Atomistry » Zinc » PDB 6s53-6scy » 6sc5
Atomistry »
  Zinc »
    PDB 6s53-6scy »
      6sc5 »

Zinc in PDB 6sc5: DAB3/Hoip-Rbr-LIGAND2

Enzymatic activity of DAB3/Hoip-Rbr-LIGAND2

All present enzymatic activity of DAB3/Hoip-Rbr-LIGAND2:
2.3.2.31;

Protein crystallography data

The structure of DAB3/Hoip-Rbr-LIGAND2, PDB code: 6sc5 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) 63.26 / 2.10
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 65.578, 86.661, 240.223, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 25.2

Other elements in 6sc5:

The structure of DAB3/Hoip-Rbr-LIGAND2 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the DAB3/Hoip-Rbr-LIGAND2 (pdb code 6sc5). 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-LIGAND2, PDB code: 6sc5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6sc5

Go back to Zinc Binding Sites List in 6sc5
Zinc binding site 1 out of 8 in the DAB3/Hoip-Rbr-LIGAND2


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-LIGAND2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:63.4
occ:1.00
 SG A:CYS702 2.4 61.6 1.0
SG A:CYS722 2.5 63.7 1.0
SG A:CYS699 2.6 65.4 1.0
SG A:CYS725 2.7 64.4 1.0
CB A:CYS725 3.2 60.2 1.0
CB A:CYS702 3.3 61.3 1.0
CB A:CYS722 3.4 62.2 1.0
CB A:CYS699 3.5 68.3 1.0
CG2 A:VAL701 3.9 62.3 1.0
N A:CYS722 4.1 70.4 1.0
N A:CYS702 4.1 70.8 1.0
CA A:CYS702 4.2 68.7 1.0
CA A:CYS722 4.3 66.3 1.0
N A:CYS725 4.3 57.6 1.0
CA A:CYS725 4.4 59.7 1.0
CB A:TRP704 4.9 66.8 1.0
CA A:CYS699 4.9 70.2 1.0
C A:CYS702 4.9 69.8 1.0
C A:CYS722 5.0 56.9 1.0
O A:CYS722 5.0 61.6 1.0

Zinc binding site 2 out of 8 in 6sc5

Go back to Zinc Binding Sites List in 6sc5
Zinc binding site 2 out of 8 in the DAB3/Hoip-Rbr-LIGAND2


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-LIGAND2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2003

b:88.7
occ:1.00
 SG A:CYS719 2.4 88.9 1.0
SG A:CYS717 2.4 83.4 1.0
SG A:CYS744 2.5 79.6 1.0
SG A:CYS747 2.5 91.7 1.0
CB A:CYS719 2.8 79.0 1.0
CB A:CYS747 3.3 79.5 1.0
CB A:CYS744 3.3 74.2 1.0
CB A:CYS717 3.3 86.2 1.0
N A:CYS747 3.5 86.2 1.0
CA A:CYS747 3.9 82.6 1.0
CA A:CYS719 4.1 82.2 1.0
N A:CYS719 4.3 88.8 1.0
O A:CYS747 4.3 88.8 1.0
CB A:ALA746 4.4 74.8 1.0
C A:CYS747 4.5 84.8 1.0
CD1 A:LEU714 4.6 79.5 1.0
C A:ALA746 4.6 87.9 1.0
CA A:CYS717 4.7 88.9 1.0
C A:CYS717 4.8 85.6 1.0
O A:CYS717 4.8 86.1 1.0
CA A:CYS744 4.8 75.4 1.0
CA A:ALA746 4.9 82.3 1.0

Zinc binding site 3 out of 8 in 6sc5

Go back to Zinc Binding Sites List in 6sc5
Zinc binding site 3 out of 8 in the DAB3/Hoip-Rbr-LIGAND2


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-LIGAND2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2004

b:52.5
occ:1.00
 SG A:CYS817 2.3 51.0 1.0
SG A:CYS820 2.3 55.8 1.0
SG A:CYS802 2.4 48.1 1.0
SG A:CYS799 2.4 44.9 1.0
CB A:CYS817 3.0 47.1 1.0
CB A:CYS799 3.2 40.8 1.0
CB A:CYS802 3.2 49.9 1.0
CB A:CYS820 3.2 58.4 1.0
N A:CYS820 3.6 57.3 1.0
N A:CYS802 3.8 47.7 1.0
CA A:CYS820 4.0 58.6 1.0
CA A:CYS802 4.1 47.1 1.0
O A:HOH2145 4.3 55.4 1.0
CA A:CYS817 4.5 50.7 1.0
CB A:GLN819 4.5 62.0 1.0
CA A:CYS799 4.6 46.6 1.0
C A:CYS802 4.6 51.0 1.0
CB A:PHE804 4.7 52.6 1.0
C A:CYS820 4.7 56.4 1.0
C A:GLN819 4.7 57.9 1.0
CB A:GLN801 4.8 55.1 1.0
C A:GLN801 4.8 52.8 1.0
N A:HIS821 4.9 59.1 1.0
CA A:GLN819 5.0 59.4 1.0
N A:GLN819 5.0 57.4 1.0

Zinc binding site 4 out of 8 in 6sc5

Go back to Zinc Binding Sites List in 6sc5
Zinc binding site 4 out of 8 in the DAB3/Hoip-Rbr-LIGAND2


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-LIGAND2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2005

b:49.8
occ:1.00
 NE2 A:HIS836 2.1 57.8 1.0
SG A:CYS828 2.3 46.2 1.0
SG A:CYS825 2.4 51.1 1.0
SG A:CYS841 2.4 48.8 1.0
CE1 A:HIS836 3.0 51.9 1.0
CB A:CYS828 3.1 45.0 1.0
CD2 A:HIS836 3.1 54.0 1.0
CB A:CYS825 3.1 48.5 1.0
CB A:CYS841 3.1 49.9 1.0
N A:CYS828 3.7 43.0 1.0
CA A:CYS841 3.8 53.4 1.0
CA A:CYS828 4.0 52.0 1.0
ND1 A:HIS836 4.1 51.5 1.0
CG A:HIS836 4.2 61.4 1.0
N A:CYS841 4.5 45.1 1.0
CA A:CYS825 4.6 51.5 1.0
C A:ARG827 4.8 42.0 1.0
C A:CYS828 4.8 47.6 1.0

Zinc binding site 5 out of 8 in 6sc5

Go back to Zinc Binding Sites List in 6sc5
Zinc binding site 5 out of 8 in the DAB3/Hoip-Rbr-LIGAND2


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-LIGAND2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2006

b:53.1
occ:1.00
 SG A:CYS893 2.1 57.8 1.0
SG A:CYS874 2.3 58.0 1.0
SG A:CYS871 2.4 46.8 1.0
SG A:CYS890 2.5 54.9 1.0
CB A:CYS893 3.0 59.8 1.0
CB A:CYS874 3.0 50.5 1.0
CB A:CYS871 3.3 55.9 1.0
CB A:CYS890 3.3 53.4 1.0
N A:CYS874 3.6 55.1 1.0
N A:CYS893 3.8 59.7 1.0
CA A:CYS874 3.9 61.8 1.0
CA A:CYS893 3.9 58.9 1.0
C A:CYS874 4.5 54.8 1.0
CB A:LYS873 4.5 55.2 1.0
C A:LYS873 4.7 56.8 1.0
C A:CYS893 4.7 59.9 1.0
CA A:CYS871 4.7 50.2 1.0
CA A:CYS890 4.8 58.1 1.0
C A:GLN892 4.8 66.8 1.0
CB A:HIS895 4.8 54.0 1.0
CB A:GLN892 4.9 64.4 1.0
N A:LYS875 4.9 52.1 1.0
CB A:PHE876 4.9 61.3 1.0
CA A:LYS873 5.0 50.4 1.0
N A:ARG894 5.0 54.2 1.0
N A:LYS873 5.0 46.0 1.0

Zinc binding site 6 out of 8 in 6sc5

Go back to Zinc Binding Sites List in 6sc5
Zinc binding site 6 out of 8 in the DAB3/Hoip-Rbr-LIGAND2


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-LIGAND2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2007

b:39.8
occ:1.00
 ND1 A:HIS926 2.0 38.9 1.0
SG A:CYS901 2.3 39.9 1.0
SG A:CYS898 2.3 38.1 1.0
SG A:CYS930 2.4 40.0 1.0
CE1 A:HIS926 3.0 39.4 1.0
CG A:HIS926 3.1 42.3 1.0
CB A:CYS898 3.2 44.9 1.0
CB A:CYS901 3.3 36.8 1.0
CB A:HIS926 3.4 39.5 1.0
CB A:CYS930 3.6 39.0 1.0
N A:CYS901 3.6 39.9 1.0
CB A:PHE932 3.9 43.6 1.0
CA A:CYS901 4.0 41.0 1.0
NE2 A:HIS926 4.1 44.5 1.0
CD2 A:HIS926 4.2 38.5 1.0
CA A:HIS926 4.2 35.8 1.0
C A:GLY900 4.4 42.2 1.0
CA A:GLY900 4.6 40.1 1.0
CA A:CYS898 4.7 40.4 1.0
N A:GLY900 4.7 41.7 1.0
CD A:PRO927 4.7 37.9 1.0
N A:PHE932 4.8 41.5 1.0
CG A:PHE932 4.8 44.3 1.0
C A:CYS901 4.8 45.1 1.0
O A:HIS925 4.9 48.8 1.0
CA A:CYS930 5.0 37.1 1.0

Zinc binding site 7 out of 8 in 6sc5

Go back to Zinc Binding Sites List in 6sc5
Zinc binding site 7 out of 8 in the DAB3/Hoip-Rbr-LIGAND2


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-LIGAND2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2008

b:44.8
occ:1.00
 NE2 A:HIS923 2.0 42.7 1.0
NE2 A:HIS925 2.0 45.3 1.0
SG A:CYS916 2.3 53.5 1.0
SG A:CYS911 2.3 49.3 1.0
CE1 A:HIS925 2.9 57.1 1.0
CD2 A:HIS923 3.0 43.6 1.0
CE1 A:HIS923 3.1 49.0 1.0
CD2 A:HIS925 3.1 49.2 1.0
CB A:CYS916 3.1 57.9 1.0
CB A:CYS911 3.2 39.9 1.0
ND1 A:HIS925 4.1 54.1 1.0
CG A:HIS923 4.1 48.0 1.0
ND1 A:HIS923 4.1 44.1 1.0
CG A:HIS925 4.2 53.0 1.0
CB A:GLU913 4.3 59.3 1.0
CA A:CYS916 4.5 61.4 1.0
CG2 A:VAL918 4.5 46.7 1.0
CA A:CYS911 4.7 47.7 1.0

Zinc binding site 8 out of 8 in 6sc5

Go back to Zinc Binding Sites List in 6sc5
Zinc binding site 8 out of 8 in the DAB3/Hoip-Rbr-LIGAND2


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-LIGAND2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2009

b:59.2
occ:1.00
 ND1 A:HIS1001 2.2 63.1 1.0
SG A:CYS998 2.4 58.4 1.0
SG A:CYS986 2.5 56.8 1.0
SG A:CYS969 2.5 61.7 1.0
CE1 A:HIS1001 3.0 66.0 1.0
CB A:CYS969 3.1 69.9 1.0
CB A:CYS998 3.1 57.5 1.0
CB A:CYS986 3.3 63.1 1.0
CG A:HIS1001 3.3 59.7 1.0
N A:CYS998 3.7 56.3 1.0
CB A:HIS1001 3.8 55.4 1.0
CA A:CYS998 4.0 53.9 1.0
NE2 A:HIS1001 4.2 65.7 1.0
CD2 A:HIS1001 4.4 58.0 1.0
CB A:VAL971 4.4 66.4 1.0
CG2 A:VAL971 4.4 65.8 1.0
CA A:CYS969 4.5 67.9 1.0
N A:HIS1001 4.7 48.1 1.0
CA A:CYS986 4.8 71.9 1.0
CB A:LYS988 4.9 61.5 1.0
CA A:HIS1001 4.9 50.7 1.0
C A:LEU997 4.9 54.6 1.0
C A:CYS998 4.9 56.4 1.0
C A:CYS969 5.0 71.9 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 07:08:19 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy