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Sodium in PDB 7rga: Crystal Structure of NANOCLAMP3:Vhh in Complex with Mtx

Protein crystallography data

The structure of Crystal Structure of NANOCLAMP3:Vhh in Complex with Mtx, PDB code: 7rga was solved by Z.Guo, K.Alexandrov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.38 / 2.90
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 173.2, 143.969, 181.814, 90, 94.34, 90
R / Rfree (%) 19.5 / 24.2

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of NANOCLAMP3:Vhh in Complex with Mtx (pdb code 7rga). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 14 binding sites of Sodium where determined in the Crystal Structure of NANOCLAMP3:Vhh in Complex with Mtx, PDB code: 7rga:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in 7rga

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Sodium binding site 1 out of 14 in the Crystal Structure of NANOCLAMP3:Vhh in Complex with Mtx


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of NANOCLAMP3:Vhh in Complex with Mtx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:63.6
occ:1.00
 O A:ASP24 2.0 75.9 1.0
OG1 A:THR27 2.1 69.4 1.0
O A:ASN19 2.5 64.6 1.0
O A:THR27 2.5 68.3 1.0
O A:SER133 2.6 61.8 1.0
OD1 A:ASP22 3.0 74.7 1.0
C A:ASP24 3.1 76.2 1.0
OE1 A:GLU134 3.3 74.5 1.0
CB A:THR27 3.5 70.4 1.0
C A:THR27 3.5 68.5 1.0
C A:ASN19 3.6 64.7 1.0
C A:SER133 3.6 59.8 1.0
N A:THR27 3.6 72.1 1.0
CG A:ASP22 3.7 72.9 1.0
OD2 A:ASP22 3.7 77.4 1.0
CA A:THR27 3.8 70.0 1.0
CA A:ASP24 4.0 76.4 1.0
N A:ASP24 4.0 75.5 1.0
N A:ASP25 4.0 76.4 1.0
N A:ASN26 4.2 75.2 1.0
CA A:ASP25 4.2 75.8 1.0
C A:ASP25 4.3 75.6 1.0
CA A:SER133 4.4 57.4 1.0
CG2 A:THR27 4.4 70.0 1.0
CA A:ASN19 4.4 64.3 1.0
CB A:GLU134 4.5 64.8 1.0
CD A:GLU134 4.5 75.1 1.0
CB A:SER133 4.5 57.0 1.0
CA A:GLU134 4.5 64.1 1.0
N A:GLU134 4.5 61.7 1.0
CB A:ASN19 4.6 64.1 1.0
N A:LEU20 4.6 64.1 1.0
CB A:ASP24 4.6 77.5 1.0
N A:GLY28 4.7 65.7 1.0
CA A:LEU20 4.7 64.0 1.0
C A:ASN26 4.8 74.0 1.0
CG A:ASP24 4.9 81.3 1.0
O A:ASP25 4.9 74.9 1.0
OD1 A:ASP24 5.0 84.2 1.0
CG A:GLU134 5.0 69.2 1.0

Sodium binding site 2 out of 14 in 7rga

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Sodium binding site 2 out of 14 in the Crystal Structure of NANOCLAMP3:Vhh in Complex with Mtx


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of NANOCLAMP3:Vhh in Complex with Mtx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:69.1
occ:1.00
 O A:GLY284 2.6 59.5 1.0
OD1 A:ASP274 2.8 65.2 1.0
OD2 A:ASP286 3.3 70.4 1.0
O A:HOH402 3.5 66.7 1.0
OG1 A:THR278 3.5 60.2 1.0
C A:GLY284 3.6 59.1 1.0
OD1 A:ASP286 3.9 69.2 1.0
CG A:ASP286 4.0 64.5 1.0
CG A:ASP274 4.0 66.1 1.0
CA A:GLY284 4.3 60.5 1.0
N A:ASP274 4.5 62.2 1.0
OD2 A:ASP274 4.6 71.0 1.0
N A:PRO285 4.6 57.4 1.0
CB A:ASN275 4.7 62.5 1.0
CB A:THR278 4.7 60.9 1.0
CB A:ASP273 4.8 30.0 1.0
N A:ASN275 4.8 61.8 1.0
C A:PRO285 5.0 56.2 1.0

Sodium binding site 3 out of 14 in 7rga

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Sodium binding site 3 out of 14 in the Crystal Structure of NANOCLAMP3:Vhh in Complex with Mtx


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of NANOCLAMP3:Vhh in Complex with Mtx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:87.5
occ:1.00
 O B:ASN19 2.0 74.2 1.0
O B:SER133 2.3 66.2 1.0
OG1 B:THR27 2.3 77.7 1.0
O B:ASP24 2.4 81.7 1.0
O B:THR27 2.4 77.2 1.0
OD1 B:ASP22 2.6 85.1 1.0
C B:ASN19 3.0 74.8 1.0
C B:THR27 3.3 77.2 1.0
C B:SER133 3.5 64.8 1.0
OE1 B:GLU134 3.5 84.3 1.0
C B:ASP24 3.5 82.5 1.0
CG B:ASP22 3.5 83.5 1.0
CB B:THR27 3.6 79.2 1.0
CA B:ASN19 3.9 75.8 1.0
OD2 B:ASP22 3.9 83.2 1.0
CA B:THR27 3.9 78.6 1.0
CB B:ASN19 4.0 76.1 1.0
N B:LEU20 4.0 74.5 1.0
N B:ASP24 4.2 82.6 1.0
N B:THR27 4.2 80.2 1.0
CA B:ASP24 4.3 83.1 1.0
CA B:LEU20 4.3 74.2 1.0
CB B:GLU134 4.3 67.7 1.0
CA B:GLU134 4.3 67.0 1.0
O B:LEU20 4.4 77.0 1.0
N B:GLY28 4.4 75.5 1.0
N B:GLU134 4.4 65.4 1.0
CA B:SER133 4.4 63.1 1.0
C B:LEU20 4.4 75.8 1.0
CD B:GLU134 4.6 82.5 1.0
N B:ASP25 4.6 83.0 1.0
CA B:GLY28 4.7 73.2 1.0
CG2 B:THR27 4.7 80.8 1.0
N B:ASP22 4.7 78.9 1.0
CB B:ASP24 4.7 83.7 1.0
CB B:ASP22 4.8 81.8 1.0
CA B:ASP25 4.9 82.8 1.0
CB B:SER133 4.9 62.4 1.0

Sodium binding site 4 out of 14 in 7rga

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Sodium binding site 4 out of 14 in the Crystal Structure of NANOCLAMP3:Vhh in Complex with Mtx


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of NANOCLAMP3:Vhh in Complex with Mtx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na303

b:79.2
occ:1.00
 O B:PRO285 2.8 62.2 1.0
NE1 B:TRP288 3.0 58.0 1.0
O B:ARG282 3.1 70.0 1.0
C B:PRO285 3.7 61.9 1.0
CA B:SER283 3.9 69.8 1.0
C B:SER283 3.9 69.5 1.0
CE2 B:TRP288 3.9 54.1 1.0
CB B:PRO285 4.0 61.5 1.0
CD1 B:TRP288 4.0 54.9 1.0
O B:SER283 4.0 70.7 1.0
NH1 B:ARG282 4.1 89.0 1.0
CZ2 B:TRP288 4.2 55.4 1.0
N B:PRO285 4.2 63.5 1.0
C B:ARG282 4.2 69.1 1.0
CA B:PRO285 4.2 62.0 1.0
N B:GLY284 4.5 67.6 1.0
N B:SER283 4.5 69.3 1.0
CD B:PRO285 4.6 63.8 1.0
C B:GLY284 4.6 65.5 1.0
CG B:PRO285 4.7 60.5 1.0
N B:ASP286 4.7 60.9 1.0
CZ B:ARG282 4.9 89.2 1.0
O B:GLY284 5.0 67.6 1.0
CB B:SER283 5.0 70.2 1.0

Sodium binding site 5 out of 14 in 7rga

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Sodium binding site 5 out of 14 in the Crystal Structure of NANOCLAMP3:Vhh in Complex with Mtx


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of NANOCLAMP3:Vhh in Complex with Mtx within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na302

b:63.9
occ:1.00
 O C:SER133 2.3 71.5 1.0
O C:ASN19 2.3 70.7 1.0
O C:ASP24 2.4 78.8 1.0
OG1 C:THR27 2.5 71.3 1.0
O C:THR27 2.7 70.0 1.0
C C:SER133 3.3 70.2 1.0
OD1 C:ASP22 3.3 76.2 1.0
C C:THR27 3.4 70.7 1.0
OE1 C:GLU134 3.4 90.3 1.0
C C:ASN19 3.4 70.6 1.0
C C:ASP24 3.6 79.2 1.0
CB C:THR27 3.7 72.9 1.0
CA C:THR27 3.9 72.4 1.0
CB C:GLU134 3.9 74.7 1.0
CG C:ASP22 3.9 77.2 1.0
N C:THR27 4.0 74.7 1.0
CA C:GLU134 4.0 73.0 1.0
OD2 C:ASP22 4.1 77.8 1.0
N C:GLU134 4.1 71.1 1.0
CA C:SER133 4.2 68.4 1.0
CA C:LEU20 4.2 70.4 1.0
N C:ASP24 4.2 80.3 1.0
N C:LEU20 4.3 70.5 1.0
CA C:ASP24 4.3 80.5 1.0
N C:GLY28 4.3 68.8 1.0
CA C:ASN19 4.4 71.0 1.0
CB C:ASN19 4.5 71.2 1.0
CD C:GLU134 4.5 89.1 1.0
CB C:ASP24 4.5 80.9 1.0
CB C:SER133 4.6 68.7 1.0
C C:LEU20 4.7 71.5 1.0
N C:ASP25 4.7 78.8 1.0
CA C:ASP25 4.8 78.0 1.0
CG2 C:THR27 4.8 73.3 1.0
CA C:GLY28 4.8 65.9 1.0
CG C:GLU134 4.8 80.5 1.0
C C:ASP25 4.9 77.8 1.0
O C:LEU20 4.9 72.2 1.0
N C:ASN26 4.9 77.9 1.0
N C:ASP22 4.9 76.6 1.0

Sodium binding site 6 out of 14 in 7rga

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Sodium binding site 6 out of 14 in the Crystal Structure of NANOCLAMP3:Vhh in Complex with Mtx


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of NANOCLAMP3:Vhh in Complex with Mtx within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na303

b:55.3
occ:1.00
 OD1 C:ASP273 2.5 66.9 1.0
O C:GLY284 2.8 55.5 1.0
OD1 C:ASP286 2.8 64.6 1.0
OD1 C:ASP274 2.8 66.1 1.0
CG C:ASP273 3.5 60.9 1.0
CG C:ASP286 3.6 62.2 1.0
OD2 C:ASP286 3.6 64.2 1.0
OD2 C:ASP273 3.9 58.3 1.0
OG1 C:THR278 3.9 57.3 1.0
C C:GLY284 4.0 54.6 1.0
CG C:ASP274 4.0 63.1 1.0
N C:ASP274 4.4 59.1 1.0
CA C:GLY284 4.6 55.2 1.0
OD2 C:ASP274 4.6 66.1 1.0
N C:ASN275 4.6 57.5 1.0
CB C:ASN275 4.8 58.8 1.0
CB C:ASP273 4.8 57.7 1.0
CA C:ASP273 4.9 57.7 1.0
N C:ASP286 4.9 55.1 1.0
CB C:ASP286 5.0 57.6 1.0

Sodium binding site 7 out of 14 in 7rga

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Sodium binding site 7 out of 14 in the Crystal Structure of NANOCLAMP3:Vhh in Complex with Mtx


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of NANOCLAMP3:Vhh in Complex with Mtx within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na302

b:52.8
occ:1.00
 O D:THR27 2.2 77.2 1.0
O D:ASN19 2.3 76.8 1.0
O D:ASP24 2.3 83.2 1.0
OG1 D:THR27 2.4 79.4 1.0
O D:SER133 2.6 65.6 1.0
OD1 D:ASP22 2.9 84.0 1.0
C D:THR27 3.3 77.3 1.0
OE1 D:GLU134 3.3 76.6 1.0
C D:ASN19 3.4 76.2 1.0
OD2 D:ASP22 3.4 86.7 1.0
CG D:ASP22 3.5 84.2 1.0
C D:ASP24 3.5 83.5 1.0
CB D:THR27 3.6 80.0 1.0
C D:SER133 3.8 64.7 1.0
CA D:THR27 3.9 79.4 1.0
N D:THR27 4.0 81.6 1.0
N D:ASP24 4.1 84.3 1.0
CA D:ASN19 4.1 77.2 1.0
CA D:ASP24 4.2 84.9 1.0
CB D:ASP24 4.3 86.2 1.0
N D:LEU20 4.3 74.8 1.0
CB D:ASN19 4.3 77.4 1.0
N D:GLY28 4.4 75.0 1.0
CB D:GLU134 4.4 68.2 1.0
CA D:LEU20 4.5 73.7 1.0
CD D:GLU134 4.6 78.8 1.0
N D:ASP25 4.6 82.6 1.0
CA D:GLU134 4.6 66.7 1.0
CA D:SER133 4.6 63.8 1.0
CA D:ASP25 4.7 81.7 1.0
CA D:GLY28 4.7 71.1 1.0
N D:GLU134 4.7 65.2 1.0
CG2 D:THR27 4.7 81.8 1.0
C D:ASP25 4.7 82.0 1.0
C D:LEU20 4.9 74.8 1.0
N D:ASN26 4.9 83.2 1.0
N D:ASP22 4.9 80.7 1.0
CB D:ASP22 4.9 83.4 1.0
CG D:ASP24 4.9 88.6 1.0

Sodium binding site 8 out of 14 in 7rga

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Sodium binding site 8 out of 14 in the Crystal Structure of NANOCLAMP3:Vhh in Complex with Mtx


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of NANOCLAMP3:Vhh in Complex with Mtx within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na303

b:74.3
occ:1.00
 O D:GLY284 3.0 72.7 1.0
OD2 D:ASP274 3.0 79.1 1.0
OD1 D:ASP273 3.2 77.4 1.0
OD1 D:ASP286 3.3 73.0 1.0
OD2 D:ASP273 3.7 72.7 1.0
CG D:ASP273 3.8 71.7 1.0
OD2 D:ASP286 3.8 71.8 1.0
CG D:ASP286 3.9 72.5 1.0
CG D:ASP274 3.9 75.5 1.0
OG1 D:THR278 3.9 71.2 1.0
C D:GLY284 4.0 70.8 1.0
OD1 D:ASP274 4.1 79.4 1.0
CA D:GLY284 4.4 70.9 1.0
N D:ASP274 4.8 69.0 1.0

Sodium binding site 9 out of 14 in 7rga

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Sodium binding site 9 out of 14 in the Crystal Structure of NANOCLAMP3:Vhh in Complex with Mtx


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of NANOCLAMP3:Vhh in Complex with Mtx within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na302

b:77.8
occ:1.00
 O E:ASP24 2.2 82.8 1.0
O E:SER133 2.2 68.7 1.0
O E:ASN19 2.3 71.1 1.0
OG1 E:THR27 2.5 74.8 1.0
OD1 E:ASP22 2.6 86.9 1.0
O E:THR27 3.1 73.1 1.0
C E:ASP24 3.3 82.8 1.0
C E:SER133 3.4 69.2 1.0
C E:ASN19 3.5 71.0 1.0
C E:THR27 3.5 73.3 1.0
OE1 E:GLU134 3.6 85.6 1.0
CB E:THR27 3.7 75.8 1.0
CG E:ASP22 3.8 85.4 1.0
N E:ASP24 3.9 82.8 1.0
N E:THR27 3.9 77.3 1.0
CA E:ASP24 4.0 83.7 1.0
CA E:THR27 4.0 75.0 1.0
CB E:GLU134 4.0 72.6 1.0
CA E:GLU134 4.2 71.4 1.0
CB E:ASP24 4.2 84.3 1.0
N E:GLU134 4.2 70.2 1.0
N E:GLY28 4.3 71.2 1.0
N E:ASP25 4.3 82.1 1.0
OD2 E:ASP22 4.3 85.3 1.0
CA E:ASN19 4.4 71.4 1.0
CA E:SER133 4.5 68.3 1.0
N E:LEU20 4.5 71.0 1.0
CA E:LEU20 4.5 70.9 1.0
CA E:ASP25 4.5 81.3 1.0
N E:ASP22 4.6 78.5 1.0
C E:LEU20 4.6 72.0 1.0
C E:ASP25 4.6 81.0 1.0
CD E:GLU134 4.6 84.0 1.0
CB E:ASN19 4.6 71.2 1.0
N E:ASN26 4.8 80.8 1.0
O E:LEU20 4.8 71.3 1.0
CB E:SER133 4.8 67.9 1.0
CA E:GLY28 4.8 69.7 1.0
CG E:GLU134 4.9 78.2 1.0
CG2 E:THR27 4.9 75.4 1.0
N E:GLY23 4.9 81.5 1.0
N E:LEU21 5.0 74.2 1.0

Sodium binding site 10 out of 14 in 7rga

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Sodium binding site 10 out of 14 in the Crystal Structure of NANOCLAMP3:Vhh in Complex with Mtx


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of NANOCLAMP3:Vhh in Complex with Mtx within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na303

b:76.1
occ:1.00
 O E:GLY284 2.4 79.6 1.0
OD1 E:ASP273 2.6 75.0 1.0
OD1 E:ASP274 2.7 82.2 1.0
OD1 E:ASP286 2.8 80.6 1.0
C E:GLY284 3.6 79.0 1.0
CG E:ASP286 3.6 78.3 1.0
CG E:ASP273 3.7 74.9 1.0
OD2 E:ASP286 3.7 82.2 1.0
CG E:ASP274 3.8 78.8 1.0
OD2 E:ASP273 4.1 78.1 1.0
OG1 E:THR278 4.2 77.0 1.0
OD2 E:ASP274 4.3 83.4 1.0
CA E:GLY284 4.3 79.9 1.0
N E:ASP274 4.5 73.2 1.0
N E:PRO285 4.6 77.5 1.0
C E:PRO285 4.9 75.4 1.0
CB E:ASP273 4.9 73.0 1.0
CA E:PRO285 4.9 75.9 1.0
N E:ASP286 4.9 74.5 1.0
N E:ASN275 4.9 75.1 1.0
CA E:ASP273 5.0 72.4 1.0

Reference:

Z.Guo, O.Smutok, W.A.Johnston, P.Walden, J.P.J.Ungerer, T.S.Peat, J.Newman, J.Parker, T.Nebl, C.Hepburn, A.Melman, R.J.Suderman, E.Katz, K.Alexandrov. Design of A Methotrexate-Controlled Chemical Dimerization System and Its Use in Bio-Electronic Devices. Nat Commun V. 12 7137 2021.
ISSN: ESSN 2041-1723
PubMed: 34880210
DOI: 10.1038/S41467-021-27184-W
Page generated: Fri Apr 7 15:57:59 2023

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