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Zinc in PDB 3zpv: Crystal Structure of Drosophila Pygo Phd Finger in Complex with Legless HD1 Domain

Protein crystallography data

The structure of Crystal Structure of Drosophila Pygo Phd Finger in Complex with Legless HD1 Domain, PDB code: 3zpv was solved by T.C.R.Miller, J.Mieszczanek, M.J.Sanchez-Barrena, T.J.Rutherford, M.Fiedler, M.Bienz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.24 / 2.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.210, 111.960, 190.760, 90.00, 90.00, 90.00
R / Rfree (%) 22.389 / 26.231

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Drosophila Pygo Phd Finger in Complex with Legless HD1 Domain (pdb code 3zpv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 36 binding sites of Zinc where determined in the Crystal Structure of Drosophila Pygo Phd Finger in Complex with Legless HD1 Domain, PDB code: 3zpv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 36 in 3zpv

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Zinc binding site 1 out of 36 in the Crystal Structure of Drosophila Pygo Phd Finger in Complex with Legless HD1 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Drosophila Pygo Phd Finger in Complex with Legless HD1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Zn805

b:26.5
occ:1.00
 SG 1:CYS799 2.2 36.9 1.0
SG 1:CYS802 2.2 44.9 1.0
SG 1:CYS766 2.3 25.5 1.0
SG 1:CYS770 2.3 33.7 1.0
CB 1:CYS802 3.1 54.4 1.0
CB 1:CYS766 3.2 26.2 1.0
CB 1:CYS770 3.3 29.1 1.0
CB 1:CYS799 3.4 36.0 1.0
N 1:CYS770 3.7 30.9 1.0
N 1:CYS799 4.0 36.5 1.0
CA 1:CYS770 4.1 28.9 1.0
N 1:CYS802 4.2 41.8 1.0
CA 1:CYS799 4.3 37.5 1.0
CA 1:CYS802 4.3 52.7 1.0
CA 1:CYS766 4.7 24.6 1.0
C 1:CYS799 4.8 37.6 1.0
O 1:CYS799 4.8 39.9 1.0
N 1:GLY769 4.9 35.5 1.0
CZ 1:PHE774 4.9 16.5 1.0
CE1 1:PHE774 4.9 17.2 1.0
C 1:GLY769 4.9 33.8 1.0
C 1:CYS770 5.0 26.9 1.0

Zinc binding site 2 out of 36 in 3zpv

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Zinc binding site 2 out of 36 in the Crystal Structure of Drosophila Pygo Phd Finger in Complex with Legless HD1 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Drosophila Pygo Phd Finger in Complex with Legless HD1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Zn806

b:19.8
occ:1.00
 ND1 1:HIS775 2.1 20.6 1.0
SG 1:CYS778 2.2 23.3 1.0
SG 1:CYS753 2.3 23.0 1.0
SG 1:CYS750 2.3 19.7 1.0
CB 1:CYS750 3.0 20.1 1.0
CE1 1:HIS775 3.1 21.4 1.0
CG 1:HIS775 3.2 19.8 1.0
CB 1:CYS753 3.3 21.8 1.0
CB 1:CYS778 3.3 26.0 1.0
CB 1:HIS775 3.5 19.7 1.0
N 1:CYS753 3.8 26.5 1.0
N 1:HIS775 4.1 19.9 1.0
CA 1:CYS753 4.1 24.3 1.0
NE2 1:HIS775 4.2 22.2 1.0
CD2 1:HIS775 4.3 21.2 1.0
CA 1:HIS775 4.4 20.0 1.0
CA 1:CYS750 4.5 20.6 1.0
CB 1:MET752 4.6 38.0 1.0
CA 1:CYS778 4.7 28.2 1.0
C 1:CYS753 4.8 25.3 1.0
N 1:HIS754 4.9 24.0 1.0
C 1:MET752 4.9 28.5 1.0

Zinc binding site 3 out of 36 in 3zpv

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Zinc binding site 3 out of 36 in the Crystal Structure of Drosophila Pygo Phd Finger in Complex with Legless HD1 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Drosophila Pygo Phd Finger in Complex with Legless HD1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Zn805

b:42.5
occ:1.00
 SG 3:CYS799 2.1 32.3 1.0
SG 3:CYS766 2.2 30.3 1.0
SG 3:CYS770 2.3 35.1 1.0
SG 3:CYS802 2.5 49.0 1.0
CB 3:CYS766 3.0 35.2 1.0
CB 3:CYS799 3.2 33.3 1.0
CB 3:CYS802 3.3 57.6 1.0
CB 3:CYS770 3.4 34.9 1.0
N 3:CYS770 3.9 41.3 1.0
N 3:CYS799 3.9 32.7 1.0
CA 3:CYS799 4.1 33.7 1.0
CA 3:CYS770 4.2 38.0 1.0
N 3:CYS802 4.3 59.3 1.0
CA 3:CYS802 4.4 58.5 1.0
CA 3:CYS766 4.5 35.7 1.0
CZ 3:PHE774 4.7 30.7 1.0
CE1 3:PHE774 4.7 31.5 1.0
C 3:CYS799 4.7 36.8 1.0
O 3:CYS799 4.8 36.0 1.0
C 3:CYS766 5.0 39.6 1.0

Zinc binding site 4 out of 36 in 3zpv

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Zinc binding site 4 out of 36 in the Crystal Structure of Drosophila Pygo Phd Finger in Complex with Legless HD1 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Drosophila Pygo Phd Finger in Complex with Legless HD1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Zn806

b:31.4
occ:1.00
 ND1 3:HIS775 2.1 25.7 1.0
SG 3:CYS750 2.2 33.4 1.0
SG 3:CYS778 2.3 32.9 1.0
SG 3:CYS753 2.4 32.6 1.0
CB 3:CYS750 2.9 33.1 1.0
CE1 3:HIS775 3.1 25.2 1.0
CG 3:HIS775 3.1 26.1 1.0
CB 3:CYS778 3.3 36.4 1.0
CB 3:CYS753 3.4 34.1 1.0
CB 3:HIS775 3.4 26.4 1.0
N 3:CYS753 3.9 39.5 1.0
N 3:HIS775 3.9 26.3 1.0
CA 3:CYS753 4.2 37.6 1.0
NE2 3:HIS775 4.2 24.6 1.0
CD2 3:HIS775 4.2 24.1 1.0
CA 3:HIS775 4.3 27.4 1.0
CA 3:CYS750 4.4 30.4 1.0
CA 3:CYS778 4.7 39.4 1.0
CB 3:MET752 4.7 55.8 1.0
C 3:CYS753 4.9 41.5 1.0
N 3:HIS754 5.0 42.9 1.0
O 3:HIS775 5.0 28.8 1.0
C 3:MET752 5.0 43.5 1.0
N 3:CYS778 5.0 41.3 1.0

Zinc binding site 5 out of 36 in 3zpv

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Zinc binding site 5 out of 36 in the Crystal Structure of Drosophila Pygo Phd Finger in Complex with Legless HD1 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Drosophila Pygo Phd Finger in Complex with Legless HD1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
5:Zn805

b:32.7
occ:1.00
 SG 5:CYS802 2.2 36.7 1.0
SG 5:CYS770 2.2 34.2 1.0
SG 5:CYS799 2.3 34.6 1.0
SG 5:CYS766 2.3 25.9 1.0
CB 5:CYS802 3.2 41.4 1.0
CB 5:CYS770 3.2 31.3 1.0
CB 5:CYS766 3.2 28.8 1.0
CB 5:CYS799 3.5 38.0 1.0
N 5:CYS770 3.7 30.0 1.0
CA 5:CYS770 4.0 28.9 1.0
N 5:CYS799 4.1 31.7 1.0
N 5:CYS802 4.2 41.6 1.0
CA 5:CYS802 4.3 42.2 1.0
CA 5:CYS799 4.4 33.9 1.0
CA 5:CYS766 4.7 28.3 1.0
N 5:GLY769 4.8 40.5 1.0
C 5:GLY769 4.8 32.7 1.0
C 5:CYS770 4.9 26.3 1.0
O 5:CYS799 4.9 35.6 1.0
C 5:CYS799 4.9 35.2 1.0
CZ 5:PHE774 4.9 28.5 1.0
N 5:ASN771 4.9 27.3 1.0
CE1 5:PHE774 4.9 30.3 1.0

Zinc binding site 6 out of 36 in 3zpv

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Zinc binding site 6 out of 36 in the Crystal Structure of Drosophila Pygo Phd Finger in Complex with Legless HD1 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Drosophila Pygo Phd Finger in Complex with Legless HD1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
5:Zn806

b:23.3
occ:1.00
 ND1 5:HIS775 2.1 24.3 1.0
SG 5:CYS778 2.2 25.1 1.0
SG 5:CYS750 2.3 26.4 1.0
SG 5:CYS753 2.3 29.6 1.0
CB 5:CYS750 3.0 23.5 1.0
CE1 5:HIS775 3.1 25.4 1.0
CG 5:HIS775 3.1 23.5 1.0
CB 5:CYS778 3.3 26.0 1.0
CB 5:CYS753 3.3 27.9 1.0
CB 5:HIS775 3.4 24.6 1.0
N 5:CYS753 3.8 31.8 1.0
N 5:HIS775 4.0 27.4 1.0
CA 5:CYS753 4.1 29.2 1.0
NE2 5:HIS775 4.2 25.6 1.0
CD2 5:HIS775 4.3 23.5 1.0
CA 5:HIS775 4.3 26.3 1.0
CA 5:CYS750 4.5 25.1 1.0
CB 5:MET752 4.6 45.5 1.0
CA 5:CYS778 4.7 28.6 1.0
C 5:CYS753 4.9 30.1 1.0
C 5:MET752 4.9 35.5 1.0
N 5:HIS754 5.0 29.5 1.0

Zinc binding site 7 out of 36 in 3zpv

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Zinc binding site 7 out of 36 in the Crystal Structure of Drosophila Pygo Phd Finger in Complex with Legless HD1 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Drosophila Pygo Phd Finger in Complex with Legless HD1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
7:Zn805

b:31.8
occ:1.00
 SG 7:CYS802 2.1 50.9 1.0
SG 7:CYS799 2.2 39.6 1.0
SG 7:CYS770 2.3 38.3 1.0
SG 7:CYS766 2.3 40.1 1.0
CB 7:CYS802 3.1 51.4 1.0
CB 7:CYS770 3.2 38.8 1.0
CB 7:CYS766 3.3 34.7 1.0
CB 7:CYS799 3.5 38.4 1.0
N 7:CYS770 3.7 41.8 1.0
CA 7:CYS770 4.0 39.9 1.0
N 7:CYS799 4.1 35.8 1.0
N 7:CYS802 4.2 52.2 1.0
CA 7:CYS802 4.2 53.6 1.0
CA 7:CYS799 4.3 37.9 1.0
CA 7:CYS766 4.7 33.5 1.0
N 7:GLY769 4.8 46.5 1.0
O 7:CYS799 4.9 34.0 1.0
C 7:CYS799 4.9 38.2 1.0
C 7:GLY769 4.9 43.3 1.0
CZ 7:PHE774 4.9 35.8 1.0
C 7:CYS770 4.9 37.7 1.0
CE1 7:PHE774 5.0 35.2 1.0
N 7:ASN771 5.0 38.0 1.0

Zinc binding site 8 out of 36 in 3zpv

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Zinc binding site 8 out of 36 in the Crystal Structure of Drosophila Pygo Phd Finger in Complex with Legless HD1 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Drosophila Pygo Phd Finger in Complex with Legless HD1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
7:Zn806

b:48.7
occ:1.00
 SG 7:CYS778 2.2 48.8 1.0
SG 7:CYS753 2.2 40.9 1.0
ND1 7:HIS775 2.3 31.2 1.0
SG 7:CYS750 2.3 34.6 1.0
CB 7:CYS750 3.0 32.6 1.0
CB 7:CYS753 3.2 40.8 1.0
CE1 7:HIS775 3.2 30.5 1.0
CG 7:HIS775 3.3 32.9 1.0
CB 7:CYS778 3.3 46.4 1.0
CB 7:HIS775 3.6 36.3 1.0
N 7:CYS753 3.7 49.3 1.0
CA 7:CYS753 4.0 44.1 1.0
N 7:HIS775 4.2 35.0 1.0
NE2 7:HIS775 4.3 30.9 1.0
CD2 7:HIS775 4.4 33.4 1.0
CA 7:HIS775 4.5 36.3 1.0
CA 7:CYS750 4.5 32.2 1.0
CB 7:MET752 4.5 61.3 1.0
CA 7:CYS778 4.7 46.0 1.0
C 7:CYS753 4.8 46.8 1.0
C 7:MET752 4.9 50.9 1.0
N 7:HIS754 4.9 48.2 1.0

Zinc binding site 9 out of 36 in 3zpv

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Zinc binding site 9 out of 36 in the Crystal Structure of Drosophila Pygo Phd Finger in Complex with Legless HD1 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Drosophila Pygo Phd Finger in Complex with Legless HD1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
9:Zn805

b:33.9
occ:1.00
 SG 9:CYS802 2.1 57.2 1.0
SG 9:CYS799 2.3 34.6 1.0
SG 9:CYS770 2.3 30.8 1.0
SG 9:CYS766 2.3 36.3 1.0
CB 9:CYS802 3.1 63.3 1.0
CB 9:CYS770 3.2 31.3 1.0
CB 9:CYS766 3.3 34.2 1.0
CB 9:CYS799 3.5 42.1 1.0
N 9:CYS770 3.7 41.6 1.0
CA 9:CYS770 4.0 35.0 1.0
N 9:CYS799 4.2 39.7 1.0
N 9:CYS802 4.2 60.4 1.0
CA 9:CYS802 4.2 63.3 1.0
CA 9:CYS799 4.4 43.0 1.0
CA 9:CYS766 4.7 35.6 1.0
N 9:GLY769 4.8 48.0 1.0
O 9:CYS799 4.9 43.9 1.0
C 9:GLY769 4.9 45.2 1.0
C 9:CYS799 4.9 48.9 1.0
CZ 9:PHE774 4.9 28.1 1.0
C 9:CYS770 4.9 34.6 1.0
CE1 9:PHE774 5.0 30.3 1.0
N 9:ASN771 5.0 33.8 1.0

Zinc binding site 10 out of 36 in 3zpv

Go back to Zinc Binding Sites List in 3zpv
Zinc binding site 10 out of 36 in the Crystal Structure of Drosophila Pygo Phd Finger in Complex with Legless HD1 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Drosophila Pygo Phd Finger in Complex with Legless HD1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
9:Zn806

b:34.8
occ:1.00
 ND1 9:HIS775 1.9 29.7 1.0
SG 9:CYS750 2.2 34.9 1.0
SG 9:CYS778 2.4 43.3 1.0
SG 9:CYS753 2.5 37.8 1.0
CB 9:CYS750 2.8 35.1 1.0
CE1 9:HIS775 2.9 30.5 1.0
CG 9:HIS775 2.9 31.6 1.0
CB 9:HIS775 3.3 35.1 1.0
CB 9:CYS778 3.4 48.5 1.0
CB 9:CYS753 3.5 35.7 1.0
N 9:HIS775 3.8 34.2 1.0
N 9:CYS753 4.0 40.5 1.0
NE2 9:HIS775 4.0 30.2 1.0
CD2 9:HIS775 4.0 31.7 1.0
CA 9:HIS775 4.2 36.1 1.0
CA 9:CYS753 4.3 38.0 1.0
CA 9:CYS750 4.3 32.6 1.0
CB 9:MET752 4.8 64.9 1.0
CA 9:CYS778 4.8 45.4 1.0
O 9:HIS775 5.0 34.6 1.0
C 9:PHE774 5.0 33.1 1.0

Reference:

T.C.R.Miller, J.Mieszczanek, M.J.Sanchez-Barrena, T.J.Rutherford, M.Fiedler, M.Bienz. Evolutionary Adaptation of the Fly Pygo Phd Finger Towards Recognizing Histone H3 Tail Methylated at Arginine 2 Structure V. 21 2208 2013.
ISSN: ISSN 0969-2126
PubMed: 24183574
DOI: 10.1016/J.STR.2013.09.013
Page generated: Sat Oct 26 18:32:32 2024

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