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Zinc in PDB 5llo: Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 3- [(1S)-2,3-Dihydro-1H-Inden-1-Ylamino]-2,5,6-Trifluoro-4-[(2-Hy- Droxyethyl)Sulfonyl]Benzenesulfonamide

Enzymatic activity of Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 3- [(1S)-2,3-Dihydro-1H-Inden-1-Ylamino]-2,5,6-Trifluoro-4-[(2-Hy- Droxyethyl)Sulfonyl]Benzenesulfonamide

All present enzymatic activity of Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 3- [(1S)-2,3-Dihydro-1H-Inden-1-Ylamino]-2,5,6-Trifluoro-4-[(2-Hy- Droxyethyl)Sulfonyl]Benzenesulfonamide:
4.2.1.1;

Protein crystallography data

The structure of Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 3- [(1S)-2,3-Dihydro-1H-Inden-1-Ylamino]-2,5,6-Trifluoro-4-[(2-Hy- Droxyethyl)Sulfonyl]Benzenesulfonamide, PDB code: 5llo was solved by A.Smirnov, E.Manakova, S.Grazulis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.10 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.291, 74.111, 91.585, 90.00, 108.95, 90.00
R / Rfree (%) 18.5 / 22.5

Other elements in 5llo:

The structure of Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 3- [(1S)-2,3-Dihydro-1H-Inden-1-Ylamino]-2,5,6-Trifluoro-4-[(2-Hy- Droxyethyl)Sulfonyl]Benzenesulfonamide also contains other interesting chemical elements:

Fluorine (F) 12 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 3- [(1S)-2,3-Dihydro-1H-Inden-1-Ylamino]-2,5,6-Trifluoro-4-[(2-Hy- Droxyethyl)Sulfonyl]Benzenesulfonamide (pdb code 5llo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 3- [(1S)-2,3-Dihydro-1H-Inden-1-Ylamino]-2,5,6-Trifluoro-4-[(2-Hy- Droxyethyl)Sulfonyl]Benzenesulfonamide, PDB code: 5llo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5llo

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 3- [(1S)-2,3-Dihydro-1H-Inden-1-Ylamino]-2,5,6-Trifluoro-4-[(2-Hy- Droxyethyl)Sulfonyl]Benzenesulfonamide


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 Isozyme XII with 3- [(1S)-2,3-Dihydro-1H-Inden-1-Ylamino]-2,5,6-Trifluoro-4-[(2-Hy- Droxyethyl)Sulfonyl]Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:10.1
occ:1.00
 ND1 A:HIS117 2.0 9.1 1.0
N4 A:5EF303 2.0 13.7 1.0
NE2 A:HIS93 2.1 10.3 1.0
NE2 A:HIS91 2.1 9.2 1.0
F11 A:5EF303 2.9 16.7 1.0
CE1 A:HIS117 2.9 8.5 1.0
CD2 A:HIS91 2.9 9.1 1.0
CD2 A:HIS93 3.0 9.5 1.0
S1 A:5EF303 3.0 13.9 1.0
CE1 A:HIS93 3.1 9.7 1.0
CG A:HIS117 3.1 9.4 1.0
O3 A:5EF303 3.2 12.5 1.0
CE1 A:HIS91 3.2 8.7 1.0
CB A:HIS117 3.6 8.5 1.0
C6 A:5EF303 3.6 15.9 1.0
C5 A:5EF303 3.7 15.3 1.0
OE1 A:GLU104 3.8 10.5 1.0
OG1 A:THR198 4.0 13.1 1.0
NE2 A:HIS117 4.0 9.5 1.0
CD2 A:HIS117 4.2 9.4 1.0
CG A:HIS91 4.2 9.8 1.0
ND1 A:HIS93 4.2 9.6 1.0
CG A:HIS93 4.2 8.9 1.0
ND1 A:HIS91 4.2 9.7 1.0
O2 A:5EF303 4.4 16.4 1.0
CD A:GLU104 4.7 11.0 1.0
C7 A:5EF303 4.8 17.2 1.0
C10 A:5EF303 5.0 17.8 1.0
CH2 A:TRP208 5.0 10.3 1.0

Zinc binding site 2 out of 4 in 5llo

Go back to Zinc Binding Sites List in 5llo
Zinc binding site 2 out of 4 in the Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 3- [(1S)-2,3-Dihydro-1H-Inden-1-Ylamino]-2,5,6-Trifluoro-4-[(2-Hy- Droxyethyl)Sulfonyl]Benzenesulfonamide


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 Isozyme XII with 3- [(1S)-2,3-Dihydro-1H-Inden-1-Ylamino]-2,5,6-Trifluoro-4-[(2-Hy- Droxyethyl)Sulfonyl]Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:9.4
occ:1.00
 N4 B:5EF303 1.8 12.7 1.0
NE2 B:HIS93 2.0 7.2 1.0
ND1 B:HIS117 2.1 8.4 1.0
NE2 B:HIS91 2.1 8.5 1.0
CE1 B:HIS117 2.9 7.4 1.0
CD2 B:HIS91 3.0 7.4 1.0
F11 B:5EF303 3.0 17.9 1.0
CE1 B:HIS93 3.0 8.5 1.0
CD2 B:HIS93 3.0 6.3 1.0
S1 B:5EF303 3.1 13.3 1.0
CG B:HIS117 3.1 7.5 1.0
CE1 B:HIS91 3.2 7.7 1.0
O3 B:5EF303 3.2 12.2 1.0
CB B:HIS117 3.6 7.4 1.0
C6 B:5EF303 3.7 14.5 1.0
C5 B:5EF303 3.7 15.3 1.0
OE1 B:GLU104 3.8 10.6 1.0
OG1 B:THR198 4.0 9.3 1.0
NE2 B:HIS117 4.1 7.3 1.0
ND1 B:HIS93 4.2 7.2 1.0
CG B:HIS91 4.2 7.0 1.0
ND1 B:HIS91 4.2 8.2 1.0
CD2 B:HIS117 4.2 7.1 1.0
CG B:HIS93 4.2 7.2 1.0
O2 B:5EF303 4.4 14.7 1.0
C7 B:5EF303 4.8 16.2 1.0
CD B:GLU104 4.8 10.9 1.0
C10 B:5EF303 5.0 17.3 1.0
CH2 B:TRP208 5.0 9.4 1.0
CA B:HIS117 5.0 7.7 1.0

Zinc binding site 3 out of 4 in 5llo

Go back to Zinc Binding Sites List in 5llo
Zinc binding site 3 out of 4 in the Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 3- [(1S)-2,3-Dihydro-1H-Inden-1-Ylamino]-2,5,6-Trifluoro-4-[(2-Hy- Droxyethyl)Sulfonyl]Benzenesulfonamide


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 Isozyme XII with 3- [(1S)-2,3-Dihydro-1H-Inden-1-Ylamino]-2,5,6-Trifluoro-4-[(2-Hy- Droxyethyl)Sulfonyl]Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:14.0
occ:1.00
 N4 C:5EF302 1.9 17.8 1.0
ND1 C:HIS117 2.0 13.1 1.0
NE2 C:HIS93 2.0 11.3 1.0
NE2 C:HIS91 2.1 11.9 1.0
CE1 C:HIS117 2.9 13.2 1.0
CD2 C:HIS91 2.9 14.3 1.0
F11 C:5EF302 2.9 17.1 1.0
CD2 C:HIS93 3.0 11.7 1.0
CE1 C:HIS93 3.0 11.0 1.0
S1 C:5EF302 3.1 17.2 1.0
CG C:HIS117 3.2 12.6 1.0
O3 C:5EF302 3.2 16.2 1.0
CE1 C:HIS91 3.2 13.7 1.0
C6 C:5EF302 3.6 18.2 1.0
CB C:HIS117 3.6 12.9 1.0
C5 C:5EF302 3.7 18.2 1.0
OE1 C:GLU104 3.8 12.8 1.0
OG1 C:THR198 4.0 11.8 1.0
NE2 C:HIS117 4.1 11.6 1.0
ND1 C:HIS93 4.2 12.5 1.0
CG C:HIS93 4.2 10.5 1.0
CG C:HIS91 4.2 16.1 1.0
ND1 C:HIS91 4.2 15.4 1.0
CD2 C:HIS117 4.3 13.5 1.0
O2 C:5EF302 4.3 18.9 1.0
CD C:GLU104 4.7 14.2 1.0
C7 C:5EF302 4.7 18.3 1.0
C10 C:5EF302 4.9 18.9 1.0
CH2 C:TRP208 5.0 13.2 1.0
CA C:HIS117 5.0 12.0 1.0

Zinc binding site 4 out of 4 in 5llo

Go back to Zinc Binding Sites List in 5llo
Zinc binding site 4 out of 4 in the Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 3- [(1S)-2,3-Dihydro-1H-Inden-1-Ylamino]-2,5,6-Trifluoro-4-[(2-Hy- Droxyethyl)Sulfonyl]Benzenesulfonamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 3- [(1S)-2,3-Dihydro-1H-Inden-1-Ylamino]-2,5,6-Trifluoro-4-[(2-Hy- Droxyethyl)Sulfonyl]Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:10.4
occ:1.00
 N4 D:5EF303 2.0 13.2 1.0
NE2 D:HIS93 2.0 9.2 1.0
ND1 D:HIS117 2.0 10.1 1.0
NE2 D:HIS91 2.1 10.5 1.0
CE1 D:HIS117 2.9 9.5 1.0
CD2 D:HIS91 3.0 8.2 1.0
F11 D:5EF303 3.0 16.4 1.0
CE1 D:HIS93 3.0 9.9 1.0
S1 D:5EF303 3.0 13.9 1.0
CD2 D:HIS93 3.0 10.0 1.0
CG D:HIS117 3.2 9.7 1.0
CE1 D:HIS91 3.2 10.2 1.0
O3 D:5EF303 3.3 14.3 1.0
C6 D:5EF303 3.6 15.0 1.0
CB D:HIS117 3.6 9.3 1.0
C5 D:5EF303 3.7 14.4 1.0
OE1 D:GLU104 3.8 10.5 1.0
OG1 D:THR198 4.0 9.8 1.0
NE2 D:HIS117 4.1 8.9 1.0
ND1 D:HIS93 4.2 10.9 1.0
CG D:HIS93 4.2 10.8 1.0
CG D:HIS91 4.2 9.7 1.0
ND1 D:HIS91 4.2 10.0 1.0
CD2 D:HIS117 4.3 9.3 1.0
O2 D:5EF303 4.3 14.6 1.0
CD D:GLU104 4.8 11.4 1.0
C7 D:5EF303 4.8 20.3 1.0
CH2 D:TRP208 4.9 12.2 1.0
C10 D:5EF303 4.9 17.7 1.0
O D:HOH401 5.0 23.2 1.0

Reference:

A.Smirnov, A.Zubriene, E.Manakova, S.Grazulis, D.Matulis. Crystal Structure Correlations with the Intrinsic Thermodynamics of Human Carbonic Anhydrase Inhibitor Binding. Peerj V. 6 E4412 2018.
ISSN: ESSN 2167-8359
PubMed: 29503769
DOI: 10.7717/PEERJ.4412
Page generated: Sun Oct 27 21:09:11 2024

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