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Cadmium in PDB 3d4c: Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form I)

Protein crystallography data

The structure of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form I), PDB code: 3d4c was solved by L.Jovine, M.Monne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 16.50 / 2.90
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.040, 95.120, 141.700, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 22.7

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form I) (pdb code 3d4c). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form I), PDB code: 3d4c:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in 3d4c

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Cadmium binding site 1 out of 7 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form I)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd483

b:0.9
occ:0.76
OE2 A:GLU427 2.7 0.2 1.0
NE2 A:HIS426 3.0 0.8 1.0
CE1 A:HIS426 3.2 0.3 1.0
CD A:GLU427 3.5 0.6 1.0
CG A:GLU427 3.7 80.4 1.0
CD2 A:HIS426 4.3 0.4 1.0
ND1 A:HIS426 4.5 0.9 1.0
OE1 A:GLU427 4.6 97.0 1.0

Cadmium binding site 2 out of 7 in 3d4c

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Cadmium binding site 2 out of 7 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form I)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd484

b:0.6
occ:1.00
NE2 A:HIS204 2.5 0.1 1.0
ND2 A:ASN202 2.6 0.7 1.0
NZ A:LYS138 3.3 0.7 1.0
CG A:ASN202 3.4 0.8 1.0
CD2 A:HIS204 3.4 0.9 1.0
CE1 A:HIS204 3.5 0.7 1.0
CB A:ASN202 3.6 0.5 1.0
CB A:PRO134 4.2 0.4 1.0
OD1 A:ASN202 4.3 0.4 1.0
O A:PRO134 4.6 0.5 1.0
ND1 A:HIS204 4.6 0.1 1.0
CE A:LYS138 4.6 0.2 1.0
CG A:HIS204 4.6 0.4 1.0
CA A:PRO134 4.8 0.8 1.0
CA A:ASN202 4.9 0.6 1.0
C A:PRO134 4.9 0.3 1.0

Cadmium binding site 3 out of 7 in 3d4c

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Cadmium binding site 3 out of 7 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form I)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd485

b:0.9
occ:0.97
OE2 A:GLU380 2.5 0.2 1.0
OE1 A:GLU380 2.5 0.9 1.0
CD A:GLU380 2.8 0.1 1.0
NH2 A:ARG411 4.3 88.3 1.0
CG A:GLU380 4.3 0.8 1.0
OE1 A:GLN424 4.4 0.1 1.0

Cadmium binding site 4 out of 7 in 3d4c

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Cadmium binding site 4 out of 7 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form I)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd486

b:0.6
occ:0.92
OE1 A:GLU464 2.6 0.4 1.0
OE2 A:GLU464 3.0 0.4 1.0
CD A:GLU464 3.1 0.9 1.0
CG A:GLU464 4.6 90.6 1.0
NH2 A:ARG462 4.8 0.3 1.0

Cadmium binding site 5 out of 7 in 3d4c

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Cadmium binding site 5 out of 7 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form I)


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd487

b:0.6
occ:1.00
O A:HIS40 2.4 99.3 1.0
ND1 A:HIS40 2.6 0.9 1.0
CE1 A:HIS40 3.1 0.2 1.0
C A:HIS40 3.5 92.4 1.0
CG A:HIS40 3.5 0.6 1.0
CB A:HIS40 4.0 0.9 1.0
NE2 A:HIS40 4.1 0.2 1.0
CD2 A:HIS40 4.3 0.2 1.0
CA A:HIS40 4.4 0.7 1.0
N A:PRO41 4.4 75.6 1.0
CA A:PRO41 4.5 76.8 1.0
C A:PRO41 4.6 80.2 1.0
N A:ASP42 4.7 74.1 1.0

Cadmium binding site 6 out of 7 in 3d4c

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Cadmium binding site 6 out of 7 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form I)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd488

b:0.6
occ:1.00
OE2 A:GLU39 2.7 0.3 1.0
OE1 A:GLU39 2.9 0.9 1.0
CD A:GLU39 3.1 0.1 1.0
CG A:GLU39 4.6 0.1 1.0
NE1 A:TRP11 4.9 91.8 1.0

Cadmium binding site 7 out of 7 in 3d4c

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Cadmium binding site 7 out of 7 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form I)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd489

b:0.7
occ:0.80
OD2 A:ASP437 2.3 0.3 1.0
OD2 A:ASP210 2.6 0.2 1.0
OG A:SER212 3.0 0.4 1.0
CG A:ASP210 3.4 0.8 1.0
OD1 A:ASP210 3.5 0.7 1.0
CG A:ASP437 3.5 0.9 1.0
CB A:SER212 4.1 0.9 1.0
OD1 A:ASP437 4.2 0.7 1.0
CB A:ASP437 4.6 0.4 1.0
CB A:LYS436 4.6 0.7 1.0
CD A:LYS436 4.8 0.6 1.0
CB A:ASP210 4.8 0.8 1.0
N A:SER212 4.9 0.3 1.0

Reference:

M.Monne, L.Han, T.Schwend, S.Burendahl, L.Jovine. Crystal Structure of the Zp-N Domain of ZP3 Reveals the Core Fold of Animal Egg Coats Nature V. 456 653 2008.
ISSN: ISSN 0028-0836
PubMed: 19052627
DOI: 10.1038/NATURE07599
Page generated: Fri Aug 28 13:33:08 2020
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