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Zinc in PDB 3ef7: Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form III)

Protein crystallography data

The structure of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form III), PDB code: 3ef7 was solved by M.Monne, L.Jovine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.16 / 3.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 86.200, 98.580, 143.680, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.6

Other elements in 3ef7:

The structure of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form III) also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Zinc atom in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form III) (pdb code 3ef7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 13 binding sites of Zinc where determined in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form III), PDB code: 3ef7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 13 in 3ef7

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Zinc binding site 1 out of 13 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form III)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form III) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn484

b:65.2
occ:0.94
O A:HIS40 2.0 74.1 1.0
ND1 A:HIS40 2.1 89.7 1.0
CE1 A:HIS40 2.9 90.9 1.0
CG A:HIS40 3.0 85.2 1.0
C A:HIS40 3.1 69.5 1.0
CB A:HIS40 3.5 67.7 1.0
CA A:HIS40 3.8 68.2 1.0
NE2 A:HIS40 3.8 90.9 1.0
CD2 A:HIS40 3.9 86.0 1.0
N A:PRO41 4.2 69.6 1.0
OD1 A:ASP42 4.4 0.8 1.0
N A:HIS40 4.4 69.3 1.0
CA A:PRO41 4.5 71.0 1.0
C A:PRO41 4.6 85.3 1.0
N A:ASP42 4.9 84.4 1.0
O A:PRO41 4.9 91.1 1.0

Zinc binding site 2 out of 13 in 3ef7

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Zinc binding site 2 out of 13 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form III)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form III) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn485

b:73.1
occ:1.00
ND1 A:HIS426 2.1 1.0 1.0
CE1 A:HIS426 2.7 0.3 1.0
CG A:HIS426 3.3 0.6 1.0
CB A:HIS426 4.0 98.7 1.0
NE2 A:HIS426 4.0 0.8 1.0
CD2 A:HIS426 4.3 1.0 1.0

Zinc binding site 3 out of 13 in 3ef7

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Zinc binding site 3 out of 13 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form III)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form III) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn486

b:72.6
occ:1.00
NE2 A:HIS204 2.2 90.2 1.0
CE1 A:HIS204 3.0 87.1 1.0
CD2 A:HIS204 3.2 86.4 1.0
CE A:LYS138 3.4 0.5 1.0
NZ A:LYS138 3.7 0.3 1.0
CB A:ASN202 4.0 73.9 1.0
CB A:PRO134 4.1 80.4 1.0
ND1 A:HIS204 4.2 82.2 1.0
ND2 A:ASN202 4.2 79.4 1.0
CG A:ASN202 4.3 75.6 1.0
CG A:HIS204 4.3 78.2 1.0
CD A:LYS138 4.4 0.7 1.0
O A:PRO134 4.5 81.6 1.0
C A:PRO134 4.6 89.0 1.0
CA A:PRO134 4.7 80.4 1.0
O A:ASN202 4.8 81.9 1.0
CG A:LYS138 4.8 0.0 1.0

Zinc binding site 4 out of 13 in 3ef7

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Zinc binding site 4 out of 13 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form III)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form III) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn489

b:0.1
occ:1.00
OE2 B:GLU378 2.0 0.6 1.0
OE2 A:GLU378 2.0 0.7 1.0
CD B:GLU378 2.5 0.5 1.0
OE2 A:GLU475 3.0 0.8 1.0
OE1 B:GLU378 3.1 1.0 1.0
CD A:GLU378 3.1 0.2 1.0
CG A:GLU475 3.3 0.5 1.0
CG B:GLU378 3.4 0.9 1.0
CD A:GLU475 3.5 0.9 1.0
OE1 A:GLU378 3.5 0.0 1.0
OE1 B:GLU475 4.0 0.2 1.0
CB A:GLU475 4.4 0.8 1.0
O A:HIS480 4.4 0.5 1.0
CG A:GLU378 4.4 0.5 1.0
OE1 A:GLU475 4.6 0.7 1.0
CB B:GLU378 4.7 0.8 1.0
CA A:GLU475 4.7 0.3 1.0
CD B:GLU475 4.9 0.0 1.0

Zinc binding site 5 out of 13 in 3ef7

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Zinc binding site 5 out of 13 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form III)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form III) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn490

b:0.7
occ:0.87
NE2 A:HIS479 2.1 0.5 1.0
CD2 A:HIS479 2.7 0.0 1.0
CE1 A:HIS479 3.3 0.5 1.0
OE1 B:GLU380 3.3 0.7 1.0
CD B:GLU380 3.6 0.7 1.0
OE2 B:GLU380 3.9 0.6 1.0
CG A:HIS479 4.0 0.1 1.0
ND1 A:HIS479 4.2 0.8 1.0
CG B:GLU380 4.3 0.1 1.0
OE1 B:GLN424 4.9 0.6 1.0

Zinc binding site 6 out of 13 in 3ef7

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Zinc binding site 6 out of 13 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form III)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form III) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn483

b:87.3
occ:1.00
OE2 A:GLU4 2.0 0.6 1.0
ND1 B:HIS480 2.1 0.2 1.0
CE1 B:HIS480 2.3 0.4 1.0
CD A:GLU4 2.3 0.6 1.0
OE1 A:GLU4 2.7 0.9 1.0
CG A:GLU4 3.1 0.0 1.0
CG B:HIS480 3.2 0.7 1.0
ND2 B:ASN19 3.3 0.6 1.0
NE2 B:HIS480 3.5 0.4 1.0
CD2 B:HIS480 3.9 98.0 1.0
CB B:HIS480 4.0 0.7 1.0
CA B:HIS480 4.3 0.7 1.0
CG B:ASN19 4.4 0.3 1.0
CB A:GLU4 4.5 98.3 1.0
O A:MET1 4.6 90.3 1.0
CD1 B:TYR18 4.8 0.5 1.0
CE1 B:TYR18 4.9 0.2 1.0
CA B:ASN19 5.0 0.6 1.0
C B:HIS480 5.0 0.6 1.0

Zinc binding site 7 out of 13 in 3ef7

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Zinc binding site 7 out of 13 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form III)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form III) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn484

b:85.2
occ:1.00
NE2 B:HIS476 2.0 0.1 1.0
OD2 A:ASP56 2.1 0.6 1.0
NE2 B:HIS478 2.2 0.2 1.0
CD2 B:HIS476 2.5 98.2 1.0
CD2 B:HIS478 2.7 85.8 1.0
CG A:ASP56 2.8 0.4 1.0
OD1 A:ASP56 2.8 0.8 1.0
CE1 B:HIS476 3.1 0.5 1.0
CE1 B:HIS478 3.4 0.3 1.0
CG B:HIS476 3.7 99.3 1.0
ND1 B:HIS476 3.9 0.8 1.0
CG B:HIS478 4.0 0.2 1.0
CB A:ASP56 4.2 78.8 1.0
ND1 B:HIS478 4.3 0.5 1.0
O B:HIS477 4.5 84.8 1.0
N A:GLY57 4.5 78.8 1.0
CG1 A:VAL51 4.7 59.1 1.0
CB A:LYS2 4.7 95.6 1.0
CB A:VAL51 4.7 66.3 1.0
CD A:LYS2 4.8 88.8 1.0
N A:LYS2 4.9 88.1 1.0
CB B:HIS476 4.9 99.4 1.0
C B:HIS477 5.0 96.8 1.0

Zinc binding site 8 out of 13 in 3ef7

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Zinc binding site 8 out of 13 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form III)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form III) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn485

b:68.3
occ:1.00
OE2 B:GLU39 2.0 1.0 1.0
NE2 B:HIS477 2.1 0.9 1.0
N B:MET1 2.1 0.4 1.0
NE2 B:HIS479 2.2 0.7 1.0
CD2 B:HIS477 2.5 0.7 1.0
CD2 B:HIS479 2.9 0.8 1.0
CA B:MET1 3.0 0.0 1.0
CD B:GLU39 3.2 98.6 1.0
CE1 B:HIS479 3.3 0.3 1.0
CE1 B:HIS477 3.3 0.6 1.0
CB B:MET1 3.5 0.4 1.0
CG B:HIS477 3.7 0.4 1.0
O B:HIS478 3.8 0.8 1.0
OE1 B:GLU39 3.9 90.6 1.0
ND1 B:HIS477 4.1 0.7 1.0
CG B:HIS479 4.1 0.6 1.0
ND1 B:HIS479 4.2 0.1 1.0
CG B:GLU39 4.2 96.4 1.0
C B:MET1 4.3 0.9 1.0
CG B:MET1 4.4 1.0 1.0
O B:MET1 4.7 0.3 1.0
CB B:HIS477 4.9 92.1 1.0

Zinc binding site 9 out of 13 in 3ef7

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Zinc binding site 9 out of 13 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form III)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form III) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn486

b:93.3
occ:1.00
ND1 B:HIS476 2.2 0.8 1.0
CE1 B:HIS476 2.8 0.5 1.0
CE A:LYS47 3.1 96.7 1.0
CG B:HIS476 3.3 99.3 1.0
NZ A:LYS47 3.4 93.0 1.0
CA B:HIS476 3.9 0.5 1.0
CB B:HIS476 3.9 99.4 1.0
NE2 B:HIS476 4.0 0.1 1.0
N B:HIS477 4.0 0.3 1.0
CD2 B:HIS476 4.2 98.2 1.0
C B:HIS476 4.5 0.1 1.0
CD A:LYS47 4.6 92.1 1.0
O B:HIS477 4.6 84.8 1.0
O B:GLU475 4.9 0.1 1.0

Zinc binding site 10 out of 13 in 3ef7

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Zinc binding site 10 out of 13 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form III)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form III) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn487

b:0.9
occ:1.00
OE1 B:GLU427 2.0 0.4 1.0
OE2 B:GLU427 2.5 0.9 1.0
CD B:GLU427 2.6 0.7 1.0
CG B:GLU427 4.1 0.2 1.0
CG B:GLN424 4.6 0.1 1.0
CB B:GLU427 4.7 0.7 1.0
CB B:GLN424 4.8 0.2 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: Wed Dec 16 04:15:50 2020

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