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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

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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

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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

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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

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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

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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

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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

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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

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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

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