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Zinc in PDB 3e2w: H. Influenzae Beta-Carbonic Anhydrase, Variant Y181F with 1M Bicarbonate

Enzymatic activity of H. Influenzae Beta-Carbonic Anhydrase, Variant Y181F with 1M Bicarbonate

All present enzymatic activity of H. Influenzae Beta-Carbonic Anhydrase, Variant Y181F with 1M Bicarbonate:
4.2.1.1;

Protein crystallography data

The structure of H. Influenzae Beta-Carbonic Anhydrase, Variant Y181F with 1M Bicarbonate, PDB code: 3e2w was solved by R.S.Rowlett, J.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.20 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 250.141, 145.225, 53.499, 90.00, 93.78, 90.00
R / Rfree (%) 20.5 / 24.2

Zinc Binding Sites:

The binding sites of Zinc atom in the H. Influenzae Beta-Carbonic Anhydrase, Variant Y181F with 1M Bicarbonate (pdb code 3e2w). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the H. Influenzae Beta-Carbonic Anhydrase, Variant Y181F with 1M Bicarbonate, PDB code: 3e2w:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3e2w

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Zinc binding site 1 out of 6 in the H. Influenzae Beta-Carbonic Anhydrase, Variant Y181F with 1M Bicarbonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of H. Influenzae Beta-Carbonic Anhydrase, Variant Y181F with 1M Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn230

b:67.5
occ:1.00
OD1 A:ASP44 2.0 70.0 1.0
NE2 A:HIS98 2.1 65.9 1.0
SG A:CYS101 2.3 65.5 1.0
SG A:CYS42 2.3 65.8 1.0
CG A:ASP44 2.9 69.8 1.0
CE1 A:HIS98 2.9 65.0 1.0
OD2 A:ASP44 3.1 70.9 1.0
CD2 A:HIS98 3.2 65.6 1.0
CB A:CYS101 3.4 66.7 1.0
CB A:CYS42 3.4 66.0 1.0
CA A:CYS101 3.7 66.9 1.0
N A:GLY102 4.0 66.8 1.0
ND1 A:HIS98 4.1 63.4 1.0
O A:HOH243 4.2 54.7 1.0
C A:CYS101 4.2 66.8 1.0
CB A:ASP44 4.2 69.5 1.0
CG A:HIS98 4.2 64.6 1.0
N A:GLY103 4.4 67.4 1.0
N A:SER45 4.4 71.8 1.0
C A:ASP44 4.4 70.6 1.0
CA A:ASP44 4.6 69.8 1.0
N A:ASP44 4.7 69.2 1.0
CA A:ALA67 4.8 64.5 1.0
N A:ALA67 4.8 64.3 1.0
CA A:CYS42 4.8 66.3 1.0
O A:ASP44 4.9 70.6 1.0
OD1 A:ASN68 4.9 64.9 1.0

Zinc binding site 2 out of 6 in 3e2w

Go back to Zinc Binding Sites List in 3e2w
Zinc binding site 2 out of 6 in the H. Influenzae Beta-Carbonic Anhydrase, Variant Y181F with 1M Bicarbonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of H. Influenzae Beta-Carbonic Anhydrase, Variant Y181F with 1M Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn230

b:65.0
occ:1.00
OD2 B:ASP44 2.0 67.8 1.0
NE2 B:HIS98 2.1 63.5 1.0
SG B:CYS42 2.3 64.8 1.0
SG B:CYS101 2.5 65.0 1.0
CE1 B:HIS98 2.9 63.4 1.0
CG B:ASP44 2.9 67.9 1.0
CD2 B:HIS98 3.2 64.5 1.0
CB B:ASP44 3.3 68.9 1.0
CB B:CYS42 3.4 64.3 1.0
CB B:CYS101 3.5 65.6 1.0
CA B:CYS101 3.8 66.0 1.0
OD1 B:ASP44 3.9 70.3 1.0
N B:GLY102 4.0 65.8 1.0
ND1 B:HIS98 4.0 62.8 1.0
CG B:HIS98 4.2 64.8 1.0
C B:CYS101 4.3 66.0 1.0
O B:HOH232 4.3 45.5 1.0
N B:GLY103 4.5 65.5 1.0
CA B:ASP44 4.5 68.5 1.0
N B:ASP44 4.6 67.6 1.0
N B:SER45 4.7 71.7 1.0
CA B:CYS42 4.8 64.4 1.0
N B:ALA67 4.9 61.7 1.0
CA B:ALA67 4.9 61.9 1.0
OD1 B:ASN68 5.0 58.7 1.0

Zinc binding site 3 out of 6 in 3e2w

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Zinc binding site 3 out of 6 in the H. Influenzae Beta-Carbonic Anhydrase, Variant Y181F with 1M Bicarbonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of H. Influenzae Beta-Carbonic Anhydrase, Variant Y181F with 1M Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn230

b:66.8
occ:1.00
OD2 C:ASP44 2.0 71.2 1.0
NE2 C:HIS98 2.1 66.6 1.0
SG C:CYS42 2.3 64.3 1.0
SG C:CYS101 2.3 67.1 1.0
CG C:ASP44 2.8 70.5 1.0
CE1 C:HIS98 2.9 65.1 1.0
CB C:ASP44 3.1 70.3 1.0
CD2 C:HIS98 3.2 65.1 1.0
CB C:CYS101 3.3 67.1 1.0
CB C:CYS42 3.3 64.6 1.0
CA C:CYS101 3.6 67.2 1.0
OD1 C:ASP44 3.9 74.6 1.0
ND1 C:HIS98 4.0 65.6 1.0
N C:GLY102 4.1 67.4 1.0
C C:CYS101 4.2 67.5 1.0
CG C:HIS98 4.2 64.9 1.0
CA C:ASP44 4.2 70.0 1.0
N C:ASP44 4.2 68.7 1.0
O C:HOH234 4.4 44.7 1.0
CA C:CYS42 4.7 65.0 1.0
N C:GLY103 4.7 68.2 1.0
C C:ASP44 4.9 70.9 1.0
N C:CYS101 4.9 67.3 1.0
N C:SER45 4.9 71.0 1.0
N C:ALA67 4.9 63.9 1.0

Zinc binding site 4 out of 6 in 3e2w

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Zinc binding site 4 out of 6 in the H. Influenzae Beta-Carbonic Anhydrase, Variant Y181F with 1M Bicarbonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of H. Influenzae Beta-Carbonic Anhydrase, Variant Y181F with 1M Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn230

b:66.5
occ:1.00
OD2 D:ASP44 2.0 64.5 1.0
NE2 D:HIS98 2.1 65.5 1.0
SG D:CYS101 2.3 65.0 1.0
SG D:CYS42 2.3 61.2 1.0
CG D:ASP44 2.8 64.3 1.0
CE1 D:HIS98 2.9 65.9 1.0
OD1 D:ASP44 3.1 65.8 1.0
CD2 D:HIS98 3.3 64.7 1.0
CB D:CYS42 3.3 61.6 1.0
CB D:CYS101 3.3 66.3 1.0
CA D:CYS101 3.7 66.2 1.0
N D:GLY102 4.0 66.5 1.0
C D:ASP44 4.0 64.3 1.0
CB D:ASP44 4.1 63.9 1.0
ND1 D:HIS98 4.1 64.9 1.0
N D:SER45 4.1 65.1 1.0
C D:CYS101 4.2 66.4 1.0
CA D:ASP44 4.3 63.6 1.0
CG D:HIS98 4.3 64.6 1.0
O D:HOH238 4.3 51.4 1.0
N D:ASP44 4.3 63.1 1.0
O D:ASP44 4.4 64.6 1.0
N D:GLY103 4.4 66.2 1.0
CA D:CYS42 4.7 61.4 1.0
CA D:SER45 4.9 65.2 1.0
C D:CYS42 5.0 61.5 1.0

Zinc binding site 5 out of 6 in 3e2w

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Zinc binding site 5 out of 6 in the H. Influenzae Beta-Carbonic Anhydrase, Variant Y181F with 1M Bicarbonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of H. Influenzae Beta-Carbonic Anhydrase, Variant Y181F with 1M Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn230

b:64.5
occ:1.00
OD2 E:ASP44 2.0 62.5 1.0
NE2 E:HIS98 2.1 62.9 1.0
SG E:CYS101 2.3 64.8 1.0
SG E:CYS42 2.3 61.7 1.0
CG E:ASP44 2.7 64.9 1.0
OD1 E:ASP44 2.8 66.6 1.0
CE1 E:HIS98 2.8 63.2 1.0
CD2 E:HIS98 3.3 62.8 1.0
CB E:CYS42 3.3 61.6 1.0
CB E:CYS101 3.3 64.3 1.0
CA E:CYS101 3.8 64.4 1.0
ND1 E:HIS98 4.0 62.6 1.0
CB E:ASP44 4.0 65.0 1.0
N E:GLY102 4.1 64.4 1.0
C E:CYS101 4.2 64.3 1.0
O E:HOH254 4.2 51.4 1.0
CG E:HIS98 4.3 63.1 1.0
C E:ASP44 4.3 66.4 1.0
N E:GLY103 4.4 64.5 1.0
CA E:ASP44 4.4 65.5 1.0
N E:ASP44 4.4 64.5 1.0
N E:SER45 4.4 67.7 1.0
O E:ASP44 4.6 65.9 1.0
CA E:CYS42 4.7 61.9 1.0
OD1 E:ASN68 5.0 60.7 1.0
O E:CYS101 5.0 64.2 1.0

Zinc binding site 6 out of 6 in 3e2w

Go back to Zinc Binding Sites List in 3e2w
Zinc binding site 6 out of 6 in the H. Influenzae Beta-Carbonic Anhydrase, Variant Y181F with 1M Bicarbonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of H. Influenzae Beta-Carbonic Anhydrase, Variant Y181F with 1M Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn230

b:68.4
occ:1.00
OD2 F:ASP44 2.0 70.1 1.0
NE2 F:HIS98 2.1 66.1 1.0
SG F:CYS42 2.3 65.2 1.0
SG F:CYS101 2.3 64.5 1.0
CG F:ASP44 2.8 70.0 1.0
OD1 F:ASP44 2.9 73.0 1.0
CE1 F:HIS98 3.0 65.4 1.0
CD2 F:HIS98 3.1 65.3 1.0
CB F:CYS101 3.3 66.1 1.0
CB F:CYS42 3.3 65.4 1.0
CA F:CYS101 3.6 66.1 1.0
ND1 F:HIS98 4.1 64.3 1.0
N F:GLY102 4.2 66.2 1.0
CB F:ASP44 4.2 70.3 1.0
CG F:HIS98 4.2 65.0 1.0
C F:CYS101 4.2 66.1 1.0
O F:HOH237 4.4 47.6 1.0
N F:ASP44 4.5 69.0 1.0
N F:GLY103 4.6 66.8 1.0
CA F:ASP44 4.6 70.1 1.0
C F:ASP44 4.6 71.2 1.0
CA F:CYS42 4.7 65.5 1.0
N F:SER45 4.8 72.2 1.0
N F:CYS101 4.9 66.1 1.0
N F:ALA67 4.9 63.1 1.0
O F:ASP44 5.0 71.8 1.0

Reference:

R.S.Rowlett, C.Tu, J.Lee, A.G.Herman, D.A.Chapnick, S.H.Shah, P.C.Gareiss. Allosteric Site Variants of Haemophilus Influenzae Beta-Carbonic Anhydrase. Biochemistry V. 48 6146 2009.
ISSN: ISSN 0006-2960
PubMed: 19459702
DOI: 10.1021/BI900663H
Page generated: Wed Dec 16 04:14:45 2020

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