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Zinc in PDB 7ae5: Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form

Enzymatic activity of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form

All present enzymatic activity of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form:
4.1.1.61; 4.1.1.63;

Protein crystallography data

The structure of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form, PDB code: 7ae5 was solved by S.A.Marshall, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.14 / 2.19
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 98.23, 108.3, 111.42, 117.72, 101.32, 91.8
R / Rfree (%) 22.3 / 26.3

Other elements in 7ae5:

The structure of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form also contains other interesting chemical elements:

Rubidium (Rb) 12 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form (pdb code 7ae5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form, PDB code: 7ae5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7ae5

Go back to Zinc Binding Sites List in 7ae5
Zinc binding site 1 out of 6 in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Zn701

b:51.2
occ:1.00
 SG b:CYS603 2.3 58.8 1.0
SG b:CYS628 2.3 59.8 1.0
SG b:CYS631 2.3 58.6 1.0
SG b:CYS606 2.3 53.8 1.0
CB b:CYS628 3.1 59.1 1.0
CB b:CYS603 3.2 59.5 1.0
CB b:CYS606 3.4 49.5 1.0
CB b:CYS631 3.4 61.3 1.0
N b:CYS606 3.9 50.8 1.0
N b:CYS631 3.9 63.0 1.0
CA b:CYS606 4.2 49.1 1.0
CA b:CYS631 4.2 62.0 1.0
CA b:CYS628 4.6 60.8 1.0
CB b:TYR633 4.6 57.4 1.0
CA b:CYS603 4.7 59.9 1.0
CB b:LYS630 4.7 82.0 1.0
CB b:ARG605 4.7 61.3 1.0
CB b:SER608 4.8 62.4 1.0
C b:CYS631 4.8 60.4 1.0
C b:CYS606 4.8 49.7 1.0
C b:LYS630 4.8 80.4 1.0
C b:ARG605 4.9 61.1 1.0
N b:TYR633 4.9 60.4 1.0
N b:GLY607 4.9 76.4 1.0
N b:CYS632 5.0 68.8 1.0
CD b:LYS630 5.0 83.5 1.0
N b:SER608 5.0 59.9 1.0

Zinc binding site 2 out of 6 in 7ae5

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Zinc binding site 2 out of 6 in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Zn701

b:40.2
occ:1.00
 SG c:CYS631 2.3 43.7 1.0
SG c:CYS606 2.3 48.4 1.0
SG c:CYS603 2.3 38.4 1.0
SG c:CYS628 2.3 45.3 1.0
CB c:CYS628 3.0 44.8 1.0
CB c:CYS603 3.2 41.9 1.0
CB c:CYS606 3.4 40.0 1.0
CB c:CYS631 3.4 46.7 1.0
N c:CYS606 3.8 54.5 1.0
N c:CYS631 3.9 51.3 1.0
CA c:CYS606 4.1 47.5 1.0
CA c:CYS631 4.2 50.6 1.0
CB c:TYR633 4.5 39.8 1.0
CA c:CYS628 4.5 46.1 1.0
C c:CYS631 4.7 50.9 1.0
CB c:SER608 4.7 54.3 1.0
CA c:CYS603 4.7 46.4 1.0
C c:CYS606 4.7 53.3 1.0
CB c:ARG605 4.7 57.1 1.0
CB c:LYS630 4.8 49.3 1.0
N c:TYR633 4.8 43.7 1.0
N c:GLY607 4.8 45.4 1.0
N c:SER608 4.9 64.2 1.0
C c:ARG605 4.9 58.3 1.0
N c:CYS632 4.9 47.1 1.0
C c:LYS630 4.9 52.0 1.0

Zinc binding site 3 out of 6 in 7ae5

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Zinc binding site 3 out of 6 in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
d:Zn701

b:40.0
occ:1.00
 SG d:CYS606 2.3 41.6 1.0
SG d:CYS603 2.3 37.1 1.0
SG d:CYS631 2.3 44.8 1.0
SG d:CYS628 2.3 50.3 1.0
CB d:CYS628 3.1 49.5 1.0
CB d:CYS603 3.2 41.6 1.0
CB d:CYS631 3.4 47.2 1.0
CB d:CYS606 3.4 42.3 1.0
N d:CYS606 3.7 51.5 1.0
N d:CYS631 3.9 47.8 1.0
CA d:CYS606 4.1 49.1 1.0
CA d:CYS631 4.1 48.0 1.0
CB d:TYR633 4.4 37.8 1.0
CB d:ARG605 4.6 50.3 1.0
CA d:CYS628 4.6 50.3 1.0
C d:CYS631 4.6 47.3 1.0
CA d:CYS603 4.7 48.6 1.0
CB d:SER608 4.7 48.1 1.0
C d:CYS606 4.7 54.1 1.0
C d:ARG605 4.8 56.4 1.0
N d:GLY607 4.8 49.1 1.0
N d:TYR633 4.8 38.3 1.0
CB d:LYS630 4.9 52.8 1.0
N d:SER608 4.9 58.0 1.0
N d:CYS632 4.9 47.3 1.0
C d:LYS630 5.0 52.5 1.0
N d:ARG605 5.0 62.0 1.0

Zinc binding site 4 out of 6 in 7ae5

Go back to Zinc Binding Sites List in 7ae5
Zinc binding site 4 out of 6 in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Zn701

b:68.3
occ:1.00
 SG e:CYS631 2.3 78.1 1.0
SG e:CYS628 2.3 85.8 1.0
SG e:CYS606 2.3 73.3 1.0
SG e:CYS603 2.3 89.1 1.0
CB e:CYS628 3.2 80.6 1.0
CB e:CYS603 3.2 91.7 1.0
CB e:CYS631 3.4 81.6 1.0
CB e:CYS606 3.4 72.3 1.0
N e:CYS606 3.7 77.0 1.0
N e:CYS631 3.8 84.2 1.0
CA e:CYS631 4.0 82.6 1.0
CA e:CYS606 4.1 75.6 1.0
CB e:ARG605 4.5 79.9 1.0
C e:CYS631 4.5 79.6 1.0
CB e:TYR633 4.6 61.9 1.0
CB e:LYS630 4.6 87.2 1.0
CA e:CYS628 4.7 80.3 1.0
C e:CYS606 4.7 77.5 1.0
CA e:CYS603 4.7 94.8 1.0
C e:ARG605 4.7 77.2 1.0
C e:LYS630 4.7 84.7 1.0
CB e:SER608 4.9 74.0 1.0
N e:ARG605 4.9 85.1 1.0
CA e:ARG605 5.0 79.7 1.0
N e:GLY607 5.0 92.5 1.0
N e:TYR633 5.0 63.9 1.0

Zinc binding site 5 out of 6 in 7ae5

Go back to Zinc Binding Sites List in 7ae5
Zinc binding site 5 out of 6 in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Zn701

b:87.1
occ:1.00
 SG f:CYS631 2.3 87.8 1.0
SG f:CYS603 2.3 85.5 1.0
SG f:CYS606 2.3 98.4 1.0
SG f:CYS628 2.3 93.8 1.0
CB f:CYS603 3.0 87.6 1.0
CB f:CYS628 3.2 93.0 1.0
CB f:CYS606 3.5 96.5 1.0
CB f:CYS631 3.5 88.7 1.0
N f:CYS631 3.8 90.0 1.0
N f:CYS606 3.9 94.4 1.0
CA f:CYS631 4.1 89.2 1.0
CA f:CYS606 4.2 95.3 1.0
C f:CYS631 4.5 88.6 1.0
CA f:CYS603 4.5 87.7 1.0
CB f:TYR633 4.6 82.8 1.0
CB f:LYS630 4.6 88.6 1.0
CA f:CYS628 4.6 93.6 1.0
CB f:SER608 4.8 95.8 1.0
C f:LYS630 4.8 87.5 1.0
O f:CYS631 4.8 87.8 1.0
CB f:ARG605 4.8 83.4 1.0
C f:CYS606 4.8 96.9 1.0
N f:GLY607 4.9 93.3 1.0
N f:SER608 4.9 94.0 1.0
C f:ARG605 4.9 84.5 1.0
N f:TYR633 5.0 83.8 1.0

Zinc binding site 6 out of 6 in 7ae5

Go back to Zinc Binding Sites List in 7ae5
Zinc binding site 6 out of 6 in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Zn701

b:55.9
occ:1.00
 SG a:CYS631 2.3 58.7 1.0
SG a:CYS603 2.3 53.1 1.0
SG a:CYS606 2.3 58.8 1.0
SG a:CYS628 2.3 75.5 1.0
CB a:CYS628 3.1 73.0 1.0
CB a:CYS603 3.2 55.5 1.0
CB a:CYS606 3.4 56.4 1.0
CB a:CYS631 3.4 63.9 1.0
N a:CYS631 3.8 64.3 1.0
N a:CYS606 3.9 58.4 1.0
CA a:CYS631 4.1 64.7 1.0
CA a:CYS606 4.2 55.7 1.0
CB a:SER608 4.5 64.3 1.0
CA a:CYS628 4.6 73.1 1.0
CB a:TYR633 4.6 59.8 1.0
C a:CYS631 4.7 61.2 1.0
CB a:LYS630 4.7 84.2 1.0
CA a:CYS603 4.7 59.0 1.0
CB a:ARG605 4.7 52.5 1.0
C a:CYS606 4.8 55.5 1.0
C a:LYS630 4.9 84.9 1.0
C a:ARG605 4.9 51.9 1.0
N a:SER608 4.9 62.4 1.0
N a:CYS632 4.9 71.5 1.0
N a:TYR633 4.9 61.0 1.0
N a:GLY607 5.0 66.4 1.0

Reference:

S.A.Marshall, K.A.P.Payne, D.Leys. Domain Mobility and Allosteric Activation of Ubid Decarboxylases To Be Published.
Page generated: Tue Oct 29 16:41:13 2024

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