Atomistry » Zinc » PDB 6s53-6scy » 6sc9
Atomistry »
  Zinc »
    PDB 6s53-6scy »
      6sc9 »

Zinc in PDB 6sc9: DAB3/Hoip-Rbr-Hoipin-8

Enzymatic activity of DAB3/Hoip-Rbr-Hoipin-8

All present enzymatic activity of DAB3/Hoip-Rbr-Hoipin-8:
2.3.2.31;

Protein crystallography data

The structure of DAB3/Hoip-Rbr-Hoipin-8, PDB code: 6sc9 was solved by Y.-C.I.Tsai, H.Johansson, D.House, K.Rittinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.90 / 2.47
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 66.127, 87.052, 241.538, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 25.2

Other elements in 6sc9:

The structure of DAB3/Hoip-Rbr-Hoipin-8 also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the DAB3/Hoip-Rbr-Hoipin-8 (pdb code 6sc9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the DAB3/Hoip-Rbr-Hoipin-8, PDB code: 6sc9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6sc9

Go back to Zinc Binding Sites List in 6sc9
Zinc binding site 1 out of 8 in the DAB3/Hoip-Rbr-Hoipin-8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of DAB3/Hoip-Rbr-Hoipin-8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:79.0
occ:1.00
 SG A:CYS702 2.3 83.9 1.0
SG A:CYS722 2.6 69.6 1.0
SG A:CYS699 2.6 75.3 1.0
SG A:CYS725 2.6 84.5 1.0
CB A:CYS702 3.2 66.0 1.0
CB A:CYS725 3.2 72.5 1.0
CB A:CYS722 3.4 69.6 1.0
CB A:CYS699 3.6 73.2 1.0
CG2 A:VAL701 3.7 83.9 1.0
N A:CYS702 3.9 88.8 1.0
N A:CYS722 4.1 74.8 1.0
CA A:CYS702 4.1 73.6 1.0
CA A:CYS722 4.3 71.6 1.0
CA A:CYS725 4.5 70.2 1.0
N A:CYS725 4.5 66.5 1.0
C A:VAL701 4.8 93.0 1.0
O A:CYS722 4.9 68.3 1.0
C A:CYS722 4.9 66.6 1.0
C A:CYS702 4.9 84.9 1.0
CB A:TRP704 5.0 76.3 1.0
CA A:CYS699 5.0 76.4 1.0

Zinc binding site 2 out of 8 in 6sc9

Go back to Zinc Binding Sites List in 6sc9
Zinc binding site 2 out of 8 in the DAB3/Hoip-Rbr-Hoipin-8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of DAB3/Hoip-Rbr-Hoipin-8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2003

b:0.1
occ:1.00
 SG A:CYS747 2.5 1.0 1.0
SG A:CYS717 2.6 1.0 1.0
SG A:CYS744 2.6 95.1 1.0
SG A:CYS719 2.7 0.5 1.0
CB A:CYS747 3.0 0.0 1.0
CB A:CYS719 3.0 86.2 1.0
CB A:CYS717 3.2 0.3 1.0
N A:CYS747 3.3 0.9 1.0
CB A:CYS744 3.7 91.6 1.0
CA A:CYS747 3.7 0.4 1.0
CB A:ALA746 4.2 91.9 1.0
CA A:CYS719 4.3 95.6 1.0
N A:CYS719 4.4 0.7 1.0
C A:ALA746 4.5 0.3 1.0
CD2 A:LEU714 4.6 0.2 1.0
C A:CYS747 4.6 0.2 1.0
CA A:CYS717 4.6 0.1 1.0
CA A:ALA746 4.7 91.7 1.0
C A:CYS717 4.8 0.7 1.0
N A:ALA746 4.8 0.5 1.0
O A:CYS717 4.9 0.9 1.0

Zinc binding site 3 out of 8 in 6sc9

Go back to Zinc Binding Sites List in 6sc9
Zinc binding site 3 out of 8 in the DAB3/Hoip-Rbr-Hoipin-8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of DAB3/Hoip-Rbr-Hoipin-8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2004

b:61.5
occ:1.00
 SG A:CYS802 2.3 58.3 1.0
SG A:CYS817 2.3 61.5 1.0
SG A:CYS820 2.4 68.1 1.0
SG A:CYS799 2.5 58.8 1.0
CB A:CYS820 3.0 55.7 1.0
CB A:CYS817 3.0 55.2 1.0
CB A:CYS802 3.2 48.2 1.0
CB A:CYS799 3.2 48.4 1.0
N A:CYS820 3.5 63.9 1.0
CA A:CYS820 3.8 61.7 1.0
N A:CYS802 4.0 58.9 1.0
CA A:CYS802 4.1 53.5 1.0
CA A:CYS817 4.5 67.4 1.0
CB A:GLN819 4.6 74.5 1.0
C A:GLN819 4.6 69.1 1.0
C A:CYS820 4.6 67.2 1.0
CA A:CYS799 4.7 53.8 1.0
C A:CYS802 4.7 60.2 1.0
CB A:PHE804 4.7 60.0 1.0
N A:HIS821 4.8 72.8 1.0
C A:GLN801 4.9 67.3 1.0
CA A:GLN819 5.0 63.7 1.0
N A:GLN819 5.0 62.8 1.0

Zinc binding site 4 out of 8 in 6sc9

Go back to Zinc Binding Sites List in 6sc9
Zinc binding site 4 out of 8 in the DAB3/Hoip-Rbr-Hoipin-8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of DAB3/Hoip-Rbr-Hoipin-8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2005

b:61.0
occ:1.00
 NE2 A:HIS836 2.2 63.1 1.0
SG A:CYS841 2.3 58.2 1.0
SG A:CYS828 2.3 63.6 1.0
SG A:CYS825 2.4 62.4 1.0
CB A:CYS841 3.1 55.2 1.0
CD2 A:HIS836 3.2 63.5 1.0
CE1 A:HIS836 3.2 58.0 1.0
CB A:CYS825 3.2 56.5 1.0
CB A:CYS828 3.4 59.7 1.0
CA A:CYS841 3.8 69.2 1.0
N A:CYS828 3.8 56.8 1.0
CA A:CYS828 4.2 58.4 1.0
ND1 A:HIS836 4.3 69.0 1.0
CG A:HIS836 4.3 69.1 1.0
N A:CYS841 4.4 52.1 1.0
CB A:ARG827 4.6 77.3 1.0
CA A:CYS825 4.7 54.4 1.0
C A:ARG827 4.9 61.7 1.0

Zinc binding site 5 out of 8 in 6sc9

Go back to Zinc Binding Sites List in 6sc9
Zinc binding site 5 out of 8 in the DAB3/Hoip-Rbr-Hoipin-8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of DAB3/Hoip-Rbr-Hoipin-8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2006

b:64.7
occ:1.00
 SG A:CYS893 2.1 78.3 1.0
SG A:CYS874 2.3 62.0 1.0
SG A:CYS871 2.5 63.2 1.0
SG A:CYS890 2.6 67.3 1.0
CB A:CYS874 2.7 52.2 1.0
CB A:CYS893 3.2 68.6 1.0
CB A:CYS871 3.2 58.0 1.0
CB A:CYS890 3.5 66.7 1.0
N A:CYS874 3.5 65.4 1.0
CA A:CYS874 3.6 70.6 1.0
N A:CYS893 4.0 68.8 1.0
CA A:CYS893 4.2 65.9 1.0
C A:CYS874 4.4 68.8 1.0
N A:LYS875 4.7 70.0 1.0
CB A:HIS895 4.7 64.1 1.0
CA A:CYS871 4.7 67.1 1.0
C A:LYS873 4.7 57.8 1.0
CB A:GLN892 4.8 79.1 1.0
C A:GLN892 4.9 73.9 1.0
CA A:CYS890 4.9 71.6 1.0
C A:CYS893 4.9 61.2 1.0

Zinc binding site 6 out of 8 in 6sc9

Go back to Zinc Binding Sites List in 6sc9
Zinc binding site 6 out of 8 in the DAB3/Hoip-Rbr-Hoipin-8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of DAB3/Hoip-Rbr-Hoipin-8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2007

b:50.8
occ:1.00
 ND1 A:HIS926 2.1 46.7 1.0
SG A:CYS901 2.3 46.3 1.0
SG A:CYS898 2.4 46.7 1.0
SG A:CYS930 2.5 50.6 1.0
CG A:HIS926 3.0 49.1 1.0
CE1 A:HIS926 3.1 49.5 1.0
CB A:CYS901 3.1 34.6 1.0
CB A:CYS898 3.3 53.8 1.0
CB A:HIS926 3.3 42.6 1.0
N A:CYS901 3.5 47.8 1.0
CB A:CYS930 3.6 43.2 1.0
CA A:CYS901 3.9 54.6 1.0
CB A:PHE932 3.9 49.4 1.0
CA A:HIS926 4.1 55.5 1.0
NE2 A:HIS926 4.2 58.5 1.0
CD2 A:HIS926 4.2 51.8 1.0
C A:GLY900 4.4 50.9 1.0
CA A:CYS898 4.7 50.2 1.0
CA A:GLY900 4.7 47.8 1.0
C A:CYS901 4.8 52.1 1.0
CG A:PHE932 4.8 50.0 1.0
N A:GLY900 4.8 48.0 1.0
CD A:PRO927 4.8 46.8 1.0
N A:PHE932 4.8 41.6 1.0
CA A:CYS930 5.0 47.5 1.0
CA A:PHE932 5.0 46.8 1.0

Zinc binding site 7 out of 8 in 6sc9

Go back to Zinc Binding Sites List in 6sc9
Zinc binding site 7 out of 8 in the DAB3/Hoip-Rbr-Hoipin-8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of DAB3/Hoip-Rbr-Hoipin-8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2008

b:60.6
occ:1.00
 NE2 A:HIS925 2.1 62.4 1.0
NE2 A:HIS923 2.1 58.0 1.0
SG A:CYS916 2.3 66.7 1.0
SG A:CYS911 2.3 68.4 1.0
CE1 A:HIS925 3.1 62.5 1.0
CD2 A:HIS923 3.1 49.3 1.0
CE1 A:HIS923 3.1 64.7 1.0
CB A:CYS916 3.1 72.0 1.0
CD2 A:HIS925 3.1 56.1 1.0
CB A:CYS911 3.4 53.9 1.0
ND1 A:HIS925 4.2 65.8 1.0
ND1 A:HIS923 4.2 59.5 1.0
CG A:HIS923 4.2 52.1 1.0
CG A:HIS925 4.3 56.5 1.0
CB A:GLU913 4.5 64.2 1.0
CA A:CYS916 4.5 76.0 1.0
CG A:GLU913 4.7 83.3 1.0
CG2 A:VAL918 4.7 54.4 1.0
CA A:CYS911 4.8 64.8 1.0

Zinc binding site 8 out of 8 in 6sc9

Go back to Zinc Binding Sites List in 6sc9
Zinc binding site 8 out of 8 in the DAB3/Hoip-Rbr-Hoipin-8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of DAB3/Hoip-Rbr-Hoipin-8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2009

b:66.7
occ:1.00
 ND1 A:HIS1001 2.0 75.1 1.0
CB A:CYS998 2.3 57.3 1.0
SG A:CYS969 2.5 64.9 1.0
SG A:CYS986 2.5 62.7 1.0
CE1 A:HIS1001 2.9 73.3 1.0
CB A:CYS969 3.1 70.0 1.0
CG A:HIS1001 3.1 69.5 1.0
CB A:CYS986 3.2 78.5 1.0
SG A:CYS998 3.5 90.6 1.0
CA A:CYS998 3.5 63.0 1.0
CB A:HIS1001 3.6 53.2 1.0
N A:CYS998 3.6 58.4 1.0
NE2 A:HIS1001 4.0 72.2 1.0
CD2 A:HIS1001 4.1 68.5 1.0
CB A:VAL971 4.4 81.9 1.0
CA A:CYS969 4.6 77.1 1.0
CG2 A:VAL971 4.6 68.9 1.0
N A:HIS1001 4.6 66.1 1.0
CB A:LYS988 4.6 70.8 1.0
C A:CYS998 4.7 66.3 1.0
CA A:CYS986 4.7 87.9 1.0
CA A:HIS1001 4.7 60.4 1.0
C A:LEU997 4.9 62.8 1.0
C A:CYS969 5.0 77.7 1.0
O A:CYS969 5.0 82.3 1.0

Reference:

Y.-C.I.Tsai, D.House, K.Rittinger. DAB3/Hoip-Rbr Apo Structure Cell Chem Biol 2019.
ISSN: ESSN 2451-9456
Page generated: Tue Oct 29 07:10:14 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy