Calcium in PDB 8ys4: Overall Structure of Eastern Equine Encephalitis Virus Vlp in Complex with the Receptor Vldlr LA3-5

Enzymatic activity of Overall Structure of Eastern Equine Encephalitis Virus Vlp in Complex with the Receptor Vldlr LA3-5

All present enzymatic activity of Overall Structure of Eastern Equine Encephalitis Virus Vlp in Complex with the Receptor Vldlr LA3-5:
3.4.21.90;

Calcium Binding Sites:

The binding sites of Calcium atom in the Overall Structure of Eastern Equine Encephalitis Virus Vlp in Complex with the Receptor Vldlr LA3-5 (pdb code 8ys4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Overall Structure of Eastern Equine Encephalitis Virus Vlp in Complex with the Receptor Vldlr LA3-5, PDB code: 8ys4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 8ys4

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Calcium binding site 1 out of 8 in the Overall Structure of Eastern Equine Encephalitis Virus Vlp in Complex with the Receptor Vldlr LA3-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Overall Structure of Eastern Equine Encephalitis Virus Vlp in Complex with the Receptor Vldlr LA3-5 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca301

b:113.0
occ:1.00
 O M:ASP215 2.4 106.3 1.0
O M:TRP210 2.4 104.6 1.0
OD1 M:ASP213 2.4 113.7 1.0
OD2 M:ASP223 2.4 115.9 1.0
OD2 M:ASP217 2.4 101.3 1.0
CG M:ASP217 3.0 100.6 1.0
CG M:ASP213 3.2 113.7 1.0
OD2 M:ASP213 3.3 112.6 1.0
OD1 M:ASP217 3.3 100.8 1.0
OE2 M:GLU224 3.4 117.0 1.0
C M:TRP210 3.4 103.3 1.0
C M:ASP215 3.5 106.3 1.0
CG M:ASP223 3.6 117.3 1.0
NZ B:LYS156 3.8 63.5 1.0
CB M:ASP215 3.8 106.7 1.0
OE1 M:GLU224 3.9 117.7 1.0
CA M:ASP215 4.0 106.3 1.0
CB M:ASP217 4.0 100.6 1.0
CD M:GLU224 4.0 117.0 1.0
N M:ASP215 4.1 106.2 1.0
N M:ASP217 4.2 101.4 1.0
CA M:TRP210 4.2 101.5 1.0
CE B:LYS156 4.3 60.1 1.0
N M:VAL211 4.4 111.7 1.0
CB M:TRP210 4.4 102.6 1.0
CB M:ASP223 4.4 117.4 1.0
N M:ASP213 4.5 113.6 1.0
CB M:ASP213 4.6 113.0 1.0
OD1 M:ASP223 4.6 117.1 1.0
CA M:VAL211 4.6 110.9 1.0
N M:ALA216 4.6 95.3 1.0
CA M:ASP217 4.8 101.2 1.0
N M:CYS212 4.8 123.2 1.0
C M:VAL211 4.9 112.1 1.0
CA M:ASP213 4.9 113.7 1.0
CA M:ALA216 5.0 95.2 1.0
CD1 M:ILE206 5.0 120.8 1.0

Calcium binding site 2 out of 8 in 8ys4

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Calcium binding site 2 out of 8 in the Overall Structure of Eastern Equine Encephalitis Virus Vlp in Complex with the Receptor Vldlr LA3-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Overall Structure of Eastern Equine Encephalitis Virus Vlp in Complex with the Receptor Vldlr LA3-5 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Ca301

b:98.0
occ:1.00
 O N:ASP215 2.4 104.5 1.0
OD1 N:ASP213 2.4 105.3 1.0
OD2 N:ASP223 2.4 115.1 1.0
OD2 N:ASP217 2.4 104.0 1.0
O N:TRP210 2.4 94.8 1.0
CG N:ASP217 3.1 102.8 1.0
OE1 N:GLU224 3.3 112.0 1.0
OD1 N:ASP217 3.4 102.0 1.0
CG N:ASP213 3.4 104.5 1.0
C N:ASP215 3.5 104.6 1.0
CG N:ASP223 3.5 116.3 1.0
C N:TRP210 3.6 93.2 1.0
OD2 N:ASP213 3.8 103.8 1.0
OD1 N:ASP223 4.0 115.8 1.0
CG N:GLU224 4.1 113.8 1.0
CD N:GLU224 4.1 112.4 1.0
CA N:ASP215 4.2 104.8 1.0
CB N:ASP215 4.2 105.0 1.0
N N:ASP217 4.2 103.4 1.0
N N:ASP215 4.2 104.8 1.0
NZ E:LYS156 4.3 50.7 1.0
CB N:ASP217 4.3 102.8 1.0
N N:ASP213 4.4 105.5 1.0
CA N:TRP210 4.4 92.6 1.0
N N:VAL211 4.5 98.7 1.0
N N:ALA216 4.5 99.4 1.0
N N:CYS212 4.6 106.2 1.0
CB N:TRP210 4.6 92.7 1.0
CA N:VAL211 4.6 99.4 1.0
CE E:LYS156 4.7 55.2 1.0
CB N:ASP223 4.7 116.2 1.0
CB N:ASP213 4.7 103.8 1.0
CA N:ALA216 4.8 99.9 1.0
C N:VAL211 4.9 99.4 1.0
C N:ALA216 4.9 101.8 1.0
CA N:ASP217 4.9 103.0 1.0
CA N:ASP213 4.9 104.6 1.0

Calcium binding site 3 out of 8 in 8ys4

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Calcium binding site 3 out of 8 in the Overall Structure of Eastern Equine Encephalitis Virus Vlp in Complex with the Receptor Vldlr LA3-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Overall Structure of Eastern Equine Encephalitis Virus Vlp in Complex with the Receptor Vldlr LA3-5 within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca301

b:92.4
occ:1.00
 O O:TRP210 2.4 99.8 1.0
O O:ASP215 2.4 101.9 1.0
OD1 O:ASP213 2.4 105.6 1.0
OE1 O:GLU224 3.2 123.4 1.0
OD2 O:ASP223 3.3 122.7 1.0
CG O:ASP213 3.3 106.9 1.0
C O:TRP210 3.5 98.5 1.0
C O:ASP215 3.5 100.7 1.0
OD2 O:ASP213 3.5 104.7 1.0
OD2 O:ASP217 3.5 116.4 1.0
CG O:ASP217 3.5 113.9 1.0
CB O:ASP215 3.8 101.1 1.0
OD1 O:ASP217 3.8 113.8 1.0
CA O:ASP215 4.1 99.9 1.0
CB O:ASP217 4.1 111.9 1.0
N O:ASP217 4.1 112.0 1.0
NZ H:LYS156 4.2 49.4 1.0
CA O:TRP210 4.2 95.9 1.0
N O:ASP215 4.3 99.9 1.0
CG O:ASP223 4.4 123.9 1.0
CB O:TRP210 4.4 97.6 1.0
N O:VAL211 4.4 108.4 1.0
CD O:GLU224 4.4 123.2 1.0
CD1 O:ILE206 4.5 110.8 1.0
CA O:VAL211 4.6 108.2 1.0
N O:ALA216 4.6 105.4 1.0
N O:ASP213 4.7 107.3 1.0
CE H:LYS156 4.7 52.8 1.0
CB O:ASP213 4.7 106.7 1.0
CA O:ASP217 4.7 112.7 1.0
CB O:ASP223 4.9 123.9 1.0
N O:CYS212 4.9 119.0 1.0
CA O:ALA216 4.9 106.6 1.0
OE2 O:GLU224 4.9 123.6 1.0

Calcium binding site 4 out of 8 in 8ys4

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Calcium binding site 4 out of 8 in the Overall Structure of Eastern Equine Encephalitis Virus Vlp in Complex with the Receptor Vldlr LA3-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Overall Structure of Eastern Equine Encephalitis Virus Vlp in Complex with the Receptor Vldlr LA3-5 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca301

b:83.7
occ:1.00
 OD1 P:ASP213 2.4 102.0 1.0
O P:TRP210 2.4 85.8 1.0
OD2 P:ASP217 2.4 98.0 1.0
OD2 P:ASP223 2.5 117.9 1.0
OE1 P:GLU224 2.6 117.6 1.0
CG P:ASP217 3.2 99.4 1.0
O P:ASP215 3.2 91.8 1.0
CG P:ASP213 3.5 102.2 1.0
CG P:ASP223 3.6 116.4 1.0
C P:TRP210 3.6 88.2 1.0
CB P:ASP215 3.8 94.1 1.0
C P:ASP215 3.8 92.0 1.0
OD1 P:ASP217 3.8 99.0 1.0
CD P:GLU224 3.8 118.4 1.0
OD2 P:ASP213 4.0 99.9 1.0
CB P:ASP223 4.1 116.6 1.0
CB P:ASP217 4.1 99.4 1.0
N P:ASP215 4.1 95.4 1.0
CA P:ASP215 4.1 93.8 1.0
CA P:VAL211 4.3 101.3 1.0
N P:ASP217 4.4 97.0 1.0
N P:VAL211 4.4 100.5 1.0
N P:ASP213 4.5 104.3 1.0
N P:CYS212 4.5 111.8 1.0
CG P:GLU224 4.6 119.3 1.0
OD1 P:ASP223 4.6 116.1 1.0
CA P:TRP210 4.7 88.0 1.0
C P:VAL211 4.7 100.9 1.0
NZ K:LYS156 4.7 48.5 1.0
N P:ALA216 4.7 91.3 1.0
CB P:ASP213 4.8 102.4 1.0
OE2 P:GLU224 4.8 117.1 1.0
CB P:TRP210 4.8 85.7 1.0
CA P:ASP217 4.9 98.7 1.0
CD1 P:ILE206 4.9 109.5 1.0
CA P:ASP213 5.0 103.6 1.0

Calcium binding site 5 out of 8 in 8ys4

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Calcium binding site 5 out of 8 in the Overall Structure of Eastern Equine Encephalitis Virus Vlp in Complex with the Receptor Vldlr LA3-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Overall Structure of Eastern Equine Encephalitis Virus Vlp in Complex with the Receptor Vldlr LA3-5 within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Ca201

b:138.8
occ:1.00
 OD1 Q:ASP135 2.4 130.7 1.0
OD2 Q:ASP145 2.4 154.1 1.0
OD2 Q:ASP135 2.4 130.2 1.0
OD2 Q:ASP139 2.6 141.5 1.0
O Q:TRP132 2.7 126.5 1.0
CG Q:ASP135 2.8 129.9 1.0
O Q:GLU137 3.0 122.4 1.0
CG Q:ASP145 3.1 153.8 1.0
OD1 Q:ASP145 3.3 154.4 1.0
OE2 Q:GLU146 3.3 149.1 1.0
C Q:TRP132 3.5 127.5 1.0
CG Q:ASP139 3.7 141.3 1.0
CB Q:TRP132 4.1 125.0 1.0
CB Q:ASP139 4.2 142.3 1.0
NZ E:LYS206 4.2 91.4 1.0
C Q:GLU137 4.3 121.5 1.0
CB Q:ASP135 4.3 129.2 1.0
CA Q:TRP132 4.3 126.2 1.0
N Q:ARG133 4.3 159.6 1.0
CB Q:ASP145 4.4 153.6 1.0
CA Q:ARG133 4.5 160.3 1.0
CD Q:GLU146 4.5 150.1 1.0
N Q:ASP139 4.5 142.4 1.0
OD1 Q:ASP139 4.7 140.9 1.0
N Q:ASP135 4.7 132.2 1.0
O Q:ASP145 4.7 153.5 1.0
C Q:ASN138 4.9 140.7 1.0
N Q:GLU137 5.0 119.3 1.0
CG Q:GLU137 5.0 118.5 1.0
OE1 Q:GLU146 5.0 151.2 1.0

Calcium binding site 6 out of 8 in 8ys4

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Calcium binding site 6 out of 8 in the Overall Structure of Eastern Equine Encephalitis Virus Vlp in Complex with the Receptor Vldlr LA3-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Overall Structure of Eastern Equine Encephalitis Virus Vlp in Complex with the Receptor Vldlr LA3-5 within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ca201

b:131.9
occ:1.00
 OD2 R:ASP139 2.4 157.2 1.0
OD2 R:ASP145 2.4 162.8 1.0
OD1 R:ASP135 2.4 143.5 1.0
O R:TRP132 3.1 133.1 1.0
O R:GLU137 3.2 151.3 1.0
CG R:ASP145 3.2 162.5 1.0
CG R:ASP135 3.2 143.4 1.0
OD2 R:ASP135 3.3 142.9 1.0
OE2 R:GLU146 3.4 158.4 1.0
OD1 R:ASP145 3.5 161.9 1.0
CG R:ASP139 3.5 157.0 1.0
C R:TRP132 3.6 133.0 1.0
NZ B:LYS206 3.7 91.4 1.0
CB R:ASP139 4.1 157.7 1.0
N R:ARG133 4.1 146.5 1.0
CA R:ARG133 4.2 146.6 1.0
CB R:TRP132 4.3 131.4 1.0
N R:CYS134 4.3 154.1 1.0
C R:GLU137 4.4 150.8 1.0
CA R:TRP132 4.4 131.9 1.0
CB R:ASP145 4.4 162.1 1.0
N R:ASP135 4.4 145.4 1.0
OD1 R:ASP139 4.5 157.1 1.0
C R:ARG133 4.5 147.0 1.0
CD R:GLU146 4.6 158.4 1.0
N R:ASP139 4.6 158.4 1.0
CB R:ASP135 4.6 143.3 1.0
CE B:LYS206 4.7 92.1 1.0
O R:ASP145 4.8 161.4 1.0
CG R:GLU137 4.8 149.2 1.0

Calcium binding site 7 out of 8 in 8ys4

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Calcium binding site 7 out of 8 in the Overall Structure of Eastern Equine Encephalitis Virus Vlp in Complex with the Receptor Vldlr LA3-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Overall Structure of Eastern Equine Encephalitis Virus Vlp in Complex with the Receptor Vldlr LA3-5 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Ca201

b:156.3
occ:1.00
 OD2 S:ASP139 2.4 145.2 1.0
OD1 S:ASP135 2.5 134.6 1.0
OD2 S:ASP145 2.5 157.4 1.0
O S:TRP132 2.5 134.2 1.0
OD2 S:ASP135 2.5 135.1 1.0
CG S:ASP135 2.8 134.6 1.0
CG S:ASP139 3.2 145.4 1.0
O S:GLU137 3.3 133.8 1.0
CG S:ASP145 3.3 156.9 1.0
C S:TRP132 3.5 134.2 1.0
OD1 S:ASP145 3.5 157.2 1.0
OE2 S:GLU146 3.5 153.9 1.0
CB S:ASP139 3.7 145.4 1.0
OD1 S:ASP139 4.0 145.2 1.0
CB S:TRP132 4.2 133.2 1.0
NZ H:LYS206 4.2 91.4 1.0
N S:ARG133 4.3 144.3 1.0
CB S:ASP135 4.3 133.6 1.0
CA S:TRP132 4.3 133.4 1.0
CA S:ARG133 4.4 144.0 1.0
C S:GLU137 4.4 133.7 1.0
N S:ASP139 4.5 146.2 1.0
CB S:ASP145 4.7 156.8 1.0
CD S:GLU146 4.7 154.2 1.0
N S:ASP135 4.7 135.4 1.0
CA S:ASP139 4.8 145.7 1.0
C S:ASN138 4.9 146.1 1.0
C S:ARG133 5.0 144.9 1.0
N S:CYS134 5.0 147.8 1.0
CG S:GLU137 5.0 132.1 1.0

Calcium binding site 8 out of 8 in 8ys4

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Calcium binding site 8 out of 8 in the Overall Structure of Eastern Equine Encephalitis Virus Vlp in Complex with the Receptor Vldlr LA3-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Overall Structure of Eastern Equine Encephalitis Virus Vlp in Complex with the Receptor Vldlr LA3-5 within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Ca201

b:108.7
occ:1.00
 O T:TRP132 2.4 116.5 1.0
OD2 T:ASP139 2.5 123.0 1.0
OD2 T:ASP135 2.5 114.0 1.0
OD1 T:ASP135 2.5 115.2 1.0
OD2 T:ASP145 2.7 129.2 1.0
CG T:ASP135 2.8 114.3 1.0
OE2 T:GLU146 3.2 124.8 1.0
C T:TRP132 3.2 116.6 1.0
CG T:ASP145 3.6 128.9 1.0
CB T:TRP132 3.6 115.6 1.0
CG T:ASP139 3.6 123.0 1.0
CA T:TRP132 3.9 115.9 1.0
O T:ASP145 4.0 126.7 1.0
NZ K:LYS206 4.1 91.4 1.0
N T:ARG133 4.1 132.2 1.0
CD T:GLU146 4.2 124.0 1.0
O T:GLU137 4.2 112.6 1.0
CB T:ASP135 4.2 113.8 1.0
OD1 T:ASP139 4.2 122.8 1.0
CB T:ASP145 4.2 127.8 1.0
N T:ASP135 4.3 116.2 1.0
OD1 T:ASP145 4.3 129.2 1.0
OE1 T:GLU146 4.4 123.7 1.0
CA T:ARG133 4.4 133.4 1.0
N T:CYS134 4.5 132.7 1.0
C T:ASP145 4.7 128.2 1.0
C T:ARG133 4.7 133.5 1.0
CB T:ASP139 4.8 123.7 1.0
CA T:ASP135 4.9 115.0 1.0
CG T:TRP132 4.9 116.0 1.0

Reference:

D.Cao, B.Ma, Z.Cao, X.Xu, X.Zhang, Y.Xiang. The Receptor Vldlr Binds Eastern Equine Encephalitis Virus Through Multiple Distinct Modes. Nat Commun V. 15 6866 2024.
ISSN: ESSN 2041-1723
PubMed: 39127734
DOI: 10.1038/S41467-024-51293-X
Page generated: Sat Sep 28 09:26:12 2024

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