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Zinc in PDB 2a8d: Haemophilus Influenzae Beta-Carbonic Anhydrase Complexed with Bicarbonate

Enzymatic activity of Haemophilus Influenzae Beta-Carbonic Anhydrase Complexed with Bicarbonate

All present enzymatic activity of Haemophilus Influenzae Beta-Carbonic Anhydrase Complexed with Bicarbonate:
4.2.1.1;

Protein crystallography data

The structure of Haemophilus Influenzae Beta-Carbonic Anhydrase Complexed with Bicarbonate, PDB code: 2a8d was solved by J.D.Cronk, R.S.Rowlett, K.Y.J.Zhang, C.Tu, J.A.Endrizzi, J.Lee, P.C.Gareiss, J.R.Preiss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 232.807, 144.602, 52.101, 90.00, 94.10, 90.00
R / Rfree (%) 20.6 / 24

Zinc Binding Sites:

The binding sites of Zinc atom in the Haemophilus Influenzae Beta-Carbonic Anhydrase Complexed with Bicarbonate (pdb code 2a8d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Haemophilus Influenzae Beta-Carbonic Anhydrase Complexed with Bicarbonate, PDB code: 2a8d:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2a8d

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Zinc binding site 1 out of 6 in the Haemophilus Influenzae Beta-Carbonic Anhydrase Complexed with Bicarbonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Haemophilus Influenzae Beta-Carbonic Anhydrase Complexed with Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1230

b:31.2
occ:1.00
 OD2 A:ASP44 2.0 26.9 1.0
NE2 A:HIS98 2.0 33.0 1.0
SG A:CYS42 2.4 27.7 1.0
SG A:CYS101 2.4 32.1 1.0
CE1 A:HIS98 2.7 30.6 1.0
CG A:ASP44 2.9 29.1 1.0
CD2 A:HIS98 3.1 29.5 1.0
CB A:CYS42 3.2 26.7 1.0
CB A:CYS101 3.3 32.4 1.0
CB A:ASP44 3.3 27.1 1.0
CA A:CYS101 3.6 33.5 1.0
ND1 A:HIS98 3.9 33.4 1.0
OD1 A:ASP44 4.0 31.1 1.0
N A:GLY102 4.0 30.8 1.0
CG A:HIS98 4.1 31.5 1.0
C A:CYS101 4.1 32.6 1.0
O A:HOH1236 4.3 27.6 1.0
N A:GLY103 4.4 29.7 1.0
N A:ASP44 4.4 28.6 1.0
CA A:ASP44 4.5 30.6 1.0
CA A:CYS42 4.6 27.6 1.0
O A:HOH1239 4.8 32.3 1.0
N A:ALA67 4.8 25.3 1.0
CA A:ALA67 4.9 27.8 1.0
N A:CYS101 4.9 36.7 1.0

Zinc binding site 2 out of 6 in 2a8d

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Zinc binding site 2 out of 6 in the Haemophilus Influenzae Beta-Carbonic Anhydrase Complexed with Bicarbonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Haemophilus Influenzae Beta-Carbonic Anhydrase Complexed with Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2230

b:40.4
occ:1.00
 OD2 B:ASP44 1.9 27.9 1.0
NE2 B:HIS98 2.1 44.6 1.0
SG B:CYS101 2.2 35.4 1.0
SG B:CYS42 2.3 35.6 1.0
CG B:ASP44 2.9 32.5 1.0
CE1 B:HIS98 3.0 43.2 1.0
CD2 B:HIS98 3.1 43.0 1.0
CB B:CYS42 3.2 36.1 1.0
CB B:CYS101 3.3 39.0 1.0
CB B:ASP44 3.3 34.9 1.0
CA B:CYS101 3.7 41.8 1.0
OD1 B:ASP44 4.0 28.8 1.0
N B:GLY102 4.0 39.1 1.0
ND1 B:HIS98 4.1 43.2 1.0
C B:CYS101 4.2 39.3 1.0
CG B:HIS98 4.2 42.4 1.0
O B:HOH2240 4.2 37.1 1.0
N B:GLY103 4.4 38.0 1.0
N B:ASP44 4.5 34.3 1.0
CA B:ASP44 4.5 36.1 1.0
CA B:CYS42 4.7 33.8 1.0
O B:HOH2248 4.8 40.2 1.0
N B:ALA67 4.9 29.5 1.0
CA B:ALA67 4.9 29.0 1.0
N B:CYS101 5.0 42.5 1.0

Zinc binding site 3 out of 6 in 2a8d

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Zinc binding site 3 out of 6 in the Haemophilus Influenzae Beta-Carbonic Anhydrase Complexed with Bicarbonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Haemophilus Influenzae Beta-Carbonic Anhydrase Complexed with Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn3230

b:46.8
occ:1.00
 SG C:CYS101 2.2 43.8 1.0
SG C:CYS42 2.2 44.6 1.0
OD2 C:ASP44 2.3 43.4 1.0
NE2 C:HIS98 2.3 52.8 1.0
CE1 C:HIS98 2.9 50.1 1.0
CB C:CYS42 3.2 41.5 1.0
CG C:ASP44 3.2 44.4 1.0
CB C:CYS101 3.3 45.6 1.0
CD2 C:HIS98 3.4 50.8 1.0
CB C:ASP44 3.4 43.8 1.0
CA C:CYS101 3.8 46.6 1.0
ND1 C:HIS98 4.0 51.7 1.0
N C:GLY102 4.1 43.0 1.0
O C:HOH3245 4.1 33.4 1.0
C C:CYS101 4.3 45.4 1.0
CG C:HIS98 4.3 50.5 1.0
OD1 C:ASP44 4.4 45.8 1.0
N C:GLY103 4.5 41.5 1.0
N C:ASP44 4.5 41.8 1.0
CA C:ASP44 4.6 43.8 1.0
CA C:CYS42 4.6 40.5 1.0
N C:ALA67 4.8 35.6 1.0
CA C:ALA67 4.8 34.8 1.0
O C:HOH3242 5.0 38.8 1.0

Zinc binding site 4 out of 6 in 2a8d

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Zinc binding site 4 out of 6 in the Haemophilus Influenzae Beta-Carbonic Anhydrase Complexed with Bicarbonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Haemophilus Influenzae Beta-Carbonic Anhydrase Complexed with Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn4230

b:38.7
occ:1.00
 OD2 D:ASP44 2.0 34.9 1.0
NE2 D:HIS98 2.1 30.9 1.0
SG D:CYS101 2.3 35.5 1.0
SG D:CYS42 2.4 30.3 1.0
CE1 D:HIS98 2.9 29.6 1.0
CG D:ASP44 2.9 34.3 1.0
CB D:CYS42 3.1 26.6 1.0
CD2 D:HIS98 3.1 29.2 1.0
CB D:CYS101 3.2 34.9 1.0
CB D:ASP44 3.2 32.1 1.0
CA D:CYS101 3.6 36.6 1.0
ND1 D:HIS98 4.0 31.4 1.0
OD1 D:ASP44 4.1 33.1 1.0
N D:GLY102 4.1 35.5 1.0
CG D:HIS98 4.2 31.4 1.0
O D:HOH4242 4.2 29.4 1.0
C D:CYS101 4.2 36.6 1.0
N D:ASP44 4.4 32.4 1.0
CA D:ASP44 4.4 33.9 1.0
N D:GLY103 4.4 31.8 1.0
CA D:CYS42 4.6 30.0 1.0
O D:HOH4233 4.7 29.1 1.0
N D:ALA67 4.8 30.4 1.0
CA D:ALA67 4.8 31.4 1.0
OD1 D:ASN68 4.9 31.1 1.0
N D:CYS101 4.9 39.8 1.0

Zinc binding site 5 out of 6 in 2a8d

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Zinc binding site 5 out of 6 in the Haemophilus Influenzae Beta-Carbonic Anhydrase Complexed with Bicarbonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Haemophilus Influenzae Beta-Carbonic Anhydrase Complexed with Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn5230

b:46.1
occ:1.00
 SG E:CYS101 2.0 38.7 1.0
NE2 E:HIS98 2.2 58.4 1.0
SG E:CYS42 2.3 50.0 1.0
OD2 E:ASP44 2.3 45.5 1.0
CE1 E:HIS98 2.9 56.6 1.0
CB E:CYS42 3.2 46.7 1.0
CG E:ASP44 3.2 43.5 1.0
CD2 E:HIS98 3.3 57.3 1.0
CB E:CYS101 3.3 46.2 1.0
CB E:ASP44 3.6 41.9 1.0
CA E:CYS101 3.8 46.9 1.0
ND1 E:HIS98 4.0 57.8 1.0
N E:GLY102 4.1 44.3 1.0
O E:HOH5246 4.2 42.8 1.0
CG E:HIS98 4.2 57.5 1.0
C E:CYS101 4.3 45.1 1.0
OD1 E:ASP44 4.3 48.3 1.0
N E:GLY103 4.4 42.8 1.0
N E:ASP44 4.5 41.0 1.0
CA E:CYS42 4.6 45.5 1.0
CA E:ASP44 4.7 43.8 1.0
N E:ALA67 4.8 39.8 1.0
CA E:ALA67 4.8 37.5 1.0
O E:HOH5261 4.9 46.1 1.0

Zinc binding site 6 out of 6 in 2a8d

Go back to Zinc Binding Sites List in 2a8d
Zinc binding site 6 out of 6 in the Haemophilus Influenzae Beta-Carbonic Anhydrase Complexed with Bicarbonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Haemophilus Influenzae Beta-Carbonic Anhydrase Complexed with Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn6230

b:37.0
occ:1.00
 OD2 F:ASP44 2.0 32.5 1.0
NE2 F:HIS98 2.0 36.5 1.0
SG F:CYS101 2.4 38.9 1.0
SG F:CYS42 2.4 30.1 1.0
CE1 F:HIS98 2.8 36.8 1.0
CG F:ASP44 3.0 31.8 1.0
CD2 F:HIS98 3.1 37.9 1.0
CB F:CYS42 3.2 29.2 1.0
CB F:CYS101 3.2 41.1 1.0
CB F:ASP44 3.4 31.5 1.0
CA F:CYS101 3.6 42.1 1.0
ND1 F:HIS98 3.9 38.6 1.0
N F:GLY102 4.0 39.6 1.0
OD1 F:ASP44 4.1 32.7 1.0
CG F:HIS98 4.1 39.0 1.0
C F:CYS101 4.2 41.2 1.0
O F:HOH6242 4.3 31.4 1.0
N F:ASP44 4.5 35.4 1.0
N F:GLY103 4.5 37.6 1.0
CA F:ASP44 4.5 35.1 1.0
CA F:CYS42 4.6 31.4 1.0
O F:HOH6234 4.6 36.0 1.0
N F:ALA67 4.8 34.2 1.0
N F:CYS101 4.9 44.4 1.0
CA F:ALA67 4.9 36.1 1.0

Reference:

J.D.Cronk, R.S.Rowlett, K.Y.J.Zhang, C.Tu, J.A.Endrizzi, J.Lee, P.C.Gareiss, J.R.Preiss. Identification of A Novel Noncatalytic Bicarbonate Binding Site in Eubacterial Beta-Carbonic Anhydrase Biochemistry V. 45 4351 2006.
ISSN: ISSN 0006-2960
PubMed: 16584170
DOI: 10.1021/BI052272Q
Page generated: Wed Oct 16 21:33:41 2024

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