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Zinc in PDB 6sc6: DAB3/Hoip-Rbr Apo Structure

Enzymatic activity of DAB3/Hoip-Rbr Apo Structure

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

Protein crystallography data

The structure of DAB3/Hoip-Rbr Apo Structure, PDB code: 6sc6 was solved by Y.-C.I.Tsai, D.House, K.Rittinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.48 / 2.25
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 65.948, 87.490, 241.927, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 24.6

Other elements in 6sc6:

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

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the DAB3/Hoip-Rbr Apo Structure (pdb code 6sc6). 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 Apo Structure, PDB code: 6sc6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6sc6

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Zinc binding site 1 out of 8 in the DAB3/Hoip-Rbr Apo Structure


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 Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1101

b:62.3
occ:1.00
 SG A:CYS722 2.2 60.8 1.0
SG A:CYS702 2.3 63.1 1.0
SG A:CYS699 2.5 65.6 1.0
SG A:CYS725 2.8 57.4 1.0
CB A:CYS725 3.3 52.3 1.0
CB A:CYS702 3.3 66.4 1.0
CB A:CYS699 3.5 66.9 1.0
CB A:CYS722 3.5 58.5 1.0
N A:CYS702 3.7 71.8 1.0
N A:CYS722 4.1 64.3 1.0
CA A:CYS702 4.1 70.6 1.0
CA A:CYS722 4.4 59.1 1.0
CB A:VAL701 4.4 62.4 1.0
N A:CYS725 4.4 52.5 1.0
CA A:CYS725 4.5 50.1 1.0
C A:VAL701 4.7 69.7 1.0
CG1 A:VAL701 4.8 63.8 1.0
C A:CYS702 4.9 74.8 1.0
CA A:CYS699 4.9 68.7 1.0
N A:VAL701 4.9 59.8 1.0
CA A:VAL701 4.9 63.0 1.0
CB A:TRP704 5.0 55.7 1.0

Zinc binding site 2 out of 8 in 6sc6

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


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 Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1102

b:72.2
occ:1.00
 SG A:CYS717 2.3 63.8 1.0
SG A:CYS747 2.3 74.8 1.0
SG A:CYS719 2.4 77.6 1.0
SG A:CYS744 2.5 66.5 1.0
CB A:CYS719 2.9 74.0 1.0
CB A:CYS717 3.2 70.3 1.0
CB A:CYS744 3.3 64.6 1.0
CB A:CYS747 3.6 74.8 1.0
N A:CYS747 3.9 73.0 1.0
CA A:CYS719 4.2 75.3 1.0
CB A:ALA746 4.2 78.6 1.0
N A:CYS719 4.3 78.7 1.0
CA A:CYS747 4.4 73.7 1.0
CA A:CYS717 4.5 74.1 1.0
C A:CYS717 4.7 73.6 1.0
C A:ALA746 4.7 76.3 1.0
O A:CYS717 4.8 73.1 1.0
O A:HOH1270 4.8 73.4 1.0
CA A:CYS744 4.8 61.9 1.0
CD1 A:LEU714 4.8 69.1 1.0
CA A:ALA746 4.8 77.2 1.0
N A:ALA746 4.9 74.6 1.0

Zinc binding site 3 out of 8 in 6sc6

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


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 Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1103

b:42.0
occ:1.00
 SG A:CYS799 2.3 39.2 1.0
SG A:CYS820 2.3 44.4 1.0
SG A:CYS802 2.4 41.6 1.0
SG A:CYS817 2.5 41.0 1.0
CB A:CYS817 3.1 39.5 1.0
CB A:CYS820 3.1 45.6 1.0
CB A:CYS799 3.2 35.6 1.0
CB A:CYS802 3.2 37.5 1.0
N A:CYS820 3.5 48.6 1.0
N A:CYS802 3.7 43.6 1.0
CA A:CYS820 3.9 48.4 1.0
CA A:CYS802 4.0 39.9 1.0
O A:HOH1236 4.1 50.3 1.0
CA A:CYS817 4.6 41.3 1.0
CB A:GLN801 4.6 48.5 1.0
CB A:GLN819 4.6 52.2 1.0
CA A:CYS799 4.6 39.6 1.0
C A:GLN819 4.7 45.2 1.0
C A:CYS802 4.7 40.4 1.0
C A:GLN801 4.7 43.9 1.0
C A:CYS820 4.7 48.0 1.0
CB A:PHE804 4.8 36.9 1.0
N A:HIS821 5.0 48.0 1.0
N A:SER803 5.0 35.6 1.0

Zinc binding site 4 out of 8 in 6sc6

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


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 Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1104

b:42.9
occ:1.00
 NE2 A:HIS836 2.1 39.1 1.0
SG A:CYS828 2.4 40.8 1.0
SG A:CYS825 2.4 44.8 1.0
SG A:CYS841 2.4 47.0 1.0
CE1 A:HIS836 3.0 40.8 1.0
CD2 A:HIS836 3.1 39.0 1.0
CB A:CYS825 3.1 37.8 1.0
CB A:CYS841 3.2 43.4 1.0
CB A:CYS828 3.3 34.5 1.0
N A:CYS828 3.7 33.6 1.0
CA A:CYS841 3.8 47.5 1.0
ND1 A:HIS836 4.1 41.2 1.0
CA A:CYS828 4.1 36.9 1.0
CG A:HIS836 4.2 43.8 1.0
N A:CYS841 4.5 41.8 1.0
CA A:CYS825 4.6 35.3 1.0
CB A:ARG827 4.7 41.6 1.0
C A:ARG827 4.8 36.2 1.0
C A:CYS828 4.9 39.9 1.0
C A:CYS841 5.0 49.9 1.0

Zinc binding site 5 out of 8 in 6sc6

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


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 Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1105

b:55.0
occ:1.00
 SG A:CYS893 2.0 59.1 1.0
SG A:CYS874 2.2 51.5 1.0
SG A:CYS890 2.4 54.6 1.0
SG A:CYS871 2.4 50.7 1.0
CB A:CYS874 2.9 45.4 1.0
CB A:CYS871 3.2 49.0 1.0
CB A:CYS890 3.3 62.2 1.0
CB A:CYS893 3.5 64.6 1.0
N A:CYS874 3.5 49.4 1.0
CA A:CYS874 3.8 51.0 1.0
N A:CYS893 3.9 74.6 1.0
CA A:CYS893 4.3 68.0 1.0
C A:CYS874 4.5 51.2 1.0
CA A:CYS871 4.6 46.7 1.0
CA A:CYS890 4.6 67.0 1.0
CB A:HIS895 4.6 53.0 1.0
C A:LYS873 4.7 48.3 1.0
N A:LYS875 4.7 46.1 1.0
CB A:PHE876 4.7 66.3 1.0
N A:GLN892 4.8 89.6 1.0
CB A:LYS873 4.9 52.1 1.0
C A:GLN892 4.9 84.5 1.0
C A:CYS890 4.9 76.2 1.0
CB A:GLN892 4.9 93.3 1.0
N A:PHE876 4.9 54.8 1.0
C A:CYS871 5.0 45.1 1.0

Zinc binding site 6 out of 8 in 6sc6

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


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 Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1106

b:35.7
occ:1.00
 ND1 A:HIS926 2.1 29.7 1.0
SG A:CYS901 2.4 29.6 1.0
SG A:CYS930 2.4 31.4 1.0
SG A:CYS898 2.4 33.0 1.0
CE1 A:HIS926 3.0 26.2 1.0
CG A:HIS926 3.1 29.8 1.0
CB A:CYS901 3.1 26.3 1.0
CB A:CYS898 3.3 34.2 1.0
CB A:HIS926 3.5 26.9 1.0
N A:CYS901 3.5 36.5 1.0
CB A:CYS930 3.5 27.0 1.0
CA A:CYS901 3.9 30.1 1.0
CB A:PHE932 4.0 32.1 1.0
NE2 A:HIS926 4.1 32.3 1.0
CA A:HIS926 4.2 31.0 1.0
CD2 A:HIS926 4.2 29.6 1.0
C A:GLY900 4.4 36.5 1.0
CD A:PRO927 4.7 31.0 1.0
CA A:GLY900 4.7 37.4 1.0
CA A:CYS898 4.7 38.6 1.0
N A:GLY900 4.7 43.4 1.0
CE A:MET886 4.8 60.1 1.0
C A:CYS901 4.8 35.3 1.0
N A:PHE932 4.8 31.7 1.0
CG A:PHE932 4.9 37.6 1.0
O A:HIS925 4.9 42.2 1.0
CA A:CYS930 4.9 28.6 1.0

Zinc binding site 7 out of 8 in 6sc6

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Zinc binding site 7 out of 8 in the DAB3/Hoip-Rbr Apo Structure


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 Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1107

b:39.9
occ:1.00
 NE2 A:HIS923 2.0 39.2 1.0
NE2 A:HIS925 2.0 39.4 1.0
SG A:CYS911 2.2 42.9 1.0
SG A:CYS916 2.2 46.7 1.0
CE1 A:HIS925 2.9 39.3 1.0
CE1 A:HIS923 3.0 42.1 1.0
CB A:CYS916 3.0 51.1 1.0
CD2 A:HIS923 3.0 37.0 1.0
CD2 A:HIS925 3.1 37.9 1.0
CB A:CYS911 3.2 39.8 1.0
ND1 A:HIS925 4.1 39.1 1.0
ND1 A:HIS923 4.1 40.4 1.0
CG A:HIS923 4.1 41.0 1.0
CG A:HIS925 4.2 38.3 1.0
CA A:CYS916 4.4 54.0 1.0
CB A:GLU913 4.5 57.6 1.0
CA A:CYS911 4.6 40.0 1.0
CG A:GLU913 4.7 61.5 1.0
CG2 A:VAL918 4.7 38.1 1.0
CG A:LYS919 4.8 59.4 1.0

Zinc binding site 8 out of 8 in 6sc6

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


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 Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1108

b:56.2
occ:1.00
 ND1 A:HIS1001 2.1 54.7 1.0
SG A:CYS998 2.3 53.3 1.0
SG A:CYS969 2.4 55.3 1.0
SG A:CYS986 2.4 56.5 1.0
CE1 A:HIS1001 2.9 54.9 1.0
CB A:CYS986 3.2 61.9 1.0
CB A:CYS969 3.2 60.5 1.0
CG A:HIS1001 3.2 54.2 1.0
CB A:CYS998 3.5 51.3 1.0
CB A:HIS1001 3.6 51.8 1.0
N A:CYS998 3.9 52.2 1.0
NE2 A:HIS1001 4.1 54.8 1.0
CG2 A:VAL971 4.2 57.2 1.0
CB A:VAL971 4.2 60.7 1.0
CD2 A:HIS1001 4.2 52.5 1.0
CA A:CYS998 4.3 51.9 1.0
CA A:CYS969 4.6 65.6 1.0
N A:HIS1001 4.6 49.5 1.0
CA A:CYS986 4.6 69.3 1.0
CA A:HIS1001 4.8 45.8 1.0
C A:CYS969 4.9 66.6 1.0
CB A:LYS988 4.9 64.5 1.0
N A:VAL971 5.0 68.1 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: Thu Aug 21 19:31:20 2025

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