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Zinc in PDB 8j9q: Crystal Structure of Ubr Box of UBR4 Apo

Enzymatic activity of Crystal Structure of Ubr Box of UBR4 Apo

All present enzymatic activity of Crystal Structure of Ubr Box of UBR4 Apo:
2.3.2.27;

Protein crystallography data

The structure of Crystal Structure of Ubr Box of UBR4 Apo, PDB code: 8j9q was solved by D.-E.Jeong, S.-J.Kim, H.-C.Shin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.76 / 2.18
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.67, 80.75, 81.32, 90, 90, 90
R / Rfree (%) 21.9 / 26.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ubr Box of UBR4 Apo (pdb code 8j9q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of Ubr Box of UBR4 Apo, PDB code: 8j9q:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 8j9q

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Zinc binding site 1 out of 9 in the Crystal Structure of Ubr Box of UBR4 Apo


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 Ubr Box of UBR4 Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:55.2
occ:1.00
 SG A:CYS1694 2.3 41.1 1.0
SG A:CYS1724 2.4 39.8 1.0
SG A:CYS1716 2.5 46.9 1.0
SG A:CYS1698 2.5 50.6 1.0
CB A:CYS1694 3.2 48.4 1.0
CB A:CYS1724 3.3 44.7 1.0
CB A:CYS1716 3.4 43.3 1.0
CB A:CYS1698 3.6 53.3 1.0
CA A:CYS1724 3.8 46.5 1.0
N A:LEU1725 4.1 49.4 1.0
CA A:CYS1694 4.1 42.3 1.0
C A:CYS1716 4.2 42.9 1.0
ZN A:ZN1802 4.2 51.2 1.0
N A:GLY1717 4.3 41.6 1.0
C A:CYS1724 4.3 51.0 1.0
CA A:CYS1716 4.4 41.0 1.0
N A:ALA1726 4.4 42.0 1.0
CB A:ALA1726 4.5 43.2 1.0
O A:CYS1716 4.5 43.0 1.0
CA A:GLY1717 4.7 41.4 1.0
CB A:CYS1662 4.8 39.2 1.0
CA A:CYS1698 4.9 51.3 1.0
SG A:CYS1662 5.0 32.9 1.0

Zinc binding site 2 out of 9 in 8j9q

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Zinc binding site 2 out of 9 in the Crystal Structure of Ubr Box of UBR4 Apo


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 Ubr Box of UBR4 Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:51.2
occ:1.00
 SG A:CYS1694 2.4 41.1 1.0
SG A:CYS1691 2.4 39.2 1.0
SG A:CYS1662 2.4 32.9 1.0
SG A:CYS1714 2.6 37.5 1.0
CB A:CYS1662 3.2 39.2 1.0
CB A:CYS1714 3.3 36.6 1.0
CB A:CYS1694 3.4 48.4 1.0
CB A:CYS1691 3.5 48.0 1.0
CA A:CYS1662 3.6 38.6 1.0
N A:CYS1691 3.9 39.1 1.0
N A:THR1663 4.1 40.9 1.0
ZN A:ZN1801 4.2 55.2 1.0
N A:CYS1694 4.2 44.9 1.0
C A:CYS1662 4.3 43.6 1.0
CA A:CYS1691 4.3 39.2 1.0
N A:GLY1717 4.3 41.6 1.0
CA A:CYS1694 4.4 42.3 1.0
CB A:CYS1716 4.6 43.3 1.0
CA A:GLY1717 4.7 41.4 1.0
OG1 A:THR1663 4.8 37.6 1.0
CA A:CYS1714 4.8 37.4 1.0
N A:PHE1664 4.8 35.4 1.0
N A:CYS1662 4.9 44.7 1.0
C A:CYS1691 4.9 36.0 1.0
SG A:CYS1724 5.0 39.8 1.0

Zinc binding site 3 out of 9 in 8j9q

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Zinc binding site 3 out of 9 in the Crystal Structure of Ubr Box of UBR4 Apo


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 Ubr Box of UBR4 Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1803

b:71.0
occ:1.00
 ND1 A:HIS1699 2.1 54.6 1.0
SG A:CYS1679 2.4 57.6 1.0
ND1 A:HIS1702 2.4 59.1 1.0
SG A:CYS1682 2.5 58.2 1.0
CE1 A:HIS1699 3.0 51.7 1.0
CG A:HIS1699 3.2 49.0 1.0
CG A:HIS1702 3.3 64.1 1.0
CE1 A:HIS1702 3.4 64.1 1.0
CB A:CYS1682 3.5 55.9 1.0
CB A:HIS1702 3.5 63.2 1.0
CB A:HIS1699 3.7 48.0 1.0
CB A:CYS1679 3.7 50.9 1.0
N A:CYS1682 4.1 58.4 1.0
NE2 A:HIS1699 4.1 48.8 1.0
CD2 A:HIS1699 4.3 46.0 1.0
CA A:HIS1699 4.4 56.2 1.0
O A:HIS1702 4.4 77.6 1.0
CA A:CYS1682 4.4 56.3 1.0
CB A:THR1681 4.4 64.6 1.0
CD2 A:HIS1702 4.5 63.6 1.0
NE2 A:HIS1702 4.5 72.1 1.0
C A:THR1681 4.8 59.5 1.0
CA A:HIS1702 4.8 61.4 1.0

Zinc binding site 4 out of 9 in 8j9q

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Zinc binding site 4 out of 9 in the Crystal Structure of Ubr Box of UBR4 Apo


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 Ubr Box of UBR4 Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1801

b:61.8
occ:1.00
 ND1 B:HIS1699 2.2 47.0 1.0
ND1 B:HIS1702 2.3 44.8 1.0
SG B:CYS1679 2.4 47.9 1.0
SG B:CYS1682 2.4 48.2 1.0
CE1 B:HIS1702 3.2 45.2 1.0
CE1 B:HIS1699 3.2 44.4 1.0
CG B:HIS1699 3.2 43.6 1.0
CG B:HIS1702 3.3 45.7 1.0
CB B:CYS1679 3.4 39.1 1.0
CB B:CYS1682 3.5 46.4 1.0
CB B:HIS1699 3.5 49.7 1.0
CB B:HIS1702 3.7 49.4 1.0
N B:CYS1682 4.0 43.5 1.0
NE2 B:HIS1702 4.3 48.4 1.0
NE2 B:HIS1699 4.3 41.0 1.0
CA B:HIS1699 4.3 46.4 1.0
CD2 B:HIS1699 4.3 43.0 1.0
CD2 B:HIS1702 4.4 50.9 1.0
CA B:CYS1682 4.4 46.3 1.0
CB B:THR1681 4.5 50.2 1.0
CA B:CYS1679 4.8 45.9 1.0
C B:THR1681 4.9 44.2 1.0

Zinc binding site 5 out of 9 in 8j9q

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Zinc binding site 5 out of 9 in the Crystal Structure of Ubr Box of UBR4 Apo


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 Ubr Box of UBR4 Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1802

b:50.7
occ:1.00
 SG B:CYS1662 2.4 37.6 1.0
SG B:CYS1714 2.4 38.6 1.0
SG B:CYS1691 2.4 39.0 1.0
SG B:CYS1694 2.6 41.3 1.0
CB B:CYS1662 3.2 41.5 1.0
CB B:CYS1714 3.3 42.2 1.0
CB B:CYS1691 3.3 46.8 1.0
CB B:CYS1694 3.5 43.9 1.0
CA B:CYS1662 3.7 39.2 1.0
N B:CYS1691 3.8 42.0 1.0
N B:THR1663 4.1 36.5 1.0
CA B:CYS1691 4.1 46.0 1.0
N B:CYS1694 4.3 46.6 1.0
N B:GLY1717 4.3 38.2 1.0
C B:CYS1662 4.3 41.4 1.0
ZN B:ZN1803 4.4 54.8 1.0
OG1 B:THR1663 4.5 41.6 1.0
CA B:CYS1694 4.5 48.4 1.0
CB B:CYS1716 4.6 40.4 1.0
C B:CYS1691 4.7 46.7 1.0
CA B:CYS1714 4.7 38.0 1.0
CA B:GLY1717 4.8 40.0 1.0
N B:PHE1664 4.9 39.8 1.0
O B:CYS1691 4.9 45.1 1.0
C B:VAL1690 5.0 44.7 1.0
N B:CYS1662 5.0 42.6 1.0

Zinc binding site 6 out of 9 in 8j9q

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Zinc binding site 6 out of 9 in the Crystal Structure of Ubr Box of UBR4 Apo


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 Ubr Box of UBR4 Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1803

b:54.8
occ:1.00
 SG B:CYS1694 2.2 41.3 1.0
SG B:CYS1724 2.3 45.9 1.0
SG B:CYS1716 2.4 43.6 1.0
SG B:CYS1698 2.5 51.9 1.0
CB B:CYS1724 3.1 38.9 1.0
CB B:CYS1694 3.3 43.9 1.0
CB B:CYS1716 3.4 40.4 1.0
CB B:CYS1698 3.4 46.0 1.0
CA B:CYS1724 3.7 42.2 1.0
N B:LEU1725 4.0 43.9 1.0
N B:GLY1717 4.0 38.2 1.0
CA B:CYS1694 4.2 48.4 1.0
C B:CYS1716 4.2 35.5 1.0
C B:CYS1724 4.2 44.8 1.0
N B:ALA1726 4.4 43.6 1.0
ZN B:ZN1802 4.4 50.7 1.0
CA B:CYS1716 4.4 38.9 1.0
CA B:GLY1717 4.5 40.0 1.0
CB B:ALA1726 4.6 43.3 1.0
CB B:CYS1662 4.7 41.5 1.0
O B:CYS1716 4.7 35.3 1.0
CA B:CYS1698 4.8 51.0 1.0
SG B:CYS1662 4.9 37.6 1.0
N B:CYS1724 5.0 45.5 1.0

Zinc binding site 7 out of 9 in 8j9q

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Zinc binding site 7 out of 9 in the Crystal Structure of Ubr Box of UBR4 Apo


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 Ubr Box of UBR4 Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1801

b:66.8
occ:1.00
 ND1 C:HIS1699 2.2 47.8 1.0
SG C:CYS1682 2.3 57.8 1.0
ND1 C:HIS1702 2.3 50.1 1.0
SG C:CYS1679 2.4 53.3 1.0
CE1 C:HIS1699 3.2 49.8 1.0
CG C:HIS1699 3.2 51.2 1.0
CE1 C:HIS1702 3.2 49.8 1.0
CB C:CYS1682 3.2 52.5 1.0
CG C:HIS1702 3.4 54.1 1.0
CB C:CYS1679 3.4 50.6 1.0
CB C:HIS1699 3.5 50.9 1.0
CB C:HIS1702 3.7 50.5 1.0
N C:CYS1682 3.9 53.4 1.0
CA C:CYS1682 4.2 52.2 1.0
NE2 C:HIS1699 4.2 49.5 1.0
CD2 C:HIS1699 4.3 46.3 1.0
CA C:HIS1699 4.3 53.8 1.0
NE2 C:HIS1702 4.4 52.2 1.0
CB C:THR1681 4.4 52.9 1.0
CD2 C:HIS1702 4.5 53.9 1.0
C C:THR1681 4.7 52.2 1.0
CA C:CYS1679 4.8 53.4 1.0

Zinc binding site 8 out of 9 in 8j9q

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Zinc binding site 8 out of 9 in the Crystal Structure of Ubr Box of UBR4 Apo


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 Ubr Box of UBR4 Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1802

b:57.1
occ:1.00
 SG C:CYS1691 2.3 44.9 1.0
SG C:CYS1694 2.4 44.4 1.0
SG C:CYS1662 2.4 42.5 1.0
SG C:CYS1714 2.5 43.2 1.0
CB C:CYS1662 3.1 47.5 1.0
CB C:CYS1694 3.2 46.3 1.0
CB C:CYS1714 3.4 50.5 1.0
CB C:CYS1691 3.5 48.4 1.0
CA C:CYS1662 3.8 46.6 1.0
N C:CYS1691 3.9 41.5 1.0
N C:THR1663 4.2 49.0 1.0
ZN C:ZN1803 4.2 60.8 1.0
CA C:CYS1691 4.2 43.6 1.0
N C:CYS1694 4.2 46.3 1.0
CA C:CYS1694 4.3 43.8 1.0
N C:GLY1717 4.3 58.8 1.0
C C:CYS1662 4.4 48.9 1.0
CB C:CYS1716 4.4 52.9 1.0
OG1 C:THR1663 4.6 44.6 1.0
C C:CYS1691 4.8 44.9 1.0
CA C:GLY1717 4.9 59.3 1.0
N C:PHE1664 4.9 53.2 1.0
CA C:CYS1714 4.9 42.5 1.0
SG C:CYS1724 4.9 49.9 1.0
O C:CYS1691 5.0 39.5 1.0
C C:VAL1690 5.0 46.1 1.0

Zinc binding site 9 out of 9 in 8j9q

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Zinc binding site 9 out of 9 in the Crystal Structure of Ubr Box of UBR4 Apo


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 Ubr Box of UBR4 Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1803

b:60.8
occ:1.00
 SG C:CYS1694 2.2 44.4 1.0
SG C:CYS1724 2.3 49.9 1.0
SG C:CYS1716 2.4 51.7 1.0
SG C:CYS1698 2.5 50.7 1.0
CB C:CYS1724 3.2 55.1 1.0
CB C:CYS1716 3.3 52.9 1.0
CB C:CYS1698 3.3 46.2 1.0
CB C:CYS1694 3.4 46.3 1.0
CA C:CYS1724 3.7 58.8 1.0
N C:LEU1725 4.1 57.4 1.0
CA C:CYS1694 4.2 43.8 1.0
N C:GLY1717 4.2 58.8 1.0
ZN C:ZN1802 4.2 57.1 1.0
C C:CYS1716 4.2 56.8 1.0
C C:CYS1724 4.3 60.5 1.0
CB C:ALA1726 4.4 46.7 1.0
N C:ALA1726 4.4 51.2 1.0
CA C:CYS1716 4.4 53.6 1.0
O C:CYS1716 4.7 61.7 1.0
CA C:GLY1717 4.7 59.3 1.0
CA C:CYS1698 4.8 45.5 1.0
CB C:CYS1662 4.9 47.5 1.0
NE2 C:HIS1699 4.9 49.5 1.0
N C:CYS1724 5.0 62.5 1.0
CA C:ALA1726 5.0 48.9 1.0

Reference:

D.E.Jeong, H.S.Lee, B.Ku, C.H.Kim, S.J.Kim, H.C.Shin. Insights Into the Recognition Mechanism in the Ubr Box of UBR4 For Its Specific Substrates. Commun Biol V. 6 1214 2023.
ISSN: ESSN 2399-3642
PubMed: 38030679
DOI: 10.1038/S42003-023-05602-7
Page generated: Thu Dec 28 13:21:27 2023

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