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Zinc in PDB 6sc8: DAB3/Hoip-Rbr-LIGAND4

Enzymatic activity of DAB3/Hoip-Rbr-LIGAND4

All present enzymatic activity of DAB3/Hoip-Rbr-LIGAND4:
2.3.2.31;

Protein crystallography data

The structure of DAB3/Hoip-Rbr-LIGAND4, PDB code: 6sc8 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) 51.03 / 2.11
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 65.919, 87.770, 241.831, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 26.1

Other elements in 6sc8:

The structure of DAB3/Hoip-Rbr-LIGAND4 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the DAB3/Hoip-Rbr-LIGAND4 (pdb code 6sc8). 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-LIGAND4, PDB code: 6sc8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6sc8

Go back to Zinc Binding Sites List in 6sc8
Zinc binding site 1 out of 8 in the DAB3/Hoip-Rbr-LIGAND4


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-LIGAND4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:75.0
occ:1.00
 SG A:CYS699 2.4 77.8 1.0
SG A:CYS702 2.5 73.5 1.0
SG A:CYS722 2.6 75.4 1.0
SG A:CYS725 2.7 66.3 1.0
CB A:CYS722 3.1 71.2 1.0
CB A:CYS702 3.2 69.9 1.0
CB A:CYS725 3.3 70.6 1.0
CB A:CYS699 3.5 81.5 1.0
N A:CYS702 3.6 73.3 1.0
N A:CYS722 4.0 83.6 1.0
CA A:CYS702 4.0 80.4 1.0
CA A:CYS722 4.1 82.4 1.0
CB A:VAL701 4.3 65.8 1.0
N A:CYS725 4.3 68.6 1.0
CA A:CYS725 4.4 67.2 1.0
C A:VAL701 4.6 83.3 1.0
CG1 A:VAL701 4.6 63.2 1.0
C A:CYS702 4.8 84.3 1.0
C A:CYS722 4.8 68.8 1.0
CA A:VAL701 4.8 69.6 1.0
CA A:CYS699 4.9 83.8 1.0
O A:CYS722 4.9 73.2 1.0
N A:VAL701 4.9 71.5 1.0
N A:GLY703 5.0 87.8 1.0

Zinc binding site 2 out of 8 in 6sc8

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Zinc binding site 2 out of 8 in the DAB3/Hoip-Rbr-LIGAND4


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-LIGAND4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2003

b:1.0
occ:1.00
 SG A:CYS719 2.4 0.5 1.0
SG A:CYS717 2.5 90.2 1.0
SG A:CYS744 2.5 92.4 1.0
SG A:CYS747 2.5 0.6 1.0
CB A:CYS747 2.7 97.4 1.0
CB A:CYS717 3.2 95.8 1.0
CB A:CYS744 3.2 89.1 1.0
CB A:CYS719 3.3 88.0 1.0
N A:CYS747 3.7 97.2 1.0
CA A:CYS747 3.8 97.5 1.0
CA A:CYS719 4.5 94.6 1.0
CA A:CYS717 4.5 0.0 1.0
N A:GLY748 4.6 0.4 1.0
O A:CYS717 4.6 86.5 1.0
N A:CYS719 4.6 0.0 1.0
CA A:CYS744 4.7 89.7 1.0
C A:CYS717 4.7 91.0 1.0
C A:CYS747 4.7 98.9 1.0
C A:ALA746 4.8 0.9 1.0
O A:HOH2164 4.8 78.4 1.0
CB A:ALA746 4.8 87.1 1.0

Zinc binding site 3 out of 8 in 6sc8

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Zinc binding site 3 out of 8 in the DAB3/Hoip-Rbr-LIGAND4


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-LIGAND4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2004

b:56.8
occ:1.00
 SG A:CYS817 2.3 51.7 1.0
SG A:CYS820 2.3 61.0 1.0
SG A:CYS799 2.4 51.7 1.0
SG A:CYS802 2.4 55.6 1.0
CB A:CYS820 3.1 65.0 1.0
CB A:CYS817 3.1 59.2 1.0
CB A:CYS799 3.2 48.4 1.0
CB A:CYS802 3.4 57.9 1.0
N A:CYS820 3.5 67.0 1.0
N A:CYS802 3.8 55.7 1.0
CA A:CYS820 3.9 66.0 1.0
CA A:CYS802 4.1 59.5 1.0
CA A:CYS817 4.6 62.7 1.0
C A:CYS820 4.6 63.6 1.0
CB A:GLN819 4.6 74.3 1.0
CA A:CYS799 4.6 56.8 1.0
CB A:GLN801 4.7 66.2 1.0
C A:GLN819 4.7 69.8 1.0
CB A:PHE804 4.7 58.5 1.0
C A:CYS802 4.7 58.5 1.0
C A:GLN801 4.8 65.5 1.0
N A:HIS821 4.8 67.7 1.0
N A:GLN819 5.0 67.4 1.0

Zinc binding site 4 out of 8 in 6sc8

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Zinc binding site 4 out of 8 in the DAB3/Hoip-Rbr-LIGAND4


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-LIGAND4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2005

b:60.4
occ:1.00
 NE2 A:HIS836 2.2 66.0 1.0
SG A:CYS841 2.4 60.4 1.0
SG A:CYS825 2.4 57.5 1.0
SG A:CYS828 2.4 61.0 1.0
CE1 A:HIS836 3.0 60.6 1.0
CB A:CYS841 3.1 57.3 1.0
CB A:CYS828 3.1 49.4 1.0
CB A:CYS825 3.2 56.6 1.0
CD2 A:HIS836 3.2 64.4 1.0
CA A:CYS841 3.6 67.8 1.0
N A:CYS828 3.6 55.0 1.0
CA A:CYS828 4.0 55.3 1.0
ND1 A:HIS836 4.2 62.7 1.0
CG A:HIS836 4.3 67.2 1.0
N A:CYS841 4.4 62.6 1.0
CA A:CYS825 4.7 56.6 1.0
CB A:ARG827 4.7 60.5 1.0
C A:ARG827 4.8 60.1 1.0
C A:CYS828 4.8 59.5 1.0
C A:CYS841 4.9 68.5 1.0

Zinc binding site 5 out of 8 in 6sc8

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Zinc binding site 5 out of 8 in the DAB3/Hoip-Rbr-LIGAND4


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-LIGAND4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2006

b:63.1
occ:1.00
 SG A:CYS874 2.1 79.5 1.0
SG A:CYS893 2.1 65.8 1.0
SG A:CYS890 2.4 63.4 1.0
SG A:CYS871 2.5 62.1 1.0
CB A:CYS874 2.7 65.4 1.0
CB A:CYS871 3.2 65.2 1.0
CB A:CYS890 3.3 67.9 1.0
CB A:CYS893 3.3 74.8 1.0
N A:CYS874 3.8 56.0 1.0
CA A:CYS874 3.8 70.0 1.0
N A:CYS893 3.8 68.7 1.0
CA A:CYS893 4.1 69.1 1.0
CG A:LYS873 4.3 73.2 1.0
C A:CYS874 4.6 65.0 1.0
CB A:HIS895 4.6 63.8 1.0
CA A:CYS871 4.7 65.5 1.0
CA A:CYS890 4.7 68.5 1.0
CB A:GLN892 4.7 79.4 1.0
C A:CYS893 4.8 69.1 1.0
C A:GLN892 4.8 75.5 1.0
C A:LYS873 4.9 66.2 1.0
N A:LYS875 4.9 65.5 1.0
N A:HIS895 5.0 66.2 1.0

Zinc binding site 6 out of 8 in 6sc8

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Zinc binding site 6 out of 8 in the DAB3/Hoip-Rbr-LIGAND4


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-LIGAND4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2007

b:50.0
occ:1.00
 ND1 A:HIS926 2.0 45.9 1.0
SG A:CYS901 2.2 48.0 1.0
SG A:CYS898 2.3 48.1 1.0
SG A:CYS930 2.4 49.3 1.0
CE1 A:HIS926 3.0 49.7 1.0
CG A:HIS926 3.0 53.5 1.0
CB A:CYS898 3.3 54.8 1.0
CB A:CYS901 3.3 38.2 1.0
CB A:HIS926 3.3 43.2 1.0
CB A:CYS930 3.6 45.5 1.0
N A:CYS901 3.6 50.9 1.0
CB A:PHE932 3.9 52.0 1.0
CA A:CYS901 4.0 55.3 1.0
NE2 A:HIS926 4.1 53.9 1.0
CA A:HIS926 4.1 50.3 1.0
CD2 A:HIS926 4.1 49.3 1.0
C A:GLY900 4.4 49.1 1.0
CA A:GLY900 4.6 50.6 1.0
CA A:CYS898 4.7 56.2 1.0
CD A:PRO927 4.7 50.7 1.0
N A:GLY900 4.7 55.0 1.0
CG A:PHE932 4.7 53.4 1.0
N A:PHE932 4.8 47.6 1.0
C A:CYS901 4.9 54.1 1.0
O A:HIS925 4.9 58.6 1.0
CA A:CYS930 5.0 47.9 1.0

Zinc binding site 7 out of 8 in 6sc8

Go back to Zinc Binding Sites List in 6sc8
Zinc binding site 7 out of 8 in the DAB3/Hoip-Rbr-LIGAND4


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-LIGAND4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2008

b:57.7
occ:1.00
 NE2 A:HIS925 2.0 59.5 1.0
NE2 A:HIS923 2.0 52.3 1.0
SG A:CYS916 2.3 62.1 1.0
SG A:CYS911 2.3 57.4 1.0
CE1 A:HIS925 3.0 59.9 1.0
CE1 A:HIS923 3.0 58.8 1.0
CD2 A:HIS923 3.0 52.2 1.0
CD2 A:HIS925 3.1 62.6 1.0
CB A:CYS916 3.2 69.7 1.0
CB A:CYS911 3.2 53.5 1.0
ND1 A:HIS925 4.1 62.1 1.0
ND1 A:HIS923 4.1 55.8 1.0
CG A:HIS923 4.1 51.6 1.0
CG A:HIS925 4.2 60.0 1.0
CB A:GLU913 4.4 72.9 1.0
CA A:CYS916 4.5 66.1 1.0
CG A:GLU913 4.6 77.6 1.0
CA A:CYS911 4.6 57.2 1.0
CG2 A:VAL918 4.7 57.1 1.0
CG A:LYS919 5.0 69.8 1.0

Zinc binding site 8 out of 8 in 6sc8

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Zinc binding site 8 out of 8 in the DAB3/Hoip-Rbr-LIGAND4


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-LIGAND4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2009

b:65.5
occ:1.00
 ND1 A:HIS1001 2.0 60.2 1.0
SG A:CYS998 2.3 60.6 1.0
SG A:CYS986 2.4 65.5 1.0
SG A:CYS969 2.4 66.8 1.0
CE1 A:HIS1001 2.8 68.2 1.0
CB A:CYS969 3.0 69.2 1.0
CB A:CYS998 3.0 55.9 1.0
CG A:HIS1001 3.1 61.1 1.0
CB A:CYS986 3.2 72.9 1.0
CB A:HIS1001 3.6 54.9 1.0
N A:CYS998 3.7 61.5 1.0
CA A:CYS998 4.0 62.5 1.0
NE2 A:HIS1001 4.0 67.6 1.0
CD2 A:HIS1001 4.2 62.7 1.0
CB A:VAL971 4.3 68.0 1.0
CA A:CYS969 4.5 71.8 1.0
CG2 A:VAL971 4.5 65.8 1.0
N A:HIS1001 4.6 56.1 1.0
CA A:CYS986 4.7 79.6 1.0
CA A:HIS1001 4.7 57.4 1.0
C A:CYS998 4.8 60.0 1.0
C A:LEU997 4.9 61.1 1.0
C A:CYS969 4.9 69.7 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 07:09:20 2024

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