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Zinc in PDB 1ddz: X-Ray Structure of A Beta-Carbonic Anhydrase From the Red Alga, Porphyridium Purpureum R-1

Enzymatic activity of X-Ray Structure of A Beta-Carbonic Anhydrase From the Red Alga, Porphyridium Purpureum R-1

All present enzymatic activity of X-Ray Structure of A Beta-Carbonic Anhydrase From the Red Alga, Porphyridium Purpureum R-1:
4.2.1.1;

Protein crystallography data

The structure of X-Ray Structure of A Beta-Carbonic Anhydrase From the Red Alga, Porphyridium Purpureum R-1, PDB code: 1ddz was solved by S.Mitsuhashi, T.Mizushima, E.Yamashita, S.Miyachi, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.500, 112.800, 73.200, 90.00, 103.60, 90.00
R / Rfree (%) 20.8 / 27.4

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Structure of A Beta-Carbonic Anhydrase From the Red Alga, Porphyridium Purpureum R-1 (pdb code 1ddz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the X-Ray Structure of A Beta-Carbonic Anhydrase From the Red Alga, Porphyridium Purpureum R-1, PDB code: 1ddz:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1ddz

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Zinc binding site 1 out of 4 in the X-Ray Structure of A Beta-Carbonic Anhydrase From the Red Alga, Porphyridium Purpureum R-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of A Beta-Carbonic Anhydrase From the Red Alga, Porphyridium Purpureum R-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:28.6
occ:1.00
OD2 A:ASP151 1.9 31.9 1.0
NE2 A:HIS205 2.0 7.0 1.0
SG A:CYS208 2.3 16.4 1.0
SG A:CYS149 2.4 17.0 1.0
CE1 A:HIS205 2.8 7.0 1.0
CG A:ASP151 3.0 34.7 1.0
CB A:CYS208 3.1 12.1 1.0
O A:HOH881 3.2 33.2 1.0
CD2 A:HIS205 3.2 7.0 1.0
CA A:CYS208 3.3 12.9 1.0
CB A:CYS149 3.6 9.0 1.0
OD1 A:ASP151 3.6 42.6 1.0
N A:GLY209 3.7 13.1 1.0
C A:CYS208 3.8 15.3 1.0
ND1 A:HIS205 4.0 9.6 1.0
O A:HOH589 4.1 15.4 1.0
CG A:HIS205 4.2 8.7 1.0
N A:GLY210 4.2 13.2 1.0
CB A:ASP151 4.3 31.8 1.0
O A:ASP151 4.4 38.8 1.0
N A:CYS208 4.5 14.5 1.0
N A:ASP151 4.6 21.4 1.0
CA A:ASP151 4.7 29.0 1.0
C A:ASP151 4.7 34.4 1.0
CA A:GLY209 4.8 8.7 1.0
O A:CYS208 4.8 15.0 1.0
N A:ALA174 4.8 9.8 1.0
CA A:ALA174 4.8 8.2 1.0
CA A:CYS149 5.0 13.5 1.0

Zinc binding site 2 out of 4 in 1ddz

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Zinc binding site 2 out of 4 in the X-Ray Structure of A Beta-Carbonic Anhydrase From the Red Alga, Porphyridium Purpureum R-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of A Beta-Carbonic Anhydrase From the Red Alga, Porphyridium Purpureum R-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:13.5
occ:1.00
OD2 A:ASP405 1.8 17.0 1.0
NE2 A:HIS459 2.0 8.0 1.0
SG A:CYS462 2.3 19.4 1.0
SG A:CYS403 2.3 17.8 1.0
CG A:ASP405 2.8 19.9 1.0
CE1 A:HIS459 2.8 9.4 1.0
CD2 A:HIS459 3.1 11.0 1.0
O A:HOH880 3.2 35.5 1.0
CB A:ASP405 3.3 22.5 1.0
CB A:CYS403 3.3 9.5 1.0
CB A:CYS462 3.3 12.5 1.0
CA A:CYS462 3.7 14.8 1.0
OD1 A:ASP405 3.9 22.7 1.0
N A:GLY463 4.0 11.1 1.0
ND1 A:HIS459 4.0 10.7 1.0
O A:HOH638 4.0 30.9 1.0
C A:CYS462 4.1 11.8 1.0
CG A:HIS459 4.2 8.5 1.0
N A:GLY464 4.3 8.6 1.0
O A:HOH575 4.3 9.8 1.0
N A:ASP405 4.4 24.7 1.0
CA A:ASP405 4.4 30.1 1.0
CA A:CYS403 4.7 11.1 1.0
N A:ALA428 4.8 16.0 1.0
CA A:ALA428 4.9 9.6 1.0
N A:CYS462 5.0 20.2 1.0

Zinc binding site 3 out of 4 in 1ddz

Go back to Zinc Binding Sites List in 1ddz
Zinc binding site 3 out of 4 in the X-Ray Structure of A Beta-Carbonic Anhydrase From the Red Alga, Porphyridium Purpureum R-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Structure of A Beta-Carbonic Anhydrase From the Red Alga, Porphyridium Purpureum R-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3

b:14.7
occ:1.00
NE2 B:HIS205 1.9 10.3 1.0
OD2 B:ASP151 1.9 31.1 1.0
SG B:CYS149 2.3 11.9 1.0
SG B:CYS208 2.3 16.2 1.0
CE1 B:HIS205 2.8 9.6 1.0
CD2 B:HIS205 3.0 7.0 1.0
CG B:ASP151 3.1 31.1 1.0
CB B:CYS208 3.2 7.0 1.0
CB B:CYS149 3.3 11.4 1.0
CA B:CYS208 3.4 11.8 1.0
O B:HOH822 3.6 39.7 1.0
OD1 B:ASP151 3.6 39.0 1.0
O B:HOH873 3.9 40.9 1.0
ND1 B:HIS205 3.9 12.3 1.0
N B:GLY209 3.9 13.2 1.0
C B:CYS208 4.1 12.2 1.0
CG B:HIS205 4.1 13.0 1.0
O B:ASP151 4.2 41.0 1.0
O B:HOH600 4.2 7.0 1.0
CB B:ASP151 4.2 29.7 1.0
N B:ASP151 4.4 18.1 1.0
N B:GLY210 4.5 8.0 1.0
C B:ASP151 4.5 33.5 1.0
CA B:ASP151 4.6 28.8 1.0
N B:CYS208 4.7 13.3 1.0
CA B:CYS149 4.7 11.4 1.0
OG B:SER152 4.8 50.8 1.0
N B:ALA174 4.9 11.5 1.0
CA B:ALA174 4.9 8.4 1.0

Zinc binding site 4 out of 4 in 1ddz

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Zinc binding site 4 out of 4 in the X-Ray Structure of A Beta-Carbonic Anhydrase From the Red Alga, Porphyridium Purpureum R-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Structure of A Beta-Carbonic Anhydrase From the Red Alga, Porphyridium Purpureum R-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4

b:29.5
occ:1.00
OD2 B:ASP405 1.9 31.4 1.0
NE2 B:HIS459 1.9 9.3 1.0
SG B:CYS403 2.3 17.2 1.0
SG B:CYS462 2.3 19.6 1.0
CE1 B:HIS459 2.8 7.0 1.0
CG B:ASP405 2.9 33.3 1.0
CD2 B:HIS459 3.0 8.4 1.0
CB B:CYS403 3.2 7.0 1.0
CB B:CYS462 3.3 13.0 1.0
CB B:ASP405 3.4 27.7 1.0
O B:HOH872 3.5 37.0 1.0
CA B:CYS462 3.7 14.9 1.0
ND1 B:HIS459 3.9 7.0 1.0
OD1 B:ASP405 4.0 33.6 1.0
CG B:HIS459 4.0 8.8 1.0
N B:GLY463 4.1 13.3 1.0
O B:HOH586 4.2 15.8 1.0
C B:CYS462 4.2 13.0 1.0
O B:HOH649 4.2 28.6 1.0
N B:GLY464 4.4 8.5 1.0
N B:ASP405 4.5 25.6 1.0
CA B:ASP405 4.5 31.2 1.0
CA B:CYS403 4.6 11.2 1.0
N B:ALA428 4.8 15.7 1.0
CA B:ALA428 4.8 11.8 1.0
N B:CYS462 4.9 18.2 1.0
C B:CYS403 5.0 11.2 1.0

Reference:

S.Mitsuhashi, T.Mizushima, E.Yamashita, M.Yamamoto, T.Kumasaka, H.Moriyama, T.Ueki, S.Miyachi, T.Tsukihara. X-Ray Structure of Beta-Carbonic Anhydrase From the Red Alga, Porphyridium Purpureum, Reveals A Novel Catalytic Site For Co(2) Hydration. J.Biol.Chem. V. 275 5521 2000.
ISSN: ISSN 0021-9258
PubMed: 10681531
DOI: 10.1074/JBC.275.8.5521
Page generated: Mon Jan 25 16:08:19 2021

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