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Zinc in PDB 5gm3: Crystal Structure of Fi-Cmcase From Aspergillus Aculeatus F-50

Enzymatic activity of Crystal Structure of Fi-Cmcase From Aspergillus Aculeatus F-50

All present enzymatic activity of Crystal Structure of Fi-Cmcase From Aspergillus Aculeatus F-50:
3.2.1.4;

Protein crystallography data

The structure of Crystal Structure of Fi-Cmcase From Aspergillus Aculeatus F-50, PDB code: 5gm3 was solved by J.W.Huang, W.D.Liu, Y.Y.Zheng, C.C.Chen, R.T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.59
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 74.215, 75.089, 188.385, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 19

Other elements in 5gm3:

The structure of Crystal Structure of Fi-Cmcase From Aspergillus Aculeatus F-50 also contains other interesting chemical elements:

Arsenic (As) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Fi-Cmcase From Aspergillus Aculeatus F-50 (pdb code 5gm3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Fi-Cmcase From Aspergillus Aculeatus F-50, PDB code: 5gm3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5gm3

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Zinc binding site 1 out of 8 in the Crystal Structure of Fi-Cmcase From Aspergillus Aculeatus F-50


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 Fi-Cmcase From Aspergillus Aculeatus F-50 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:19.1
occ:1.00
 O2 A:CAC307 1.7 25.9 1.0
O2 A:CAC306 1.8 13.0 0.5
ND1 A:HIS185 2.0 19.1 1.0
CE1 A:HIS185 3.0 19.4 1.0
CG A:HIS185 3.1 18.7 1.0
AS A:CAC306 3.2 23.4 0.5
AS A:CAC307 3.3 23.1 1.0
CB A:HIS185 3.4 18.2 1.0
O1 A:CAC306 3.7 17.1 0.5
C2 A:CAC306 3.8 16.7 0.5
CA A:HIS185 3.9 16.6 1.0
O1 A:CAC307 3.9 22.6 1.0
C2 A:CAC307 4.1 35.6 1.0
NE2 A:HIS185 4.1 21.5 1.0
CD2 A:HIS185 4.2 21.3 1.0
OH A:TYR159 4.3 19.8 1.0
CD1 A:ILE136 4.4 19.9 1.0
O A:HIS185 4.5 22.1 1.0
O A:ASN184 4.5 21.8 1.0
C A:HIS185 4.6 15.7 1.0
C1 A:CAC307 4.8 33.4 1.0
C1 A:CAC306 4.9 22.0 0.5
N A:HIS185 5.0 17.9 1.0
CE1 A:TYR159 5.0 18.3 1.0

Zinc binding site 2 out of 8 in 5gm3

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Zinc binding site 2 out of 8 in the Crystal Structure of Fi-Cmcase From Aspergillus Aculeatus F-50


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 Fi-Cmcase From Aspergillus Aculeatus F-50 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:48.5
occ:1.00
 O A:HOH425 2.3 30.4 1.0
O A:HOH651 2.5 45.7 1.0
O A:HOH652 3.3 23.1 1.0
O A:HOH626 3.3 13.7 1.0
O A:HOH535 3.8 26.0 1.0
OD1 A:ASP116 4.2 21.6 1.0
ZN A:ZN304 4.2 32.9 1.0
NZ A:LYS157 4.3 22.8 1.0
O A:HOH508 4.4 34.2 1.0
CB A:SER155 4.5 35.5 1.0
O A:SER155 4.6 28.3 1.0
CG A:ASP116 4.8 20.0 1.0
O A:HOH646 4.9 25.2 1.0
CA A:SER155 5.0 28.5 1.0

Zinc binding site 3 out of 8 in 5gm3

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Zinc binding site 3 out of 8 in the Crystal Structure of Fi-Cmcase From Aspergillus Aculeatus F-50


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 Fi-Cmcase From Aspergillus Aculeatus F-50 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:25.6
occ:1.00
 O B:HOH419 1.8 26.8 1.0
O B:HOH615 2.1 25.1 1.0
OD2 B:ASP107 2.1 23.9 1.0
OD1 A:ASP7 2.1 19.1 1.0
O A:HOH577 2.2 25.6 1.0
OD2 A:ASP7 2.6 24.1 1.0
CG A:ASP7 2.6 23.1 1.0
CG B:ASP107 3.0 24.1 1.0
OD1 B:ASP107 3.1 19.4 1.0
O B:HOH697 4.0 40.0 1.0
ND2 B:ASN109 4.1 20.5 1.0
CB A:ASP7 4.2 18.2 1.0
O B:HOH630 4.2 33.8 1.0
CB B:ASP107 4.4 19.3 1.0
O A:HOH566 4.4 17.0 1.0
O B:HOH593 4.5 20.3 1.0
CA A:ASP7 4.8 19.5 1.0
N A:ASP7 4.9 18.3 1.0
CB B:ASN109 5.0 14.6 1.0

Zinc binding site 4 out of 8 in 5gm3

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Zinc binding site 4 out of 8 in the Crystal Structure of Fi-Cmcase From Aspergillus Aculeatus F-50


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 Fi-Cmcase From Aspergillus Aculeatus F-50 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:32.9
occ:1.00
 OD1 A:ASP116 2.0 21.6 1.0
O A:HOH605 2.3 13.7 1.0
OD2 A:ASP116 2.6 20.7 1.0
CG A:ASP116 2.6 20.0 1.0
O A:HOH646 3.2 25.2 1.0
O A:HOH626 3.3 13.7 1.0
O A:HOH652 3.3 23.1 1.0
O A:HOH425 4.1 30.4 1.0
CB A:ASP116 4.1 18.5 1.0
ZN A:ZN302 4.2 48.5 1.0
ZN A:ZN305 4.3 46.5 1.0
CB A:ALA106 4.4 18.0 1.0
N A:ALA106 4.5 15.2 1.0
CD2 A:HIS110 4.8 18.9 1.0
CA A:ASP116 4.8 16.7 1.0
O A:HOH535 4.9 26.0 1.0

Zinc binding site 5 out of 8 in 5gm3

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Zinc binding site 5 out of 8 in the Crystal Structure of Fi-Cmcase From Aspergillus Aculeatus F-50


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Fi-Cmcase From Aspergillus Aculeatus F-50 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:46.5
occ:1.00
 NE2 A:HIS110 2.3 18.5 1.0
O A:HOH646 3.1 25.2 1.0
CD2 A:HIS110 3.2 18.9 1.0
CE1 A:HIS110 3.3 18.6 1.0
O A:HOH476 3.7 30.7 1.0
OD1 A:ASP116 3.9 21.6 1.0
OG A:SER155 4.0 38.2 1.0
ZN A:ZN304 4.3 32.9 1.0
CG A:HIS110 4.3 16.1 1.0
ND1 A:HIS110 4.4 17.9 1.0
O A:HOH652 4.4 23.1 1.0
C A:GLY115 4.5 18.1 1.0
CB A:SER155 4.7 35.5 1.0
O A:GLY115 4.7 19.0 1.0
O A:HOH605 4.7 13.7 1.0
N A:ASP116 4.8 16.3 1.0

Zinc binding site 6 out of 8 in 5gm3

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Zinc binding site 6 out of 8 in the Crystal Structure of Fi-Cmcase From Aspergillus Aculeatus F-50


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Fi-Cmcase From Aspergillus Aculeatus F-50 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:18.9
occ:1.00
 O1 B:CAC304 1.7 24.2 0.5
O1 B:CAC305 1.8 23.2 1.0
ND1 B:HIS185 2.0 18.2 1.0
CE1 B:HIS185 2.9 19.2 1.0
CG B:HIS185 3.1 18.8 1.0
AS B:CAC304 3.2 17.7 0.5
AS B:CAC305 3.3 21.1 1.0
CB B:HIS185 3.6 18.5 1.0
O2 B:CAC304 3.7 16.7 0.5
O2 B:CAC305 3.7 26.2 1.0
CA B:HIS185 3.9 17.1 1.0
C2 B:CAC304 4.0 18.4 0.5
NE2 B:HIS185 4.0 18.9 1.0
CD2 B:HIS185 4.2 18.6 1.0
C1 B:CAC305 4.2 30.9 1.0
CD1 B:ILE136 4.4 28.1 1.0
O B:ASN184 4.4 21.0 1.0
O B:HOH643 4.4 33.5 1.0
OH B:TYR159 4.6 18.1 1.0
O B:HIS185 4.6 20.3 1.0
C2 B:CAC305 4.6 28.9 1.0
C1 B:CAC304 4.6 19.9 0.5
C B:HIS185 4.7 15.0 1.0
O B:HOH443 4.8 40.9 1.0
N B:HIS185 4.9 16.5 1.0

Zinc binding site 7 out of 8 in 5gm3

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Zinc binding site 7 out of 8 in the Crystal Structure of Fi-Cmcase From Aspergillus Aculeatus F-50


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Fi-Cmcase From Aspergillus Aculeatus F-50 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:31.5
occ:1.00
 O B:HOH507 2.0 27.9 1.0
NE2 B:HIS110 2.1 16.1 1.0
CE1 B:HIS110 3.1 18.8 1.0
CD2 B:HIS110 3.1 18.1 1.0
O B:HOH689 3.2 15.8 1.0
O B:HOH454 3.8 37.4 1.0
ND1 B:HIS110 4.2 15.9 1.0
CG B:HIS110 4.2 14.8 1.0
OG B:SER155 4.2 36.0 1.0
OD1 B:ASP116 4.3 22.1 1.0
ZN B:ZN303 4.6 30.9 1.0
OG B:SER114 4.6 19.8 1.0
C B:GLY115 4.7 18.1 1.0
O B:HOH678 4.7 28.9 1.0
O A:HOH507 4.7 34.9 1.0
O B:HOH600 4.7 21.2 1.0
O B:GLY115 4.8 17.9 1.0
N B:ASP116 4.9 13.8 1.0
O B:HOH633 5.0 15.2 1.0

Zinc binding site 8 out of 8 in 5gm3

Go back to Zinc Binding Sites List in 5gm3
Zinc binding site 8 out of 8 in the Crystal Structure of Fi-Cmcase From Aspergillus Aculeatus F-50


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Fi-Cmcase From Aspergillus Aculeatus F-50 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:30.9
occ:1.00
 OD1 B:ASP116 2.1 22.1 1.0
O B:HOH633 2.3 15.2 1.0
OD2 B:ASP116 2.7 17.1 1.0
CG B:ASP116 2.7 16.7 1.0
O B:HOH678 3.2 28.9 1.0
O B:HOH651 3.3 12.8 1.0
O B:HOH689 3.3 15.8 1.0
O B:HOH507 3.8 27.9 1.0
O B:HOH541 4.2 30.3 1.0
CB B:ASP116 4.2 16.0 1.0
N B:ALA106 4.4 13.9 1.0
CB B:ALA106 4.5 15.3 1.0
O B:HOH682 4.5 17.1 1.0
CD2 B:HIS110 4.6 18.1 1.0
ZN B:ZN302 4.6 31.5 1.0
CA B:ASP116 4.9 14.1 1.0
NE2 B:HIS110 5.0 16.1 1.0

Reference:

J.W.Huang, W.Liu, H.L.Lai, Y.S.Cheng, Y.Zheng, Q.Li, H.Sun, C.J.Kuo, R.T.Guo, C.C.Chen. Crystal Structure and Genetic Modifications of Fi-Cmcase From Aspergillus Aculeatus F-50 Biochem. Biophys. Res. V. 478 565 2016COMMUN..
ISSN: ESSN 1090-2104
PubMed: 27470581
DOI: 10.1016/J.BBRC.2016.07.101
Page generated: Sun Oct 27 17:07:12 2024

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