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Zinc in PDB 3kwc: Oxidized, Active Structure of the Beta-Carboxysomal Gamma-Carbonic Anhydrase, Ccmm

Enzymatic activity of Oxidized, Active Structure of the Beta-Carboxysomal Gamma-Carbonic Anhydrase, Ccmm

All present enzymatic activity of Oxidized, Active Structure of the Beta-Carboxysomal Gamma-Carbonic Anhydrase, Ccmm:
4.2.1.1;

Protein crystallography data

The structure of Oxidized, Active Structure of the Beta-Carboxysomal Gamma-Carbonic Anhydrase, Ccmm, PDB code: 3kwc was solved by M.S.Kimber, S.E.Castel, K.L.Pena, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 16.88 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.900, 105.040, 196.130, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 24.7

Other elements in 3kwc:

The structure of Oxidized, Active Structure of the Beta-Carboxysomal Gamma-Carbonic Anhydrase, Ccmm also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Oxidized, Active Structure of the Beta-Carboxysomal Gamma-Carbonic Anhydrase, Ccmm (pdb code 3kwc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Oxidized, Active Structure of the Beta-Carboxysomal Gamma-Carbonic Anhydrase, Ccmm, PDB code: 3kwc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3kwc

Go back to Zinc Binding Sites List in 3kwc
Zinc binding site 1 out of 6 in the Oxidized, Active Structure of the Beta-Carboxysomal Gamma-Carbonic Anhydrase, Ccmm


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Oxidized, Active Structure of the Beta-Carboxysomal Gamma-Carbonic Anhydrase, Ccmm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn300

b:32.7
occ:1.00
O A:HOH244 2.3 19.4 1.0
ND1 A:HIS75 2.3 23.8 1.0
O C:HOH832 2.3 34.4 1.0
NE2 A:HIS107 2.3 24.5 1.0
NE2 C:HIS102 2.4 24.6 1.0
CE1 A:HIS75 3.1 23.9 1.0
CE1 A:HIS107 3.2 25.5 1.0
CE1 C:HIS102 3.4 24.7 1.0
CG A:HIS75 3.4 25.6 1.0
CD2 A:HIS107 3.4 27.6 1.0
CD2 C:HIS102 3.4 23.5 1.0
CB A:HIS75 3.8 25.9 1.0
O C:HOH232 4.0 21.7 1.0
OE1 C:GLN69 4.1 24.8 1.0
NE2 A:HIS75 4.2 25.9 1.0
OE1 A:GLU56 4.3 29.0 1.0
ND1 A:HIS107 4.4 27.1 1.0
CD2 A:HIS75 4.4 24.6 1.0
CG A:HIS107 4.5 25.0 1.0
ND1 C:HIS102 4.5 25.2 1.0
CG C:HIS102 4.6 25.6 1.0
CZ C:PHE120 4.7 27.6 1.0
N A:GLY76 4.7 25.5 1.0
CE2 C:PHE120 4.7 26.4 1.0
O A:GLY76 4.7 24.1 1.0
O A:HOH664 4.8 37.0 1.0
C A:GLY76 4.9 24.6 1.0
CD C:GLN69 5.0 25.4 1.0

Zinc binding site 2 out of 6 in 3kwc

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Zinc binding site 2 out of 6 in the Oxidized, Active Structure of the Beta-Carboxysomal Gamma-Carbonic Anhydrase, Ccmm


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Oxidized, Active Structure of the Beta-Carboxysomal Gamma-Carbonic Anhydrase, Ccmm within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn300

b:38.2
occ:1.00
NE2 B:HIS107 2.3 25.3 1.0
NE2 A:HIS102 2.3 27.0 1.0
ND1 B:HIS75 2.4 25.3 1.0
O B:HOH874 2.5 34.2 1.0
O2 A:IPA301 2.7 33.6 1.0
CE1 B:HIS75 3.1 21.4 1.0
CE1 A:HIS102 3.2 26.9 1.0
CE1 B:HIS107 3.2 23.5 1.0
CD2 B:HIS107 3.2 24.3 1.0
CD2 A:HIS102 3.4 25.0 1.0
CG B:HIS75 3.5 24.7 1.0
C1 A:IPA301 3.6 34.1 1.0
C2 A:IPA301 3.7 34.0 1.0
OE1 A:GLN69 3.9 28.2 1.0
CB B:HIS75 4.0 24.6 1.0
O B:HOH225 4.2 22.2 1.0
NE2 B:HIS75 4.3 23.8 1.0
ND1 B:HIS107 4.3 22.8 1.0
ND1 A:HIS102 4.4 25.9 1.0
CG B:HIS107 4.4 24.2 1.0
CG A:HIS102 4.5 25.8 1.0
CD2 B:HIS75 4.5 24.7 1.0
CZ A:PHE120 4.6 26.1 1.0
CE2 A:PHE120 4.7 26.8 1.0
OE1 B:GLU56 4.8 29.4 1.0
N B:GLY76 4.8 25.2 1.0
C3 A:IPA301 4.8 34.1 1.0
O B:GLY76 4.8 24.9 1.0
CD A:GLN69 4.9 26.9 1.0
OE2 B:GLU56 4.9 33.9 1.0

Zinc binding site 3 out of 6 in 3kwc

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Zinc binding site 3 out of 6 in the Oxidized, Active Structure of the Beta-Carboxysomal Gamma-Carbonic Anhydrase, Ccmm


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Oxidized, Active Structure of the Beta-Carboxysomal Gamma-Carbonic Anhydrase, Ccmm within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn300

b:35.7
occ:1.00
NE2 C:HIS107 2.2 25.7 1.0
ND1 C:HIS75 2.4 27.1 1.0
O C:HOH616 2.4 26.7 1.0
NE2 B:HIS102 2.4 23.8 1.0
O2 B:IPA301 3.0 35.8 1.0
CE1 C:HIS75 3.1 25.9 1.0
CE1 C:HIS107 3.1 27.1 1.0
CD2 C:HIS107 3.2 27.9 1.0
CD2 B:HIS102 3.3 25.1 1.0
CE1 B:HIS102 3.4 25.8 1.0
CG C:HIS75 3.5 26.9 1.0
C1 B:IPA301 3.8 35.4 1.0
CB C:HIS75 3.9 26.1 1.0
O C:HOH833 4.0 28.8 1.0
C2 B:IPA301 4.0 35.5 1.0
OE1 B:GLN69 4.1 23.6 1.0
ND1 C:HIS107 4.2 25.1 1.0
NE2 C:HIS75 4.3 27.6 1.0
CG C:HIS107 4.3 25.4 1.0
CD2 C:HIS75 4.5 28.1 1.0
OE1 C:GLU56 4.5 25.4 0.5
CG B:HIS102 4.5 25.3 1.0
ND1 B:HIS102 4.5 25.5 1.0
CZ B:PHE120 4.7 27.1 1.0
CE2 B:PHE120 4.7 26.9 1.0
N C:GLY76 4.7 26.5 1.0
O C:GLY76 4.7 26.3 1.0
OE1 C:GLU56 4.8 27.1 0.5
C3 B:IPA301 4.8 35.8 1.0
CD B:GLN69 4.9 25.9 1.0
C C:GLY76 5.0 26.2 1.0

Zinc binding site 4 out of 6 in 3kwc

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Zinc binding site 4 out of 6 in the Oxidized, Active Structure of the Beta-Carboxysomal Gamma-Carbonic Anhydrase, Ccmm


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Oxidized, Active Structure of the Beta-Carboxysomal Gamma-Carbonic Anhydrase, Ccmm within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn300

b:36.5
occ:1.00
O F:HOH491 2.2 32.0 1.0
NE2 D:HIS107 2.2 26.9 1.0
NE2 F:HIS102 2.3 23.3 1.0
ND1 D:HIS75 2.4 26.6 1.0
O D:HOH500 2.4 19.5 1.0
CE1 D:HIS75 3.1 24.6 1.0
CE1 D:HIS107 3.1 27.2 1.0
O F:HOH590 3.2 44.3 1.0
CE1 F:HIS102 3.2 24.8 1.0
CD2 D:HIS107 3.3 25.9 1.0
CD2 F:HIS102 3.3 23.2 1.0
CG D:HIS75 3.5 25.1 1.0
CB D:HIS75 4.0 25.5 1.0
OE1 F:GLN69 4.0 28.5 1.0
O D:HOH291 4.2 27.3 1.0
ND1 D:HIS107 4.3 25.0 1.0
NE2 D:HIS75 4.3 24.1 1.0
ND1 F:HIS102 4.4 22.7 1.0
CG D:HIS107 4.4 25.5 1.0
CG F:HIS102 4.4 25.0 1.0
CD2 D:HIS75 4.5 24.2 1.0
OE2 D:GLU56 4.7 31.3 1.0
CZ F:PHE120 4.7 25.1 1.0
N D:GLY76 4.7 26.0 1.0
CE2 F:PHE120 4.7 26.2 1.0
O D:GLY76 4.8 25.8 1.0
OE1 D:GLU56 4.8 27.9 1.0
CD F:GLN69 4.9 27.4 1.0
C D:GLY76 4.9 25.9 1.0

Zinc binding site 5 out of 6 in 3kwc

Go back to Zinc Binding Sites List in 3kwc
Zinc binding site 5 out of 6 in the Oxidized, Active Structure of the Beta-Carboxysomal Gamma-Carbonic Anhydrase, Ccmm


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Oxidized, Active Structure of the Beta-Carboxysomal Gamma-Carbonic Anhydrase, Ccmm within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn300

b:29.9
occ:1.00
NE2 E:HIS107 2.2 25.8 1.0
O D:HOH787 2.3 26.6 1.0
O E:HOH258 2.3 16.7 1.0
NE2 D:HIS102 2.4 23.1 1.0
ND1 E:HIS75 2.5 26.1 1.0
CE1 E:HIS107 3.2 26.7 1.0
CD2 E:HIS107 3.2 26.5 1.0
CE1 E:HIS75 3.3 24.0 1.0
CE1 D:HIS102 3.4 25.5 1.0
CD2 D:HIS102 3.4 24.0 1.0
CG E:HIS75 3.5 25.4 1.0
O E:HOH624 3.7 44.2 1.0
CB E:HIS75 3.9 25.4 1.0
O E:HOH467 4.0 21.8 1.0
OE1 D:GLN69 4.1 27.3 1.0
ND1 E:HIS107 4.3 26.5 1.0
CG E:HIS107 4.4 25.2 1.0
OE1 E:GLU56 4.4 25.9 1.0
NE2 E:HIS75 4.5 24.3 1.0
ND1 D:HIS102 4.5 24.3 1.0
CG D:HIS102 4.6 24.4 1.0
CD2 E:HIS75 4.6 25.3 1.0
N E:GLY76 4.6 26.1 1.0
CZ D:PHE120 4.7 25.1 1.0
CE2 D:PHE120 4.7 25.9 1.0
O E:GLY76 4.7 24.7 1.0
C E:GLY76 4.8 25.2 1.0

Zinc binding site 6 out of 6 in 3kwc

Go back to Zinc Binding Sites List in 3kwc
Zinc binding site 6 out of 6 in the Oxidized, Active Structure of the Beta-Carboxysomal Gamma-Carbonic Anhydrase, Ccmm


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Oxidized, Active Structure of the Beta-Carboxysomal Gamma-Carbonic Anhydrase, Ccmm within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn300

b:35.2
occ:1.00
O F:HOH235 2.2 15.7 1.0
NE2 F:HIS107 2.2 25.9 1.0
ND1 F:HIS75 2.4 25.6 1.0
NE2 E:HIS102 2.4 26.7 1.0
O2 E:IPA301 2.8 30.4 1.0
CE1 F:HIS75 3.1 22.9 1.0
CE1 F:HIS107 3.1 26.1 1.0
CD2 F:HIS107 3.2 26.9 1.0
CD2 E:HIS102 3.4 26.2 1.0
CE1 E:HIS102 3.4 25.8 1.0
CG F:HIS75 3.5 25.6 1.0
O F:HOH792 3.9 18.5 1.0
CB F:HIS75 3.9 25.6 1.0
C2 E:IPA301 4.0 30.3 1.0
OE1 E:GLN69 4.1 25.0 1.0
C1 E:IPA301 4.1 30.0 1.0
ND1 F:HIS107 4.3 27.4 1.0
NE2 F:HIS75 4.3 24.7 1.0
CG F:HIS107 4.4 25.2 1.0
CD2 F:HIS75 4.5 25.1 1.0
ND1 E:HIS102 4.5 27.0 1.0
OE2 F:GLU56 4.6 31.4 1.0
CG E:HIS102 4.6 25.9 1.0
N F:GLY76 4.7 26.3 1.0
CZ E:PHE120 4.8 26.8 1.0
CE2 E:PHE120 4.8 26.7 1.0
OE1 F:GLU56 4.8 32.4 1.0
O F:GLY76 4.8 24.8 1.0
C F:GLY76 4.9 25.6 1.0
CD E:GLN69 4.9 25.5 1.0
CD F:GLU56 5.0 28.7 1.0

Reference:

K.L.Pena, S.E.Castel, C.De Araujo, G.S.Espie, M.S.Kimber. Structural Basis of the Oxidative Activation of the Carboxysomal {Gamma}-Carbonic Anhydrase, Ccmm. Proc.Natl.Acad.Sci.Usa V. 107 2455 2010.
ISSN: ISSN 0027-8424
PubMed: 20133749
DOI: 10.1073/PNAS.0910866107
Page generated: Wed Dec 16 04:31:16 2020

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