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Zinc in PDB 5dvx: Crystal Structure of the Catalytic-Domain of Human Carbonic Anhydrase IX at 1.6 Angstrom Resolution

Enzymatic activity of Crystal Structure of the Catalytic-Domain of Human Carbonic Anhydrase IX at 1.6 Angstrom Resolution

All present enzymatic activity of Crystal Structure of the Catalytic-Domain of Human Carbonic Anhydrase IX at 1.6 Angstrom Resolution:
4.2.1.1;

Protein crystallography data

The structure of Crystal Structure of the Catalytic-Domain of Human Carbonic Anhydrase IX at 1.6 Angstrom Resolution, PDB code: 5dvx was solved by B.P.Mahon, L.Socorro, J.M.Driscoll, R.Mckenna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.84 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.877, 102.744, 108.964, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 19.1

Other elements in 5dvx:

The structure of Crystal Structure of the Catalytic-Domain of Human Carbonic Anhydrase IX at 1.6 Angstrom Resolution also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Catalytic-Domain of Human Carbonic Anhydrase IX at 1.6 Angstrom Resolution (pdb code 5dvx). 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 the Catalytic-Domain of Human Carbonic Anhydrase IX at 1.6 Angstrom Resolution, PDB code: 5dvx:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5dvx

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Zinc binding site 1 out of 4 in the Crystal Structure of the Catalytic-Domain of Human Carbonic Anhydrase IX at 1.6 Angstrom Resolution


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 the Catalytic-Domain of Human Carbonic Anhydrase IX at 1.6 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:8.6
occ:1.00
 O A:HOH606 1.9 9.6 1.0
NE2 A:HIS226 2.0 5.9 1.0
ND1 A:HIS251 2.0 7.0 1.0
NE2 A:HIS228 2.1 7.6 1.0
CE1 A:HIS251 2.9 7.7 1.0
CD2 A:HIS226 3.0 6.7 1.0
CE1 A:HIS228 3.1 8.0 1.0
CE1 A:HIS226 3.1 8.6 1.0
CD2 A:HIS228 3.1 7.8 1.0
CG A:HIS251 3.2 6.4 1.0
CB A:HIS251 3.6 9.3 1.0
O A:HOH662 3.8 10.0 1.0
OG1 A:THR332 3.9 9.3 1.0
OE2 A:GLU238 3.9 9.2 1.0
NE2 A:HIS251 4.0 8.0 1.0
CG A:HIS226 4.1 7.1 1.0
ND1 A:HIS226 4.1 8.1 1.0
ND1 A:HIS228 4.2 9.1 1.0
CD2 A:HIS251 4.2 6.1 1.0
CG A:HIS228 4.2 7.7 1.0
O A:HOH705 4.2 12.1 1.0
CD A:GLU238 4.8 11.1 1.0
O A:HOH835 5.0 9.9 1.0

Zinc binding site 2 out of 4 in 5dvx

Go back to Zinc Binding Sites List in 5dvx
Zinc binding site 2 out of 4 in the Crystal Structure of the Catalytic-Domain of Human Carbonic Anhydrase IX at 1.6 Angstrom Resolution


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 the Catalytic-Domain of Human Carbonic Anhydrase IX at 1.6 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:11.3
occ:1.00
 ND1 A:HIS140 2.0 16.6 0.5
NE2 A:HIS200 2.1 9.2 1.0
N A:TRP141 2.2 29.6 1.0
O A:TRP141 2.3 11.5 1.0
CE1 A:HIS140 2.5 33.5 0.5
CA A:TRP141 2.9 15.2 1.0
C A:TRP141 2.9 11.8 1.0
CE1 A:HIS200 3.0 10.0 1.0
C A:HIS140 3.0 50.4 1.0
CD2 A:HIS200 3.1 10.4 1.0
CG A:HIS140 3.1 44.0 0.5
CG A:TRP141 3.4 12.1 1.0
CD1 A:TRP141 3.5 11.6 1.0
CA A:HIS140 3.5 43.6 1.0
CB A:TRP141 3.7 13.1 1.0
NE2 A:HIS140 3.8 22.5 0.5
CD2 A:TRP141 3.8 10.0 1.0
CB A:HIS140 3.9 48.0 1.0
NE1 A:TRP141 3.9 10.8 1.0
CD2 A:HIS140 4.1 43.9 0.5
O A:HIS140 4.1 66.0 1.0
ND1 A:HIS200 4.1 11.4 1.0
CE2 A:TRP141 4.1 12.0 1.0
CG A:HIS200 4.2 9.0 1.0
N A:ARG142 4.2 11.6 1.0
CE3 A:TRP141 4.5 11.4 1.0
CG A:PRO366 4.7 11.8 1.0
ND1 A:HIS140 4.7 16.6 0.5
CG A:HIS140 4.8 44.0 0.5
O A:HOH571 4.9 18.4 1.0
O A:HOH682 5.0 16.2 1.0
N A:HIS140 5.0 54.2 1.0

Zinc binding site 3 out of 4 in 5dvx

Go back to Zinc Binding Sites List in 5dvx
Zinc binding site 3 out of 4 in the Crystal Structure of the Catalytic-Domain of Human Carbonic Anhydrase IX at 1.6 Angstrom Resolution


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 the Catalytic-Domain of Human Carbonic Anhydrase IX at 1.6 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn409

b:12.5
occ:1.00
 N B:TRP141 2.1 13.6 1.0
NE2 A:HIS244 2.1 10.3 1.0
NE2 B:HIS200 2.1 10.3 1.0
O B:HOH671 2.1 16.4 1.0
O B:TRP141 2.3 13.7 1.0
CE1 B:HIS200 3.0 11.6 1.0
C B:TRP141 3.0 13.0 1.0
CA B:TRP141 3.0 14.2 1.0
CE1 A:HIS244 3.0 9.2 1.0
CD2 A:HIS244 3.1 13.3 1.0
CD2 B:HIS200 3.1 11.2 1.0
CG B:TRP141 3.3 11.7 1.0
CD1 B:TRP141 3.4 12.3 1.0
CB B:TRP141 3.7 15.2 1.0
CD2 B:TRP141 3.7 9.7 1.0
NE1 B:TRP141 3.9 12.9 1.0
CE2 B:TRP141 4.1 9.8 1.0
O A:HOH803 4.1 20.2 1.0
ND1 B:HIS200 4.1 14.2 1.0
O A:HOH581 4.1 33.9 1.0
ND1 A:HIS244 4.1 10.1 1.0
CG A:HIS244 4.2 11.5 1.0
CG B:HIS200 4.2 8.9 1.0
N B:ARG142 4.3 13.5 1.0
CE3 B:TRP141 4.5 13.3 1.0
O A:GLU242 4.7 13.3 1.0
CG B:PRO366 4.7 12.3 1.0
OE2 A:GLU242 4.9 22.2 1.0
CA B:ARG142 5.0 12.0 1.0

Zinc binding site 4 out of 4 in 5dvx

Go back to Zinc Binding Sites List in 5dvx
Zinc binding site 4 out of 4 in the Crystal Structure of the Catalytic-Domain of Human Carbonic Anhydrase IX at 1.6 Angstrom Resolution


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 the Catalytic-Domain of Human Carbonic Anhydrase IX at 1.6 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:10.1
occ:1.00
 O B:HOH575 1.9 10.6 1.0
ND1 B:HIS251 2.0 9.1 1.0
NE2 B:HIS226 2.0 7.5 1.0
NE2 B:HIS228 2.1 9.2 1.0
CE1 B:HIS251 2.9 9.1 1.0
CD2 B:HIS226 3.0 8.3 1.0
CE1 B:HIS228 3.0 8.8 1.0
CD2 B:HIS228 3.0 9.2 1.0
CE1 B:HIS226 3.1 12.7 1.0
CG B:HIS251 3.1 8.2 1.0
CB B:HIS251 3.6 10.2 1.0
O B:HOH571 3.8 11.5 1.0
OG1 B:THR332 3.9 10.1 1.0
OE2 B:GLU238 3.9 10.8 1.0
NE2 B:HIS251 4.0 9.8 1.0
CG B:HIS226 4.1 9.3 1.0
ND1 B:HIS226 4.2 11.2 1.0
ND1 B:HIS228 4.2 8.9 1.0
O B:HOH665 4.2 14.2 1.0
CD2 B:HIS251 4.2 11.9 1.0
CG B:HIS228 4.2 8.9 1.0
CD B:GLU238 4.8 9.2 1.0

Reference:

B.P.Mahon, A.Bhatt, L.Socorro, J.M.Driscoll, C.Okoh, C.L.Lomelino, M.Y.Mboge, J.J.Kurian, C.Tu, M.Agbandje-Mckenna, S.C.Frost, R.Mckenna. The Structure of Carbonic Anhydrase IX Is Adapted For Low-pH Catalysis. Biochemistry V. 55 4642 2016.
ISSN: ISSN 0006-2960
PubMed: 27439028
DOI: 10.1021/ACS.BIOCHEM.6B00243
Page generated: Sun Oct 27 14:55:48 2024

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