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Zinc 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:

Fluorine (F) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Human Carbonic Anhydrase I in Complex with Polmacoxib, PDB code: 5gmm:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5gmm

Go back to Zinc Binding Sites List in 5gmm
Zinc binding site 1 out of 3 in the Crystal Structure of Human Carbonic Anhydrase I in Complex with Polmacoxib


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn301

b:20.5
occ:1.00
N22 A:949302 2.0 18.3 1.0
NE2 A:HIS94 2.0 18.3 1.0
NE2 A:HIS96 2.0 19.3 1.0
ND1 A:HIS119 2.1 18.3 1.0
CD2 A:HIS96 2.8 17.0 1.0
O20 A:949302 2.9 16.1 1.0
CE1 A:HIS94 2.9 18.3 1.0
CE1 A:HIS119 3.0 21.1 1.0
S19 A:949302 3.0 20.9 1.0
CD2 A:HIS94 3.0 19.6 1.0
CE1 A:HIS96 3.1 16.6 1.0
CG A:HIS119 3.2 20.4 1.0
CB A:HIS119 3.6 17.8 1.0
O21 A:949302 4.0 15.7 1.0
OG1 A:THR199 4.0 17.4 1.0
ND1 A:HIS94 4.0 18.9 1.0
CG A:HIS96 4.0 18.2 1.0
OE1 A:GLU106 4.1 17.6 1.0
C16 A:949302 4.1 23.1 1.0
CG A:HIS94 4.1 19.8 1.0
NE2 A:HIS119 4.1 20.2 1.0
ND1 A:HIS96 4.1 16.5 1.0
CD2 A:HIS119 4.2 16.3 1.0
O A:HOH465 4.5 22.0 1.0
O A:HOH455 4.6 18.5 1.0
C15 A:949302 4.7 20.0 1.0
C17 A:949302 5.0 19.7 1.0

Zinc binding site 2 out of 3 in 5gmm

Go back to Zinc Binding Sites List in 5gmm
Zinc binding site 2 out of 3 in the Crystal Structure of Human Carbonic Anhydrase I in Complex with Polmacoxib


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
B:Zn301

b:22.3
occ:1.00
N22 B:949303 1.9 18.7 1.0
NE2 B:HIS94 2.0 18.5 1.0
NE2 B:HIS96 2.0 19.1 1.0
ND1 B:HIS119 2.1 19.5 1.0
O20 B:949303 2.8 23.1 1.0
S19 B:949303 2.9 23.2 1.0
CD2 B:HIS94 2.9 18.9 1.0
CE1 B:HIS119 3.0 20.4 1.0
CE1 B:HIS96 3.0 23.2 1.0
CD2 B:HIS96 3.0 22.6 1.0
CE1 B:HIS94 3.0 22.3 1.0
CG B:HIS119 3.2 23.7 1.0
CB B:HIS119 3.6 20.2 1.0
OG1 B:THR199 3.8 22.2 1.0
O21 B:949303 4.0 24.6 1.0
C16 B:949303 4.0 27.2 1.0
OE1 B:GLU106 4.1 21.1 1.0
CG B:HIS94 4.1 20.1 1.0
ND1 B:HIS96 4.1 18.3 1.0
ND1 B:HIS94 4.1 21.2 1.0
NE2 B:HIS119 4.1 22.4 1.0
CG B:HIS96 4.2 19.2 1.0
CD2 B:HIS119 4.3 21.1 1.0
O B:HOH480 4.6 21.5 1.0
O B:HOH512 4.6 29.5 1.0
O B:HOH450 4.6 23.2 1.0
C15 B:949303 4.7 27.3 1.0
C17 B:949303 4.9 27.6 1.0

Zinc binding site 3 out of 3 in 5gmm

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
B:Zn302

b:60.2
occ:1.00
O B:HOH435 3.8 35.9 1.0
ND2 B:ASN245 3.8 21.6 1.0
N B:SER99 3.8 30.5 1.0
O B:HOH412 3.9 28.6 1.0
CB B:HIS243 4.0 29.4 1.0
OG B:SER99 4.1 36.7 1.0
O B:HOH503 4.1 39.0 1.0
CG B:HIS243 4.1 31.9 1.0
CA B:GLY98 4.2 25.5 1.0
ND1 B:HIS243 4.2 39.8 1.0
CB B:SER99 4.5 30.2 1.0
C B:GLY98 4.6 24.7 1.0
OD1 B:ASN245 4.6 34.4 1.0
CG B:ASN245 4.7 28.4 1.0
O B:HIS103 4.7 35.5 1.0
CA B:SER99 4.8 30.5 1.0
CD2 B:HIS243 4.9 36.1 1.0
CE1 B:HIS243 4.9 36.5 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: Wed Dec 16 06:19:35 2020

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