Atomistry » Sodium » PDB 7e21-7f4x » 7f35
Atomistry »
  Sodium »
    PDB 7e21-7f4x »
      7f35 »

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

Go back to Sodium Binding Sites List in 7f35
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy