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Sodium in PDB 7b7n: Human Herpesvirus-8 Gh/Gl in Complex with EPHA2

Enzymatic activity of Human Herpesvirus-8 Gh/Gl in Complex with EPHA2

All present enzymatic activity of Human Herpesvirus-8 Gh/Gl in Complex with EPHA2:
2.7.10.1;

Protein crystallography data

The structure of Human Herpesvirus-8 Gh/Gl in Complex with EPHA2, PDB code: 7b7n was solved by R.Pederzoli, P.Guardado-Calvo, F.A.Rey, M.Backovic, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.44 / 2.69
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 72.94, 129, 267.69, 90, 90, 90
R / Rfree (%) 22.3 / 26.5

Other elements in 7b7n:

The structure of Human Herpesvirus-8 Gh/Gl in Complex with EPHA2 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Herpesvirus-8 Gh/Gl in Complex with EPHA2 (pdb code 7b7n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Human Herpesvirus-8 Gh/Gl in Complex with EPHA2, PDB code: 7b7n:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 7b7n

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Sodium binding site 1 out of 10 in the Human Herpesvirus-8 Gh/Gl in Complex with EPHA2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Herpesvirus-8 Gh/Gl in Complex with EPHA2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na304

b:55.2
occ:1.00
 CA E:GLY131 3.5 55.6 1.0
C E:GLY131 3.6 56.3 1.0
N E:THR132 3.9 56.8 1.0
CG2 E:THR132 4.0 48.5 1.0
O E:GLY131 4.0 56.3 1.0
O E:HOH405 4.2 46.1 1.0
CA E:THR132 4.7 54.5 1.0
N E:GLY131 4.8 57.5 1.0
OD2 E:ASP129 5.0 57.0 1.0
CB E:THR132 5.0 53.0 1.0

Sodium binding site 2 out of 10 in 7b7n

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Sodium binding site 2 out of 10 in the Human Herpesvirus-8 Gh/Gl in Complex with EPHA2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Herpesvirus-8 Gh/Gl in Complex with EPHA2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na305

b:69.6
occ:1.00
 O E:TRP43 3.0 49.5 1.0
OH E:TYR67 3.3 56.8 1.0
OD2 L:ASP68 3.9 94.8 1.0
CE1 E:TYR67 4.1 59.0 1.0
CZ E:TYR67 4.2 61.0 1.0
C E:TRP43 4.2 49.0 1.0
OG1 E:THR45 4.2 49.2 1.0
N E:TRP43 4.5 50.4 1.0
CG2 E:THR45 4.5 52.4 1.0
CG L:ASP68 4.6 91.6 1.0
CB L:ASP68 4.6 81.2 1.0
CE1 E:TYR48 4.8 107.5 1.0
CB E:LEU54 4.9 59.6 1.0
CA E:TRP43 5.0 49.8 1.0

Sodium binding site 3 out of 10 in 7b7n

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Sodium binding site 3 out of 10 in the Human Herpesvirus-8 Gh/Gl in Complex with EPHA2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Herpesvirus-8 Gh/Gl in Complex with EPHA2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na802

b:56.2
occ:1.00
 NA L:NA305 3.1 72.4 1.0
CD1 H:TRP78 3.2 58.1 1.0
N L:PHE40 3.2 63.5 1.0
CB L:PHE40 3.8 61.5 1.0
CG H:TRP78 3.8 59.9 1.0
CD2 L:LEU39 3.8 45.4 1.0
CA L:LEU39 3.8 60.1 1.0
CB H:TRP78 3.9 56.1 1.0
CA H:THR75 3.9 59.3 1.0
C L:LEU39 4.0 64.8 1.0
CG2 H:THR75 4.0 56.0 1.0
OG1 H:THR75 4.0 73.5 1.0
CB L:LEU39 4.1 53.2 1.0
CA L:PHE40 4.1 59.9 1.0
NE1 H:TRP78 4.2 60.4 1.0
O H:THR75 4.2 54.6 1.0
CB H:THR75 4.2 62.1 1.0
C H:THR75 4.6 55.9 1.0
CG L:LEU39 4.6 49.6 1.0
OG1 H:THR79 4.7 69.0 1.0
O L:HOH414 4.8 64.2 1.0
CE2 L:PHE41 4.9 68.8 1.0
CD2 L:PHE41 4.9 65.0 1.0
N H:THR75 5.0 61.7 1.0

Sodium binding site 4 out of 10 in 7b7n

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Sodium binding site 4 out of 10 in the Human Herpesvirus-8 Gh/Gl in Complex with EPHA2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Human Herpesvirus-8 Gh/Gl in Complex with EPHA2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na803

b:57.3
occ:1.00
 OE2 H:GLU167 3.9 83.3 1.0
CD2 H:TYR195 4.2 69.5 1.0
OG1 H:THR206 4.3 56.1 1.0
O H:TYR195 4.4 68.6 1.0
CD H:GLU167 4.4 84.8 1.0
CG1 H:VAL204 4.5 59.7 1.0
CG2 H:VAL197 4.5 61.6 1.0
CE1 H:PHE161 4.5 64.6 1.0
CE2 H:TYR195 4.6 70.1 1.0
O H:VAL204 4.7 72.5 1.0
CB H:VAL197 4.7 59.1 1.0
CA H:GLY196 4.8 63.3 1.0
CG H:GLU167 4.8 86.2 1.0
CD2 H:LEU160 4.9 73.5 1.0
C H:GLY196 4.9 62.3 1.0
C H:TYR195 4.9 65.0 1.0
CD1 H:PHE161 5.0 63.7 1.0

Sodium binding site 5 out of 10 in 7b7n

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Sodium binding site 5 out of 10 in the Human Herpesvirus-8 Gh/Gl in Complex with EPHA2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Human Herpesvirus-8 Gh/Gl in Complex with EPHA2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na804

b:82.9
occ:1.00
 OG1 H:THR383 3.3 92.0 1.0
N H:LYS384 3.9 75.3 1.0
CB H:LYS384 4.0 80.8 1.0
CA H:LYS384 4.1 77.7 1.0
OG H:SER381 4.1 94.2 1.0
CD H:LYS384 4.3 94.7 1.0
CB H:THR383 4.4 84.1 1.0
C H:THR383 4.5 75.7 1.0
CG H:LYS384 4.8 85.6 1.0

Sodium binding site 6 out of 10 in 7b7n

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Sodium binding site 6 out of 10 in the Human Herpesvirus-8 Gh/Gl in Complex with EPHA2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Human Herpesvirus-8 Gh/Gl in Complex with EPHA2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na805

b:63.6
occ:1.00
 OE1 H:GLU438 3.1 98.8 1.0
O H:THR433 3.3 65.4 1.0
CD H:GLU438 3.7 95.9 1.0
OE2 H:GLU438 4.1 101.5 1.0
CA H:TYR428 4.2 73.6 1.0
CG2 H:VAL431 4.3 81.1 1.0
C H:THR433 4.4 64.5 1.0
CD2 H:LEU434 4.4 58.7 1.0
N H:TYR428 4.4 72.2 1.0
CA H:LEU434 4.5 65.9 1.0
O H:ALA427 4.6 71.0 1.0
C H:ALA427 4.6 69.2 1.0
CB H:TYR428 4.7 75.9 1.0
CG H:GLU438 4.7 85.6 1.0
N H:LEU434 4.9 67.0 1.0
O H:MET424 5.0 52.4 1.0

Sodium binding site 7 out of 10 in 7b7n

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Sodium binding site 7 out of 10 in the Human Herpesvirus-8 Gh/Gl in Complex with EPHA2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Human Herpesvirus-8 Gh/Gl in Complex with EPHA2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na806

b:109.2
occ:1.00
 O H:LEU510 3.5 91.1 1.0
CB H:LEU510 4.0 77.0 1.0
C H:LEU510 4.2 89.0 1.0
O H:ARG507 4.3 75.7 1.0
N H:LEU510 4.3 85.2 1.0
CD2 H:HIS545 4.4 106.3 1.0
CA H:LEU510 4.4 84.1 1.0
CA H:TYR508 4.5 80.8 1.0
CG H:HIS545 4.5 105.4 1.0
O H:TYR508 4.5 82.6 1.0
C H:TYR508 4.6 81.2 1.0
NE2 H:HIS545 4.7 106.5 1.0
O H:LEU541 4.8 89.7 1.0
ND1 H:HIS545 4.8 108.4 1.0
CB H:LEU541 4.9 79.8 1.0
CG H:LEU510 4.9 70.1 1.0
CB H:HIS545 4.9 98.2 1.0
CE1 H:HIS545 4.9 106.9 1.0
CD2 H:LEU541 5.0 84.9 1.0
CE1 H:HIS511 5.0 108.5 1.0

Sodium binding site 8 out of 10 in 7b7n

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Sodium binding site 8 out of 10 in the Human Herpesvirus-8 Gh/Gl in Complex with EPHA2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Human Herpesvirus-8 Gh/Gl in Complex with EPHA2 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na303

b:58.3
occ:1.00
 O L:PRO25 2.8 69.0 1.0
O L:HIS47 3.3 46.8 1.0
CG H:GLU52 3.6 54.3 1.0
C L:PRO25 3.7 56.6 1.0
CA L:PRO25 3.7 62.5 1.0
CB L:HIS47 3.8 44.8 1.0
C L:HIS47 3.9 44.1 1.0
CB L:LYS61 4.1 42.2 1.0
CB L:PRO25 4.2 64.2 1.0
CB H:GLU52 4.4 54.9 1.0
C L:PHE48 4.4 49.1 1.0
N L:LYS61 4.4 42.5 1.0
O L:PHE48 4.5 52.5 1.0
N L:ALA49 4.5 54.9 1.0
CA L:HIS47 4.5 41.6 1.0
N L:PHE48 4.5 40.2 1.0
CG L:LYS61 4.7 47.8 1.0
CB L:ALA49 4.7 62.7 1.0
CD H:GLU52 4.7 57.3 1.0
CD L:LYS61 4.8 50.6 1.0
CA L:PHE48 4.8 44.2 1.0
CA L:ALA49 4.9 60.4 1.0
C L:ALA60 4.9 43.2 1.0
CD1 L:ILE59 4.9 39.4 1.0
CA L:ALA60 4.9 43.9 1.0
CA L:LYS61 4.9 47.0 1.0
N L:CYS26 4.9 44.1 1.0
O L:LEU24 5.0 55.7 1.0

Sodium binding site 9 out of 10 in 7b7n

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Sodium binding site 9 out of 10 in the Human Herpesvirus-8 Gh/Gl in Complex with EPHA2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Human Herpesvirus-8 Gh/Gl in Complex with EPHA2 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na304

b:86.1
occ:1.00
 CA L:ALA112 3.7 62.6 1.0
CB L:ALA112 4.0 60.1 1.0
N L:ALA112 4.1 60.4 1.0
CG1 L:VAL115 4.3 69.3 1.0
O L:THR111 4.5 80.0 1.0
C L:THR111 4.5 66.9 1.0
CG2 L:VAL115 4.5 76.8 1.0
C L:ALA112 4.9 63.8 1.0
OG1 L:THR111 5.0 78.9 1.0

Sodium binding site 10 out of 10 in 7b7n

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Sodium binding site 10 out of 10 in the Human Herpesvirus-8 Gh/Gl in Complex with EPHA2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Human Herpesvirus-8 Gh/Gl in Complex with EPHA2 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na305

b:72.4
occ:1.00
 OG1 H:THR75 2.7 73.5 1.0
NA H:NA802 3.1 56.2 1.0
CE2 L:PHE41 3.4 68.8 1.0
CD2 L:PHE41 3.5 65.0 1.0
CB H:THR75 3.8 62.1 1.0
CG2 H:THR75 3.8 56.0 1.0
CD2 L:LEU39 4.1 45.4 1.0
CD1 L:LEU39 4.1 52.6 1.0
CB L:LEU39 4.2 53.2 1.0
CG L:LEU39 4.3 49.6 1.0
CA H:THR75 4.4 59.3 1.0
CZ L:PHE41 4.7 71.0 1.0
CG L:PHE41 4.8 63.9 1.0
N L:PHE40 4.9 63.5 1.0

Reference:

M.Backovic, R.Pederzoli, F.A.Rey. Human Herpesvirus-8 Gh/Gl in Complex with EPHA2 To Be Published.
Page generated: Mon Aug 18 09:15:58 2025

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