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
Go back to
Zinc Binding Sites List in 6bmm
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: Mon Oct 28 18:07:31 2024
|