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Sodium in PDB 7u64: Crystal Structure of Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl

Protein crystallography data

The structure of Crystal Structure of Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl, PDB code: 7u64 was solved by J.V.Rodarte, M.P.Pancera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.33 / 1.75
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 218.139, 218.139, 89.023, 90, 90, 120
R / Rfree (%) 19.7 / 22.5

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 Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl (pdb code 7u64). 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 Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl, PDB code: 7u64:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in 7u64

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Sodium binding site 1 out of 14 in the Crystal Structure of Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl


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 Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na301

b:22.0
occ:1.00
 O D:ASN138 2.3 20.3 1.0
O D:ALA112 2.3 19.2 1.0
O D:HOH488 2.6 35.0 1.0
O D:HOH461 2.6 34.4 1.0
O D:ASN137 3.3 21.2 1.0
C D:ASN138 3.4 22.1 1.0
C D:ALA112 3.6 20.2 1.0
CB D:ASN138 3.9 23.2 1.0
N D:SER114 4.0 21.3 1.0
CA D:PRO113 4.0 19.7 1.0
CA D:ASN138 4.2 21.9 1.0
C D:PRO113 4.2 25.6 1.0
N D:PRO113 4.3 18.4 1.0
C D:ASN137 4.3 22.5 1.0
N D:PHE139 4.4 19.9 1.0
OG D:SER114 4.4 29.7 1.0
CA D:PHE139 4.5 18.4 1.0
N D:ALA112 4.5 16.6 1.0
CA D:ALA112 4.7 20.6 1.0
C D:ALA111 4.7 18.1 1.0
CB D:ALA111 4.7 20.7 1.0
O D:HOH457 4.7 29.5 1.0
N D:ASN138 4.7 18.7 1.0
O D:ALA111 4.9 16.5 1.0
CB D:PHE139 4.9 19.9 1.0

Sodium binding site 2 out of 14 in 7u64

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Sodium binding site 2 out of 14 in the Crystal Structure of Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl


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 Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na302

b:20.3
occ:1.00
 O E:HOH538 2.3 26.7 1.0
OG E:SER82B 2.3 14.9 1.0
O E:HOH424 2.4 11.8 1.0
O E:HOH556 2.5 24.4 1.0
CB E:SER82B 3.5 14.7 1.0
O E:HOH504 4.0 27.9 1.0
O E:HOH562 4.2 44.1 1.0
CA E:SER82B 4.2 8.0 1.0
O E:HOH569 4.5 31.6 1.0
O E:SER15 4.6 11.7 1.0
N E:SER82B 4.6 7.6 1.0

Sodium binding site 3 out of 14 in 7u64

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Sodium binding site 3 out of 14 in the Crystal Structure of Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl


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 Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na301

b:11.3
occ:1.00
 O F:ASN138 2.2 11.0 1.0
OXT F:ACT302 2.3 14.6 1.0
O F:ALA112 2.3 11.0 1.0
O F:HOH516 2.4 26.1 1.0
O F:HOH425 2.7 26.8 1.0
O F:ASN137 3.1 11.7 1.0
C F:ASN138 3.3 10.5 1.0
C F:ACT302 3.3 15.3 1.0
C F:ALA112 3.5 7.7 1.0
CH3 F:ACT302 3.8 13.7 1.0
O F:HOH527 3.8 33.9 1.0
N F:SER114 3.8 12.0 1.0
CB F:ASN138 3.8 8.0 1.0
CA F:PRO113 3.9 9.6 1.0
CA F:ASN138 4.1 7.6 1.0
C F:PRO113 4.1 11.8 1.0
C F:ASN137 4.2 13.9 1.0
OG F:SER114 4.2 23.9 1.0
N F:PRO113 4.2 7.8 1.0
N F:PHE139 4.3 9.6 1.0
O F:ACT302 4.4 11.7 1.0
CA F:PHE139 4.5 8.2 1.0
N F:ALA112 4.5 8.2 1.0
O F:HOH543 4.6 30.2 1.0
N F:ASN138 4.6 8.7 1.0
CA F:ALA112 4.6 8.4 1.0
O F:HOH512 4.7 21.5 1.0
C F:ALA111 4.7 10.8 1.0
CB F:ALA111 4.7 8.2 1.0
CB F:PHE139 4.9 8.5 1.0
CB F:SER114 4.9 16.2 1.0
CA F:SER114 4.9 10.1 1.0
O F:PRO113 4.9 14.8 1.0

Sodium binding site 4 out of 14 in 7u64

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Sodium binding site 4 out of 14 in the Crystal Structure of Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl


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 Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na301

b:29.3
occ:1.00
 O H:LEU201 2.3 23.1 1.0
O H:HIS198 2.3 17.5 1.0
O H:HOH462 2.3 33.7 1.0
O H:HOH495 2.4 24.6 1.0
O H:HOH512 2.4 38.4 1.0
O H:HOH499 2.6 36.6 1.0
C H:HIS198 3.3 19.5 1.0
C H:LEU201 3.4 25.3 1.0
O H:HOH516 3.6 35.0 1.0
N H:HIS198 3.9 14.5 1.0
N H:LEU201 4.0 16.6 1.0
CA H:LEU201 4.1 20.4 1.0
N H:GLN199 4.1 15.1 1.0
CB H:LEU201 4.1 18.5 1.0
O H:GLN199 4.1 19.2 1.0
CA H:GLN199 4.1 21.8 1.0
C H:GLN199 4.2 24.9 1.0
CA H:HIS198 4.2 17.0 1.0
C H:SER202 4.5 30.0 1.0
N H:SER202 4.5 27.0 1.0
CG2 H:THR197 4.6 28.3 1.0
N H:SER203 4.6 27.1 1.0
O H:SER202 4.7 32.4 1.0
CA H:SER202 4.7 28.3 1.0
N H:GLY200 4.8 17.2 1.0
O H:HOH518 5.0 41.8 1.0
C H:THR197 5.0 19.6 1.0

Sodium binding site 5 out of 14 in 7u64

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Sodium binding site 5 out of 14 in the Crystal Structure of Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl


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 Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na302

b:33.4
occ:1.00
 O H:GLY101 2.3 17.5 1.0
O H:GLN6 2.6 25.0 1.0
O H:HOH450 2.7 38.5 1.0
O H:ALA8 2.8 22.8 1.0
C H:GLY101 3.5 17.5 1.0
C H:ALA8 3.6 25.3 1.0
C H:GLN6 3.7 20.4 1.0
CB H:GLN6 3.9 19.1 1.0
C H:GLY100 4.0 19.4 1.0
CA H:PHE9 4.0 22.1 1.0
N H:GLY101 4.0 15.4 1.0
OG1 H:THR102 4.1 16.6 1.0
N H:PHE9 4.1 20.2 1.0
O H:GLY100 4.2 20.3 1.0
O H:HOH496 4.3 23.4 1.0
CA H:GLY101 4.4 17.4 1.0
CA H:GLN6 4.4 18.9 1.0
N H:ALA8 4.4 26.6 1.0
C H:ALA7 4.4 28.9 1.0
CA H:GLY100 4.4 16.4 1.0
N H:THR102 4.5 18.8 1.0
CD1 H:PHE9 4.5 44.7 1.0
O H:ALA7 4.5 35.8 1.0
O H:HOH520 4.6 47.4 1.0
CA H:THR102 4.6 14.7 1.0
O H:HOH487 4.6 35.8 1.0
CA H:ALA8 4.6 21.8 1.0
N H:ALA7 4.8 24.2 1.0
CG H:PHE9 4.8 43.9 1.0
N H:GLY100 4.9 15.4 1.0
C H:PHE9 4.9 23.6 1.0
CE1 H:PHE9 5.0 43.3 1.0
CB H:PHE9 5.0 22.0 1.0
CA H:ALA7 5.0 35.0 1.0
O H:PHE9 5.0 18.5 1.0

Sodium binding site 6 out of 14 in 7u64

Go back to Sodium Binding Sites List in 7u64
Sodium binding site 6 out of 14 in the Crystal Structure of Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl


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 Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na303

b:16.0
occ:1.00
 O H:ACT304 2.3 18.7 1.0
O H:ASN138 2.3 14.1 1.0
O H:ALA112 2.3 13.9 1.0
O H:HOH501 2.3 30.3 1.0
O H:HOH467 2.5 28.0 1.0
O H:ASN137 3.3 16.3 1.0
C H:ACT304 3.3 17.2 1.0
C H:ASN138 3.4 13.7 1.0
C H:ALA112 3.5 14.8 1.0
CH3 H:ACT304 3.7 12.1 1.0
N H:SER114 3.9 17.3 1.0
CB H:ASN138 3.9 16.4 1.0
CA H:PRO113 4.0 14.0 1.0
C H:PRO113 4.2 20.0 1.0
CA H:ASN138 4.2 11.2 1.0
N H:PRO113 4.2 13.4 1.0
OG H:SER114 4.3 26.5 1.0
C H:ASN137 4.3 14.4 1.0
N H:PHE139 4.4 14.1 1.0
OXT H:ACT304 4.5 16.3 1.0
N H:ALA112 4.5 10.5 1.0
CA H:PHE139 4.5 12.0 1.0
CA H:ALA112 4.6 13.9 1.0
C H:ALA111 4.7 12.1 1.0
N H:ASN138 4.7 12.0 1.0
CB H:ALA111 4.8 13.0 1.0
O H:HOH477 4.8 25.8 1.0
O H:ALA111 4.9 12.8 1.0
CB H:PHE139 4.9 12.4 1.0
CB H:SER114 5.0 22.2 1.0
O H:PRO113 5.0 19.1 1.0
CA H:SER114 5.0 18.7 1.0

Sodium binding site 7 out of 14 in 7u64

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Sodium binding site 7 out of 14 in the Crystal Structure of Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl


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 Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na301

b:26.3
occ:1.00
 O J:LEU201 2.2 19.2 1.0
O J:HOH511 2.3 26.7 1.0
O J:HIS198 2.4 14.8 1.0
O J:HOH538 2.5 31.7 1.0
O J:HOH535 2.5 30.1 1.0
O J:HOH528 2.5 21.1 1.0
C J:LEU201 3.3 12.6 1.0
C J:HIS198 3.4 14.0 1.0
O J:HOH539 3.7 32.4 1.0
N J:LEU201 4.0 14.4 1.0
N J:HIS198 4.0 9.4 1.0
CA J:LEU201 4.0 14.3 1.0
O J:GLN199 4.1 15.1 1.0
N J:GLN199 4.2 13.8 1.0
CA J:GLN199 4.2 15.4 1.0
CB J:LEU201 4.2 17.4 1.0
C J:GLN199 4.2 15.9 1.0
CA J:HIS198 4.3 12.6 1.0
N J:SER202 4.4 18.9 1.0
C J:SER202 4.5 25.0 1.0
CG2 J:THR197 4.6 24.6 1.0
CA J:SER202 4.6 27.4 1.0
N J:SER203 4.7 19.7 1.0
O J:SER202 4.8 25.4 1.0
N J:GLY200 4.9 13.0 1.0

Sodium binding site 8 out of 14 in 7u64

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Sodium binding site 8 out of 14 in the Crystal Structure of Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl


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 Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na302

b:14.1
occ:1.00
 O J:ASN138 2.2 12.2 1.0
OXT J:ACT303 2.3 13.8 1.0
O J:ALA112 2.3 11.1 1.0
O J:HOH510 2.4 23.3 1.0
O J:HOH437 2.7 29.0 1.0
O J:ASN137 3.1 11.7 1.0
C J:ASN138 3.3 9.5 1.0
C J:ACT303 3.4 15.6 1.0
C J:ALA112 3.5 11.8 1.0
N J:SER114 3.8 12.3 1.0
CH3 J:ACT303 3.8 13.6 1.0
CB J:ASN138 3.8 10.3 1.0
O J:HOH532 3.9 34.9 1.0
CA J:PRO113 3.9 8.5 1.0
CA J:ASN138 4.1 8.8 1.0
C J:PRO113 4.1 13.0 1.0
C J:ASN137 4.1 12.9 1.0
N J:PRO113 4.2 9.8 1.0
OG J:SER114 4.2 18.8 1.0
N J:PHE139 4.3 8.4 1.0
CA J:PHE139 4.5 10.1 1.0
O J:ACT303 4.5 11.4 1.0
N J:ASN138 4.5 10.9 1.0
N J:ALA112 4.6 9.0 1.0
CA J:ALA112 4.7 6.8 1.0
O J:HOH509 4.7 21.1 1.0
C J:ALA111 4.8 8.1 1.0
CB J:ALA111 4.8 9.4 1.0
CB J:PHE139 4.8 9.0 1.0
CB J:SER114 4.8 15.2 1.0
CA J:SER114 4.9 9.2 1.0
O J:PRO113 4.9 13.7 1.0

Sodium binding site 9 out of 14 in 7u64

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Sodium binding site 9 out of 14 in the Crystal Structure of Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl


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 Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Na302

b:20.3
occ:1.00
 O K:HOH554 2.3 29.8 1.0
OG K:SER82B 2.4 16.0 1.0
O K:HOH425 2.4 14.8 1.0
O K:HOH563 2.5 26.1 1.0
CB K:SER82B 3.6 17.8 1.0
O K:HOH516 4.2 29.0 1.0
CA K:SER82B 4.4 10.4 1.0
O K:SER15 4.6 13.2 1.0
N K:SER82B 4.8 8.5 1.0

Sodium binding site 10 out of 14 in 7u64

Go back to Sodium Binding Sites List in 7u64
Sodium binding site 10 out of 14 in the Crystal Structure of Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl


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 Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na301

b:13.4
occ:1.00
 O L:ASN138 2.2 11.1 1.0
O L:ALA112 2.3 11.1 1.0
O L:ACT302 2.3 13.2 1.0
O L:HOH517 2.4 24.2 1.0
O L:HOH437 2.8 32.5 1.0
O L:ASN137 3.1 13.5 1.0
C L:ASN138 3.2 10.5 1.0
C L:ACT302 3.3 13.4 1.0
C L:ALA112 3.5 9.8 1.0
CH3 L:ACT302 3.6 17.2 1.0
N L:SER114 3.8 12.6 1.0
CB L:ASN138 3.8 10.3 1.0
O L:HOH519 3.9 34.6 1.0
CA L:PRO113 3.9 9.8 1.0
CA L:ASN138 4.0 10.5 1.0
C L:PRO113 4.1 12.8 1.0
C L:ASN137 4.1 13.5 1.0
N L:PRO113 4.2 10.2 1.0
N L:PHE139 4.2 10.2 1.0
OG L:SER114 4.3 27.1 1.0
CA L:PHE139 4.4 9.8 1.0
N L:ALA112 4.5 10.1 1.0
OXT L:ACT302 4.5 11.3 1.0
N L:ASN138 4.5 11.7 1.0
O L:HOH511 4.6 24.4 1.0
CA L:ALA112 4.6 8.3 1.0
O L:HOH539 4.7 32.1 1.0
C L:ALA111 4.7 7.4 1.0
CB L:ALA111 4.8 11.3 1.0
CB L:SER114 4.9 16.7 1.0
CB L:PHE139 4.9 9.3 1.0
CA L:SER114 4.9 12.4 1.0
O L:PRO113 4.9 16.0 1.0
O L:HOH516 4.9 34.3 1.0

Reference:

J.V.Rodarte, C.Baehr, D.Hicks, T.L.Liban, C.Weidle, P.B.Rupert, R.Jahan, A.Wall, A.T.Mcguire, R.K.Strong, S.Runyon, M.Pravetoni, M.Pancera. Structures of Drug-Specific Monoclonal Antibodies Bound to Opioids and Nicotine Reveal A Common Mode of Binding. Structure 2022.
ISSN: ISSN 0969-2126
PubMed: 36513069
DOI: 10.1016/J.STR.2022.11.008
Page generated: Wed Oct 9 09:10:58 2024

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