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Zinc in PDB 5v3g: PRDM9-Allele-C ZNF8-13

Enzymatic activity of PRDM9-Allele-C ZNF8-13

All present enzymatic activity of PRDM9-Allele-C ZNF8-13:
2.1.1.43;

Protein crystallography data

The structure of PRDM9-Allele-C ZNF8-13, PDB code: 5v3g was solved by A.Patel, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.18 / 2.42
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.151, 123.778, 70.200, 90.00, 116.07, 90.00
R / Rfree (%) 17.3 / 22.5

Zinc Binding Sites:

Pages:

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

Binding sites:

The binding sites of Zinc atom in the PRDM9-Allele-C ZNF8-13 (pdb code 5v3g). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 13 binding sites of Zinc where determined in the PRDM9-Allele-C ZNF8-13, PDB code: 5v3g:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 13 in 5v3g

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Zinc binding site 1 out of 13 in the PRDM9-Allele-C ZNF8-13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of PRDM9-Allele-C ZNF8-13 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1001

b:55.8
occ:1.00
NE2 D:HIS741 2.0 87.5 1.0
NE2 D:HIS737 2.1 44.6 1.0
SG D:CYS724 2.2 55.2 1.0
SG D:CYS721 2.4 58.2 1.0
CD2 D:HIS741 2.4 78.2 1.0
CD2 D:HIS737 3.0 46.6 1.0
CB D:CYS721 3.1 47.5 1.0
CB D:CYS724 3.1 57.3 1.0
CE1 D:HIS737 3.1 48.9 1.0
CE1 D:HIS741 3.3 87.4 1.0
N D:CYS724 3.6 74.4 1.0
CG D:HIS741 3.7 80.2 1.0
CA D:CYS724 3.9 64.3 1.0
OE1 D:GLU723 4.0 0.5 1.0
ND1 D:HIS741 4.1 88.9 1.0
CG D:HIS737 4.2 45.1 1.0
ND1 D:HIS737 4.2 45.3 1.0
C D:GLU723 4.5 82.8 1.0
CA D:CYS721 4.5 49.8 1.0
CB D:GLU723 4.6 64.8 1.0
C D:CYS724 4.7 61.8 1.0
N D:GLY725 4.9 55.2 1.0
CA D:GLU723 4.9 71.7 1.0
C D:CYS721 4.9 47.9 1.0
O D:CYS721 5.0 56.8 1.0

Zinc binding site 2 out of 13 in 5v3g

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Zinc binding site 2 out of 13 in the PRDM9-Allele-C ZNF8-13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of PRDM9-Allele-C ZNF8-13 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1002

b:59.2
occ:1.00
NE2 D:HIS765 1.8 70.0 1.0
NE2 D:HIS769 2.1 96.3 1.0
SG D:CYS752 2.2 51.1 1.0
SG D:CYS749 2.2 61.5 1.0
CD2 D:HIS769 2.3 87.1 1.0
CE1 D:HIS765 2.7 67.0 1.0
CD2 D:HIS765 2.8 53.5 1.0
CB D:CYS749 3.2 59.5 1.0
CE1 D:HIS769 3.3 97.1 1.0
CB D:CYS752 3.3 54.6 1.0
N D:CYS752 3.5 67.7 1.0
CG D:HIS769 3.7 75.2 1.0
ND1 D:HIS765 3.9 75.0 1.0
CG D:HIS765 3.9 70.3 1.0
ND1 D:HIS769 4.0 89.6 1.0
CA D:CYS752 4.0 57.7 1.0
CB D:GLU751 4.4 77.3 1.0
C D:GLU751 4.5 70.4 1.0
CA D:CYS749 4.6 67.0 1.0
C D:CYS752 4.7 59.3 1.0
CA D:GLU751 4.8 72.0 1.0
CB D:HIS769 4.9 57.7 1.0
N D:GLU751 4.9 72.5 1.0
N D:GLY753 4.9 59.0 1.0

Zinc binding site 3 out of 13 in 5v3g

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Zinc binding site 3 out of 13 in the PRDM9-Allele-C ZNF8-13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of PRDM9-Allele-C ZNF8-13 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1003

b:66.0
occ:1.00
NE2 D:HIS793 1.8 60.6 1.0
NE2 D:HIS797 1.9 80.5 1.0
SG D:CYS777 2.2 62.6 1.0
SG D:CYS780 2.3 62.7 1.0
CE1 D:HIS793 2.7 78.2 1.0
CD2 D:HIS797 2.8 72.3 1.0
CD2 D:HIS793 3.0 49.1 1.0
CB D:CYS780 3.0 65.3 1.0
CE1 D:HIS797 3.0 76.3 1.0
CB D:CYS777 3.2 54.0 1.0
N D:CYS780 3.6 75.4 1.0
ND1 D:HIS793 3.8 61.9 1.0
CA D:CYS780 3.9 67.1 1.0
CG D:HIS797 4.0 72.5 1.0
CG D:HIS793 4.0 48.6 1.0
ND1 D:HIS797 4.0 79.2 1.0
CA D:CYS777 4.6 66.7 1.0
C D:CYS780 4.7 66.5 1.0
C D:GLU779 4.7 83.4 1.0
N D:GLY781 4.8 69.5 1.0
CB D:GLU779 4.8 86.1 1.0
CB D:ARG782 4.9 60.8 1.0

Zinc binding site 4 out of 13 in 5v3g

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Zinc binding site 4 out of 13 in the PRDM9-Allele-C ZNF8-13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of PRDM9-Allele-C ZNF8-13 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1004

b:51.5
occ:1.00
NE2 D:HIS821 1.7 52.3 1.0
SG D:CYS808 2.3 45.9 1.0
NE2 D:HIS825 2.3 62.2 1.0
SG D:CYS805 2.3 54.0 1.0
CE1 D:HIS821 2.6 71.6 1.0
CD2 D:HIS825 2.8 54.5 1.0
CD2 D:HIS821 2.9 45.2 1.0
CB D:CYS805 3.2 43.5 1.0
CB D:CYS808 3.2 46.3 1.0
CE1 D:HIS825 3.6 80.5 1.0
ND1 D:HIS821 3.7 51.7 1.0
N D:CYS808 3.8 56.4 1.0
CG D:HIS821 3.9 48.4 1.0
CA D:CYS808 4.1 52.5 1.0
CG D:HIS825 4.1 58.0 1.0
CB D:GLU807 4.3 62.1 1.0
ND1 D:HIS825 4.4 64.9 1.0
CA D:CYS805 4.6 41.7 1.0
C D:CYS808 4.7 53.4 1.0
C D:GLU807 4.8 56.0 1.0
CB D:ARG810 4.8 49.8 1.0
N D:ARG810 4.8 47.3 1.0
CG D:GLU807 4.9 79.9 1.0
O D:CYS805 4.9 56.2 1.0
CA D:GLU807 5.0 51.7 1.0
N D:GLY809 5.0 46.0 1.0

Zinc binding site 5 out of 13 in 5v3g

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Zinc binding site 5 out of 13 in the PRDM9-Allele-C ZNF8-13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of PRDM9-Allele-C ZNF8-13 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1005

b:80.4
occ:1.00
NE2 D:HIS853 2.0 0.0 1.0
SG D:CYS836 2.3 96.7 1.0
SG D:CYS833 2.3 77.5 1.0
NE2 D:HIS849 2.4 84.8 1.0
CB D:CYS836 2.6 94.7 1.0
CD2 D:HIS853 2.8 94.2 1.0
CE1 D:HIS849 3.0 0.3 1.0
CE1 D:HIS853 3.1 96.1 1.0
CD2 D:HIS849 3.2 73.5 1.0
CB D:CYS833 3.3 72.0 1.0
N D:CYS836 3.4 97.5 1.0
CA D:CYS836 3.6 94.7 1.0
ND1 D:HIS849 4.0 82.0 1.0
CG D:HIS853 4.0 91.9 1.0
CG D:HIS849 4.1 66.2 1.0
ND1 D:HIS853 4.1 95.7 1.0
C D:CYS836 4.4 94.3 1.0
C D:GLU835 4.6 96.8 1.0
CB D:GLU835 4.7 83.4 1.0
N D:GLY837 4.8 98.3 1.0
CA D:CYS833 4.8 82.7 1.0
O D:HIS849 4.8 72.3 1.0
CB D:ARG838 4.9 83.7 1.0
N D:ARG838 4.9 86.8 1.0

Zinc binding site 6 out of 13 in 5v3g

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Zinc binding site 6 out of 13 in the PRDM9-Allele-C ZNF8-13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of PRDM9-Allele-C ZNF8-13 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1006

b:88.5
occ:1.00
NE2 D:HIS881 2.1 0.2 1.0
NE2 D:HIS877 2.1 0.2 1.0
CB D:CYS864 2.3 0.5 1.0
SG D:CYS864 2.4 0.5 1.0
SG D:CYS861 2.5 93.6 1.0
CE1 D:HIS881 2.8 0.7 1.0
CE1 D:HIS877 2.9 0.8 1.0
CD2 D:HIS881 3.2 0.4 1.0
CD2 D:HIS877 3.3 1.0 1.0
CB D:CYS861 3.5 92.7 1.0
CA D:CYS864 3.6 0.7 1.0
N D:CYS864 3.6 0.8 1.0
ND1 D:HIS881 4.0 0.1 1.0
ND1 D:HIS877 4.1 0.8 1.0
CG D:HIS881 4.2 1.0 1.0
CG D:HIS877 4.3 0.1 1.0
CG D:GLU863 4.3 0.0 1.0
C D:CYS864 4.6 0.6 1.0
C D:GLU863 4.9 0.0 1.0
CA D:CYS861 4.9 99.6 1.0
N D:GLY865 5.0 99.2 1.0

Zinc binding site 7 out of 13 in 5v3g

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Zinc binding site 7 out of 13 in the PRDM9-Allele-C ZNF8-13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of PRDM9-Allele-C ZNF8-13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:55.4
occ:1.00
NE2 A:HIS741 1.9 72.9 1.0
NE2 A:HIS737 2.2 56.1 1.0
SG A:CYS721 2.2 51.2 1.0
SG A:CYS724 2.3 58.7 1.0
CD2 A:HIS741 2.8 66.1 1.0
CE1 A:HIS741 2.9 66.0 1.0
CD2 A:HIS737 3.0 44.1 1.0
CB A:CYS721 3.1 45.9 1.0
CB A:CYS724 3.1 53.7 1.0
CE1 A:HIS737 3.2 46.1 1.0
N A:CYS724 3.7 55.7 1.0
CA A:CYS724 4.0 54.7 1.0
CG A:HIS741 4.0 70.0 1.0
ND1 A:HIS741 4.0 70.1 1.0
CG A:HIS737 4.2 44.0 1.0
ND1 A:HIS737 4.3 45.3 1.0
CB A:GLU723 4.4 68.1 1.0
CA A:CYS721 4.5 41.5 1.0
C A:CYS724 4.7 57.4 1.0
C A:GLU723 4.7 64.0 1.0
CB A:ARG726 4.9 52.8 1.0
N A:GLY725 4.9 60.4 1.0
C A:CYS721 4.9 49.4 1.0
CA A:GLU723 4.9 62.9 1.0
O A:CYS721 4.9 50.6 1.0
N A:GLU723 4.9 68.5 1.0

Zinc binding site 8 out of 13 in 5v3g

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Zinc binding site 8 out of 13 in the PRDM9-Allele-C ZNF8-13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of PRDM9-Allele-C ZNF8-13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:63.8
occ:1.00
NE2 A:HIS765 1.7 65.2 1.0
NE2 A:HIS769 2.1 75.1 1.0
SG A:CYS752 2.1 70.0 1.0
SG A:CYS749 2.2 56.3 1.0
CE1 A:HIS765 2.3 75.7 1.0
CD2 A:HIS765 3.0 53.3 1.0
CD2 A:HIS769 3.0 68.7 1.0
CB A:CYS749 3.1 52.8 1.0
CE1 A:HIS769 3.1 70.9 1.0
CB A:CYS752 3.2 76.2 1.0
ND1 A:HIS765 3.6 70.2 1.0
N A:CYS752 3.8 76.3 1.0
CG A:HIS765 3.9 58.4 1.0
CA A:CYS752 4.0 73.2 1.0
CG A:HIS769 4.2 62.6 1.0
ND1 A:HIS769 4.2 68.3 1.0
CB A:GLU751 4.3 88.4 1.0
CA A:CYS749 4.5 57.3 1.0
C A:GLU751 4.7 81.0 1.0
C A:CYS752 4.8 69.5 1.0
N A:GLY753 4.9 66.2 1.0
CB A:ARG754 4.9 71.5 1.0
CA A:GLU751 4.9 81.9 1.0

Zinc binding site 9 out of 13 in 5v3g

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Zinc binding site 9 out of 13 in the PRDM9-Allele-C ZNF8-13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of PRDM9-Allele-C ZNF8-13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:55.5
occ:1.00
NE2 A:HIS797 1.9 61.8 1.0
NE2 A:HIS793 1.9 62.7 1.0
SG A:CYS780 2.3 56.6 1.0
CE1 A:HIS793 2.3 55.3 1.0
SG A:CYS777 2.3 49.1 1.0
CE1 A:HIS797 2.3 50.2 1.0
CD2 A:HIS797 3.1 52.7 1.0
CD2 A:HIS793 3.2 60.2 1.0
CB A:CYS777 3.2 49.9 1.0
CB A:CYS780 3.3 48.6 1.0
ND1 A:HIS793 3.6 47.3 1.0
ND1 A:HIS797 3.6 52.6 1.0
N A:CYS780 3.8 57.1 1.0
CG A:HIS797 4.0 52.4 1.0
CG A:HIS793 4.1 47.3 1.0
CB A:GLU779 4.1 74.7 1.0
CA A:CYS780 4.1 58.5 1.0
C A:GLU779 4.5 60.0 1.0
CA A:CYS777 4.7 49.4 1.0
CA A:GLU779 4.8 64.2 1.0
OG1 A:THR796 4.8 60.1 1.0
C A:CYS780 4.9 59.9 1.0
N A:GLU779 4.9 62.5 1.0
CB A:ARG782 4.9 58.7 1.0
N A:GLY781 5.0 53.9 1.0

Zinc binding site 10 out of 13 in 5v3g

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Zinc binding site 10 out of 13 in the PRDM9-Allele-C ZNF8-13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of PRDM9-Allele-C ZNF8-13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1004

b:48.6
occ:1.00
NE2 A:HIS825 2.0 63.9 1.0
NE2 A:HIS821 2.0 52.1 1.0
SG A:CYS808 2.2 50.4 1.0
SG A:CYS805 2.2 46.6 1.0
CE1 A:HIS825 2.9 56.4 1.0
CE1 A:HIS821 2.9 41.4 1.0
CD2 A:HIS825 3.1 52.5 1.0
CD2 A:HIS821 3.1 46.3 1.0
CB A:CYS808 3.2 50.7 1.0
CB A:CYS805 3.2 41.4 1.0
N A:CYS808 3.6 47.1 1.0
CA A:CYS808 3.9 50.9 1.0
ND1 A:HIS825 4.0 59.0 1.0
ND1 A:HIS821 4.1 39.9 1.0
CG A:HIS825 4.2 58.9 1.0
CG A:HIS821 4.2 41.2 1.0
CB A:GLU807 4.3 70.1 1.0
C A:GLU807 4.6 56.6 1.0
C A:CYS808 4.6 56.9 1.0
CA A:CYS805 4.7 46.5 1.0
CB A:ARG810 4.8 50.3 1.0
N A:GLU807 4.8 64.0 1.0
CA A:GLU807 4.8 60.2 1.0
N A:GLY809 4.9 52.0 1.0
N A:ARG810 4.9 45.3 1.0

Reference:

A.Patel, X.Zhang, R.M.Blumenthal, X.Cheng. Structural Basis of Human Pr/Set Domain 9 (PRDM9) Allele C-Specific Recognition of Its Cognate Dna Sequence. J. Biol. Chem. V. 292 15994 2017.
ISSN: ESSN 1083-351X
PubMed: 28801461
DOI: 10.1074/JBC.M117.805754
Page generated: Wed Dec 16 11:07:34 2020

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