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Cadmium in PDB 1cfz: Hydrogenase Maturating Endopeptidase Hybd From E. Coli

Protein crystallography data

The structure of Hydrogenase Maturating Endopeptidase Hybd From E. Coli, PDB code: 1cfz was solved by E.Fritsche, A.Paschos, H.-G.Beisel, A.Boeck, R.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.20
Space group P 32 1 2
Cell size a, b, c (Å), α, β, γ (°) 128.000, 128.000, 139.700, 90.00, 90.00, 120.00
R / Rfree (%) 22.4 / 25.9

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Hydrogenase Maturating Endopeptidase Hybd From E. Coli (pdb code 1cfz). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Hydrogenase Maturating Endopeptidase Hybd From E. Coli, PDB code: 1cfz:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 1cfz

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Cadmium binding site 1 out of 6 in the Hydrogenase Maturating Endopeptidase Hybd From E. Coli


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Hydrogenase Maturating Endopeptidase Hybd From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd163

b:33.8
occ:1.00
 OE1 A:GLU16 2.2 33.7 1.0
NE2 A:HIS93 2.3 30.5 1.0
OD2 A:ASP62 2.5 27.1 1.0
O A:HOH188 2.5 36.1 1.0
OE2 A:GLU16 2.5 34.3 1.0
OD1 A:ASP62 2.8 29.7 1.0
CD A:GLU16 2.8 38.1 1.0
CG A:ASP62 3.0 33.5 1.0
CD2 A:HIS93 3.1 30.1 1.0
CE1 A:HIS93 3.4 38.0 1.0
O A:ALA63 4.0 32.3 1.0
N A:ALA63 4.2 34.1 1.0
CA A:GLY9 4.2 32.4 1.0
CG A:GLU16 4.3 32.0 1.0
CG A:HIS93 4.3 33.2 1.0
NE2 A:GLN94 4.3 31.8 1.0
OG A:SER91 4.4 40.1 1.0
ND1 A:HIS93 4.4 35.2 1.0
CG A:GLN94 4.4 30.4 1.0
CB A:ASP62 4.5 23.8 1.0
CB A:ALA63 4.6 27.2 1.0
CD A:GLN94 4.7 41.5 1.0
O B:HOH184 4.7 41.8 1.0
N A:GLY9 4.7 38.0 1.0
CA A:ALA63 4.8 32.9 1.0
OXT B:SER162 4.8 39.9 1.0
C A:ALA63 4.8 29.4 1.0
O A:GLU16 4.9 28.6 1.0
O A:VAL8 5.0 34.9 1.0

Cadmium binding site 2 out of 6 in 1cfz

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Cadmium binding site 2 out of 6 in the Hydrogenase Maturating Endopeptidase Hybd From E. Coli


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Hydrogenase Maturating Endopeptidase Hybd From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd163

b:36.3
occ:1.00
 OE1 B:GLU16 2.2 33.8 1.0
NE2 B:HIS93 2.2 30.4 1.0
OE2 B:GLU16 2.3 33.4 1.0
O B:HOH189 2.5 42.1 1.0
OD2 B:ASP62 2.5 27.4 1.0
OD1 B:ASP62 2.7 29.1 1.0
CD B:GLU16 2.8 37.7 1.0
CG B:ASP62 3.0 33.9 1.0
CD2 B:HIS93 3.1 30.7 1.0
CE1 B:HIS93 3.3 37.9 1.0
O B:ALA63 4.0 32.4 1.0
NE2 B:GLN94 4.2 32.0 1.0
CA B:GLY9 4.2 32.6 1.0
CG B:GLU16 4.2 32.2 1.0
CG B:HIS93 4.3 33.0 1.0
N B:ALA63 4.3 34.4 1.0
ND1 B:HIS93 4.3 35.2 1.0
CG B:GLN94 4.4 30.8 1.0
OG B:SER91 4.4 40.5 1.0
CB B:ASP62 4.5 24.3 1.0
CD B:GLN94 4.6 41.5 1.0
CB B:ALA63 4.6 27.0 1.0
O B:HOH215 4.7 52.7 1.0
N B:GLY9 4.7 38.5 1.0
O B:GLU16 4.8 28.9 1.0
C B:ALA63 4.8 29.9 1.0
CA B:ALA63 4.8 33.2 1.0
O B:VAL8 5.0 34.5 1.0
C B:VAL8 5.0 36.8 1.0

Cadmium binding site 3 out of 6 in 1cfz

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Cadmium binding site 3 out of 6 in the Hydrogenase Maturating Endopeptidase Hybd From E. Coli


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Hydrogenase Maturating Endopeptidase Hybd From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd163

b:35.1
occ:1.00
 OE1 C:GLU16 2.2 33.5 1.0
NE2 C:HIS93 2.3 30.1 1.0
OE2 C:GLU16 2.3 34.2 1.0
OD2 C:ASP62 2.5 27.2 1.0
OD1 C:ASP62 2.7 29.0 1.0
CD C:GLU16 2.8 37.7 1.0
CG C:ASP62 3.0 33.9 1.0
CD2 C:HIS93 3.1 30.3 1.0
CE1 C:HIS93 3.4 38.0 1.0
O C:ALA63 4.1 32.4 1.0
CA C:GLY9 4.1 32.7 1.0
O C:HOH164 4.2 32.9 1.0
N C:ALA63 4.2 34.3 1.0
CG C:GLU16 4.2 32.2 1.0
CG C:HIS93 4.3 33.4 1.0
OE1 C:GLN94 4.3 37.6 1.0
O E:HOH189 4.3 49.1 1.0
ND1 C:HIS93 4.4 35.3 1.0
OG C:SER91 4.4 40.1 1.0
CG C:GLN94 4.4 30.7 1.0
CD C:GLN94 4.5 41.5 1.0
CB C:ASP62 4.5 24.4 1.0
CB C:ALA63 4.6 26.9 1.0
N C:GLY9 4.7 38.7 1.0
CA C:ALA63 4.8 33.1 1.0
C C:ALA63 4.8 29.2 1.0
O C:GLU16 4.9 29.4 1.0
OXT E:SER162 4.9 39.3 1.0
O C:VAL8 4.9 34.8 1.0

Cadmium binding site 4 out of 6 in 1cfz

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Cadmium binding site 4 out of 6 in the Hydrogenase Maturating Endopeptidase Hybd From E. Coli


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Hydrogenase Maturating Endopeptidase Hybd From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd163

b:34.1
occ:1.00
 OE1 D:GLU16 2.2 33.5 1.0
NE2 D:HIS93 2.2 30.4 1.0
OE2 D:GLU16 2.5 34.1 1.0
OD2 D:ASP62 2.5 27.3 1.0
OD1 D:ASP62 2.8 29.0 1.0
CD D:GLU16 2.8 38.0 1.0
CG D:ASP62 3.0 33.9 1.0
CD2 D:HIS93 3.1 30.1 1.0
CE1 D:HIS93 3.4 38.2 1.0
O D:HOH164 4.1 31.2 1.0
O D:ALA63 4.1 32.5 1.0
N D:ALA63 4.2 34.4 1.0
CA D:GLY9 4.2 32.5 1.0
CG D:HIS93 4.3 33.2 1.0
CG D:GLU16 4.3 32.1 1.0
NE2 D:GLN94 4.3 31.6 1.0
ND1 D:HIS93 4.4 35.1 1.0
OXT C:SER162 4.4 40.0 1.0
CG D:GLN94 4.5 30.5 1.0
O C:HOH174 4.5 41.1 1.0
CB D:ASP62 4.5 24.1 1.0
OG D:SER91 4.5 40.3 1.0
CB D:ALA63 4.5 27.0 1.0
CD D:GLN94 4.6 41.2 1.0
N D:GLY9 4.7 38.3 1.0
CA D:ALA63 4.7 33.6 1.0
C D:ALA63 4.8 29.1 1.0
O D:VAL8 4.9 34.6 1.0
C C:SER162 4.9 33.2 1.0
O D:GLU16 4.9 29.4 1.0

Cadmium binding site 5 out of 6 in 1cfz

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Cadmium binding site 5 out of 6 in the Hydrogenase Maturating Endopeptidase Hybd From E. Coli


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Hydrogenase Maturating Endopeptidase Hybd From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cd163

b:35.3
occ:1.00
 NE2 E:HIS93 2.2 30.2 1.0
OE1 E:GLU16 2.3 33.1 1.0
OE2 E:GLU16 2.3 34.0 1.0
OD2 E:ASP62 2.5 27.1 1.0
OD1 E:ASP62 2.7 29.4 1.0
CD E:GLU16 2.7 37.6 1.0
CG E:ASP62 3.0 33.7 1.0
CD2 E:HIS93 3.0 30.6 1.0
CE1 E:HIS93 3.4 37.9 1.0
O E:ALA63 4.0 32.4 1.0
CA E:GLY9 4.1 33.2 1.0
CG E:GLU16 4.2 32.1 1.0
NE2 E:GLN94 4.2 32.2 1.0
N E:ALA63 4.3 33.8 1.0
CG E:HIS93 4.3 33.1 1.0
O E:HOH164 4.4 32.1 1.0
ND1 E:HIS93 4.4 35.0 1.0
CG E:GLN94 4.4 30.3 1.0
OG E:SER91 4.5 39.9 1.0
CB E:ASP62 4.5 24.0 1.0
CD E:GLN94 4.6 41.4 1.0
CB E:ALA63 4.6 26.3 1.0
N E:GLY9 4.7 38.5 1.0
CA E:ALA63 4.8 33.4 1.0
C E:ALA63 4.8 29.2 1.0
O E:VAL8 4.9 34.4 1.0
O E:GLU16 4.9 29.2 1.0
C E:VAL8 5.0 37.2 1.0

Cadmium binding site 6 out of 6 in 1cfz

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Cadmium binding site 6 out of 6 in the Hydrogenase Maturating Endopeptidase Hybd From E. Coli


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Hydrogenase Maturating Endopeptidase Hybd From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cd163

b:37.0
occ:1.00
 NE2 F:HIS93 2.2 30.0 1.0
OE1 F:GLU16 2.2 33.9 1.0
O F:HOH192 2.4 39.6 1.0
OE2 F:GLU16 2.4 33.9 1.0
OD2 F:ASP62 2.5 28.2 1.0
OD1 F:ASP62 2.7 29.6 1.0
CD F:GLU16 2.8 37.8 1.0
CG F:ASP62 3.0 34.0 1.0
CD2 F:HIS93 3.0 30.4 1.0
CE1 F:HIS93 3.3 38.6 1.0
O F:ALA63 4.0 32.5 1.0
O F:HOH164 4.1 36.2 1.0
CA F:GLY9 4.2 32.4 1.0
N F:ALA63 4.2 34.6 1.0
NE2 F:GLN94 4.2 32.7 1.0
CG F:HIS93 4.2 33.2 1.0
CG F:GLU16 4.3 32.2 1.0
ND1 F:HIS93 4.4 35.3 1.0
OG F:SER91 4.4 40.2 1.0
CG F:GLN94 4.4 30.6 1.0
CB F:ASP62 4.5 24.1 1.0
CD F:GLN94 4.6 41.2 1.0
CB F:ALA63 4.6 26.6 1.0
N F:GLY9 4.8 38.5 1.0
O A:HOH167 4.8 46.4 1.0
OXT A:SER162 4.8 39.8 1.0
CA F:ALA63 4.8 33.0 1.0
C F:ALA63 4.8 29.2 1.0
O F:VAL8 4.9 35.2 1.0
O F:GLU16 4.9 29.5 1.0
C F:VAL8 5.0 36.9 1.0

Reference:

E.Fritsche, A.Paschos, H.G.Beisel, A.Bock, R.Huber. Crystal Structure of the Hydrogenase Maturating Endopeptidase Hybd From Escherichia Coli. J.Mol.Biol. V. 288 989 1999.
ISSN: ISSN 0022-2836
PubMed: 10331925
DOI: 10.1006/JMBI.1999.2719
Page generated: Fri Jul 19 13:06:36 2024

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