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Manganese in PDB 7ex2: Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with L-742,001 (Methyl Ester Form)

Enzymatic activity of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with L-742,001 (Methyl Ester Form)

All present enzymatic activity of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with L-742,001 (Methyl Ester Form):
2.7.7.48;

Protein crystallography data

The structure of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with L-742,001 (Methyl Ester Form), PDB code: 7ex2 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) 26.44 / 3.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.409, 70.804, 69.86, 90, 90.06, 90
R / Rfree (%) 17.9 / 22.7

Other elements in 7ex2:

The structure of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with L-742,001 (Methyl Ester Form) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with L-742,001 (Methyl Ester Form) (pdb code 7ex2). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with L-742,001 (Methyl Ester Form), PDB code: 7ex2:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 7ex2

Go back to Manganese Binding Sites List in 7ex2
Manganese binding site 1 out of 4 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with L-742,001 (Methyl Ester Form)


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 L-742,001 (Methyl Ester Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn201

b:48.2
occ:1.00
 O6 A:I0N203 2.2 35.5 1.0
O9 A:I0N203 2.3 32.9 1.0
OD1 A:ASP79 2.4 33.5 1.0
OD1 A:ASN52 2.4 42.3 1.0
CG A:ASP79 3.0 31.9 1.0
C8 A:I0N203 3.2 30.5 1.0
OD2 A:ASP79 3.2 30.6 1.0
C5 A:I0N203 3.3 34.6 1.0
CG A:ASN52 3.4 29.1 1.0
C7 A:I0N203 3.6 30.7 1.0
MN A:MN202 3.6 27.1 1.0
ND2 A:ASN52 3.7 27.9 1.0
OD1 A:ASP92 3.9 39.6 1.0
CE1 A:HIS34 4.1 33.6 1.0
OD1 A:ASN51 4.2 37.1 1.0
CB A:ASP79 4.2 33.0 1.0
CA A:ASP79 4.2 32.6 1.0
N A:ASP79 4.2 34.2 1.0
NE2 A:HIS34 4.3 35.8 1.0
O A:THR77 4.4 36.7 1.0
C10 A:I0N203 4.5 32.5 1.0
C3 A:I0N203 4.6 36.1 1.0
N A:ASN52 4.7 33.8 1.0
OD2 A:ASP92 4.7 39.9 1.0
CG A:ASP92 4.7 37.8 1.0
O2 A:I0N203 4.7 32.7 1.0
CB A:ASN52 4.7 26.7 1.0
CA A:ASN52 4.9 30.0 1.0
C19 A:I0N203 4.9 29.1 1.0
C A:PRO78 4.9 35.1 1.0
CG A:ASN51 4.9 37.5 1.0

Manganese binding site 2 out of 4 in 7ex2

Go back to Manganese Binding Sites List in 7ex2
Manganese binding site 2 out of 4 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with L-742,001 (Methyl Ester Form)


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 L-742,001 (Methyl Ester Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn202

b:27.1
occ:1.00
 OD2 A:ASP79 2.0 30.6 1.0
NE2 A:HIS34 2.2 35.8 1.0
O A:TYR93 2.2 30.8 1.0
O6 A:I0N203 2.3 35.5 1.0
OD2 A:ASP92 2.4 39.9 1.0
O2 A:I0N203 2.6 32.7 1.0
C1 A:I0N203 2.6 41.1 1.0
CD2 A:HIS34 3.0 40.8 1.0
CG A:ASP79 3.0 31.9 1.0
CG A:ASP92 3.2 37.8 1.0
CE1 A:HIS34 3.2 33.6 1.0
C A:TYR93 3.3 30.8 1.0
C5 A:I0N203 3.4 34.6 1.0
OD1 A:ASP79 3.4 33.5 1.0
N A:TYR93 3.4 32.5 1.0
OD1 A:ASP92 3.5 39.6 1.0
C3 A:I0N203 3.6 36.1 1.0
MN A:MN201 3.6 48.2 1.0
CA A:TYR93 3.7 30.2 1.0
CB A:TYR93 4.1 28.7 1.0
CG A:HIS34 4.1 32.0 1.0
ND1 A:HIS34 4.2 32.8 1.0
C A:ASP92 4.3 29.8 1.0
CB A:ASP79 4.3 33.0 1.0
CB A:ASP92 4.3 28.4 1.0
N A:LYS94 4.4 31.0 1.0
CA A:ASP92 4.6 26.9 1.0
C7 A:I0N203 4.6 30.7 1.0
O4 A:I0N203 4.7 36.4 1.0
CD2 A:TYR93 4.7 28.9 1.0
CG A:TYR93 4.7 27.1 1.0
CE A:LYS94 4.8 30.7 1.0
NZ A:LYS94 4.8 28.2 1.0
CA A:LYS94 4.9 28.8 1.0
CD A:LYS94 5.0 28.0 1.0

Manganese binding site 3 out of 4 in 7ex2

Go back to Manganese Binding Sites List in 7ex2
Manganese binding site 3 out of 4 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with L-742,001 (Methyl Ester Form)


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 L-742,001 (Methyl Ester Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn201

b:51.7
occ:1.00
 OD1 B:ASN52 1.9 48.0 1.0
OD1 B:ASP79 2.2 39.2 1.0
O6 B:I0N203 2.3 43.9 1.0
O9 B:I0N203 2.5 38.7 1.0
CG B:ASN52 3.0 33.1 1.0
CG B:ASP79 3.1 35.9 1.0
C5 B:I0N203 3.4 41.4 1.0
C8 B:I0N203 3.4 36.8 1.0
ND2 B:ASN52 3.6 32.5 1.0
C7 B:I0N203 3.7 36.4 1.0
OD2 B:ASP79 3.7 32.5 1.0
OD1 B:ASP92 3.8 40.7 1.0
OD1 B:ASN51 3.8 38.2 1.0
CA B:ASP79 3.8 34.3 1.0
N B:ASP79 3.8 33.6 1.0
MN B:MN202 3.8 27.1 1.0
CB B:ASP79 4.0 36.5 1.0
O B:THR77 4.1 35.9 1.0
N B:ASN52 4.2 30.8 1.0
CB B:ASN52 4.3 30.9 1.0
CE1 B:HIS34 4.3 41.1 1.0
CA B:ASN52 4.4 29.6 1.0
C B:PRO78 4.5 34.8 1.0
NE2 B:HIS34 4.5 42.5 1.0
C30 B:I0N203 4.6 34.1 1.0
CG B:ASP92 4.6 42.4 1.0
CG B:ASN51 4.6 40.1 1.0
C3 B:I0N203 4.7 44.9 1.0
OD2 B:ASP92 4.7 43.1 1.0
C10 B:I0N203 4.9 36.5 1.0
O B:PRO78 4.9 35.8 1.0
C B:ASN51 4.9 33.9 1.0

Manganese binding site 4 out of 4 in 7ex2

Go back to Manganese Binding Sites List in 7ex2
Manganese binding site 4 out of 4 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with L-742,001 (Methyl Ester Form)


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 L-742,001 (Methyl Ester Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn202

b:27.1
occ:1.00
 NE2 B:HIS34 2.2 42.5 1.0
O2 B:I0N203 2.3 42.8 1.0
O6 B:I0N203 2.3 43.9 1.0
O B:TYR93 2.3 33.8 1.0
OD2 B:ASP79 2.3 32.5 1.0
OD2 B:ASP92 2.4 43.1 1.0
C1 B:I0N203 2.8 55.1 1.0
OD1 B:ASP79 3.0 39.2 1.0
CG B:ASP79 3.1 35.9 1.0
C5 B:I0N203 3.1 41.4 1.0
CD2 B:HIS34 3.1 47.1 1.0
C3 B:I0N203 3.1 44.9 1.0
CG B:ASP92 3.2 42.4 1.0
CE1 B:HIS34 3.2 41.1 1.0
C B:TYR93 3.4 31.9 1.0
N B:TYR93 3.6 33.4 1.0
OD1 B:ASP92 3.6 40.7 1.0
MN B:MN201 3.8 51.7 1.0
CA B:TYR93 3.9 30.5 1.0
C B:ASP92 4.2 30.9 1.0
CB B:TYR93 4.2 30.8 1.0
CG B:HIS34 4.3 37.1 1.0
ND1 B:HIS34 4.3 38.9 1.0
CB B:ASP92 4.3 31.9 1.0
C7 B:I0N203 4.3 36.4 1.0
O4 B:I0N203 4.3 45.7 1.0
CA B:ASP92 4.5 27.1 1.0
N B:LYS94 4.5 29.4 1.0
CB B:ASP79 4.5 36.5 1.0
CD2 B:TYR93 4.8 31.0 1.0
CG B:TYR93 4.8 32.0 1.0
CE B:LYS94 4.9 29.0 1.0
NZ B:LYS94 5.0 27.2 1.0
CA B:LYS94 5.0 32.1 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 08:37:02 2024

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