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Zinc in PDB 5ll5: Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 4-(1H- Benzimidazol-1-Ylacetyl)Benzenesulfonamide

Enzymatic activity of Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 4-(1H- Benzimidazol-1-Ylacetyl)Benzenesulfonamide

All present enzymatic activity of Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 4-(1H- Benzimidazol-1-Ylacetyl)Benzenesulfonamide:
4.2.1.1;

Protein crystallography data

The structure of Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 4-(1H- Benzimidazol-1-Ylacetyl)Benzenesulfonamide, PDB code: 5ll5 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) 67.76 / 1.42
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.418, 73.962, 91.328, 90.00, 108.96, 90.00
R / Rfree (%) 16.4 / 19.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 4-(1H- Benzimidazol-1-Ylacetyl)Benzenesulfonamide (pdb code 5ll5). 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 4-(1H- Benzimidazol-1-Ylacetyl)Benzenesulfonamide, PDB code: 5ll5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5ll5

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 4-(1H- Benzimidazol-1-Ylacetyl)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 4-(1H- Benzimidazol-1-Ylacetyl)Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:8.5
occ:1.00
 N10 A:6YH302 1.9 12.5 1.0
NE2 A:HIS93 2.0 8.5 1.0
NE2 A:HIS91 2.0 8.1 1.0
ND1 A:HIS117 2.0 8.7 1.0
CE1 A:HIS117 2.9 7.6 1.0
O8 A:6YH302 3.0 13.8 1.0
S7 A:6YH302 3.0 14.3 1.0
CE1 A:HIS93 3.0 8.0 1.0
CD2 A:HIS91 3.0 9.9 1.0
CD2 A:HIS93 3.0 7.0 1.0
CE1 A:HIS91 3.1 9.4 1.0
CG A:HIS117 3.1 7.5 1.0
CB A:HIS117 3.6 8.2 1.0
OE1 A:GLU104 3.8 10.3 1.0
OG1 A:THR198 3.9 8.9 1.0
NE2 A:HIS117 4.1 7.4 1.0
C1 A:6YH302 4.1 17.1 1.0
O9 A:6YH302 4.1 11.6 1.0
ND1 A:HIS93 4.1 8.9 1.0
CG A:HIS91 4.2 9.5 1.0
CG A:HIS93 4.2 7.9 1.0
CD2 A:HIS117 4.2 7.9 1.0
ND1 A:HIS91 4.2 9.9 1.0
C2 A:6YH302 4.7 20.9 1.0
C2 A:EDO304 4.7 25.3 1.0
CD A:GLU104 4.8 9.4 1.0
C6 A:6YH302 4.9 18.9 1.0
C1 A:EDO304 5.0 25.4 1.0

Zinc binding site 2 out of 4 in 5ll5

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 4-(1H- Benzimidazol-1-Ylacetyl)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 4-(1H- Benzimidazol-1-Ylacetyl)Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:6.8
occ:1.00
 N10 B:6YH302 1.9 10.8 1.0
NE2 B:HIS91 2.0 6.1 1.0
NE2 B:HIS93 2.0 5.8 1.0
ND1 B:HIS117 2.0 6.2 1.0
CE1 B:HIS117 2.9 6.9 1.0
CD2 B:HIS91 3.0 6.9 1.0
O8 B:6YH302 3.0 10.8 1.0
S7 B:6YH302 3.0 10.3 1.0
CE1 B:HIS93 3.1 7.7 1.0
CE1 B:HIS91 3.1 6.9 1.0
CD2 B:HIS93 3.1 6.1 1.0
CG B:HIS117 3.2 6.5 1.0
CB B:HIS117 3.6 6.7 1.0
OE1 B:GLU104 3.9 8.5 1.0
OG1 B:THR198 4.0 7.7 1.0
NE2 B:HIS117 4.1 6.7 1.0
ND1 B:HIS91 4.2 6.9 1.0
O9 B:6YH302 4.2 9.5 1.0
C1 B:6YH302 4.2 11.0 1.0
CG B:HIS91 4.2 6.4 1.0
ND1 B:HIS93 4.2 6.7 1.0
CD2 B:HIS117 4.2 7.2 1.0
CG B:HIS93 4.2 6.3 1.0
C2 B:EDO304 4.5 15.5 1.0
C6 B:6YH302 4.7 13.9 1.0
C1 B:EDO304 4.8 15.3 1.0
C2 B:6YH302 4.8 13.3 1.0
CD B:GLU104 4.9 7.3 1.0

Zinc binding site 3 out of 4 in 5ll5

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Zinc binding site 3 out of 4 in the Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 4-(1H- Benzimidazol-1-Ylacetyl)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 4-(1H- Benzimidazol-1-Ylacetyl)Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:10.5
occ:1.00
 N10 C:6YH302 1.9 13.2 1.0
ND1 C:HIS117 2.0 10.8 1.0
NE2 C:HIS93 2.0 9.8 1.0
NE2 C:HIS91 2.0 10.7 1.0
CE1 C:HIS117 2.9 10.2 1.0
S7 C:6YH302 3.0 16.7 1.0
CE1 C:HIS93 3.0 10.8 1.0
CD2 C:HIS93 3.0 10.2 1.0
CE1 C:HIS91 3.0 11.5 1.0
O8 C:6YH302 3.0 16.1 1.0
CD2 C:HIS91 3.0 11.5 1.0
CG C:HIS117 3.1 9.2 1.0
CB C:HIS117 3.5 11.0 1.0
OE1 C:GLU104 3.8 10.7 1.0
OG1 C:THR198 3.9 9.7 1.0
O9 C:6YH302 4.1 13.2 1.0
NE2 C:HIS117 4.1 9.7 1.0
C1 C:6YH302 4.1 20.0 1.0
ND1 C:HIS91 4.2 12.5 1.0
ND1 C:HIS93 4.2 10.9 1.0
CG C:HIS91 4.2 11.7 1.0
CG C:HIS93 4.2 9.2 1.0
CD2 C:HIS117 4.2 10.4 1.0
C2 C:6YH302 4.4 28.1 1.0
C1 C:EDO303 4.6 38.1 1.0
CD C:GLU104 4.8 10.3 1.0
CA C:HIS117 5.0 10.3 1.0

Zinc binding site 4 out of 4 in 5ll5

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Zinc binding site 4 out of 4 in the Crystal Structure of Human Carbonic Anhydrase Isozyme XII with 4-(1H- Benzimidazol-1-Ylacetyl)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 4-(1H- Benzimidazol-1-Ylacetyl)Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:7.2
occ:1.00
 N10 D:6YH302 1.9 13.1 0.5
N10 D:6YH302 1.9 8.4 0.5
NE2 D:HIS93 2.0 6.5 1.0
NE2 D:HIS91 2.0 7.0 1.0
ND1 D:HIS117 2.0 6.3 1.0
CE1 D:HIS117 2.9 7.0 1.0
CD2 D:HIS91 3.0 6.7 1.0
S7 D:6YH302 3.0 10.2 0.5
S7 D:6YH302 3.0 15.7 0.5
O8 D:6YH302 3.0 9.6 0.5
O8 D:6YH302 3.0 15.7 0.5
CD2 D:HIS93 3.0 6.8 1.0
CE1 D:HIS93 3.0 7.9 1.0
CE1 D:HIS91 3.1 7.0 1.0
CG D:HIS117 3.1 6.4 1.0
CB D:HIS117 3.6 7.2 1.0
OE1 D:GLU104 3.9 9.4 1.0
OG1 D:THR198 4.0 7.3 1.0
NE2 D:HIS117 4.1 6.3 1.0
O9 D:6YH302 4.1 8.6 0.5
C1 D:6YH302 4.2 18.4 0.5
CG D:HIS91 4.2 6.2 1.0
ND1 D:HIS91 4.2 7.6 1.0
ND1 D:HIS93 4.2 7.8 1.0
O9 D:6YH302 4.2 14.8 0.5
CD2 D:HIS117 4.2 7.1 1.0
C1 D:6YH302 4.2 11.4 0.5
CG D:HIS93 4.2 7.3 1.0
C2 D:EDO304 4.5 19.1 1.0
C6 D:6YH302 4.7 14.4 0.5
C6 D:6YH302 4.7 22.8 0.5
C1 D:EDO304 4.9 18.1 1.0
CD D:GLU104 4.9 8.5 1.0
C2 D:6YH302 5.0 22.9 0.5

Reference:

E.Capkauskaite, V.Linkuviene, A.Smirnov, G.Milinaviciute, D.Timm, A.Kasiliauskaite, E.Manakova, S.Grazulis, D.Matulis. Combinatorial Design of Isoform-Selective N-Alkylated Benzimidazole-Based Inhibitors of Carbonic Anhydrases Chemistryselect 2017.
ISSN: ESSN 2365-6549
DOI: 10.1002/SLCT.201700531
Page generated: Sun Oct 27 21:06:46 2024

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