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Zinc in PDB 5eh2: Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence III

Enzymatic activity of Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence III

All present enzymatic activity of Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence III:
2.1.1.43;

Protein crystallography data

The structure of Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence III, PDB code: 5eh2 was solved by A.Patel, J.R.Horton, G.G.Wilson, X.Zhang, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.75 / 2.05
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 45.208, 57.756, 76.206, 90.15, 75.30, 83.30
R / Rfree (%) 20.1 / 23.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence III (pdb code 5eh2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence III, PDB code: 5eh2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5eh2

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Zinc binding site 1 out of 8 in the Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence III


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence III within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1001

b:47.8
occ:1.00
 NE2 E:HIS741 1.9 36.9 1.0
NE2 E:HIS737 2.1 48.4 1.0
SG E:CYS724 2.2 48.3 1.0
SG E:CYS721 2.2 44.6 1.0
CE1 E:HIS741 2.8 49.2 1.0
CD2 E:HIS741 3.0 54.4 1.0
CD2 E:HIS737 3.0 44.3 1.0
CE1 E:HIS737 3.1 51.1 1.0
CB E:CYS721 3.1 40.9 1.0
CB E:CYS724 3.2 50.6 1.0
N E:CYS724 3.6 47.0 1.0
ND1 E:HIS741 4.0 54.5 1.0
CA E:CYS724 4.0 45.3 1.0
CG E:HIS741 4.1 50.2 1.0
ND1 E:HIS737 4.2 47.3 1.0
CG E:HIS737 4.2 54.6 1.0
CB E:GLU723 4.5 49.1 1.0
CA E:CYS721 4.5 44.8 1.0
C E:GLU723 4.5 51.5 1.0
HD1 E:HIS741 4.7 0.8 1.0
C E:CYS724 4.7 42.3 1.0
NE E:ARG726 4.7 59.6 0.5
N E:GLY725 4.8 41.6 1.0
CA E:GLU723 4.9 44.3 1.0
C E:CYS721 4.9 49.5 1.0
HD1 E:HIS737 4.9 56.8 1.0
N E:GLU723 4.9 45.4 1.0
N E:ARG726 5.0 47.6 1.0

Zinc binding site 2 out of 8 in 5eh2

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Zinc binding site 2 out of 8 in the Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence III


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence III within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1002

b:79.6
occ:1.00
 NE2 E:HIS769 2.0 67.8 1.0
SG E:CYS752 2.0 70.5 1.0
SG E:CYS749 2.2 62.9 1.0
NE2 E:HIS765 2.3 75.4 1.0
CD2 E:HIS769 2.9 72.0 1.0
CE1 E:HIS769 3.1 75.4 1.0
CE1 E:HIS765 3.1 66.2 1.0
CB E:CYS749 3.2 72.0 1.0
CD2 E:HIS765 3.3 65.8 1.0
CB E:CYS752 3.4 85.7 1.0
N E:CYS752 3.7 81.0 1.0
CG E:HIS769 4.1 72.0 1.0
CA E:CYS752 4.1 79.8 1.0
ND1 E:HIS769 4.2 77.2 1.0
ND1 E:HIS765 4.3 69.5 1.0
C E:GLU751 4.3 80.2 1.0
CG E:HIS765 4.4 63.3 1.0
CB E:GLU751 4.4 82.6 1.0
CA E:CYS749 4.6 77.5 1.0
CA E:GLU751 4.7 78.7 1.0
N E:GLU751 4.9 74.8 1.0
N E:GLY753 4.9 78.6 1.0
C E:CYS752 4.9 75.4 1.0
HD1 E:HIS769 4.9 92.6 1.0

Zinc binding site 3 out of 8 in 5eh2

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Zinc binding site 3 out of 8 in the Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence III


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence III within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1003

b:51.2
occ:1.00
 NE2 E:HIS797 2.0 58.5 1.0
NE2 E:HIS793 2.1 52.5 1.0
SG E:CYS777 2.2 51.8 1.0
SG E:CYS780 2.2 49.2 1.0
CD2 E:HIS797 2.7 62.0 1.0
CD2 E:HIS793 2.8 44.0 1.0
CB E:CYS777 3.2 44.0 1.0
CE1 E:HIS797 3.2 67.2 1.0
CE1 E:HIS793 3.3 54.1 1.0
CB E:CYS780 3.3 55.4 1.0
N E:CYS780 3.8 63.5 1.0
CG E:HIS797 3.9 68.9 1.0
CG E:HIS793 4.1 44.5 1.0
CA E:CYS780 4.1 58.8 1.0
ND1 E:HIS797 4.1 66.7 1.0
ND1 E:HIS793 4.2 50.1 1.0
CA E:CYS777 4.6 53.4 1.0
CB E:GLU779 4.6 64.5 1.0
C E:GLU779 4.7 66.6 1.0
O E:CYS777 4.8 58.8 1.0
C E:CYS780 4.8 54.9 1.0
C E:CYS777 4.9 63.5 1.0
CG E:GLU779 5.0 67.4 1.0
N E:GLU779 5.0 56.8 1.0

Zinc binding site 4 out of 8 in 5eh2

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Zinc binding site 4 out of 8 in the Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence III


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence III within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1004

b:68.3
occ:1.00
 SG E:CYS805 2.2 69.2 1.0
NE2 E:HIS825 2.3 83.0 1.0
NE2 E:HIS821 2.4 73.0 1.0
CB E:CYS808 2.4 64.8 1.0
SG E:CYS808 2.4 87.6 1.0
CB E:CYS805 3.1 68.4 1.0
CD2 E:HIS821 3.1 67.9 1.0
CD2 E:HIS825 3.2 82.0 1.0
N E:CYS808 3.3 78.0 1.0
CE1 E:HIS825 3.3 81.8 1.0
CA E:CYS808 3.4 80.3 1.0
CE1 E:HIS821 3.5 71.0 1.0
CG E:HIS821 4.4 73.2 1.0
CG E:HIS825 4.4 90.1 1.0
ND1 E:HIS825 4.4 89.4 1.0
C E:GLU807 4.5 82.3 1.0
CA E:CYS805 4.5 63.3 1.0
ND1 E:HIS821 4.5 71.5 1.0
C E:CYS808 4.6 74.4 1.0
CB E:GLU807 4.8 76.1 1.0
N E:GLY809 4.8 70.5 1.0
CB E:ARG810 4.8 63.9 1.0
C E:CYS805 4.9 70.0 1.0
N E:GLU807 4.9 69.5 1.0
O E:CYS805 5.0 71.8 1.0
CA E:GLU807 5.0 78.6 1.0
CG E:GLU807 5.0 89.8 1.0

Zinc binding site 5 out of 8 in 5eh2

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Zinc binding site 5 out of 8 in the Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence III


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence III within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1001

b:54.7
occ:1.00
 NE2 F:HIS737 1.9 43.1 1.0
NE2 F:HIS741 2.1 59.3 1.0
SG F:CYS724 2.2 57.9 1.0
SG F:CYS721 2.4 61.5 1.0
CE1 F:HIS737 2.7 47.7 1.0
CD2 F:HIS741 3.0 53.5 1.0
CD2 F:HIS737 3.1 40.9 1.0
CE1 F:HIS741 3.2 59.2 1.0
CB F:CYS724 3.2 56.1 1.0
CB F:CYS721 3.3 66.4 1.0
N F:CYS724 3.7 66.5 1.0
ND1 F:HIS737 3.9 47.1 1.0
CA F:CYS724 4.0 63.4 1.0
CG F:HIS737 4.1 45.9 1.0
CG F:HIS741 4.2 56.6 1.0
ND1 F:HIS741 4.2 61.7 1.0
HD1 F:HIS737 4.5 56.5 1.0
CB F:GLU723 4.6 71.3 1.0
C F:GLU723 4.7 69.3 1.0
CA F:CYS721 4.7 66.1 1.0
C F:CYS724 4.8 66.5 1.0
N F:GLY725 4.8 68.1 1.0
N F:GLU723 5.0 63.7 1.0
CA F:GLU723 5.0 70.2 1.0

Zinc binding site 6 out of 8 in 5eh2

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Zinc binding site 6 out of 8 in the Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence III


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence III within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1002

b:48.5
occ:1.00
 SG F:CYS752 2.1 43.0 1.0
NE2 F:HIS769 2.2 47.5 1.0
NE2 F:HIS765 2.2 44.3 1.0
SG F:CYS749 2.2 49.2 1.0
CD2 F:HIS769 3.0 49.1 1.0
CB F:CYS749 3.1 48.5 1.0
CB F:CYS752 3.1 57.4 1.0
CD2 F:HIS765 3.1 42.1 1.0
CE1 F:HIS765 3.2 43.6 1.0
CE1 F:HIS769 3.3 56.8 1.0
N F:CYS752 3.6 51.2 1.0
CA F:CYS752 3.9 47.2 1.0
CG F:HIS769 4.2 46.8 1.0
CG F:HIS765 4.3 44.5 1.0
ND1 F:HIS765 4.3 46.7 1.0
ND1 F:HIS769 4.3 53.7 1.0
CA F:CYS749 4.5 49.8 1.0
C F:CYS752 4.6 49.3 1.0
C F:GLU751 4.6 56.5 1.0
CB F:GLU751 4.6 58.6 1.0
N F:GLY753 4.7 46.8 1.0
CG F:GLU751 4.8 56.4 1.0
CB F:ARG754 4.9 49.8 0.5
C F:CYS749 4.9 46.8 1.0
CA F:GLU751 4.9 51.5 1.0
O F:CYS749 5.0 49.6 1.0
N F:GLU751 5.0 57.5 1.0
N F:ARG754 5.0 53.2 1.0

Zinc binding site 7 out of 8 in 5eh2

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Zinc binding site 7 out of 8 in the Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence III


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence III within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1003

b:46.3
occ:1.00
 NE2 F:HIS793 2.0 43.8 1.0
NE2 F:HIS797 2.1 47.4 1.0
SG F:CYS777 2.1 45.6 1.0
SG F:CYS780 2.3 45.0 1.0
CD2 F:HIS797 2.8 43.1 1.0
CD2 F:HIS793 2.9 35.5 1.0
CE1 F:HIS793 3.0 45.7 1.0
CB F:CYS777 3.2 39.3 1.0
CE1 F:HIS797 3.2 51.8 1.0
CB F:CYS780 3.2 47.1 1.0
N F:CYS780 3.8 56.6 1.0
CA F:CYS780 4.0 53.5 1.0
CG F:HIS797 4.1 48.7 1.0
CG F:HIS793 4.1 36.4 1.0
ND1 F:HIS793 4.1 40.5 1.0
ND1 F:HIS797 4.2 50.8 1.0
O F:HOH1136 4.4 54.6 1.0
CB F:GLU779 4.5 49.5 1.0
CA F:CYS777 4.6 49.7 1.0
C F:CYS780 4.7 46.9 1.0
C F:GLU779 4.7 60.3 1.0
N F:GLY781 4.9 52.5 1.0
HD1 F:HIS793 4.9 48.6 1.0
C F:CYS777 5.0 55.4 1.0

Zinc binding site 8 out of 8 in 5eh2

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Zinc binding site 8 out of 8 in the Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence III


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence III within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1004

b:50.3
occ:1.00
 NE2 F:HIS825 2.0 59.1 1.0
NE2 F:HIS821 2.1 55.4 1.0
SG F:CYS805 2.2 50.6 1.0
SG F:CYS808 2.2 49.4 1.0
CE1 F:HIS825 3.0 59.9 1.0
CD2 F:HIS825 3.0 59.0 1.0
CB F:CYS805 3.0 44.7 1.0
CE1 F:HIS821 3.1 52.4 1.0
CD2 F:HIS821 3.1 47.2 1.0
CB F:CYS808 3.3 47.5 1.0
N F:CYS808 3.7 45.4 1.0
CA F:CYS808 4.0 46.1 1.0
ND1 F:HIS825 4.1 66.2 1.0
CG F:HIS825 4.2 63.8 1.0
ND1 F:HIS821 4.2 49.1 1.0
CG F:HIS821 4.2 47.5 1.0
CB F:GLU807 4.2 58.4 1.0
CA F:CYS805 4.5 47.8 1.0
C F:GLU807 4.6 56.6 1.0
C F:CYS808 4.8 44.4 1.0
CA F:GLU807 4.9 53.9 1.0
HD1 F:HIS825 4.9 79.5 1.0
N F:GLY809 4.9 42.4 1.0
C F:CYS805 4.9 46.0 1.0
CB F:ARG810 5.0 42.7 1.0
O F:CYS805 5.0 45.4 1.0
HD1 F:HIS821 5.0 58.9 1.0

Reference:

A.Patel, J.R.Horton, G.G.Wilson, X.Zhang, X.Cheng. Structural Basis For Human PRDM9 Action at Recombination Hot Spots. Genes Dev. V. 30 257 2016.
ISSN: ISSN 0890-9369
PubMed: 26833727
DOI: 10.1101/GAD.274928.115
Page generated: Sun Oct 27 15:16:59 2024

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