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Zinc in PDB 6sc7: DAB3/Hoip-Rbr-LIGAND3

Enzymatic activity of DAB3/Hoip-Rbr-LIGAND3

All present enzymatic activity of DAB3/Hoip-Rbr-LIGAND3:
2.3.2.31;

Protein crystallography data

The structure of DAB3/Hoip-Rbr-LIGAND3, PDB code: 6sc7 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) 63.39 / 2.56
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 65.712, 86.701, 240.551, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 26.7

Other elements in 6sc7:

The structure of DAB3/Hoip-Rbr-LIGAND3 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the DAB3/Hoip-Rbr-LIGAND3 (pdb code 6sc7). 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-LIGAND3, PDB code: 6sc7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6sc7

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Zinc binding site 1 out of 8 in the DAB3/Hoip-Rbr-LIGAND3


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-LIGAND3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:70.8
occ:1.00
 SG A:CYS702 2.3 81.9 1.0
SG A:CYS722 2.5 69.2 1.0
SG A:CYS699 2.6 77.1 1.0
SG A:CYS725 2.6 72.5 1.0
CB A:CYS702 2.9 75.4 1.0
CB A:CYS725 3.3 71.1 1.0
CB A:CYS722 3.5 75.5 1.0
CG1 A:VAL701 3.6 74.3 1.0
CB A:CYS699 3.7 76.3 1.0
N A:CYS702 3.7 77.8 1.0
CA A:CYS702 3.9 73.3 1.0
N A:CYS722 4.1 77.2 1.0
CA A:CYS722 4.3 76.1 1.0
N A:CYS725 4.4 70.6 1.0
CA A:CYS725 4.5 72.1 1.0
C A:VAL701 4.6 76.8 1.0
C A:CYS702 4.8 76.7 1.0
O A:CYS722 4.8 72.1 1.0
CB A:VAL701 4.9 71.1 1.0
C A:CYS722 4.9 72.8 1.0

Zinc binding site 2 out of 8 in 6sc7

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Zinc binding site 2 out of 8 in the DAB3/Hoip-Rbr-LIGAND3


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-LIGAND3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2003

b:0.1
occ:1.00
 SG A:CYS747 2.4 99.0 1.0
SG A:CYS717 2.6 0.0 1.0
SG A:CYS719 2.6 95.7 1.0
SG A:CYS744 2.7 92.0 1.0
CB A:CYS747 2.9 93.7 1.0
N A:CYS747 3.3 94.0 1.0
CB A:CYS717 3.4 0.2 1.0
CB A:CYS744 3.5 88.5 1.0
CA A:CYS747 3.7 93.6 1.0
CB A:CYS719 3.8 94.7 1.0
CB A:ALA746 4.1 91.4 1.0
C A:ALA746 4.3 95.7 1.0
N A:GLY748 4.5 92.1 1.0
CA A:ALA746 4.6 90.9 1.0
C A:CYS747 4.7 91.8 1.0
N A:ALA746 4.8 90.0 1.0
CA A:CYS717 4.8 0.5 1.0
O A:CYS717 4.9 0.5 1.0
CA A:CYS744 4.9 87.3 1.0
CA A:CYS719 4.9 98.1 1.0
N A:CYS719 5.0 0.2 1.0
C A:CYS717 5.0 0.7 1.0

Zinc binding site 3 out of 8 in 6sc7

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Zinc binding site 3 out of 8 in the DAB3/Hoip-Rbr-LIGAND3


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-LIGAND3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2004

b:61.2
occ:1.00
 SG A:CYS802 2.3 56.8 1.0
SG A:CYS820 2.4 68.4 1.0
SG A:CYS817 2.4 58.0 1.0
SG A:CYS799 2.5 55.9 1.0
CB A:CYS817 2.9 61.6 1.0
CB A:CYS799 3.2 55.9 1.0
CB A:CYS820 3.2 64.1 1.0
CB A:CYS802 3.3 57.7 1.0
N A:CYS820 3.5 65.5 1.0
CA A:CYS820 3.9 65.7 1.0
N A:CYS802 4.1 58.7 1.0
CA A:CYS802 4.2 56.3 1.0
CA A:CYS817 4.4 63.2 1.0
O A:HOH2101 4.4 67.1 1.0
CB A:GLN819 4.5 67.8 1.0
C A:GLN819 4.7 66.3 1.0
CA A:CYS799 4.7 59.9 1.0
C A:CYS820 4.7 68.2 1.0
CB A:PHE804 4.7 57.3 1.0
C A:CYS802 4.7 58.6 1.0
N A:HIS821 4.8 70.1 1.0
N A:GLN819 4.9 63.1 1.0
CA A:GLN819 4.9 66.2 1.0
C A:CYS817 4.9 62.4 1.0

Zinc binding site 4 out of 8 in 6sc7

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Zinc binding site 4 out of 8 in the DAB3/Hoip-Rbr-LIGAND3


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-LIGAND3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2005

b:61.7
occ:1.00
 SG A:CYS828 1.9 77.9 1.0
CB A:CYS828 2.5 60.7 1.0
SG A:CYS841 2.5 70.4 1.0
SG A:CYS825 2.5 68.0 1.0
NE2 A:HIS836 2.5 65.6 1.0
CB A:CYS825 3.1 61.4 1.0
N A:CYS828 3.4 64.0 1.0
CD2 A:HIS836 3.4 70.2 1.0
CA A:CYS828 3.4 62.2 1.0
CB A:CYS841 3.5 64.9 1.0
CE1 A:HIS836 3.5 68.7 1.0
CA A:CYS841 4.2 70.2 1.0
C A:ARG827 4.5 64.2 1.0
CA A:CYS825 4.6 60.4 1.0
ND1 A:HIS836 4.6 73.6 1.0
CG A:HIS836 4.6 73.8 1.0
C A:CYS828 4.7 64.6 1.0
CB A:ARG827 4.9 66.4 1.0
CD2 A:LEU813 4.9 72.9 1.0

Zinc binding site 5 out of 8 in 6sc7

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Zinc binding site 5 out of 8 in the DAB3/Hoip-Rbr-LIGAND3


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-LIGAND3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2006

b:61.1
occ:1.00
 SG A:CYS893 2.2 62.4 1.0
SG A:CYS874 2.3 61.3 1.0
SG A:CYS890 2.4 59.6 1.0
SG A:CYS871 2.5 61.5 1.0
CB A:CYS874 2.9 62.5 1.0
CB A:CYS890 3.3 61.6 1.0
CB A:CYS871 3.3 60.2 1.0
CB A:CYS893 3.4 66.7 1.0
N A:CYS874 3.6 65.3 1.0
CA A:CYS874 3.8 64.9 1.0
N A:CYS893 3.9 67.6 1.0
CA A:CYS893 4.2 68.2 1.0
C A:CYS874 4.5 67.2 1.0
CB A:GLN892 4.6 70.8 1.0
CB A:LYS873 4.7 65.7 1.0
C A:LYS873 4.7 67.1 1.0
CA A:CYS890 4.7 63.4 1.0
CA A:CYS871 4.7 64.0 1.0
CB A:HIS895 4.8 62.3 1.0
C A:GLN892 4.8 68.3 1.0
N A:LYS875 4.8 66.2 1.0
C A:CYS893 4.9 66.4 1.0
CB A:PHE876 4.9 68.2 1.0

Zinc binding site 6 out of 8 in 6sc7

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Zinc binding site 6 out of 8 in the DAB3/Hoip-Rbr-LIGAND3


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-LIGAND3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2007

b:46.6
occ:1.00
 ND1 A:HIS926 2.1 44.9 1.0
SG A:CYS901 2.3 46.6 1.0
SG A:CYS930 2.5 47.3 1.0
SG A:CYS898 2.6 52.0 1.0
CG A:HIS926 3.1 49.4 1.0
CE1 A:HIS926 3.1 51.3 1.0
CB A:CYS898 3.2 48.4 1.0
CB A:CYS901 3.3 43.0 1.0
CB A:HIS926 3.3 47.3 1.0
N A:CYS901 3.6 47.4 1.0
CB A:CYS930 3.7 47.4 1.0
CB A:PHE932 3.9 48.1 1.0
CA A:CYS901 4.0 48.5 1.0
CA A:HIS926 4.2 51.9 1.0
NE2 A:HIS926 4.2 53.8 1.0
CD2 A:HIS926 4.2 49.4 1.0
C A:GLY900 4.5 48.0 1.0
CA A:GLY900 4.7 47.4 1.0
CA A:CYS898 4.7 50.9 1.0
CG A:PHE932 4.7 49.4 1.0
N A:GLY900 4.7 47.6 1.0
N A:PHE932 4.8 48.7 1.0
C A:CYS901 4.9 52.8 1.0
CD A:PRO927 4.9 47.3 1.0
CE A:MET886 5.0 54.7 1.0
CA A:PHE932 5.0 48.6 1.0
O A:HIS925 5.0 54.0 1.0

Zinc binding site 7 out of 8 in 6sc7

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Zinc binding site 7 out of 8 in the DAB3/Hoip-Rbr-LIGAND3


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-LIGAND3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2008

b:55.0
occ:1.00
 NE2 A:HIS925 2.1 58.4 1.0
NE2 A:HIS923 2.1 54.6 1.0
SG A:CYS911 2.3 56.3 1.0
SG A:CYS916 2.3 63.6 1.0
CE1 A:HIS925 3.0 58.9 1.0
CD2 A:HIS923 3.0 55.7 1.0
CE1 A:HIS923 3.1 55.6 1.0
CD2 A:HIS925 3.1 56.1 1.0
CB A:CYS916 3.2 67.9 1.0
CB A:CYS911 3.3 55.0 1.0
ND1 A:HIS925 4.1 57.7 1.0
CG A:HIS923 4.2 56.9 1.0
ND1 A:HIS923 4.2 56.0 1.0
CG A:HIS925 4.2 56.5 1.0
CB A:GLU913 4.5 66.3 1.0
CG2 A:VAL918 4.6 55.6 1.0
CA A:CYS916 4.6 69.5 1.0
CA A:CYS911 4.7 56.9 1.0
CG A:GLU913 4.7 66.3 1.0
CG A:LYS919 4.9 64.6 1.0

Zinc binding site 8 out of 8 in 6sc7

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Zinc binding site 8 out of 8 in the DAB3/Hoip-Rbr-LIGAND3


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-LIGAND3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2009

b:76.8
occ:1.00
 ND1 A:HIS1001 2.1 76.7 1.0
SG A:CYS969 2.5 79.0 1.0
CB A:CYS998 2.6 70.2 1.0
SG A:CYS986 2.6 79.5 1.0
CE1 A:HIS1001 2.8 79.5 1.0
CB A:CYS969 3.1 82.3 1.0
CG A:HIS1001 3.2 72.3 1.0
CB A:CYS986 3.3 84.7 1.0
SG A:CYS998 3.7 92.3 1.0
N A:CYS998 3.7 72.5 1.0
CB A:HIS1001 3.7 69.6 1.0
CA A:CYS998 3.7 70.7 1.0
NE2 A:HIS1001 4.0 76.8 1.0
CD2 A:HIS1001 4.2 70.3 1.0
CB A:LYS988 4.5 81.7 1.0
CB A:VAL971 4.5 84.0 1.0
CG2 A:VAL971 4.6 79.7 1.0
CA A:CYS969 4.6 83.3 1.0
N A:HIS1001 4.7 67.8 1.0
CA A:CYS986 4.7 86.2 1.0
CA A:HIS1001 4.8 65.3 1.0
C A:CYS998 4.9 69.4 1.0
C A:LEU997 4.9 70.8 1.0
CG A:LYS988 5.0 84.0 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 07:09:19 2024

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