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Cadmium in PDB 1cvm: Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens

Enzymatic activity of Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens

All present enzymatic activity of Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens:
3.1.3.8;

Protein crystallography data

The structure of Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens, PDB code: 1cvm was solved by S.Shin, N.-C.Ha, B.-H.Oh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.090, 65.010, 105.540, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 27.4

Other elements in 1cvm:

The structure of Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens (pdb code 1cvm). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens, PDB code: 1cvm:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 1cvm

Go back to Cadmium Binding Sites List in 1cvm
Cadmium binding site 1 out of 5 in the Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd811

b:22.7
occ:1.00
 OE2 A:GLU227 2.6 9.9 1.0
OE1 A:GLU260 2.6 22.4 1.0
OE2 A:GLU260 2.7 21.3 1.0
CD A:GLU260 3.0 15.8 1.0
OH A:TYR159 3.3 20.1 1.0
O A:HOH559 3.3 28.8 1.0
OE1 A:GLU211 3.4 31.0 1.0
CD A:GLU227 3.6 16.8 1.0
CD A:GLU211 3.7 15.8 1.0
CD A:CD812 3.7 62.7 1.0
OE2 A:GLU211 3.8 27.9 1.0
CD A:CD813 3.9 17.4 1.0
CZ A:TYR159 3.9 15.8 1.0
OE1 A:GLU227 4.0 19.0 1.0
CE2 A:TYR159 4.1 15.9 1.0
O A:HOH558 4.2 31.3 1.0
CB A:GLU211 4.2 12.9 1.0
CG A:GLU260 4.5 9.1 1.0
CG A:GLU211 4.6 18.5 1.0
OD2 A:ASP314 4.6 13.5 1.0
CG A:GLU227 4.7 12.1 1.0
NE2 A:GLN209 4.9 31.5 1.0

Cadmium binding site 2 out of 5 in 1cvm

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Cadmium binding site 2 out of 5 in the Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd812

b:62.7
occ:1.00
 OD1 A:ASP258 2.7 20.0 1.0
OE1 A:GLN279 2.9 24.5 1.0
OE1 A:GLU260 3.0 22.4 1.0
CG A:ASP258 3.7 22.9 1.0
CD A:GLN279 3.7 17.2 1.0
CD A:CD811 3.7 22.7 1.0
NE2 A:GLN279 3.8 17.4 1.0
CD A:GLU260 3.8 15.8 1.0
O A:HOH559 3.8 28.8 1.0
O A:HOH560 3.9 34.3 1.0
CB A:ASP258 4.0 22.5 1.0
O A:HOH558 4.1 31.3 1.0
OE1 A:GLU227 4.4 19.0 1.0
OE2 A:GLU260 4.5 21.3 1.0
CG A:GLU260 4.6 9.1 1.0
OD2 A:ASP314 4.6 13.5 1.0
CD A:GLU227 4.8 16.8 1.0
OE2 A:GLU227 4.8 9.9 1.0
OD2 A:ASP258 4.9 32.2 1.0

Cadmium binding site 3 out of 5 in 1cvm

Go back to Cadmium Binding Sites List in 1cvm
Cadmium binding site 3 out of 5 in the Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd813

b:17.4
occ:1.00
 OE2 A:GLU211 2.5 27.9 1.0
OD1 A:ASP55 2.5 15.8 1.0
OE1 A:GLU211 2.6 31.0 1.0
OD2 A:ASP55 2.9 11.8 1.0
CD A:GLU211 2.9 15.8 1.0
CG A:ASP55 3.0 12.9 1.0
O A:HOH559 3.4 28.8 1.0
OE2 A:GLU260 3.7 21.3 1.0
OD2 A:ASP314 3.7 13.5 1.0
CD A:CD811 3.9 22.7 1.0
CB A:ASP314 4.1 11.9 1.0
CG A:ASP314 4.2 13.1 1.0
ND2 A:ASN99 4.2 7.5 1.0
OD1 A:ASN99 4.4 16.4 1.0
O A:HOH522 4.4 13.8 1.0
CG A:GLU211 4.4 18.5 1.0
OD1 A:ASN100 4.4 16.1 1.0
NZ A:LYS76 4.5 31.5 1.0
OH A:TYR159 4.5 20.1 1.0
CB A:ASP55 4.5 9.9 1.0
CG A:ASN99 4.7 11.8 1.0
CZ A:TYR159 4.8 15.8 1.0
CD A:GLU260 4.9 15.8 1.0
CE1 A:TYR159 4.9 10.3 1.0

Cadmium binding site 4 out of 5 in 1cvm

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Cadmium binding site 4 out of 5 in the Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd814

b:65.8
occ:1.00
 OD1 A:ASP314 2.6 28.6 1.0
OD2 A:ASP314 3.0 13.5 1.0
CG A:ASP314 3.1 13.1 1.0
OD1 A:ASP52 3.2 48.8 1.0
NZ A:LYS76 3.2 31.5 1.0
O A:HOH559 3.7 28.8 1.0
CG A:ASP52 4.0 45.5 1.0
CE A:LYS76 4.2 30.9 1.0
O A:HOH560 4.4 34.3 1.0
CB A:ASP314 4.5 11.9 1.0
CB A:ASP52 4.5 38.0 1.0
NE2 A:GLN335 4.6 5.8 1.0
OD1 A:ASP55 4.6 15.8 1.0
O A:ALA54 4.7 7.5 1.0
NE2 A:GLN279 4.7 17.4 1.0
NE2 A:GLN348 4.7 16.5 1.0
OD2 A:ASP52 4.9 50.2 1.0

Cadmium binding site 5 out of 5 in 1cvm

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Cadmium binding site 5 out of 5 in the Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd815

b:49.8
occ:1.00
 OD2 A:ASP258 2.5 32.2 1.0
OD2 A:ASP228 2.9 38.3 1.0
OD1 A:ASP228 3.0 36.3 1.0
OD1 A:ASP258 3.0 20.0 1.0
CG A:ASP258 3.1 22.9 1.0
CG A:ASP228 3.3 33.8 1.0
OE1 A:GLU227 4.1 19.0 1.0
CB A:ASP258 4.4 22.5 1.0
CB A:GLU227 4.8 12.3 1.0
CB A:ASP228 4.8 31.2 1.0

Reference:

N.C.Ha, B.C.Oh, S.Shin, H.J.Kim, T.K.Oh, Y.O.Kim, K.Y.Choi, B.H.Oh. Crystal Structures of A Novel, Thermostable Phytase in Partially and Fully Calcium-Loaded States. Nat.Struct.Biol. V. 7 147 2000.
ISSN: ISSN 1072-8368
PubMed: 10655618
DOI: 10.1038/72421
Page generated: Fri Jul 19 13:07:53 2024

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