.0
C5 D:1I6203 3.2 23.3 1.0
CD2 D:HIS34 3.3 21.1 1.0
OD1 D:ASP79 3.4 23.9 1.0
C D:TYR93 3.4 20.3 1.0
N D:TYR93 3.6 21.9 1.0
OD1 D:ASP92 3.6 20.6 1.0
CE1 D:HIS34 3.7 22.1 1.0
MN D:MN201 3.9 37.8 0.6
CA D:TYR93 3.9 22.4 1.0
CB D:ASP92 4.3 22.8 1.0
O4 D:1I6203 4.3 22.1 1.0
O D:HOH322 4.3 19.1 1.0
CB D:TYR93 4.3 22.4 1.0
C D:ASP92 4.3 22.6 1.0
CE D:LYS94 4.4 27.0 1.0
CG D:HIS34 4.5 26.0 1.0
C7 D:1I6203 4.5 25.8 1.0
CB D:ASP79 4.6 23.6 1.0
CA D:ASP92 4.6 22.4 1.0
N D:LYS94 4.6 21.4 1.0
O D:HOH315 4.6 26.1 1.0
ND1 D:HIS34 4.7 22.8 1.0
NZ D:LYS94 4.7 25.3 1.0
CD2 D:TYR93 4.8 25.0 1.0
CG D:TYR93 4.9 21.5 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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