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Zinc in PDB 6bmm: Structure of Human DHHC20 Palmitoyltransferase, Space Group P21

Enzymatic activity of Structure of Human DHHC20 Palmitoyltransferase, Space Group P21

All present enzymatic activity of Structure of Human DHHC20 Palmitoyltransferase, Space Group P21:
2.3.1.225;

Protein crystallography data

The structure of Structure of Human DHHC20 Palmitoyltransferase, Space Group P21, PDB code: 6bmm was solved by M.S.Rana, C.-J.Lee, A.Banerjee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.85 / 2.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.519, 57.700, 94.098, 90.00, 115.51, 90.00
R / Rfree (%) 24.1 / 26

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Human DHHC20 Palmitoyltransferase, Space Group P21 (pdb code 6bmm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Human DHHC20 Palmitoyltransferase, Space Group P21, PDB code: 6bmm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6bmm

Go back to Zinc Binding Sites List in 6bmm
Zinc binding site 1 out of 4 in the Structure of Human DHHC20 Palmitoyltransferase, Space Group P21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human DHHC20 Palmitoyltransferase, Space Group P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:0.4
occ:1.00
ND1 A:HIS155 2.0 85.8 1.0
SG A:CYS162 2.2 0.9 1.0
SG A:CYS142 2.3 79.4 1.0
SG A:CYS145 2.3 76.9 1.0
CG A:HIS155 2.9 79.0 1.0
CE1 A:HIS155 3.0 80.9 1.0
CB A:HIS155 3.3 67.9 1.0
CB A:CYS145 3.4 94.2 1.0
CB A:CYS142 3.4 73.9 1.0
CB A:CYS162 3.5 85.8 1.0
N A:CYS145 3.5 79.9 1.0
CA A:CYS162 4.0 71.9 1.0
NE2 A:HIS155 4.0 84.4 1.0
CA A:CYS145 4.0 81.8 1.0
CD2 A:HIS155 4.0 83.7 1.0
CB A:ALA144 4.1 82.2 1.0
N A:CYS162 4.1 65.2 1.0
CA A:HIS155 4.2 71.9 1.0
C A:ALA144 4.4 88.1 1.0
CA A:ALA144 4.7 86.3 1.0
C A:ASN161 4.7 76.8 1.0
CA A:CYS142 4.8 78.3 1.0
N A:ALA144 4.8 85.3 1.0
N A:HIS155 5.0 66.5 1.0

Zinc binding site 2 out of 4 in 6bmm

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Zinc binding site 2 out of 4 in the Structure of Human DHHC20 Palmitoyltransferase, Space Group P21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human DHHC20 Palmitoyltransferase, Space Group P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:99.2
occ:1.00
ND1 A:HIS141 2.0 72.6 1.0
SG A:CYS131 2.3 72.5 1.0
SG A:CYS128 2.3 71.4 1.0
SG A:CYS148 2.3 66.0 1.0
CG A:HIS141 2.9 61.1 1.0
CE1 A:HIS141 3.0 68.2 1.0
CB A:CYS131 3.1 85.4 1.0
CB A:HIS141 3.2 60.7 1.0
N A:CYS148 3.6 62.5 1.0
CB A:CYS148 3.6 71.1 1.0
CB A:CYS128 3.6 68.7 1.0
CA A:CYS148 3.9 65.7 1.0
C A:SER147 3.9 70.3 1.0
CA A:HIS141 4.0 75.4 1.0
CD2 A:HIS141 4.0 66.2 1.0
NE2 A:HIS141 4.1 71.7 1.0
N A:CYS131 4.1 79.1 1.0
CA A:CYS131 4.2 77.9 1.0
O A:SER147 4.3 72.8 1.0
CA A:SER147 4.5 77.7 1.0
N A:HIS141 4.9 72.3 1.0
CA A:CYS128 5.0 73.0 1.0

Zinc binding site 3 out of 4 in 6bmm

Go back to Zinc Binding Sites List in 6bmm
Zinc binding site 3 out of 4 in the Structure of Human DHHC20 Palmitoyltransferase, Space Group P21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human DHHC20 Palmitoyltransferase, Space Group P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:0.9
occ:1.00
ND1 B:HIS141 2.0 0.9 1.0
SG B:CYS131 2.3 0.2 1.0
SG B:CYS128 2.3 0.5 1.0
SG B:CYS148 2.3 0.2 1.0
CG B:HIS141 2.8 0.9 1.0
CB B:CYS131 2.9 0.1 1.0
CB B:HIS141 2.9 0.5 1.0
CE1 B:HIS141 3.1 0.6 1.0
CB B:CYS128 3.4 0.7 1.0
CB B:CYS148 3.7 0.9 1.0
CA B:HIS141 3.8 0.2 1.0
N B:CYS148 3.9 0.0 1.0
CD2 B:HIS141 3.9 0.5 1.0
CA B:CYS148 4.0 0.1 1.0
NE2 B:HIS141 4.1 0.3 1.0
CA B:CYS131 4.1 0.8 1.0
N B:CYS131 4.1 0.8 1.0
C B:SER147 4.2 0.5 1.0
O B:SER147 4.5 0.2 1.0
N B:HIS141 4.6 0.5 1.0
CA B:SER147 4.8 0.8 1.0
CA B:CYS128 4.8 0.3 1.0

Zinc binding site 4 out of 4 in 6bmm

Go back to Zinc Binding Sites List in 6bmm
Zinc binding site 4 out of 4 in the Structure of Human DHHC20 Palmitoyltransferase, Space Group P21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Human DHHC20 Palmitoyltransferase, Space Group P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:0.8
occ:1.00
ND1 B:HIS155 2.0 0.4 1.0
SG B:CYS162 2.3 0.6 1.0
SG B:CYS142 2.3 0.2 1.0
SG B:CYS145 2.3 0.7 1.0
CG B:HIS155 2.9 0.4 1.0
CB B:HIS155 3.1 95.6 1.0
CE1 B:HIS155 3.1 0.7 1.0
CB B:CYS162 3.6 98.2 1.0
CB B:CYS145 3.6 0.4 1.0
CB B:CYS142 3.6 0.5 1.0
N B:CYS145 3.7 0.9 1.0
CA B:CYS162 3.8 93.2 1.0
CA B:HIS155 3.8 92.3 1.0
N B:CYS162 4.0 86.8 1.0
CB B:ALA144 4.0 0.5 1.0
CD2 B:HIS155 4.1 0.0 1.0
NE2 B:HIS155 4.1 0.6 1.0
CA B:CYS145 4.2 0.7 1.0
C B:ASN161 4.5 92.7 1.0
C B:ALA144 4.5 1.0 1.0
N B:HIS155 4.6 89.8 1.0
O B:ASN161 4.6 93.0 1.0
CA B:ALA144 4.7 0.9 1.0
N B:ALA144 4.9 0.0 1.0
CE B:MET152 4.9 0.0 1.0
CA B:CYS142 5.0 0.0 1.0

Reference:

M.S.Rana, P.Kumar, C.J.Lee, R.Verardi, K.R.Rajashankar, A.Banerjee. Fatty Acyl Recognition and Transfer By An Integral Membranes-Acyltransferase. Science V. 359 2018.
ISSN: ESSN 1095-9203
PubMed: 29326245
DOI: 10.1126/SCIENCE.AAO6326
Page generated: Wed Dec 16 11:32:37 2020

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