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Zinc in PDB 6bmn: Structure of Human DHHC20 Palmitoyltransferase, Space Group P63

Enzymatic activity of Structure of Human DHHC20 Palmitoyltransferase, Space Group P63

All present enzymatic activity of Structure of Human DHHC20 Palmitoyltransferase, Space Group P63:
2.3.1.225;

Protein crystallography data

The structure of Structure of Human DHHC20 Palmitoyltransferase, Space Group P63, PDB code: 6bmn 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) 86.21 / 2.25
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 99.541, 99.541, 158.386, 90.00, 90.00, 120.00
R / Rfree (%) 25.7 / 27.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Human DHHC20 Palmitoyltransferase, Space Group P63 (pdb code 6bmn). 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 P63, PDB code: 6bmn:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6bmn

Go back to Zinc Binding Sites List in 6bmn
Zinc binding site 1 out of 4 in the Structure of Human DHHC20 Palmitoyltransferase, Space Group P63


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 P63 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:93.4
occ:1.00
ND1 A:HIS155 2.0 94.7 1.0
SG A:CYS145 2.3 93.2 1.0
SG A:CYS162 2.3 99.5 1.0
SG A:CYS142 2.4 94.7 1.0
CG A:HIS155 3.0 93.0 1.0
CB A:CYS162 3.0 92.0 1.0
CE1 A:HIS155 3.0 93.1 1.0
CB A:HIS155 3.3 81.3 1.0
CB A:CYS142 3.3 91.0 1.0
CB A:CYS145 3.5 94.4 1.0
CA A:CYS162 3.7 88.8 1.0
N A:CYS145 3.8 0.9 1.0
CA A:HIS155 4.0 87.3 1.0
N A:CYS162 4.0 93.0 1.0
NE2 A:HIS155 4.1 87.1 1.0
CD2 A:HIS155 4.1 93.0 1.0
CA A:CYS145 4.2 94.9 1.0
CB A:ALA144 4.4 88.8 1.0
C A:ASN161 4.7 94.8 1.0
C A:ALA144 4.8 0.7 1.0
CA A:CYS142 4.8 89.7 1.0
N A:HIS155 4.8 88.6 1.0
CE A:MET152 4.8 88.2 1.0
CG1 A:ILE149 4.8 78.1 1.0
O A:ASN161 5.0 91.7 1.0

Zinc binding site 2 out of 4 in 6bmn

Go back to Zinc Binding Sites List in 6bmn
Zinc binding site 2 out of 4 in the Structure of Human DHHC20 Palmitoyltransferase, Space Group P63


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 P63 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:93.8
occ:1.00
ND1 A:HIS141 2.0 94.5 1.0
SG A:CYS131 2.3 86.2 1.0
SG A:CYS128 2.3 97.4 1.0
SG A:CYS148 2.3 87.5 1.0
CG A:HIS141 3.0 89.3 1.0
CE1 A:HIS141 3.0 93.4 1.0
CB A:HIS141 3.3 88.5 1.0
CB A:CYS131 3.4 94.2 1.0
N A:CYS148 3.4 92.2 1.0
CB A:CYS148 3.5 93.6 1.0
CB A:CYS128 3.5 93.0 1.0
CA A:CYS148 3.7 89.6 1.0
C A:SER147 3.8 91.7 1.0
CA A:HIS141 4.0 91.7 1.0
CD2 A:HIS141 4.1 88.7 1.0
NE2 A:HIS141 4.1 90.2 1.0
O A:SER147 4.2 94.7 1.0
N A:CYS131 4.2 94.8 1.0
CA A:SER147 4.4 99.9 1.0
CA A:CYS131 4.4 94.6 1.0
N A:HIS141 4.8 91.2 1.0
CA A:CYS128 4.9 95.2 1.0
N A:SER147 5.0 0.6 1.0

Zinc binding site 3 out of 4 in 6bmn

Go back to Zinc Binding Sites List in 6bmn
Zinc binding site 3 out of 4 in the Structure of Human DHHC20 Palmitoyltransferase, Space Group P63


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 P63 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:69.8
occ:1.00
ND1 B:HIS141 2.0 76.5 1.0
SG B:CYS148 2.2 58.9 1.0
SG B:CYS131 2.3 73.9 1.0
SG B:CYS128 2.3 74.1 1.0
CE1 B:HIS141 3.0 76.4 1.0
CG B:HIS141 3.0 68.4 1.0
CB B:CYS131 3.2 78.6 1.0
CB B:HIS141 3.3 59.1 1.0
CB B:CYS148 3.5 75.3 1.0
CB B:CYS128 3.5 75.3 1.0
N B:CYS148 3.6 63.2 1.0
CA B:CYS148 3.8 65.1 1.0
N B:CYS131 4.0 77.8 1.0
C B:SER147 4.0 69.9 1.0
NE2 B:HIS141 4.0 70.2 1.0
CD2 B:HIS141 4.1 72.0 1.0
CA B:HIS141 4.2 64.9 1.0
CA B:CYS131 4.2 74.7 1.0
O B:SER147 4.4 70.6 1.0
CA B:SER147 4.7 73.7 1.0
CA B:CYS128 4.9 68.8 1.0
CB B:LYS130 5.0 66.4 1.0
N B:HIS141 5.0 54.1 1.0

Zinc binding site 4 out of 4 in 6bmn

Go back to Zinc Binding Sites List in 6bmn
Zinc binding site 4 out of 4 in the Structure of Human DHHC20 Palmitoyltransferase, Space Group P63


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 P63 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:70.8
occ:1.00
ND1 B:HIS155 2.0 80.2 1.0
SG B:CYS145 2.3 62.8 1.0
SG B:CYS162 2.3 72.2 1.0
SG B:CYS142 2.3 59.8 1.0
CE1 B:HIS155 2.9 67.8 1.0
CB B:CYS162 3.1 68.0 1.0
CG B:HIS155 3.1 73.7 1.0
CB B:CYS142 3.2 69.4 1.0
CB B:CYS145 3.4 68.9 1.0
CB B:HIS155 3.5 55.9 1.0
N B:CYS145 3.7 75.0 1.0
CA B:CYS162 3.8 52.1 1.0
N B:CYS162 4.0 65.2 1.0
NE2 B:HIS155 4.1 64.9 1.0
CA B:CYS145 4.1 62.1 1.0
CD2 B:HIS155 4.2 69.4 1.0
CA B:HIS155 4.2 61.5 1.0
CB B:ALA144 4.4 58.7 1.0
C B:ALA144 4.7 76.2 1.0
CA B:CYS142 4.7 66.9 1.0
C B:ASN161 4.7 71.7 1.0
CG1 B:ILE149 4.7 66.1 1.0
CE B:MET152 4.8 72.3 1.0
CA B:ALA144 5.0 75.0 1.0
N B:HIS155 5.0 56.0 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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