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Sodium in PDB 8szz: Cryoem Structure of Computationally Designed Nanocage O32-ZL4

Sodium Binding Sites:

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Sodium atom in the Cryoem Structure of Computationally Designed Nanocage O32-ZL4 (pdb code 8szz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 24 binding sites of Sodium where determined in the Cryoem Structure of Computationally Designed Nanocage O32-ZL4, PDB code: 8szz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 24 in 8szz

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Sodium binding site 1 out of 24 in the Cryoem Structure of Computationally Designed Nanocage O32-ZL4


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Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cryoem Structure of Computationally Designed Nanocage O32-ZL4 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na301

b:30.0
occ:1.00
 SG I:CYS74 3.0 35.1 1.0
OE2 I:GLU71 3.1 38.3 1.0
CG I:LYS101 3.9 42.6 1.0
CB I:CYS74 4.0 35.1 1.0
O I:PHE97 4.1 45.7 1.0
N I:ALA75 4.1 31.4 1.0
C I:CYS74 4.1 35.1 1.0
CD I:GLU71 4.2 38.3 1.0
O I:CYS74 4.3 35.1 1.0
CA I:ALA75 4.4 31.4 1.0
CB I:LYS101 4.4 42.6 1.0
SG I:CYS98 4.5 42.4 1.0
OE1 I:GLU71 4.6 38.3 1.0
CA I:CYS98 4.6 42.4 1.0
CG2 I:VAL78 4.6 30.4 1.0
CA I:CYS74 4.7 35.1 1.0
C I:PHE97 4.8 45.7 1.0
O I:GLU71 4.9 38.3 1.0
CB I:CYS98 4.9 42.4 1.0
CD I:LYS101 4.9 42.6 1.0
CB I:ALA75 4.9 31.4 1.0

Sodium binding site 2 out of 24 in 8szz

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Sodium binding site 2 out of 24 in the Cryoem Structure of Computationally Designed Nanocage O32-ZL4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cryoem Structure of Computationally Designed Nanocage O32-ZL4 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na301

b:30.0
occ:1.00
 SG J:CYS74 2.8 34.9 1.0
OE2 J:GLU71 3.2 39.8 1.0
CB J:CYS74 3.7 34.9 1.0
CG J:LYS101 4.0 44.8 1.0
C J:CYS74 4.1 34.9 1.0
SG J:CYS98 4.1 43.2 1.0
N J:ALA75 4.2 31.8 1.0
O J:CYS74 4.2 34.9 1.0
O J:PHE97 4.2 47.0 1.0
CD J:GLU71 4.3 39.8 1.0
CB J:LYS101 4.5 44.8 1.0
CG2 J:VAL78 4.5 29.8 1.0
CA J:ALA75 4.5 31.8 1.0
CA J:CYS74 4.6 34.9 1.0
OE1 J:GLU71 4.7 39.8 1.0
CA J:CYS98 4.7 43.2 1.0
C J:PHE97 4.9 47.0 1.0
CB J:CYS98 4.9 43.2 1.0
O J:GLU71 4.9 39.8 1.0

Sodium binding site 3 out of 24 in 8szz

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Sodium binding site 3 out of 24 in the Cryoem Structure of Computationally Designed Nanocage O32-ZL4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cryoem Structure of Computationally Designed Nanocage O32-ZL4 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Na301

b:30.0
occ:1.00
 SG K:CYS74 2.5 36.4 1.0
CG K:LYS101 3.2 46.0 1.0
OE2 K:GLU71 3.4 39.0 1.0
CB K:CYS74 3.7 36.4 1.0
C K:CYS74 4.0 36.4 1.0
O K:CYS74 4.1 36.4 1.0
CD K:LYS101 4.1 46.0 1.0
CB K:LYS101 4.1 46.0 1.0
N K:ALA75 4.1 32.0 1.0
CE K:LYS101 4.1 46.0 1.0
SG K:CYS98 4.3 45.5 1.0
CD K:GLU71 4.3 39.0 1.0
CG2 K:VAL78 4.4 31.6 1.0
CA K:ALA75 4.5 32.0 1.0
CA K:CYS74 4.5 36.4 1.0
OE1 K:GLU71 4.6 39.0 1.0
CA K:CYS98 4.6 45.5 1.0
O K:PHE97 4.8 46.2 1.0
N K:CYS98 4.9 45.5 1.0
CG2 K:VAL103 4.9 35.9 1.0
C K:PHE97 4.9 46.2 1.0
CB K:VAL78 4.9 31.6 1.0

Sodium binding site 4 out of 24 in 8szz

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Sodium binding site 4 out of 24 in the Cryoem Structure of Computationally Designed Nanocage O32-ZL4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Cryoem Structure of Computationally Designed Nanocage O32-ZL4 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na301

b:30.0
occ:1.00
 SG L:CYS74 2.7 35.7 1.0
CG L:LYS101 3.2 44.4 1.0
OE2 L:GLU71 3.6 39.7 1.0
CB L:CYS74 3.8 35.7 1.0
C L:CYS74 3.9 35.7 1.0
N L:ALA75 4.0 32.4 1.0
CE L:LYS101 4.0 44.4 1.0
O L:CYS74 4.0 35.7 1.0
CD L:LYS101 4.0 44.4 1.0
O L:PHE97 4.2 46.3 1.0
CB L:LYS101 4.2 44.4 1.0
CG2 L:VAL78 4.2 30.9 1.0
CA L:ALA75 4.2 32.4 1.0
CD L:GLU71 4.4 39.7 1.0
SG L:CYS98 4.4 43.3 1.0
OE1 L:GLU71 4.5 39.7 1.0
CA L:CYS74 4.5 35.7 1.0
CA L:CYS98 4.7 43.3 1.0
CB L:VAL78 4.9 30.9 1.0
CB L:ALA75 4.9 32.4 1.0
O L:GLU71 4.9 39.7 1.0
C L:PHE97 4.9 46.3 1.0
CB L:CYS98 5.0 43.3 1.0

Sodium binding site 5 out of 24 in 8szz

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Sodium binding site 5 out of 24 in the Cryoem Structure of Computationally Designed Nanocage O32-ZL4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Cryoem Structure of Computationally Designed Nanocage O32-ZL4 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Na301

b:30.0
occ:1.00
 SG M:CYS74 2.6 35.2 1.0
OE2 M:GLU71 3.4 39.2 1.0
CB M:CYS74 3.7 35.2 1.0
CG M:LYS101 3.8 46.3 1.0
C M:CYS74 4.0 35.2 1.0
N M:ALA75 4.0 31.0 1.0
O M:CYS74 4.1 35.2 1.0
O M:PHE97 4.2 46.6 1.0
CD M:GLU71 4.2 39.2 1.0
SG M:CYS98 4.4 44.4 1.0
OE1 M:GLU71 4.4 39.2 1.0
CA M:ALA75 4.4 31.0 1.0
CG2 M:VAL78 4.4 29.7 1.0
CA M:CYS74 4.5 35.2 1.0
CA M:CYS98 4.6 44.4 1.0
CB M:LYS101 4.6 46.3 1.0
CB M:CYS98 4.8 44.4 1.0
O M:GLU71 4.9 39.2 1.0
C M:PHE97 4.9 46.6 1.0
CD M:LYS101 4.9 46.3 1.0
CE M:LYS101 4.9 46.3 1.0
CB M:ALA75 5.0 31.0 1.0

Sodium binding site 6 out of 24 in 8szz

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Sodium binding site 6 out of 24 in the Cryoem Structure of Computationally Designed Nanocage O32-ZL4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Cryoem Structure of Computationally Designed Nanocage O32-ZL4 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na301

b:30.0
occ:1.00
 SG N:CYS74 2.7 34.1 1.0
OE2 N:GLU71 3.1 37.4 1.0
CB N:CYS74 3.9 34.1 1.0
CD N:GLU71 4.1 37.4 1.0
O N:PHE97 4.2 44.5 1.0
C N:CYS74 4.2 34.1 1.0
N N:ALA75 4.2 30.6 1.0
CG N:LYS101 4.2 43.0 1.0
O N:CYS74 4.3 34.1 1.0
SG N:CYS98 4.4 43.3 1.0
OE1 N:GLU71 4.5 37.4 1.0
CA N:ALA75 4.5 30.6 1.0
CG2 N:VAL78 4.5 29.2 1.0
CB N:LYS101 4.6 43.0 1.0
CA N:CYS74 4.7 34.1 1.0
C N:PHE97 4.8 44.5 1.0
O N:GLU71 4.9 37.4 1.0
CA N:CYS98 5.0 43.3 1.0
CG2 N:VAL103 5.0 35.4 1.0

Sodium binding site 7 out of 24 in 8szz

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Sodium binding site 7 out of 24 in the Cryoem Structure of Computationally Designed Nanocage O32-ZL4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Cryoem Structure of Computationally Designed Nanocage O32-ZL4 within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Na301

b:30.0
occ:1.00
 SG O:CYS74 2.7 34.5 1.0
OE2 O:GLU71 3.3 38.8 1.0
CB O:CYS74 3.9 34.5 1.0
C O:CYS74 4.0 34.5 1.0
O O:CYS74 4.1 34.5 1.0
N O:ALA75 4.1 31.9 1.0
CG O:LYS101 4.2 44.2 1.0
SG O:CYS98 4.3 42.8 1.0
CG2 O:VAL78 4.3 30.6 1.0
CA O:ALA75 4.3 31.9 1.0
CD O:GLU71 4.4 38.8 1.0
O O:PHE97 4.5 45.4 1.0
CB O:LYS101 4.5 44.2 1.0
CA O:CYS74 4.6 34.5 1.0
CA O:CYS98 4.8 42.8 1.0
CB O:VAL78 4.8 30.6 1.0
OE1 O:GLU71 4.8 38.8 1.0
CB O:ALA75 5.0 31.9 1.0
C O:PHE97 5.0 45.4 1.0

Sodium binding site 8 out of 24 in 8szz

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Sodium binding site 8 out of 24 in the Cryoem Structure of Computationally Designed Nanocage O32-ZL4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Cryoem Structure of Computationally Designed Nanocage O32-ZL4 within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Na301

b:30.0
occ:1.00
 SG U:CYS74 3.1 35.0 1.0
OE2 U:GLU71 3.3 38.4 1.0
CB U:CYS74 3.9 35.0 1.0
C U:CYS74 4.0 35.0 1.0
O U:CYS74 4.1 35.0 1.0
N U:ALA75 4.1 32.1 1.0
CG2 U:VAL78 4.3 30.4 1.0
CA U:ALA75 4.3 32.1 1.0
CD U:GLU71 4.4 38.4 1.0
SG U:CYS98 4.6 42.9 1.0
CA U:CYS74 4.6 35.0 1.0
CG U:LYS101 4.7 43.4 1.0
OE1 U:GLU71 4.7 38.4 1.0
CB U:LYS101 4.7 43.4 1.0
CB U:VAL78 4.8 30.4 1.0
O U:PHE97 4.9 45.0 1.0
CB U:ALA75 5.0 32.1 1.0
CG2 U:VAL103 5.0 36.7 1.0

Sodium binding site 9 out of 24 in 8szz

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Sodium binding site 9 out of 24 in the Cryoem Structure of Computationally Designed Nanocage O32-ZL4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Cryoem Structure of Computationally Designed Nanocage O32-ZL4 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Na301

b:30.0
occ:1.00
 SG Y:CYS74 2.8 35.7 1.0
OE2 Y:GLU71 3.3 39.6 1.0
CB Y:CYS74 3.8 35.7 1.0
C Y:CYS74 3.9 35.7 1.0
O Y:PHE97 3.9 47.4 1.0
O Y:CYS74 4.0 35.7 1.0
N Y:ALA75 4.0 33.3 1.0
CG2 Y:VAL78 4.2 31.8 1.0
CA Y:ALA75 4.3 33.3 1.0
SG Y:CYS98 4.3 45.0 1.0
CD Y:LYS101 4.4 45.0 1.0
CD Y:GLU71 4.5 39.6 1.0
CA Y:CYS74 4.5 35.7 1.0
CB Y:VAL78 4.9 31.8 1.0
NZ Y:LYS101 4.9 45.0 1.0
O Y:GLU71 4.9 39.6 1.0
OE1 Y:GLU71 5.0 39.6 1.0
CA Y:CYS98 5.0 45.0 1.0
C Y:PHE97 5.0 47.4 1.0

Sodium binding site 10 out of 24 in 8szz

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Sodium binding site 10 out of 24 in the Cryoem Structure of Computationally Designed Nanocage O32-ZL4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Cryoem Structure of Computationally Designed Nanocage O32-ZL4 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Na301

b:30.0
occ:1.00
 SG Z:CYS74 3.0 34.8 1.0
CG Z:LYS101 3.1 43.1 1.0
OE2 Z:GLU71 3.3 37.6 1.0
CB Z:CYS74 3.7 34.8 1.0
O Z:PHE97 3.9 45.0 1.0
CE Z:LYS101 4.0 43.1 1.0
CD Z:LYS101 4.0 43.1 1.0
C Z:CYS74 4.1 34.8 1.0
CB Z:LYS101 4.1 43.1 1.0
N Z:ALA75 4.1 31.9 1.0
CD Z:GLU71 4.2 37.6 1.0
SG Z:CYS98 4.2 42.3 1.0
O Z:CYS74 4.2 34.8 1.0
OE1 Z:GLU71 4.3 37.6 1.0
CA Z:ALA75 4.5 31.9 1.0
CG2 Z:VAL78 4.5 30.4 1.0
CA Z:CYS74 4.6 34.8 1.0
CA Z:CYS98 4.6 42.3 1.0
C Z:PHE97 4.7 45.0 1.0
O Z:GLU71 4.9 37.6 1.0
CB Z:CYS98 5.0 42.3 1.0

Reference:

Z.Li, S.Wang, U.Nattermann, A.K.Bera, A.J.Borst, M.Y.Yaman, M.J.Bick, E.C.Yang, W.Sheffler, B.Lee, S.Seifert, G.L.Hura, H.Nguyen, A.Kang, R.Dalal, J.M.Lubner, Y.Hsia, H.Haddox, A.Courbet, Q.Dowling, M.Miranda, A.Favor, A.Etemadi, N.I.Edman, W.Yang, C.Weidle, B.Sankaran, B.Negahdari, M.B.Ross, D.S.Ginger, D.Baker. Accurate Computational Design of Three-Dimensional Protein Crystals. Nat Mater 2023.
ISSN: ISSN 1476-4660
PubMed: 37845322
DOI: 10.1038/S41563-023-01683-1
Page generated: Mon Aug 18 15:40:21 2025

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