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Zinc in PDB 5ei9: Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence I

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

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

Protein crystallography data

The structure of Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence I, PDB code: 5ei9 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) 32.98 / 1.92
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.329, 55.740, 76.038, 89.85, 75.50, 86.58
R / Rfree (%) 21.4 / 23.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Human PRDM9 Allele-A Znf Domain with Associated Recombination Hotspot Dna Sequence I (pdb code 5ei9). 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 I, PDB code: 5ei9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5ei9

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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 I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1001

b:38.3
occ:1.00
 NE2 F:HIS741 1.8 25.8 1.0
NE2 F:HIS737 2.1 32.9 1.0
SG F:CYS721 2.2 36.4 1.0
SG F:CYS724 2.2 38.7 1.0
CD2 F:HIS741 2.8 39.1 1.0
CD2 F:HIS737 2.9 33.8 1.0
CE1 F:HIS741 2.9 41.1 1.0
CB F:CYS721 3.1 33.9 1.0
CE1 F:HIS737 3.2 41.1 1.0
CB F:CYS724 3.3 43.0 1.0
N F:CYS724 3.7 44.1 1.0
CG F:HIS741 3.9 42.3 1.0
ND1 F:HIS741 4.0 43.0 1.0
CA F:CYS724 4.0 35.0 1.0
CG F:HIS737 4.1 39.1 1.0
ND1 F:HIS737 4.2 36.6 1.0
CB F:GLU723 4.4 40.8 1.0
CA F:CYS721 4.5 33.5 1.0
C F:GLU723 4.6 40.8 1.0
C F:CYS724 4.7 33.5 1.0
HD1 F:HIS741 4.8 51.6 1.0
N F:GLY725 4.8 37.1 1.0
C F:CYS721 4.8 39.3 1.0
CA F:GLU723 4.9 38.2 1.0
O F:CYS721 4.9 37.2 1.0
N F:GLU723 4.9 39.5 1.0

Zinc binding site 2 out of 8 in 5ei9

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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 I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1002

b:76.0
occ:1.00
 NE2 F:HIS769 2.0 76.4 1.0
SG F:CYS752 2.0 67.2 1.0
CD2 F:HIS769 2.4 75.5 1.0
NE2 F:HIS765 2.4 73.2 1.0
SG F:CYS749 2.4 71.2 1.0
CD2 F:HIS765 3.0 65.6 1.0
CE1 F:HIS769 3.2 75.9 1.0
CB F:CYS752 3.5 77.2 1.0
CG F:HIS769 3.5 73.4 1.0
CB F:CYS749 3.6 69.6 1.0
CE1 F:HIS765 3.6 69.2 1.0
N F:CYS752 3.9 78.4 1.0
ND1 F:HIS769 3.9 77.4 1.0
C F:GLU751 4.1 81.2 1.0
CB F:GLU751 4.2 80.0 1.0
CA F:CYS752 4.2 79.8 1.0
CG F:HIS765 4.3 64.3 1.0
ND1 F:HIS765 4.5 66.9 1.0
O F:GLU751 4.5 81.5 1.0
CA F:GLU751 4.5 79.1 1.0
CG F:GLN766 4.6 62.6 1.0
N F:GLU751 4.7 79.5 1.0
N F:GLN766 4.7 67.3 1.0
HD1 F:HIS769 4.7 92.9 1.0
CB F:HIS769 4.8 73.0 1.0
CA F:GLN766 4.9 66.2 1.0
CA F:CYS749 4.9 67.7 1.0
CG F:GLU751 5.0 79.8 1.0

Zinc binding site 3 out of 8 in 5ei9

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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 I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1003

b:41.7
occ:1.00
 NE2 F:HIS793 2.0 42.7 1.0
SG F:CYS777 2.0 37.0 1.0
NE2 F:HIS797 2.0 44.6 1.0
SG F:CYS780 2.3 40.3 1.0
CD2 F:HIS797 2.7 47.7 1.0
CD2 F:HIS793 2.9 38.8 1.0
CE1 F:HIS793 3.0 47.1 1.0
CB F:CYS777 3.1 34.5 1.0
CE1 F:HIS797 3.2 53.1 1.0
CB F:CYS780 3.2 46.3 1.0
N F:CYS780 3.7 45.7 1.0
CG F:HIS797 4.0 51.8 1.0
CA F:CYS780 4.1 46.2 1.0
CG F:HIS793 4.1 39.5 1.0
ND1 F:HIS793 4.1 40.5 1.0
ND1 F:HIS797 4.2 48.3 1.0
CB F:GLU779 4.5 56.7 1.0
CA F:CYS777 4.6 43.1 1.0
C F:GLU779 4.6 54.0 1.0
O F:CYS777 4.8 45.5 1.0
C F:CYS780 4.8 43.5 1.0
HD1 F:HIS793 4.9 48.6 1.0
CB F:ARG782 4.9 38.3 1.0
C F:CYS777 4.9 49.0 1.0
CA F:GLU779 5.0 51.9 1.0
HD1 F:HIS797 5.0 57.9 1.0

Zinc binding site 4 out of 8 in 5ei9

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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 I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1004

b:54.6
occ:1.00
 NE2 F:HIS821 2.2 57.7 1.0
SG F:CYS808 2.2 53.6 1.0
SG F:CYS805 2.3 53.1 1.0
NE2 F:HIS825 2.3 69.5 1.0
CD2 F:HIS825 2.8 64.0 1.0
CD2 F:HIS821 3.0 55.3 1.0
CB F:CYS805 3.2 48.6 1.0
CB F:CYS808 3.3 61.0 1.0
CE1 F:HIS821 3.3 57.6 1.0
N F:CYS808 3.5 53.4 1.0
CE1 F:HIS825 3.5 64.5 1.0
CA F:CYS808 3.9 56.6 1.0
CG F:HIS825 4.1 68.6 1.0
CG F:HIS821 4.2 56.8 1.0
CB F:GLU807 4.3 63.8 1.0
ND1 F:HIS821 4.3 57.4 1.0
ND1 F:HIS825 4.4 73.0 1.0
C F:GLU807 4.5 61.5 1.0
C F:CYS808 4.6 53.1 1.0
CA F:CYS805 4.6 49.7 1.0
CG F:GLU807 4.6 66.0 1.0
N F:GLY809 4.7 55.3 1.0
CA F:GLU807 4.7 60.6 1.0
N F:GLU807 4.8 57.2 1.0
C F:CYS805 4.9 51.9 1.0
N F:ARG810 4.9 46.0 1.0
CB F:ARG810 5.0 50.9 1.0
O F:CYS805 5.0 50.5 1.0

Zinc binding site 5 out of 8 in 5ei9

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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 I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1001

b:49.8
occ:1.00
 NE2 E:HIS737 1.9 33.8 1.0
NE2 E:HIS741 2.1 49.7 1.0
SG E:CYS724 2.2 50.8 1.0
SG E:CYS721 2.3 52.0 1.0
CE1 E:HIS737 2.6 38.3 1.0
CD2 E:HIS741 2.9 48.2 1.0
CD2 E:HIS737 3.1 36.6 1.0
CB E:CYS721 3.2 52.4 1.0
CE1 E:HIS741 3.2 48.6 1.0
CB E:CYS724 3.3 43.4 1.0
N E:CYS724 3.7 56.0 1.0
ND1 E:HIS737 3.9 36.4 1.0
CA E:CYS724 4.1 54.7 1.0
CG E:HIS737 4.1 35.7 1.0
CG E:HIS741 4.2 47.4 1.0
ND1 E:HIS741 4.3 49.5 1.0
CB E:GLU723 4.3 58.5 1.0
HD1 E:HIS737 4.6 43.7 1.0
C E:GLU723 4.6 59.0 1.0
CA E:CYS721 4.6 55.1 1.0
C E:CYS724 4.8 54.8 1.0
N E:GLY725 4.8 53.4 1.0
CA E:GLU723 4.8 57.1 1.0
N E:GLU723 4.9 57.0 1.0
C E:CYS721 5.0 53.2 1.0
CB E:ARG726 5.0 50.6 0.5
CB E:ARG726 5.0 50.6 0.5

Zinc binding site 6 out of 8 in 5ei9

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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 I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1002

b:41.1
occ:1.00
 SG E:CYS752 2.0 36.5 1.0
NE2 E:HIS765 2.1 34.3 1.0
NE2 E:HIS769 2.1 41.0 1.0
SG E:CYS749 2.2 42.8 1.0
CD2 E:HIS769 2.8 39.1 1.0
CD2 E:HIS765 3.0 38.7 1.0
CE1 E:HIS765 3.1 39.9 1.0
CB E:CYS749 3.1 40.3 1.0
CB E:CYS752 3.2 48.2 1.0
CE1 E:HIS769 3.3 45.2 1.0
N E:CYS752 3.6 44.4 1.0
CA E:CYS752 3.9 42.2 1.0
CG E:HIS769 4.1 42.7 1.0
ND1 E:HIS765 4.2 36.6 1.0
CG E:HIS765 4.2 36.0 1.0
ND1 E:HIS769 4.3 42.5 1.0
CA E:CYS749 4.5 44.1 1.0
C E:GLU751 4.5 50.3 1.0
C E:CYS752 4.6 45.6 1.0
CB E:GLU751 4.6 47.8 1.0
N E:GLY753 4.7 41.4 1.0
N E:GLU751 4.9 49.1 1.0
CB E:ARG754 4.9 41.9 1.0
N E:ARG754 4.9 43.0 1.0
C E:CYS749 4.9 44.1 1.0
O E:CYS749 4.9 42.3 1.0
CA E:GLU751 4.9 45.6 1.0
CG E:GLN766 4.9 38.0 1.0
HD1 E:HIS765 5.0 43.9 1.0

Zinc binding site 7 out of 8 in 5ei9

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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 I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1003

b:37.7
occ:1.00
 NE2 E:HIS793 1.9 41.6 1.0
NE2 E:HIS797 2.0 40.1 1.0
SG E:CYS777 2.1 36.2 1.0
SG E:CYS780 2.3 36.8 1.0
CD2 E:HIS797 2.8 36.0 1.0
CE1 E:HIS793 2.9 38.6 1.0
CD2 E:HIS793 3.0 31.2 1.0
CB E:CYS777 3.1 35.0 1.0
CE1 E:HIS797 3.2 43.2 1.0
CB E:CYS780 3.2 41.7 1.0
N E:CYS780 3.7 47.4 1.0
ND1 E:HIS793 4.0 36.5 1.0
CG E:HIS797 4.0 40.4 1.0
CA E:CYS780 4.0 44.2 1.0
CG E:HIS793 4.1 35.1 1.0
ND1 E:HIS797 4.2 39.1 1.0
O E:HOH1136 4.3 42.6 1.0
CB E:GLU779 4.4 45.7 1.0
CA E:CYS777 4.6 41.8 1.0
C E:GLU779 4.6 49.6 1.0
HD1 E:HIS793 4.8 43.8 1.0
C E:CYS780 4.8 43.1 1.0
CA E:GLU779 4.9 48.1 1.0
N E:GLU779 4.9 46.9 1.0
N E:GLY781 4.9 42.9 1.0
O E:CYS777 4.9 46.8 1.0
CB E:ARG782 5.0 35.1 1.0
C E:CYS777 5.0 48.7 1.0
HD1 E:HIS797 5.0 46.9 1.0

Zinc binding site 8 out of 8 in 5ei9

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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 I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1004

b:42.2
occ:1.00
 NE2 E:HIS821 2.1 43.6 1.0
SG E:CYS808 2.2 39.1 1.0
NE2 E:HIS825 2.2 49.5 1.0
SG E:CYS805 2.3 41.2 1.0
CD2 E:HIS821 2.9 43.5 1.0
CB E:CYS805 3.0 37.6 1.0
CD2 E:HIS825 3.1 50.0 1.0
CE1 E:HIS821 3.2 43.0 1.0
CE1 E:HIS825 3.2 52.5 1.0
CB E:CYS808 3.3 41.8 1.0
N E:CYS808 3.6 42.2 1.0
CA E:CYS808 4.0 39.2 1.0
CB E:GLU807 4.1 51.4 1.0
CG E:HIS821 4.1 43.4 1.0
ND1 E:HIS821 4.2 44.0 1.0
ND1 E:HIS825 4.3 58.2 1.0
CG E:HIS825 4.3 55.6 1.0
CA E:CYS805 4.5 38.0 1.0
C E:GLU807 4.5 46.3 1.0
CG E:GLU807 4.6 53.0 1.0
C E:CYS808 4.7 37.8 1.0
CA E:GLU807 4.8 42.5 1.0
N E:GLY809 4.8 36.2 1.0
C E:CYS805 4.9 39.2 1.0
CB E:ARG810 4.9 38.1 1.0
O E:CYS805 4.9 35.3 1.0
N E:GLU807 4.9 39.5 1.0
N E:ARG810 5.0 33.5 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 15:21:34 2024

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