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Zinc in PDB 4qjo: 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: 4qjo 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) 23.59 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.498, 66.558, 80.318, 81.98, 84.31, 86.45
R / Rfree (%) 16.1 / 20.6

Other elements in 4qjo:

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

Fluorine (F) 12 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 4qjo). 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: 4qjo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4qjo

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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 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:Zn302

b:10.8
occ:1.00
 NE2 A:HIS91 2.0 8.2 1.0
NE2 A:HIS93 2.1 8.2 1.0
ND1 A:HIS117 2.1 8.4 1.0
N10 A:V1F303 2.3 16.2 1.0
F12 A:V1F303 2.7 34.7 1.0
S7 A:V1F303 3.0 19.7 1.0
CD2 A:HIS91 3.0 8.3 1.0
CD2 A:HIS93 3.0 8.1 1.0
CE1 A:HIS117 3.1 9.2 1.0
CE1 A:HIS91 3.1 9.3 1.0
CE1 A:HIS93 3.1 8.2 1.0
O9 A:V1F303 3.1 18.6 1.0
CG A:HIS117 3.1 8.7 1.0
C3 A:V1F303 3.4 32.7 1.0
CB A:HIS117 3.5 8.9 1.0
C4 A:V1F303 3.6 28.3 1.0
OE1 A:GLU104 3.9 9.3 1.0
OG1 A:THR198 4.0 7.9 1.0
ND1 A:HIS93 4.2 9.3 1.0
ND1 A:HIS91 4.2 8.9 1.0
CG A:HIS91 4.2 9.3 1.0
NE2 A:HIS117 4.2 9.0 1.0
CG A:HIS93 4.2 8.9 1.0
CD2 A:HIS117 4.3 8.6 1.0
O8 A:V1F303 4.4 18.5 1.0
C2 A:V1F303 4.6 44.7 1.0
C5 A:V1F303 4.9 35.1 1.0
CD A:GLU104 4.9 9.5 1.0
CA A:HIS117 5.0 8.2 1.0

Zinc binding site 2 out of 4 in 4qjo

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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:Zn303

b:10.1
occ:1.00
 N10 B:V1F304 1.8 17.8 1.0
NE2 B:HIS91 2.1 11.2 1.0
NE2 B:HIS93 2.1 8.0 1.0
ND1 B:HIS117 2.1 9.2 1.0
CE1 B:HIS117 3.0 8.3 1.0
CD2 B:HIS91 3.0 10.8 1.0
CD2 B:HIS93 3.0 8.3 1.0
S7 B:V1F304 3.0 17.9 1.0
O9 B:V1F304 3.1 14.7 1.0
CE1 B:HIS93 3.1 8.5 1.0
CE1 B:HIS91 3.1 11.6 1.0
CG B:HIS117 3.2 8.7 1.0
CB B:HIS117 3.6 8.3 1.0
OE1 B:GLU104 3.8 11.6 1.0
OG1 B:THR198 4.0 7.8 1.0
NE2 B:HIS117 4.1 8.8 1.0
CG B:HIS91 4.2 10.7 1.0
C4 B:V1F304 4.2 24.4 1.0
CG B:HIS93 4.2 7.8 1.0
ND1 B:HIS91 4.2 10.6 1.0
ND1 B:HIS93 4.2 8.3 1.0
O8 B:V1F304 4.2 14.7 1.0
CD2 B:HIS117 4.3 8.3 1.0
F26 B:V1F304 4.6 34.4 1.0
C5 B:V1F304 4.8 27.5 1.0
CD B:GLU104 4.8 11.0 1.0
CH2 B:TRP208 4.9 9.9 1.0
C27 B:V1F304 4.9 33.7 1.0

Zinc binding site 3 out of 4 in 4qjo

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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 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:9.8
occ:1.00
 N10 C:V1F302 1.9 16.9 1.0
NE2 C:HIS93 1.9 8.5 1.0
NE2 C:HIS91 2.0 9.9 1.0
ND1 C:HIS117 2.1 8.0 1.0
F12 C:V1F302 2.6 38.7 1.0
CD2 C:HIS93 2.9 8.5 1.0
CD2 C:HIS91 2.9 10.8 1.0
CE1 C:HIS93 3.0 8.4 1.0
S7 C:V1F302 3.0 21.7 1.0
CE1 C:HIS91 3.0 10.5 1.0
CG C:HIS117 3.1 8.4 1.0
CE1 C:HIS117 3.1 7.8 1.0
O9 C:V1F302 3.2 18.2 1.0
CB C:HIS117 3.4 7.9 1.0
C3 C:V1F302 3.5 31.8 1.0
C4 C:V1F302 3.7 30.9 1.0
OG1 C:THR198 3.9 7.6 1.0
OE1 C:GLU104 3.9 9.0 1.0
CG C:HIS93 4.1 8.7 1.0
ND1 C:HIS93 4.1 9.2 1.0
CG C:HIS91 4.1 10.1 1.0
ND1 C:HIS91 4.1 11.1 1.0
O8 C:V1F302 4.1 19.2 1.0
NE2 C:HIS117 4.2 7.5 1.0
CD2 C:HIS117 4.2 8.3 1.0
C2 C:V1F302 4.7 42.8 1.0
C5 C:V1F302 4.9 32.4 1.0
CA C:HIS117 4.9 8.3 1.0
CD C:GLU104 4.9 9.2 1.0

Zinc binding site 4 out of 4 in 4qjo

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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 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:11.7
occ:1.00
 N10 D:V1F302 1.7 16.3 1.0
NE2 D:HIS91 2.0 13.5 1.0
ND1 D:HIS117 2.1 8.2 1.0
NE2 D:HIS93 2.1 9.5 1.0
CE1 D:HIS117 2.9 7.8 1.0
CD2 D:HIS93 3.0 9.4 1.0
CD2 D:HIS91 3.0 12.4 1.0
CE1 D:HIS91 3.0 12.9 1.0
S7 D:V1F302 3.0 20.4 1.0
O9 D:V1F302 3.1 17.2 1.0
CG D:HIS117 3.1 7.9 1.0
CE1 D:HIS93 3.1 9.5 1.0
CB D:HIS117 3.6 8.1 1.0
OE1 D:GLU104 3.8 11.8 1.0
OG1 D:THR198 4.1 9.7 1.0
NE2 D:HIS117 4.1 8.5 1.0
CG D:HIS91 4.2 12.6 1.0
ND1 D:HIS91 4.2 12.1 1.0
O8 D:V1F302 4.2 19.2 1.0
CG D:HIS93 4.2 9.2 1.0
C4 D:V1F302 4.2 32.4 1.0
ND1 D:HIS93 4.2 9.7 1.0
CD2 D:HIS117 4.2 8.2 1.0
F26 D:V1F302 4.5 52.3 1.0
C5 D:V1F302 4.8 40.9 1.0
CD D:GLU104 4.8 11.5 1.0
CH2 D:TRP208 5.0 9.1 1.0
CA D:HIS117 5.0 8.9 1.0

Reference:

V.Dudutiene, A.Zubriene, A.Smirnov, D.D.Timm, J.Smirnoviene, J.Kazokaite, V.Michailoviene, A.Zaksauskas, E.Manakova, S.Grazulis, D.Matulis. Functionalization of Fluorinated Benzenesulfonamides and Their Inhibitory Properties Toward Carbonic Anhydrases Chemmedchem V. 10 662 2015.
ISSN: ISSN 1860-7179
PubMed: 25758852
DOI: 10.1002/CMDC.201402490
Page generated: Wed Aug 20 21:50:03 2025

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