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Zinc in PDB 6g98: Three Dimensional Structure of Human Carbonic Anhydrase IX in Complex with Sulfonamide

Enzymatic activity of Three Dimensional Structure of Human Carbonic Anhydrase IX in Complex with Sulfonamide

All present enzymatic activity of Three Dimensional Structure of Human Carbonic Anhydrase IX in Complex with Sulfonamide:
4.2.1.1;

Protein crystallography data

The structure of Three Dimensional Structure of Human Carbonic Anhydrase IX in Complex with Sulfonamide, PDB code: 6g98 was solved by J.Leitans, K.Tars, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 76.19 / 2.47
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 152.390, 152.390, 171.830, 90.00, 90.00, 120.00
R / Rfree (%) 16.9 / 20.9

Other elements in 6g98:

The structure of Three Dimensional Structure of Human Carbonic Anhydrase IX in Complex with Sulfonamide also contains other interesting chemical elements:

Fluorine (F) 12 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Three Dimensional Structure of Human Carbonic Anhydrase IX in Complex with Sulfonamide (pdb code 6g98). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Three Dimensional Structure of Human Carbonic Anhydrase IX in Complex with Sulfonamide, PDB code: 6g98:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6g98

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Zinc binding site 1 out of 4 in the Three Dimensional Structure of Human Carbonic Anhydrase IX in Complex with Sulfonamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Three Dimensional Structure of Human Carbonic Anhydrase IX in Complex with Sulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:25.1
occ:1.00
 N40 A:ER5302 2.0 38.4 1.0
NE2 A:HIS96 2.1 23.7 1.0
NE2 A:HIS94 2.1 24.8 1.0
ND1 A:HIS119 2.1 20.8 1.0
CE1 A:HIS119 2.9 21.5 1.0
CD2 A:HIS94 3.0 25.2 1.0
CD2 A:HIS96 3.0 23.6 1.0
CE1 A:HIS96 3.1 23.1 1.0
CE1 A:HIS94 3.1 23.9 1.0
S37 A:ER5302 3.2 39.6 1.0
CG A:HIS119 3.3 20.2 1.0
C7 A:ER5302 3.4 40.9 1.0
F13 A:ER5302 3.6 42.2 1.0
C12 A:ER5302 3.6 40.8 1.0
O38 A:ER5302 3.6 38.8 1.0
CB A:HIS119 3.7 19.8 1.0
OE2 A:GLU106 4.0 36.8 1.0
OG1 A:THR199 4.0 29.8 1.0
NE2 A:HIS119 4.1 20.9 1.0
CG A:HIS94 4.2 24.4 1.0
ND1 A:HIS96 4.2 23.7 1.0
CG A:HIS96 4.2 25.2 1.0
ND1 A:HIS94 4.2 24.3 1.0
CD2 A:HIS119 4.3 21.1 1.0
C8 A:ER5302 4.3 40.7 1.0
O39 A:ER5302 4.4 38.0 1.0
C11 A:ER5302 4.6 43.3 1.0
CD A:GLU106 4.7 36.1 1.0
CH2 A:TRP209 4.8 20.8 1.0
N16 A:ER5302 4.9 44.0 1.0

Zinc binding site 2 out of 4 in 6g98

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Zinc binding site 2 out of 4 in the Three Dimensional Structure of Human Carbonic Anhydrase IX in Complex with Sulfonamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Three Dimensional Structure of Human Carbonic Anhydrase IX in Complex with Sulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:27.1
occ:1.00
 NE2 B:HIS94 2.0 31.2 1.0
N40 B:ER5302 2.1 40.9 1.0
ND1 B:HIS119 2.1 27.4 1.0
NE2 B:HIS96 2.1 28.2 1.0
CD2 B:HIS94 2.9 32.8 1.0
CE1 B:HIS119 3.0 28.0 1.0
CE1 B:HIS94 3.0 32.4 1.0
CD2 B:HIS96 3.1 28.3 1.0
S37 B:ER5302 3.1 42.0 1.0
CE1 B:HIS96 3.1 29.1 1.0
CG B:HIS119 3.2 26.5 1.0
O38 B:ER5302 3.4 39.0 1.0
C7 B:ER5302 3.4 47.1 1.0
F13 B:ER5302 3.5 55.4 1.0
CB B:HIS119 3.6 28.4 1.0
C12 B:ER5302 3.6 51.2 1.0
OE2 B:GLU106 3.7 41.0 1.0
ND1 B:HIS94 4.1 31.6 1.0
CG B:HIS94 4.1 32.7 1.0
NE2 B:HIS119 4.1 27.5 1.0
ND1 B:HIS96 4.2 30.0 1.0
CG B:HIS96 4.2 30.4 1.0
OG1 B:THR199 4.2 25.6 1.0
CD2 B:HIS119 4.2 26.1 1.0
O39 B:ER5302 4.4 38.5 1.0
C8 B:ER5302 4.4 49.2 1.0
CH2 B:TRP209 4.6 26.0 1.0
C11 B:ER5302 4.6 52.9 1.0
CD B:GLU106 4.8 37.7 1.0
N16 B:ER5302 4.9 52.4 1.0

Zinc binding site 3 out of 4 in 6g98

Go back to Zinc Binding Sites List in 6g98
Zinc binding site 3 out of 4 in the Three Dimensional Structure of Human Carbonic Anhydrase IX in Complex with Sulfonamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Three Dimensional Structure of Human Carbonic Anhydrase IX in Complex with Sulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:29.4
occ:1.00
 N40 C:ER5302 1.9 42.7 1.0
NE2 C:HIS94 2.1 32.4 1.0
ND1 C:HIS119 2.1 28.7 1.0
NE2 C:HIS96 2.1 33.5 1.0
CE1 C:HIS119 2.9 29.1 1.0
CE1 C:HIS94 3.0 31.1 1.0
CD2 C:HIS96 3.1 33.4 1.0
CE1 C:HIS96 3.1 32.5 1.0
CD2 C:HIS94 3.1 31.7 1.0
S37 C:ER5302 3.1 41.5 1.0
CG C:HIS119 3.2 29.8 1.0
C7 C:ER5302 3.4 44.2 1.0
O39 C:ER5302 3.4 42.8 1.0
F13 C:ER5302 3.6 53.4 1.0
C12 C:ER5302 3.7 47.3 1.0
CB C:HIS119 3.7 28.8 1.0
OE2 C:GLU106 3.8 44.4 1.0
OG1 C:THR199 4.0 36.1 1.0
NE2 C:HIS119 4.1 27.3 1.0
ND1 C:HIS94 4.1 32.0 1.0
CG C:HIS94 4.2 32.2 1.0
ND1 C:HIS96 4.2 32.4 1.0
CG C:HIS96 4.2 34.2 1.0
CD2 C:HIS119 4.2 28.1 1.0
O38 C:ER5302 4.3 39.3 1.0
C8 C:ER5302 4.4 41.9 1.0
CD C:GLU106 4.6 43.8 1.0
CH2 C:TRP209 4.7 27.1 1.0
C11 C:ER5302 4.7 45.9 1.0
N16 C:ER5302 4.9 43.2 1.0

Zinc binding site 4 out of 4 in 6g98

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Zinc binding site 4 out of 4 in the Three Dimensional Structure of Human Carbonic Anhydrase IX in Complex with Sulfonamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Three Dimensional Structure of Human Carbonic Anhydrase IX in Complex with Sulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:35.0
occ:1.00
 NE2 D:HIS94 2.0 27.6 1.0
ND1 D:HIS119 2.0 30.3 1.0
NE2 D:HIS96 2.1 39.9 1.0
N40 D:ER5302 2.2 39.7 1.0
CE1 D:HIS119 2.8 31.5 1.0
CE1 D:HIS94 2.8 29.6 1.0
CD2 D:HIS94 3.0 31.6 1.0
CD2 D:HIS96 3.1 39.8 1.0
CG D:HIS119 3.1 30.1 1.0
CE1 D:HIS96 3.1 39.9 1.0
S37 D:ER5302 3.1 41.9 1.0
C7 D:ER5302 3.4 42.7 1.0
O38 D:ER5302 3.5 43.4 1.0
F13 D:ER5302 3.5 46.0 1.0
CB D:HIS119 3.6 29.7 1.0
C12 D:ER5302 3.6 43.9 1.0
OE2 D:GLU106 4.0 45.0 1.0
NE2 D:HIS119 4.0 31.0 1.0
ND1 D:HIS94 4.0 29.9 1.0
OG1 D:THR199 4.0 32.8 1.0
CG D:HIS94 4.1 31.8 1.0
CD2 D:HIS119 4.1 30.3 1.0
ND1 D:HIS96 4.2 39.3 1.0
CG D:HIS96 4.2 37.9 1.0
C8 D:ER5302 4.3 41.9 1.0
O39 D:ER5302 4.4 45.1 1.0
CH2 D:TRP209 4.6 31.3 1.0
C11 D:ER5302 4.6 42.4 1.0
CD D:GLU106 4.8 42.7 1.0
N16 D:ER5302 4.9 44.2 1.0

Reference:

J.Kazokaite, R.Niemans, V.Dudutiene, H.M.Becker, J.Leitans, A.Zubriene, L.Baranauskiene, G.Gondi, R.Zeidler, J.Matuliene, K.Tars, A.Yaromina, P.Lambin, L.J.Dubois, D.Matulis. Novel Fluorinated Carbonic Anhydrase IX Inhibitors Reduce Hypoxia-Induced Acidification and Clonogenic Survival of Cancer Cells. Oncotarget V. 9 26800 2018.
ISSN: ESSN 1949-2553
PubMed: 29928486
DOI: 10.18632/ONCOTARGET.25508
Page generated: Mon Oct 28 21:42:57 2024

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