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Sodium in PDB 7f35: Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin

Protein crystallography data

The structure of Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin, PDB code: 7f35 was solved by L.T.Wang, W.Y.Jiao, X.Shen, H.T.Lei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.64 / 2.60
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 184.071, 184.071, 100.66, 90, 90, 90
R / Rfree (%) 20 / 23.5

Other elements in 7f35:

The structure of Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin (pdb code 7f35). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin, PDB code: 7f35:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 7f35

Go back to Sodium Binding Sites List in 7f35
Sodium binding site 1 out of 8 in the Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin


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 S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:118.7
occ:1.00
 ND1 B:HIS167 3.6 89.6 1.0
OD1 A:ASP169 3.9 101.3 1.0
CE1 B:HIS167 4.1 91.1 1.0
O B:VAL166 4.4 92.2 1.0
CB A:THR166 4.7 78.2 1.0
CA B:HIS167 4.7 85.3 1.0
CG B:HIS167 4.8 83.1 1.0
O A:ASP167 4.8 86.6 1.0
CG2 A:THR166 4.9 79.5 1.0
OG1 A:THR166 4.9 77.0 1.0

Sodium binding site 2 out of 8 in 7f35

Go back to Sodium Binding Sites List in 7f35
Sodium binding site 2 out of 8 in the Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin


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 S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na305

b:108.3
occ:1.00
 OG B:SER17 3.1 92.0 1.0
CE1 B:HIS82 4.1 75.5 1.0
CB B:SER17 4.1 77.0 1.0
CB B:ASN84 4.3 68.5 1.0
NE2 B:HIS82 4.4 84.7 1.0
O1 B:EDO304 4.5 94.1 1.0
O1 B:EDO302 5.0 99.3 1.0

Sodium binding site 3 out of 8 in 7f35

Go back to Sodium Binding Sites List in 7f35
Sodium binding site 3 out of 8 in the Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin


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 S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na306

b:88.9
occ:1.00
 CB B:TYR102 3.6 58.2 1.0
CG B:TYR102 4.2 59.5 1.0
CD1 B:TYR102 4.5 61.9 1.0
O B:TYR102 4.6 63.5 1.0
CA B:TYR102 4.8 58.1 1.0
C B:TYR102 4.9 61.1 1.0

Sodium binding site 4 out of 8 in 7f35

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Sodium binding site 4 out of 8 in the Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin


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 S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin within 5.0Å range:

Sodium binding site 5 out of 8 in 7f35

Go back to Sodium Binding Sites List in 7f35
Sodium binding site 5 out of 8 in the Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin


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 S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na308

b:110.4
occ:1.00
 NZ C:LYS105 4.5 80.4 1.0
CD C:LYS105 4.6 84.1 1.0

Sodium binding site 6 out of 8 in 7f35

Go back to Sodium Binding Sites List in 7f35
Sodium binding site 6 out of 8 in the Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin


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 S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin within 5.0Å range:

Sodium binding site 7 out of 8 in 7f35

Go back to Sodium Binding Sites List in 7f35
Sodium binding site 7 out of 8 in the Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin


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 S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na303

b:96.2
occ:1.00
 OG D:SER25 2.6 97.0 1.0
O D:GLN3 3.4 74.9 1.0
CB D:SER25 3.5 88.8 1.0
C D:GLN3 3.7 76.1 1.0
CB D:GLN5 3.8 65.7 1.0
O D:LYS23 3.8 68.0 1.0
N D:GLN5 3.9 63.6 1.0
CB D:GLN3 4.0 83.6 1.0
N D:SER25 4.1 86.1 1.0
N D:LEU4 4.1 66.4 1.0
C D:LEU4 4.2 63.9 1.0
CA D:LEU4 4.3 64.1 1.0
CA D:SER25 4.4 90.0 1.0
CA D:GLN5 4.4 62.3 1.0
CA D:GLN3 4.5 80.3 1.0
C D:ALA24 4.6 79.1 1.0
C D:LYS23 4.7 69.5 1.0
O D:LEU4 4.8 71.5 1.0
CG D:GLN5 4.9 66.9 1.0
CA D:ALA24 5.0 76.8 1.0

Sodium binding site 8 out of 8 in 7f35

Go back to Sodium Binding Sites List in 7f35
Sodium binding site 8 out of 8 in the Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin


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 S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na304

b:89.6
occ:1.00
 OE1 D:GLU46 2.9 63.7 1.0
OG D:SER40 3.4 58.1 1.0
N D:SER40 3.7 53.1 1.0
CB D:SER40 3.8 60.3 1.0
CD D:GLU46 4.0 75.5 1.0
CE D:LYS38 4.1 44.6 1.0
O D:SER44 4.2 56.8 1.0
CB D:GLU46 4.4 49.2 1.0
CA D:SER40 4.4 60.2 1.0
O D:LYS38 4.4 47.2 1.0
CD D:LYS38 4.5 41.9 1.0
CG D:LYS38 4.5 47.7 1.0
CG D:GLU46 4.6 60.8 1.0
C D:GLN39 4.6 54.7 1.0
CA D:GLN39 4.7 49.3 1.0
CB D:LYS43 4.7 81.1 1.0
C D:LYS38 4.8 48.2 1.0
CD D:LYS43 4.8 84.9 1.0
N D:GLN39 5.0 47.0 1.0

Reference:

L.T.Wang, W.Xie, W.Y.Jiao, C.Zhang, X.Li, Z.Xu, X.Huang, H.T.Lei, X.Shen. Conformational Adaptability Determining Antibody Recognition to Distomer: Structure Analysis of Enantioselective Antibody Against Chiral Drug Gatifloxacin Rsc Adv V. 11 39534 2021.
ISSN: ESSN 2046-2069
DOI: 10.1039/D1RA07143B
Page generated: Tue Oct 8 16:46:37 2024

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