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Manganese in PDB 7ewu: Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease (Wt)

Enzymatic activity of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease (Wt)

All present enzymatic activity of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease (Wt):
2.7.7.48;

Protein crystallography data

The structure of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease (Wt), PDB code: 7ewu 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) 35.95 / 2.11
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.812, 41.587, 145.313, 90, 101.58, 90
R / Rfree (%) 24 / 28.5

Manganese Binding Sites:

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

Manganese binding site 1 out of 6 in 7ewu

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Manganese binding site 1 out of 6 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease (Wt)


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

b:58.5
occ:1.00
 O B:HOH315 2.2 34.1 1.0
OD1 B:ASP79 2.2 34.9 1.0
O B:HOH351 2.2 38.6 1.0
OD1 B:ASN52 2.3 45.0 1.0
O B:HOH334 2.4 48.4 1.0
O B:HOH344 2.5 44.1 1.0
CG B:ASP79 3.2 34.3 1.0
CG B:ASN52 3.4 42.6 1.0
OD2 B:ASP79 3.7 37.3 1.0
ND2 B:ASN52 3.8 47.0 1.0
CE1 B:HIS34 4.0 37.3 1.0
O B:THR77 4.3 35.4 1.0
NE2 B:HIS34 4.4 42.8 1.0
CB B:ASP79 4.4 33.0 1.0
CA B:ASP79 4.4 36.4 1.0
OD1 B:ASP92 4.5 32.9 1.0
MN B:MN202 4.5 53.5 0.6
N B:ASP79 4.6 35.0 1.0
CB B:ASN52 4.7 39.5 1.0
N B:ASN52 4.7 42.0 1.0
OE1 B:GLU31 4.9 56.5 1.0
CA B:ASN52 4.9 38.0 1.0
ND1 B:HIS34 4.9 37.2 1.0
C B:PRO78 5.0 35.2 1.0

Manganese binding site 2 out of 6 in 7ewu

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Manganese binding site 2 out of 6 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease (Wt)


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

b:53.5
occ:0.55
 O B:TYR93 2.0 32.3 1.0
O B:HOH344 2.3 44.1 1.0
OD2 B:ASP92 2.6 36.0 1.0
OD2 B:ASP79 3.0 37.3 1.0
NE2 B:HIS34 3.2 42.8 1.0
C B:TYR93 3.2 33.8 1.0
CE B:LYS94 3.3 41.0 1.0
CG B:ASP92 3.5 35.8 1.0
CD2 B:HIS34 3.6 31.2 1.0
CD B:LYS94 3.7 39.3 1.0
NZ B:LYS94 3.9 42.8 1.0
N B:TYR93 3.9 35.4 1.0
OD1 B:ASP92 4.0 32.9 1.0
CG B:ASP79 4.1 34.3 1.0
CA B:TYR93 4.1 29.6 1.0
N B:LYS94 4.1 33.8 1.0
CG B:LYS94 4.2 37.7 1.0
CE1 B:HIS34 4.2 37.3 1.0
CA B:LYS94 4.3 34.4 1.0
OD1 B:ASP79 4.5 34.9 1.0
CB B:ASP92 4.5 30.3 1.0
MN B:MN201 4.5 58.5 1.0
O B:HOH352 4.6 26.0 1.0
C B:ASP92 4.6 34.3 1.0
CG B:HIS34 4.7 39.9 1.0
CB B:TYR93 4.8 31.5 1.0
CB B:LYS94 4.8 37.8 1.0
CA B:ASP92 4.9 25.0 1.0
O B:HOH315 4.9 34.1 1.0

Manganese binding site 3 out of 6 in 7ewu

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Manganese binding site 3 out of 6 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease (Wt)


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

b:73.5
occ:1.00
 O C:HOH318 2.4 54.9 1.0
O C:HOH306 2.4 50.9 1.0
OD1 C:ASN52 2.4 52.5 1.0
OD1 C:ASP79 2.7 36.8 1.0
O C:HOH323 2.7 53.2 1.0
O C:HOH340 2.7 55.9 1.0
CG C:ASN52 3.4 53.2 1.0
ND2 C:ASN52 3.7 52.1 1.0
CG C:ASP79 3.8 37.6 1.0
O C:HOH336 4.1 54.7 1.0
O C:THR77 4.3 36.8 1.0
CE1 C:HIS34 4.3 35.5 1.0
OD1 C:ASN51 4.3 46.1 1.0
OD2 C:ASP79 4.4 34.2 1.0
NE2 C:HIS34 4.6 35.6 1.0
MN C:MN202 4.6 53.4 0.6
OD1 C:ASP92 4.7 43.1 1.0
CB C:ASN52 4.8 44.5 1.0
N C:ASP79 4.9 37.5 1.0
CA C:ASP79 5.0 38.3 1.0
CB C:ASP79 5.0 36.2 1.0

Manganese binding site 4 out of 6 in 7ewu

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Manganese binding site 4 out of 6 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease (Wt)


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

b:53.4
occ:0.56
 O C:HOH323 2.3 53.2 1.0
OD2 C:ASP92 2.3 39.8 1.0
O C:TYR93 2.5 32.6 1.0
CE C:LYS94 3.2 36.9 1.0
NZ C:LYS94 3.2 38.7 1.0
CG C:ASP92 3.4 40.3 1.0
NE2 C:HIS34 3.4 35.6 1.0
OD2 C:ASP79 3.6 34.2 1.0
CD C:LYS94 3.6 39.4 1.0
C C:TYR93 3.7 37.7 1.0
CD2 C:HIS34 3.8 31.3 1.0
OD1 C:ASP92 4.0 43.1 1.0
CG C:LYS94 4.3 38.9 1.0
N C:TYR93 4.4 34.9 1.0
CG C:ASP79 4.5 37.6 1.0
CE1 C:HIS34 4.5 35.5 1.0
N C:LYS94 4.5 39.8 1.0
OD1 C:ASP79 4.5 36.8 1.0
CA C:LYS94 4.5 33.2 1.0
CB C:ASP92 4.6 31.9 1.0
O C:HOH334 4.6 23.9 1.0
MN C:MN201 4.6 73.5 1.0
CA C:TYR93 4.7 34.0 1.0
C C:ASP92 4.9 35.3 1.0
CG C:HIS34 4.9 35.7 1.0
CB C:LYS94 5.0 38.4 1.0

Manganese binding site 5 out of 6 in 7ewu

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Manganese binding site 5 out of 6 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease (Wt)


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

b:84.8
occ:0.65
 O D:HOH337 2.1 62.4 1.0
ND2 D:ASN52 2.2 51.8 1.0
O D:HOH339 2.3 53.7 1.0
OD1 D:ASP79 2.4 42.7 1.0
O D:HOH335 2.7 49.0 1.0
O D:HOH305 2.7 45.9 1.0
CG D:ASN52 3.1 52.9 1.0
OD1 D:ASN52 3.4 57.7 1.0
CG D:ASP79 3.6 44.7 1.0
CE1 D:HIS34 3.9 40.8 1.0
O D:HOH328 4.3 46.2 1.0
OD2 D:ASP79 4.3 40.8 1.0
MN D:MN202 4.3 57.4 0.5
NE2 D:HIS34 4.4 40.6 1.0
O D:THR77 4.5 40.0 1.0
CB D:ASN52 4.5 47.2 1.0
CA D:ASP79 4.6 38.5 1.0
CB D:ASP79 4.7 40.1 1.0
CA D:ASN52 4.8 46.1 1.0
N D:ASP79 4.8 36.6 1.0
N D:ASN52 4.8 47.1 1.0
ND1 D:HIS34 4.9 39.5 1.0

Manganese binding site 6 out of 6 in 7ewu

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Manganese binding site 6 out of 6 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease (Wt)


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

b:57.4
occ:0.48
 O D:HOH335 2.1 49.0 1.0
OD2 D:ASP92 2.3 48.2 1.0
NZ D:LYS94 2.4 50.5 1.0
OD2 D:ASP79 2.9 40.8 1.0
O D:TYR93 3.0 36.5 1.0
CG D:ASP92 3.1 45.4 1.0
NE2 D:HIS34 3.4 40.6 1.0
OD1 D:ASP92 3.4 47.8 1.0
CG D:ASP79 3.7 44.7 1.0
OD1 D:ASP79 3.8 42.7 1.0
CE D:LYS94 3.8 40.6 1.0
CD2 D:HIS34 4.0 34.0 1.0
O D:HOH305 4.1 45.9 1.0
C D:TYR93 4.1 37.0 1.0
N D:TYR93 4.3 37.9 1.0
MN D:MN201 4.3 84.8 0.7
CE1 D:HIS34 4.3 40.8 1.0
CB D:ASP92 4.3 38.5 1.0
CD D:LYS94 4.7 40.3 1.0
CA D:ASP92 4.7 37.7 1.0
C D:ASP92 4.8 39.2 1.0
CA D:TYR93 4.8 36.8 1.0
O D:HOH328 4.8 46.2 1.0
O D:HOH337 4.9 62.4 1.0
CG D:LYS94 4.9 40.1 1.0
CB D:ASP79 5.0 40.1 1.0

Reference:

W.Kuang, H.Zhang, Y.Cai, G.Zhang, F.Deng, H.Li, Z.Hu, Y.Guo, M.Wang, Y.Zhou, P.Gong. Insights Into Two-Metal-Ion Catalytic Mechanism of Cap-Snatching Endonuclease of Ebinur Lake Virus in Bunyavirales. J.Virol. V. 96 08521 2022.
ISSN: ESSN 1098-5514
PubMed: 35044209
DOI: 10.1128/JVI.02085-21
Page generated: Sun Oct 6 08:34:33 2024

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