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Sodium in PDB 9mw5: D1 Herpes Virus Simplex Neutralizing Nanobody Bound to Hsv Glycoprotein Gb

Sodium Binding Sites:

The binding sites of Sodium atom in the D1 Herpes Virus Simplex Neutralizing Nanobody Bound to Hsv Glycoprotein Gb (pdb code 9mw5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the D1 Herpes Virus Simplex Neutralizing Nanobody Bound to Hsv Glycoprotein Gb, PDB code: 9mw5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 9mw5

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Sodium binding site 1 out of 6 in the D1 Herpes Virus Simplex Neutralizing Nanobody Bound to Hsv Glycoprotein Gb


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of D1 Herpes Virus Simplex Neutralizing Nanobody Bound to Hsv Glycoprotein Gb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na801

b:35.7
occ:1.00
 OD1 A:ASN540 2.6 27.2 1.0
O A:HOH1222 2.7 26.1 1.0
O C:HOH1461 3.2 41.8 1.0
CG A:ASN540 3.2 18.5 1.0
ND2 A:ASN540 3.3 18.8 1.0
NH2 A:ARG543 3.6 33.3 1.0
CB A:PHE127 3.7 15.4 1.0
O A:HOH1425 3.8 28.1 1.0
NE2 A:GLN129 4.0 32.3 1.0
CD2 A:PHE127 4.0 19.3 1.0
O A:HOH1399 4.0 43.7 1.0
O A:HOH1311 4.1 32.6 1.0
CZ A:ARG543 4.3 33.2 1.0
CG A:PHE127 4.3 19.0 1.0
NH1 A:ARG543 4.4 32.4 1.0
CD1 A:LEU536 4.5 15.6 1.0
CB A:ASN540 4.6 17.5 1.0
O C:HOH940 4.6 29.4 1.0
O A:HOH1770 4.6 45.0 1.0
CA A:PHE127 4.7 21.1 1.0
N A:PHE127 4.8 23.0 1.0
O A:PHE127 4.8 21.7 1.0
CG A:LEU536 4.8 17.0 1.0
CD A:GLN129 4.9 37.8 1.0
OE1 A:GLN129 4.9 41.5 1.0
CD2 A:LEU536 4.9 16.2 1.0

Sodium binding site 2 out of 6 in 9mw5

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Sodium binding site 2 out of 6 in the D1 Herpes Virus Simplex Neutralizing Nanobody Bound to Hsv Glycoprotein Gb


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of D1 Herpes Virus Simplex Neutralizing Nanobody Bound to Hsv Glycoprotein Gb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na802

b:29.3
occ:1.00
 O A:HOH1016 2.4 15.9 1.0
O A:HOH1874 2.7 33.5 1.0
CA A:CYS529 3.6 12.7 1.0
CD A:ARG131 3.6 21.1 1.0
NH1 A:ARG131 3.7 32.4 1.0
O C:HOH1135 3.8 29.9 1.0
CB A:GLN532 3.9 10.7 1.0
CG A:GLN532 3.9 9.4 1.0
CB A:CYS529 3.9 15.8 1.0
O A:HOH1594 4.0 33.2 1.0
SG A:CYS529 4.2 29.7 1.0
O A:CYS529 4.2 13.5 1.0
C A:CYS529 4.4 10.4 1.0
N A:CYS529 4.5 10.0 1.0
CB C:PHE670 4.6 13.9 1.0
NE A:ARG131 4.6 29.3 1.0
CG A:ARG131 4.6 20.2 1.0
CZ A:ARG131 4.6 26.9 1.0
O A:TRP528 4.6 8.0 1.0
CB A:ARG131 4.7 19.8 1.0
CG C:PHE670 4.8 17.2 1.0
O C:ILE671 4.8 16.7 1.0
OD1 A:ASN533 4.9 17.5 1.0
C A:TRP528 4.9 8.8 1.0
CD1 A:TRP528 4.9 6.5 1.0
CD2 C:PHE670 5.0 16.5 1.0

Sodium binding site 3 out of 6 in 9mw5

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Sodium binding site 3 out of 6 in the D1 Herpes Virus Simplex Neutralizing Nanobody Bound to Hsv Glycoprotein Gb


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of D1 Herpes Virus Simplex Neutralizing Nanobody Bound to Hsv Glycoprotein Gb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na801

b:30.2
occ:1.00
 O B:HOH1076 2.4 16.1 1.0
O B:HOH1868 2.8 31.5 1.0
CA B:CYS529 3.6 12.6 1.0
O A:HOH1112 3.7 29.4 1.0
CG B:GLN532 3.7 9.4 1.0
NH1 B:ARG131 3.7 33.0 1.0
CD B:ARG131 3.7 21.7 1.0
CB B:GLN532 3.8 11.6 1.0
CB B:CYS529 4.1 16.2 1.0
SG B:CYS529 4.1 30.4 1.0
O B:HOH1576 4.1 34.2 1.0
O B:CYS529 4.2 12.7 1.0
C B:CYS529 4.4 10.6 1.0
N B:CYS529 4.4 10.3 1.0
O B:TRP528 4.5 8.6 1.0
CB A:PHE670 4.6 13.8 1.0
CZ B:ARG131 4.7 27.5 1.0
NE B:ARG131 4.7 30.7 1.0
CB B:ARG131 4.7 19.4 1.0
CG B:ARG131 4.8 21.5 1.0
O A:ILE671 4.8 16.2 1.0
CG A:PHE670 4.8 16.6 1.0
C B:TRP528 4.8 8.9 1.0
CD1 B:TRP528 4.8 6.1 1.0
OD1 B:ASN533 5.0 17.8 1.0

Sodium binding site 4 out of 6 in 9mw5

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Sodium binding site 4 out of 6 in the D1 Herpes Virus Simplex Neutralizing Nanobody Bound to Hsv Glycoprotein Gb


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of D1 Herpes Virus Simplex Neutralizing Nanobody Bound to Hsv Glycoprotein Gb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na802

b:36.5
occ:1.00
 OD1 B:ASN540 2.5 28.2 1.0
O B:HOH1252 2.7 25.2 1.0
CG B:ASN540 3.2 18.8 1.0
ND2 B:ASN540 3.3 20.0 1.0
O B:HOH1699 3.3 43.4 1.0
CB B:PHE127 3.6 14.6 1.0
NH2 B:ARG543 3.7 32.8 1.0
O B:HOH1406 3.8 24.5 1.0
NE2 B:GLN129 3.9 30.5 1.0
CD2 B:PHE127 3.9 18.7 1.0
O B:HOH1394 4.0 44.4 1.0
O B:HOH1419 4.1 33.0 1.0
CG B:PHE127 4.2 18.4 1.0
CZ B:ARG543 4.3 33.8 1.0
NH1 B:ARG543 4.3 30.5 1.0
CD1 B:LEU536 4.5 15.5 1.0
CB B:ASN540 4.6 17.1 1.0
O A:HOH970 4.6 30.4 1.0
CA B:PHE127 4.7 19.9 1.0
O B:PHE127 4.7 21.8 1.0
N B:PHE127 4.7 23.6 1.0
CG B:LEU536 4.8 16.4 1.0
CD B:GLN129 4.9 36.6 1.0
CD2 B:LEU536 4.9 17.1 1.0
OE1 B:GLN129 5.0 42.5 1.0
O A:HOH1752 5.0 47.5 1.0
C B:PHE127 5.0 19.3 1.0

Sodium binding site 5 out of 6 in 9mw5

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Sodium binding site 5 out of 6 in the D1 Herpes Virus Simplex Neutralizing Nanobody Bound to Hsv Glycoprotein Gb


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of D1 Herpes Virus Simplex Neutralizing Nanobody Bound to Hsv Glycoprotein Gb within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na801

b:29.2
occ:1.00
 O C:HOH1060 2.5 15.9 1.0
O C:HOH1882 2.8 31.7 1.0
CA C:CYS529 3.6 12.2 1.0
NH1 C:ARG131 3.6 32.1 1.0
O B:HOH1118 3.7 29.1 1.0
CG C:GLN532 3.7 9.3 1.0
CD C:ARG131 3.8 23.2 1.0
CB C:GLN532 3.8 12.0 1.0
CB C:CYS529 4.0 15.9 1.0
O C:HOH1502 4.1 34.6 1.0
O C:CYS529 4.3 13.5 1.0
SG C:CYS529 4.3 31.6 1.0
C C:CYS529 4.4 10.7 1.0
N C:CYS529 4.5 10.0 1.0
O C:TRP528 4.5 9.3 1.0
CB B:PHE670 4.6 14.5 1.0
CZ C:ARG131 4.6 28.2 1.0
NE C:ARG131 4.6 30.6 1.0
O B:ILE671 4.7 17.3 1.0
CG C:ARG131 4.8 20.9 1.0
CD1 C:TRP528 4.8 7.2 1.0
CG B:PHE670 4.8 17.1 1.0
CB C:ARG131 4.8 20.8 1.0
C C:TRP528 4.8 8.9 1.0

Sodium binding site 6 out of 6 in 9mw5

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Sodium binding site 6 out of 6 in the D1 Herpes Virus Simplex Neutralizing Nanobody Bound to Hsv Glycoprotein Gb


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of D1 Herpes Virus Simplex Neutralizing Nanobody Bound to Hsv Glycoprotein Gb within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na802

b:36.7
occ:1.00
 O C:HOH1206 2.6 26.4 1.0
OD1 C:ASN540 2.6 25.3 1.0
O C:HOH1689 3.3 44.8 1.0
CG C:ASN540 3.4 17.6 1.0
ND2 C:ASN540 3.5 18.6 1.0
NH2 C:ARG543 3.5 34.6 1.0
CB C:PHE127 3.6 16.2 1.0
NE2 C:GLN129 3.8 30.7 1.0
O C:HOH1419 3.9 26.0 1.0
CD2 C:PHE127 4.0 19.7 1.0
O C:HOH1239 4.1 34.2 1.0
O C:HOH1439 4.1 43.9 1.0
CZ C:ARG543 4.2 34.9 1.0
CG C:PHE127 4.3 20.6 1.0
CD1 C:LEU536 4.5 16.3 1.0
NH1 C:ARG543 4.5 33.6 1.0
O B:HOH941 4.6 31.3 1.0
O C:PHE127 4.6 24.1 1.0
CA C:PHE127 4.6 21.3 1.0
N C:PHE127 4.6 24.6 1.0
CB C:ASN540 4.7 16.6 1.0
CD C:GLN129 4.8 38.5 1.0
O C:HOH1793 4.8 44.9 1.0
CG C:LEU536 4.8 15.3 1.0
OE1 C:GLN129 4.9 41.4 1.0
C C:PHE127 4.9 20.7 1.0
CD2 C:LEU536 4.9 15.5 1.0

Reference:

C.V.Lee, H.Viadiu, A.Kalamkar, D.I.Bernstein, A.Pae, X.Yu, S.Wong, F.J.Bravo, S.Ding, E.Seto, M.Hung, Y.Yu, W.Xing, G.A.Papalia, W.Kan, B.Carr, M.Thomas, L.Tong, P.Desai, N.Jarrousse, A.Mercier, M.M.Holdorf, S.P.Fletcher, E.Abernathy. Identification and Engineering of Potent Bispecific Antibodies That Protect Against Herpes Simplex Virus Recurrent Disease. Cell Rep V. 44 16063 2025.
ISSN: ESSN 2211-1247
PubMed: 40716063
DOI: 10.1016/J.CELREP.2025.116063
Page generated: Mon Aug 18 17:27:22 2025

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