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Zinc in PDB 4kp8: Crystal Structure of Catalytic Domain of Human Carbonic Anhydrase Isozyme XII with 3-[(Pyrimidin-2-Ylsulfanyl)Acetyl]Benzenesulfonamide

Enzymatic activity of Crystal Structure of Catalytic Domain of Human Carbonic Anhydrase Isozyme XII with 3-[(Pyrimidin-2-Ylsulfanyl)Acetyl]Benzenesulfonamide

All present enzymatic activity of Crystal Structure of Catalytic Domain of Human Carbonic Anhydrase Isozyme XII with 3-[(Pyrimidin-2-Ylsulfanyl)Acetyl]Benzenesulfonamide:
4.2.1.1;

Protein crystallography data

The structure of Crystal Structure of Catalytic Domain of Human Carbonic Anhydrase Isozyme XII with 3-[(Pyrimidin-2-Ylsulfanyl)Acetyl]Benzenesulfonamide, PDB code: 4kp8 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) 40.00 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.817, 67.258, 81.190, 81.88, 83.99, 86.51
R / Rfree (%) 19.8 / 25.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Catalytic Domain of Human Carbonic Anhydrase Isozyme XII with 3-[(Pyrimidin-2-Ylsulfanyl)Acetyl]Benzenesulfonamide (pdb code 4kp8). 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 Catalytic Domain of Human Carbonic Anhydrase Isozyme XII with 3-[(Pyrimidin-2-Ylsulfanyl)Acetyl]Benzenesulfonamide, PDB code: 4kp8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4kp8

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Zinc binding site 1 out of 4 in the Crystal Structure of Catalytic Domain of Human Carbonic Anhydrase Isozyme XII with 3-[(Pyrimidin-2-Ylsulfanyl)Acetyl]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 Catalytic Domain of Human Carbonic Anhydrase Isozyme XII with 3-[(Pyrimidin-2-Ylsulfanyl)Acetyl]Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:10.9
occ:1.00
 N20 A:E1G302 1.8 16.1 1.0
NE2 A:HIS91 2.1 9.8 1.0
NE2 A:HIS93 2.1 8.8 1.0
ND1 A:HIS117 2.1 9.7 1.0
CE1 A:HIS117 3.0 8.8 1.0
CD2 A:HIS91 3.0 10.6 1.0
S17 A:E1G302 3.1 25.4 1.0
CD2 A:HIS93 3.1 8.6 1.0
O18 A:E1G302 3.1 23.3 1.0
CE1 A:HIS93 3.1 8.7 1.0
CE1 A:HIS91 3.2 11.2 1.0
CG A:HIS117 3.2 8.9 1.0
CB A:HIS117 3.7 9.0 1.0
OG1 A:THR198 3.9 9.5 1.0
OE1 A:GLU104 4.0 10.2 1.0
O19 A:E1G302 4.1 24.0 1.0
NE2 A:HIS117 4.2 7.9 1.0
C4 A:E1G302 4.2 26.2 1.0
CG A:HIS91 4.2 11.1 1.0
CG A:HIS93 4.2 8.7 1.0
ND1 A:HIS91 4.3 10.8 1.0
ND1 A:HIS93 4.3 8.9 1.0
CD2 A:HIS117 4.3 8.4 1.0
C5 A:E1G302 4.5 27.7 1.0
CD A:GLU104 4.9 10.2 1.0

Zinc binding site 2 out of 4 in 4kp8

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Zinc binding site 2 out of 4 in the Crystal Structure of Catalytic Domain of Human Carbonic Anhydrase Isozyme XII with 3-[(Pyrimidin-2-Ylsulfanyl)Acetyl]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 Catalytic Domain of Human Carbonic Anhydrase Isozyme XII with 3-[(Pyrimidin-2-Ylsulfanyl)Acetyl]Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:10.3
occ:1.00
 N20 B:E1G302 1.8 13.5 1.0
ND1 B:HIS117 2.0 9.5 1.0
NE2 B:HIS91 2.0 10.5 1.0
NE2 B:HIS93 2.1 8.2 1.0
CE1 B:HIS117 2.9 9.7 1.0
CD2 B:HIS91 2.9 10.7 1.0
S17 B:E1G302 3.0 15.9 1.0
CD2 B:HIS93 3.0 9.5 1.0
CE1 B:HIS93 3.1 8.2 1.0
O18 B:E1G302 3.1 15.2 1.0
CG B:HIS117 3.1 10.9 1.0
CE1 B:HIS91 3.1 10.6 1.0
CB B:HIS117 3.6 10.7 1.0
OE1 B:GLU104 3.8 11.3 1.0
OG1 B:THR198 4.0 7.4 1.0
NE2 B:HIS117 4.1 9.6 1.0
CG B:HIS91 4.1 10.4 1.0
C4 B:E1G302 4.2 14.8 1.0
O19 B:E1G302 4.2 13.3 1.0
ND1 B:HIS91 4.2 10.9 1.0
CD2 B:HIS117 4.2 10.0 1.0
ND1 B:HIS93 4.2 9.0 1.0
CG B:HIS93 4.2 8.6 1.0
O2 B:PEG303 4.7 24.2 1.0
C3 B:PEG303 4.8 26.9 1.0
CD B:GLU104 4.9 9.7 1.0
C3 B:E1G302 4.9 15.4 1.0
C5 B:E1G302 4.9 15.5 1.0

Zinc binding site 3 out of 4 in 4kp8

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Zinc binding site 3 out of 4 in the Crystal Structure of Catalytic Domain of Human Carbonic Anhydrase Isozyme XII with 3-[(Pyrimidin-2-Ylsulfanyl)Acetyl]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 Catalytic Domain of Human Carbonic Anhydrase Isozyme XII with 3-[(Pyrimidin-2-Ylsulfanyl)Acetyl]Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:9.8
occ:1.00
 NE2 C:HIS91 1.9 9.9 1.0
ND1 C:HIS117 2.0 8.4 1.0
NE2 C:HIS93 2.0 10.6 1.0
CE1 C:HIS117 2.8 9.1 1.0
CD2 C:HIS91 2.9 10.0 1.0
CE1 C:HIS91 3.0 11.0 1.0
CD2 C:HIS93 3.0 9.5 1.0
CE1 C:HIS93 3.0 10.3 1.0
CG C:HIS117 3.1 8.8 1.0
CB C:HIS117 3.6 9.2 1.0
OG1 C:THR198 3.9 10.2 1.0
NE2 C:HIS117 4.0 7.9 1.0
OE1 C:GLU104 4.0 9.1 1.0
CG C:HIS91 4.1 10.8 1.0
ND1 C:HIS91 4.1 10.8 1.0
ND1 C:HIS93 4.1 9.8 1.0
CD2 C:HIS117 4.1 8.5 1.0
CG C:HIS93 4.2 9.4 1.0
CA C:HIS117 5.0 9.3 1.0

Zinc binding site 4 out of 4 in 4kp8

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Zinc binding site 4 out of 4 in the Crystal Structure of Catalytic Domain of Human Carbonic Anhydrase Isozyme XII with 3-[(Pyrimidin-2-Ylsulfanyl)Acetyl]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 Catalytic Domain of Human Carbonic Anhydrase Isozyme XII with 3-[(Pyrimidin-2-Ylsulfanyl)Acetyl]Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:9.9
occ:1.00
 N20 D:E1G302 1.8 14.1 1.0
ND1 D:HIS117 2.0 7.7 1.0
NE2 D:HIS91 2.1 9.2 1.0
NE2 D:HIS93 2.1 7.1 1.0
CE1 D:HIS117 2.9 8.0 1.0
S17 D:E1G302 3.0 17.6 1.0
O18 D:E1G302 3.0 15.4 1.0
CD2 D:HIS91 3.0 8.9 1.0
CE1 D:HIS91 3.1 9.0 1.0
CE1 D:HIS93 3.1 7.7 1.0
CD2 D:HIS93 3.1 8.2 1.0
CG D:HIS117 3.2 8.2 1.0
CB D:HIS117 3.7 8.1 1.0
OE1 D:GLU104 3.8 9.7 1.0
OG1 D:THR198 4.0 8.4 1.0
NE2 D:HIS117 4.1 9.1 1.0
O19 D:E1G302 4.1 13.9 1.0
C4 D:E1G302 4.2 19.0 1.0
ND1 D:HIS91 4.2 8.7 1.0
CG D:HIS91 4.2 9.2 1.0
CD2 D:HIS117 4.2 7.9 1.0
ND1 D:HIS93 4.3 8.2 1.0
CG D:HIS93 4.3 7.8 1.0
C2 D:PEG303 4.5 22.0 1.0
CD D:GLU104 4.8 9.8 1.0
C5 D:E1G302 4.8 19.1 1.0
C3 D:E1G302 5.0 19.6 1.0

Reference:

E.Capkauskaite, A.Zubriene, A.Smirnov, J.Torresan, M.Kisonaite, J.Kazokaite, J.Gylyte, V.Michailoviene, V.Jogaite, E.Manakova, S.Grazulis, S.Tumkevicius, D.Matulis. Benzenesulfonamides with Pyrimidine Moiety As Inhibitors of Human Carbonic Anhydrases I, II, VI, VII, XII, and XIII Bioorg.Med.Chem. V. 21 6937 2013.
ISSN: ISSN 0968-0896
PubMed: 24103428
DOI: 10.1016/J.BMC.2013.09.029
Page generated: Sun Oct 27 01:20:59 2024

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