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Zinc in PDB 4q0l: Crystal Structure of Catalytic Domain of Human Carbonic Anhydrase Isozyme XII with Inhibitor

Enzymatic activity of Crystal Structure of Catalytic Domain of Human Carbonic Anhydrase Isozyme XII with Inhibitor

All present enzymatic activity of Crystal Structure of Catalytic Domain of Human Carbonic Anhydrase Isozyme XII with Inhibitor:
4.2.1.1;

Protein crystallography data

The structure of Crystal Structure of Catalytic Domain of Human Carbonic Anhydrase Isozyme XII with Inhibitor, PDB code: 4q0l 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) 22.09 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.520, 75.211, 77.888, 109.42, 101.60, 107.95
R / Rfree (%) 26.4 / 32.8

Other elements in 4q0l:

The structure of Crystal Structure of Catalytic Domain of Human Carbonic Anhydrase Isozyme XII with Inhibitor also contains other interesting chemical elements:

Fluorine (F) 15 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Catalytic Domain of Human Carbonic Anhydrase Isozyme XII with Inhibitor (pdb code 4q0l). 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 Inhibitor, PDB code: 4q0l:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4q0l

Go back to Zinc Binding Sites List in 4q0l
Zinc binding site 1 out of 4 in the Crystal Structure of Catalytic Domain of Human Carbonic Anhydrase Isozyme XII with Inhibitor


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 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:13.0
occ:1.00
 N10 A:V14302 1.9 22.1 1.0
NE2 A:HIS91 1.9 17.6 1.0
ND1 A:HIS117 1.9 10.2 1.0
NE2 A:HIS93 2.1 12.2 1.0
CE1 A:HIS117 2.8 10.8 1.0
CE1 A:HIS91 2.9 17.4 1.0
CD2 A:HIS91 2.9 16.3 1.0
CD2 A:HIS93 2.9 12.0 1.0
CG A:HIS117 3.0 10.8 1.0
F12 A:V14302 3.0 21.6 1.0
S7 A:V14302 3.1 23.5 1.0
CE1 A:HIS93 3.2 12.2 1.0
O9 A:V14302 3.3 24.1 1.0
CB A:HIS117 3.5 10.4 1.0
C3 A:V14302 3.7 25.5 1.0
C4 A:V14302 3.8 25.0 1.0
OE1 A:GLU104 3.9 13.8 1.0
NE2 A:HIS117 4.0 11.4 1.0
ND1 A:HIS91 4.0 15.8 1.0
OG1 A:THR198 4.1 11.5 1.0
CG A:HIS91 4.1 16.4 1.0
CD2 A:HIS117 4.1 10.3 1.0
CG A:HIS93 4.2 11.9 1.0
ND1 A:HIS93 4.3 12.0 1.0
O8 A:V14302 4.4 24.2 1.0
CH2 A:TRP208 4.8 10.9 1.0
CD A:GLU104 4.9 13.8 1.0
C2 A:V14302 4.9 26.8 1.0
CA A:HIS117 4.9 11.1 1.0

Zinc binding site 2 out of 4 in 4q0l

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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 Inhibitor


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 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:14.0
occ:1.00
 ND1 B:HIS117 2.0 9.8 1.0
N10 B:V14302 2.0 13.2 1.0
NE2 B:HIS91 2.1 9.4 1.0
NE2 B:HIS93 2.3 10.2 1.0
CE1 B:HIS117 2.9 10.2 1.0
CD2 B:HIS91 2.9 9.7 1.0
F12 B:V14302 3.0 18.4 1.0
S7 B:V14302 3.0 15.4 1.0
CD2 B:HIS93 3.0 10.2 1.0
O9 B:V14302 3.0 13.2 1.0
CG B:HIS117 3.1 10.2 1.0
CE1 B:HIS91 3.3 10.0 1.0
OE1 B:GLU104 3.5 12.7 1.0
CE1 B:HIS93 3.5 9.9 1.0
CB B:HIS117 3.6 9.6 1.0
C3 B:V14302 3.6 17.4 1.0
C4 B:V14302 3.7 16.8 1.0
OG1 B:THR198 3.9 10.2 1.0
NE2 B:HIS117 4.1 10.7 1.0
CD2 B:HIS117 4.2 10.0 1.0
CG B:HIS91 4.2 9.9 1.0
CG B:HIS93 4.3 10.6 1.0
ND1 B:HIS91 4.3 9.4 1.0
O8 B:V14302 4.4 13.3 1.0
ND1 B:HIS93 4.5 10.5 1.0
CD B:GLU104 4.5 11.5 1.0
C2 B:V14302 4.8 17.7 1.0
CH2 B:TRP208 4.9 9.1 1.0
C5 B:V14302 4.9 19.0 1.0

Zinc binding site 3 out of 4 in 4q0l

Go back to Zinc Binding Sites List in 4q0l
Zinc binding site 3 out of 4 in the Crystal Structure of Catalytic Domain of Human Carbonic Anhydrase Isozyme XII with Inhibitor


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 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:14.2
occ:1.00
 ND1 C:HIS117 1.9 9.8 1.0
N10 C:V14302 2.0 21.0 1.0
NE2 C:HIS93 2.1 10.5 1.0
NE2 C:HIS91 2.2 15.3 1.0
CE1 C:HIS117 2.8 10.4 1.0
CG C:HIS117 3.0 10.6 1.0
CD2 C:HIS91 3.0 14.3 1.0
CE1 C:HIS93 3.0 10.7 1.0
F12 C:V14302 3.0 22.4 1.0
CD2 C:HIS93 3.1 10.9 1.0
S7 C:V14302 3.1 21.8 1.0
CE1 C:HIS91 3.2 14.2 1.0
O9 C:V14302 3.3 20.3 1.0
CB C:HIS117 3.4 10.3 1.0
C3 C:V14302 3.6 24.3 1.0
C4 C:V14302 3.7 23.0 1.0
OE1 C:GLU104 3.9 14.9 1.0
NE2 C:HIS117 3.9 11.1 1.0
OG1 C:THR198 4.0 11.6 1.0
CD2 C:HIS117 4.1 10.3 1.0
CG C:HIS91 4.1 13.8 1.0
ND1 C:HIS93 4.2 11.3 1.0
ND1 C:HIS91 4.2 13.5 1.0
CG C:HIS93 4.2 11.3 1.0
O8 C:V14302 4.4 20.7 1.0
CH2 C:TRP208 4.7 11.2 1.0
C2 C:V14302 4.7 24.5 1.0
CD C:GLU104 4.8 14.2 1.0
CA C:HIS117 4.9 10.9 1.0
C5 C:V14302 4.9 25.7 1.0

Zinc binding site 4 out of 4 in 4q0l

Go back to Zinc Binding Sites List in 4q0l
Zinc binding site 4 out of 4 in the Crystal Structure of Catalytic Domain of Human Carbonic Anhydrase Isozyme XII with Inhibitor


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 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:11.6
occ:1.00
 ND1 D:HIS117 1.8 9.0 1.0
N10 D:V14302 1.9 15.4 0.5
N10 D:V14302 1.9 13.0 0.5
NE2 D:HIS91 2.0 9.1 1.0
NE2 D:HIS93 2.2 12.0 1.0
CE1 D:HIS117 2.7 9.6 1.0
F12 D:V14302 3.0 19.6 0.5
CD2 D:HIS91 3.0 9.3 1.0
S7 D:V14302 3.0 16.9 0.5
CG D:HIS117 3.0 9.6 1.0
F12 D:V14302 3.0 16.1 0.5
CE1 D:HIS91 3.0 10.1 1.0
CD2 D:HIS93 3.1 11.4 1.0
O9 D:V14302 3.1 15.6 0.5
S7 D:V14302 3.2 13.7 0.5
CE1 D:HIS93 3.3 11.5 1.0
OE1 D:GLU104 3.5 14.1 1.0
O9 D:V14302 3.5 13.0 0.5
CB D:HIS117 3.5 9.3 1.0
C3 D:V14302 3.6 18.6 0.5
C3 D:V14302 3.7 14.7 0.5
C4 D:V14302 3.7 18.0 0.5
C4 D:V14302 3.8 14.6 0.5
NE2 D:HIS117 3.9 9.6 1.0
OG1 D:THR198 3.9 11.0 1.0
CD2 D:HIS117 4.0 9.3 1.0
CG D:HIS91 4.1 10.0 1.0
ND1 D:HIS91 4.1 9.6 1.0
O8 D:V14302 4.3 15.8 0.5
CG D:HIS93 4.3 12.2 1.0
ND1 D:HIS93 4.4 12.5 1.0
CD D:GLU104 4.5 12.8 1.0
O8 D:V14302 4.5 12.9 0.5
C2 D:V14302 4.8 15.0 0.5
C2 D:V14302 4.8 19.3 0.5
C5 D:V14302 5.0 19.7 0.5
CA D:HIS117 5.0 9.7 1.0
CH2 D:TRP208 5.0 8.4 1.0

Reference:

V.Dudutiene, J.Matuliene, A.Smirnov, D.D.Timm, A.Zubriene, L.Baranauskiene, V.Morkunaite, J.Smirnoviene, V.Michailoviene, V.Juozapaitiene, A.Mickeviciute, J.Kazokaite, S.Baksyte, A.Kasiliauskaite, J.Jachno, J.Revuckiene, M.Kisonaite, V.Pilipuityte, E.Ivanauskaite, G.Milinaviciute, V.Smirnovas, V.Petrikaite, V.Kairys, V.Petrauskas, P.Norvaisas, D.Linge, P.Gibieza, E.Capkauskaite, A.Zaksauskas, E.Kazlauskas, E.Manakova, S.Grazulis, J.E.Ladbury, D.Matulis. Discovery and Characterization of Novel Selective Inhibitors of Carbonic Anhydrase IX. J.Med.Chem. V. 57 9435 2014.
ISSN: ISSN 0022-2623
PubMed: 25358084
DOI: 10.1021/JM501003K
Page generated: Sun Oct 27 06:13:04 2024

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