Atomistry » Fluorine » PDB 5g48-5he1 » 5gmm
Atomistry »
  Fluorine »
    PDB 5g48-5he1 »
      5gmm »

Fluorine in PDB 5gmm: Crystal Structure of Human Carbonic Anhydrase I in Complex with Polmacoxib

Enzymatic activity of Crystal Structure of Human Carbonic Anhydrase I in Complex with Polmacoxib

All present enzymatic activity of Crystal Structure of Human Carbonic Anhydrase I in Complex with Polmacoxib:
4.2.1.1;

Protein crystallography data

The structure of Crystal Structure of Human Carbonic Anhydrase I in Complex with Polmacoxib, PDB code: 5gmm was solved by H.T.Kim, K.Y.Hwang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.02 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.265, 87.953, 142.580, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 22.7

Other elements in 5gmm:

The structure of Crystal Structure of Human Carbonic Anhydrase I in Complex with Polmacoxib also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Carbonic Anhydrase I in Complex with Polmacoxib (pdb code 5gmm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Human Carbonic Anhydrase I in Complex with Polmacoxib, PDB code: 5gmm:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5gmm

Go back to Fluorine Binding Sites List in 5gmm
Fluorine binding site 1 out of 6 in the Crystal Structure of Human Carbonic Anhydrase I in Complex with Polmacoxib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human Carbonic Anhydrase I in Complex with Polmacoxib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:27.8
occ:1.00
 F25 A:949302 0.0 27.8 1.0
C1 A:949302 1.3 22.9 1.0
C2 A:949302 2.3 23.2 1.0
C6 A:949302 2.4 21.7 1.0
CE1 A:HIS67 3.1 31.6 1.0
C18 A:949303 3.3 27.2 1.0
NE2 A:HIS64 3.4 21.9 1.0
CE1 A:HIS64 3.4 22.5 1.0
C17 A:949303 3.4 25.2 1.0
C3 A:949302 3.6 24.4 1.0
C5 A:949302 3.6 24.9 1.0
NE2 A:HIS67 3.7 25.4 1.0
C13 A:949303 3.9 29.2 1.0
ND1 A:HIS67 4.0 26.2 1.0
CE1 A:HIS200 4.1 21.2 1.0
C4 A:949302 4.1 25.1 1.0
C16 A:949303 4.1 27.5 1.0
O A:HOH465 4.1 22.0 1.0
CG2 A:VAL62 4.2 20.3 1.0
NE2 A:HIS200 4.2 16.8 1.0
C14 A:949303 4.5 28.5 1.0
CB A:VAL62 4.5 21.6 1.0
C15 A:949303 4.5 31.1 1.0
O21 A:949303 4.6 25.3 1.0
C8 A:949303 4.6 27.7 1.0
ND1 A:HIS64 4.7 20.1 1.0
CD2 A:HIS64 4.7 16.4 1.0
CG1 A:VAL62 4.8 21.2 1.0
CD2 A:HIS67 4.8 20.5 1.0
C7 A:949302 4.8 24.8 1.0
S19 A:949303 5.0 32.2 1.0
CG A:HIS67 5.0 26.1 1.0

Fluorine binding site 2 out of 6 in 5gmm

Go back to Fluorine Binding Sites List in 5gmm
Fluorine binding site 2 out of 6 in the Crystal Structure of Human Carbonic Anhydrase I in Complex with Polmacoxib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human Carbonic Anhydrase I in Complex with Polmacoxib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:30.5
occ:1.00
 F25 A:949303 0.0 30.5 1.0
C1 A:949303 1.3 28.8 1.0
C2 A:949303 2.4 27.0 1.0
C6 A:949303 2.4 25.6 1.0
CA A:VAL62 3.4 20.7 1.0
O A:ASN61 3.5 24.6 1.0
CG A:LYS170 3.5 21.6 1.0
CE A:LYS170 3.6 37.9 1.0
C5 A:949303 3.6 23.1 1.0
C3 A:949303 3.6 28.4 1.0
C A:VAL62 3.7 26.6 1.0
C24 B:949305 3.8 35.2 1.0
O A:VAL62 3.9 21.7 1.0
N A:GLY171 3.9 22.1 1.0
C4 A:949303 4.1 28.3 1.0
CA A:GLY171 4.1 24.5 1.0
CB A:VAL62 4.2 21.6 1.0
CD A:LYS170 4.2 24.1 1.0
C A:ASN61 4.4 24.7 1.0
N A:VAL62 4.4 18.0 1.0
N A:GLY63 4.5 23.5 1.0
CG1 A:VAL62 4.5 21.2 1.0
CB B:ALA132 4.7 30.4 1.0
C A:LYS170 4.7 24.4 1.0
O12 A:949303 4.8 36.6 1.0
C7 A:949303 4.8 33.9 1.0
CB A:LYS170 4.9 22.7 1.0
NZ A:LYS170 4.9 31.6 1.0

Fluorine binding site 3 out of 6 in 5gmm

Go back to Fluorine Binding Sites List in 5gmm
Fluorine binding site 3 out of 6 in the Crystal Structure of Human Carbonic Anhydrase I in Complex with Polmacoxib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human Carbonic Anhydrase I in Complex with Polmacoxib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F304

b:58.6
occ:1.00
 F25 A:949304 0.0 58.6 1.0
C1 A:949304 1.3 43.0 1.0
C6 A:949304 2.4 35.6 1.0
C2 A:949304 2.4 41.2 1.0
OH A:TYR204 3.3 29.7 1.0
O B:HOH517 3.6 45.5 1.0
C5 A:949304 3.6 32.7 1.0
C3 A:949304 3.6 35.8 1.0
C4 A:949304 4.1 33.7 1.0
O B:HOH540 4.1 44.1 1.0
CZ A:TYR204 4.5 27.3 1.0
CB A:PRO202 4.6 21.2 1.0
C18 A:949304 4.8 34.8 1.0
C23 B:949304 4.8 30.3 1.0
O12 B:949304 4.8 33.2 1.0
CG A:PRO202 4.9 21.6 1.0
OD1 B:ASP4 4.9 62.4 1.0
C7 A:949304 4.9 38.6 1.0

Fluorine binding site 4 out of 6 in 5gmm

Go back to Fluorine Binding Sites List in 5gmm
Fluorine binding site 4 out of 6 in the Crystal Structure of Human Carbonic Anhydrase I in Complex with Polmacoxib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human Carbonic Anhydrase I in Complex with Polmacoxib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F303

b:31.2
occ:1.00
 F25 B:949303 0.0 31.2 1.0
C1 B:949303 1.3 24.8 1.0
C2 B:949303 2.4 26.8 1.0
C6 B:949303 2.4 27.7 1.0
CE1 B:HIS67 3.1 21.7 1.0
NE2 B:HIS64 3.3 30.0 1.0
CE1 B:HIS64 3.4 23.8 1.0
C18 B:949304 3.5 27.0 1.0
NE2 B:HIS67 3.5 25.3 1.0
C3 B:949303 3.6 25.2 1.0
C5 B:949303 3.6 26.4 1.0
C17 B:949304 3.7 26.4 1.0
O B:HOH521 3.7 35.7 1.0
CE1 B:HIS200 3.9 28.1 1.0
C13 B:949304 4.0 25.7 1.0
CG2 B:VAL62 4.0 21.5 1.0
NE2 B:HIS200 4.1 23.9 1.0
C4 B:949303 4.1 26.9 1.0
O B:HOH480 4.1 21.5 1.0
ND1 B:HIS67 4.1 22.3 1.0
O B:HOH512 4.3 29.5 1.0
C16 B:949304 4.3 32.3 1.0
CB B:VAL62 4.4 24.1 1.0
CD2 B:HIS64 4.6 22.7 1.0
C14 B:949304 4.6 31.6 1.0
C8 B:949304 4.6 30.9 1.0
CD2 B:HIS67 4.7 18.8 1.0
CG1 B:VAL62 4.7 19.7 1.0
ND1 B:HIS64 4.7 21.6 1.0
C15 B:949304 4.8 30.3 1.0
O21 B:949304 4.9 29.8 1.0
C7 B:949303 4.9 27.2 1.0
CG B:HIS67 5.0 24.4 1.0

Fluorine binding site 5 out of 6 in 5gmm

Go back to Fluorine Binding Sites List in 5gmm
Fluorine binding site 5 out of 6 in the Crystal Structure of Human Carbonic Anhydrase I in Complex with Polmacoxib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human Carbonic Anhydrase I in Complex with Polmacoxib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F304

b:33.9
occ:1.00
 F25 B:949304 0.0 33.9 1.0
C1 B:949304 1.4 28.8 1.0
C6 B:949304 2.4 24.8 1.0
C2 B:949304 2.4 22.5 1.0
NZ B:LYS170 2.7 40.4 1.0
CG B:LYS170 3.4 28.8 1.0
CA B:VAL62 3.4 21.3 1.0
O B:ASN61 3.5 22.6 1.0
C5 B:949304 3.6 27.4 1.0
C B:VAL62 3.6 25.4 1.0
CE B:LYS170 3.7 41.5 1.0
C3 B:949304 3.7 28.4 1.0
C15 A:949304 3.7 36.3 1.0
O B:VAL62 3.8 24.3 1.0
N B:GLY171 3.9 17.9 1.0
C14 A:949304 4.1 34.8 1.0
O20 A:949304 4.1 45.2 1.0
CD B:LYS170 4.1 29.9 1.0
C4 B:949304 4.1 21.8 1.0
CA B:GLY171 4.3 20.8 1.0
CB B:VAL62 4.3 24.1 1.0
C B:ASN61 4.3 22.5 1.0
N B:GLY63 4.3 22.4 1.0
N B:VAL62 4.4 23.9 1.0
CB A:ALA132 4.5 24.3 1.0
CG1 B:VAL62 4.6 19.7 1.0
C B:LYS170 4.7 25.8 1.0
CB B:LYS170 4.7 25.6 1.0
C16 A:949304 4.8 37.7 1.0
O B:HOH521 4.9 35.7 1.0
O12 B:949304 4.9 33.2 1.0
C7 B:949304 4.9 28.8 1.0
CA B:LYS170 4.9 23.2 1.0

Fluorine binding site 6 out of 6 in 5gmm

Go back to Fluorine Binding Sites List in 5gmm
Fluorine binding site 6 out of 6 in the Crystal Structure of Human Carbonic Anhydrase I in Complex with Polmacoxib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human Carbonic Anhydrase I in Complex with Polmacoxib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F305

b:49.7
occ:1.00
 F25 B:949305 0.0 49.7 1.0
C1 B:949305 1.3 47.3 1.0
C6 B:949305 2.4 42.8 1.0
O12 A:949304 2.4 37.2 1.0
C2 B:949305 2.4 45.1 1.0
C24 A:949304 3.2 35.0 1.0
C11 A:949304 3.3 32.4 1.0
C14 A:949303 3.5 28.5 1.0
C3 B:949305 3.6 36.8 1.0
C5 B:949305 3.6 43.4 1.0
C10 A:949304 3.7 37.5 1.0
C8 A:949303 4.0 27.7 1.0
C13 A:949303 4.0 29.2 1.0
O9 A:949303 4.1 30.6 1.0
C4 B:949305 4.1 43.1 1.0
C23 A:949304 4.1 35.5 1.0
C15 A:949303 4.3 31.1 1.0
C23 B:949304 4.4 30.3 1.0
C23 A:949303 4.5 34.4 1.0
C7 A:949304 4.5 38.6 1.0
C7 A:949303 4.6 33.9 1.0
C10 A:949303 4.8 29.9 1.0
C7 B:949305 4.9 35.1 1.0
O9 B:949304 4.9 34.0 1.0
C4 A:949304 4.9 33.7 1.0
O9 A:949304 5.0 35.6 1.0

Reference:

H.T.Kim, H.Cha, K.Y.Hwang. Structural Insight Into the Inhibition of Carbonic Anhydrase By the Cox-2-Selective Inhibitor Polmacoxib (CG100649). Biochem. Biophys. Res. V. 478 1 2016COMMUN..
ISSN: ESSN 1090-2104
PubMed: 27475498
DOI: 10.1016/J.BBRC.2016.07.114
Page generated: Thu Aug 1 09:39:34 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy