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Zinc in PDB 5llp: Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 3- [(1S)-1,2,3,4-Tetrahydronapthalen-1-Ylamino)-2,5,6-Trifluoro-4-[(2- Hydroxyethyl)Sulfonyl]Benzenesulfonamide

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

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

Protein crystallography data

The structure of Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 3- [(1S)-1,2,3,4-Tetrahydronapthalen-1-Ylamino)-2,5,6-Trifluoro-4-[(2- Hydroxyethyl)Sulfonyl]Benzenesulfonamide, PDB code: 5llp 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) 73.28 / 1.48
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.488, 74.288, 91.658, 90.00, 108.97, 90.00
R / Rfree (%) 16.4 / 19.9

Other elements in 5llp:

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

Fluorine (F) 15 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 3- [(1S)-1,2,3,4-Tetrahydronapthalen-1-Ylamino)-2,5,6-Trifluoro-4-[(2- Hydroxyethyl)Sulfonyl]Benzenesulfonamide (pdb code 5llp). 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)-1,2,3,4-Tetrahydronapthalen-1-Ylamino)-2,5,6-Trifluoro-4-[(2- Hydroxyethyl)Sulfonyl]Benzenesulfonamide, PDB code: 5llp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5llp

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 3- [(1S)-1,2,3,4-Tetrahydronapthalen-1-Ylamino)-2,5,6-Trifluoro-4-[(2- Hydroxyethyl)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)-1,2,3,4-Tetrahydronapthalen-1-Ylamino)-2,5,6-Trifluoro-4-[(2- Hydroxyethyl)Sulfonyl]Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:6.7
occ:1.00
 N29 A:6Z9302 1.9 10.5 0.5
N29 A:6Z9302 1.9 9.3 0.5
ND1 A:HIS117 2.0 7.7 1.0
NE2 A:HIS93 2.0 5.7 1.0
NE2 A:HIS91 2.0 4.9 1.0
F5 A:6Z9302 2.9 15.7 0.5
CE1 A:HIS117 2.9 5.5 1.0
F5 A:6Z9302 2.9 13.9 0.5
CD2 A:HIS91 3.0 5.7 1.0
CE1 A:HIS93 3.0 6.6 1.0
S2 A:6Z9302 3.0 10.4 0.5
S2 A:6Z9302 3.0 11.5 0.5
CD2 A:HIS93 3.1 5.5 1.0
CE1 A:HIS91 3.1 6.1 1.0
CG A:HIS117 3.1 5.8 1.0
O30 A:6Z9302 3.2 12.6 0.5
O30 A:6Z9302 3.2 11.1 0.5
C4 A:6Z9302 3.5 15.4 0.5
CB A:HIS117 3.6 6.0 1.0
C4 A:6Z9302 3.6 14.0 0.5
C3 A:6Z9302 3.6 14.0 0.5
C3 A:6Z9302 3.6 12.6 0.5
OE1 A:GLU104 3.8 8.7 1.0
OG1 A:THR198 4.0 7.7 1.0
NE2 A:HIS117 4.1 6.5 1.0
ND1 A:HIS93 4.1 6.0 1.0
CG A:HIS91 4.2 6.2 1.0
ND1 A:HIS91 4.2 6.3 1.0
CG A:HIS93 4.2 5.8 1.0
CD2 A:HIS117 4.2 6.9 1.0
O1 A:6Z9302 4.3 12.5 0.5
O1 A:6Z9302 4.3 14.0 0.5
CD A:GLU104 4.7 8.2 1.0
C6 A:6Z9302 4.7 17.3 0.5
C6 A:6Z9302 4.8 15.5 0.5
C27 A:6Z9302 4.9 16.1 0.5
C27 A:6Z9302 4.9 14.7 0.5
CA A:HIS117 5.0 6.1 1.0
CH2 A:TRP208 5.0 7.0 1.0

Zinc binding site 2 out of 4 in 5llp

Go back to Zinc Binding Sites List in 5llp
Zinc binding site 2 out of 4 in the Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 3- [(1S)-1,2,3,4-Tetrahydronapthalen-1-Ylamino)-2,5,6-Trifluoro-4-[(2- Hydroxyethyl)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)-1,2,3,4-Tetrahydronapthalen-1-Ylamino)-2,5,6-Trifluoro-4-[(2- Hydroxyethyl)Sulfonyl]Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:4.9
occ:1.00
 N29 B:6Z9302 1.9 8.7 1.0
ND1 B:HIS117 2.0 4.4 1.0
NE2 B:HIS91 2.0 3.2 1.0
NE2 B:HIS93 2.0 3.8 1.0
CE1 B:HIS117 2.9 4.8 1.0
CD2 B:HIS91 3.0 4.0 1.0
S2 B:6Z9302 3.0 9.8 1.0
F5 B:6Z9302 3.0 16.7 1.0
CE1 B:HIS93 3.1 5.1 1.0
CD2 B:HIS93 3.1 3.9 1.0
CE1 B:HIS91 3.1 4.0 1.0
CG B:HIS117 3.1 4.5 1.0
O30 B:6Z9302 3.2 9.7 1.0
CB B:HIS117 3.6 4.2 1.0
C3 B:6Z9302 3.6 13.2 1.0
C4 B:6Z9302 3.7 14.7 1.0
OE1 B:GLU104 3.8 7.1 1.0
OG1 B:THR198 4.0 5.4 1.0
NE2 B:HIS117 4.1 4.5 1.0
CG B:HIS91 4.1 3.7 1.0
ND1 B:HIS93 4.2 4.5 1.0
ND1 B:HIS91 4.2 4.1 1.0
CG B:HIS93 4.2 4.3 1.0
CD2 B:HIS117 4.2 5.2 1.0
O1 B:6Z9302 4.3 12.2 1.0
C6 B:6Z9302 4.8 19.5 1.0
C27 B:6Z9302 4.8 16.4 1.0
CD B:GLU104 4.9 6.1 1.0
CH2 B:TRP208 5.0 4.6 1.0

Zinc binding site 3 out of 4 in 5llp

Go back to Zinc Binding Sites List in 5llp
Zinc binding site 3 out of 4 in the Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 3- [(1S)-1,2,3,4-Tetrahydronapthalen-1-Ylamino)-2,5,6-Trifluoro-4-[(2- Hydroxyethyl)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)-1,2,3,4-Tetrahydronapthalen-1-Ylamino)-2,5,6-Trifluoro-4-[(2- Hydroxyethyl)Sulfonyl]Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:7.8
occ:1.00
 N29 C:6Z9302 1.9 10.1 1.0
ND1 C:HIS117 2.0 8.6 1.0
NE2 C:HIS91 2.0 6.2 1.0
NE2 C:HIS93 2.0 5.9 1.0
F5 C:6Z9302 2.9 16.2 1.0
CE1 C:HIS117 2.9 7.5 1.0
CE1 C:HIS93 3.0 7.8 1.0
CD2 C:HIS91 3.0 8.3 1.0
S2 C:6Z9302 3.0 12.3 1.0
CD2 C:HIS93 3.0 7.3 1.0
CE1 C:HIS91 3.1 7.4 1.0
CG C:HIS117 3.1 6.5 1.0
O30 C:6Z9302 3.2 12.0 1.0
CB C:HIS117 3.5 7.8 1.0
C4 C:6Z9302 3.6 15.1 1.0
C3 C:6Z9302 3.6 15.7 1.0
OE1 C:GLU104 3.8 8.8 1.0
OG1 C:THR198 4.0 6.4 1.0
NE2 C:HIS117 4.1 6.4 1.0
ND1 C:HIS93 4.1 7.6 1.0
CG C:HIS91 4.1 7.4 1.0
ND1 C:HIS91 4.1 8.4 1.0
CG C:HIS93 4.2 6.9 1.0
CD2 C:HIS117 4.2 8.6 1.0
O1 C:6Z9302 4.3 14.4 1.0
CD C:GLU104 4.7 8.7 1.0
C6 C:6Z9302 4.7 19.3 1.0
C27 C:6Z9302 4.9 17.2 1.0
CA C:HIS117 4.9 6.9 1.0

Zinc binding site 4 out of 4 in 5llp

Go back to Zinc Binding Sites List in 5llp
Zinc binding site 4 out of 4 in the Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 3- [(1S)-1,2,3,4-Tetrahydronapthalen-1-Ylamino)-2,5,6-Trifluoro-4-[(2- Hydroxyethyl)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)-1,2,3,4-Tetrahydronapthalen-1-Ylamino)-2,5,6-Trifluoro-4-[(2- Hydroxyethyl)Sulfonyl]Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:5.0
occ:1.00
 N29 D:6Z9302 1.9 7.5 1.0
NE2 D:HIS91 2.0 3.7 1.0
NE2 D:HIS93 2.0 3.5 1.0
ND1 D:HIS117 2.0 4.5 1.0
CE1 D:HIS117 2.9 4.8 1.0
CD2 D:HIS91 2.9 3.9 1.0
F5 D:6Z9302 3.0 15.1 1.0
S2 D:6Z9302 3.0 8.9 1.0
CE1 D:HIS93 3.0 4.4 1.0
CE1 D:HIS91 3.0 3.6 1.0
CD2 D:HIS93 3.1 4.0 1.0
CG D:HIS117 3.1 4.3 1.0
O30 D:6Z9302 3.2 8.4 1.0
CB D:HIS117 3.6 4.1 1.0
C3 D:6Z9302 3.6 12.8 1.0
C4 D:6Z9302 3.7 14.3 1.0
OE1 D:GLU104 3.8 7.6 1.0
OG1 D:THR198 4.0 4.8 1.0
NE2 D:HIS117 4.1 4.4 1.0
CG D:HIS91 4.1 3.5 1.0
ND1 D:HIS91 4.2 4.2 1.0
ND1 D:HIS93 4.2 5.0 1.0
CG D:HIS93 4.2 4.6 1.0
O1 D:6Z9302 4.3 10.8 1.0
CD2 D:HIS117 4.3 5.2 1.0
C27 D:6Z9302 4.8 13.4 1.0
C6 D:6Z9302 4.9 17.2 1.0
CD D:GLU104 4.9 7.1 1.0
CH2 D:TRP208 4.9 6.0 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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