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Zinc in PDB 6bms: Palmitoyltransferase Structure

Enzymatic activity of Palmitoyltransferase Structure

All present enzymatic activity of Palmitoyltransferase Structure:
2.3.1.225;

Protein crystallography data

The structure of Palmitoyltransferase Structure, PDB code: 6bms was solved by P.Kumar, K.Rajashankar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.21 / 2.44
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 186.402, 186.402, 90.177, 90.00, 90.00, 90.00
R / Rfree (%) 23.3 / 26.1

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 6bms

Go back to Zinc Binding Sites List in 6bms
Zinc binding site 1 out of 4 in the Palmitoyltransferase Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Palmitoyltransferase Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:58.7
occ:1.00
ND1 A:HIS128 2.2 83.5 1.0
SG A:CYS115 2.4 55.3 1.0
SG A:CYS135 2.4 54.6 1.0
SG A:CYS118 2.5 63.5 1.0
CE1 A:HIS128 2.8 71.8 1.0
CG A:HIS128 3.0 71.9 1.0
N A:CYS135 3.2 55.7 1.0
CB A:CYS118 3.2 63.0 1.0
CB A:CYS135 3.4 49.8 1.0
CB A:CYS115 3.4 58.0 1.0
CB A:HIS128 3.5 50.0 1.0
CA A:CYS135 3.6 49.0 1.0
NE2 A:HIS128 3.7 77.0 1.0
CD2 A:HIS128 3.8 81.2 1.0
C A:THR134 3.9 55.1 1.0
N A:CYS118 4.0 66.9 1.0
CA A:HIS128 4.2 54.4 1.0
CA A:CYS118 4.3 64.5 1.0
CA A:THR134 4.4 67.6 1.0
O A:THR134 4.5 56.5 1.0
CA A:CYS115 4.9 63.4 1.0
CB A:ARG117 4.9 70.8 1.0

Zinc binding site 2 out of 4 in 6bms

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Zinc binding site 2 out of 4 in the Palmitoyltransferase Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Palmitoyltransferase Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:62.0
occ:1.00
SG A:CYS149 2.1 58.6 1.0
ND1 A:HIS142 2.2 70.5 1.0
SG A:CYS129 2.3 50.9 1.0
SG A:CYS132 2.3 72.2 1.0
CE1 A:HIS142 3.1 63.3 1.0
CG A:HIS142 3.1 70.7 1.0
CB A:CYS149 3.2 53.4 1.0
CB A:CYS129 3.3 48.3 1.0
CB A:CYS132 3.4 72.7 1.0
CB A:HIS142 3.4 45.9 1.0
N A:CYS132 3.7 64.3 1.0
CA A:CYS149 3.7 52.7 1.0
N A:CYS149 3.8 57.2 1.0
NE2 A:HIS142 4.1 73.0 1.0
CD2 A:HIS142 4.1 60.6 1.0
CA A:CYS132 4.1 58.0 1.0
CA A:HIS142 4.2 53.7 1.0
CB A:VAL131 4.4 66.4 1.0
C A:ASN148 4.5 64.2 1.0
CA A:CYS129 4.7 57.9 1.0
C A:VAL131 4.7 73.6 1.0
O A:ASN148 4.9 68.8 1.0
CA A:VAL131 5.0 65.3 1.0

Zinc binding site 3 out of 4 in 6bms

Go back to Zinc Binding Sites List in 6bms
Zinc binding site 3 out of 4 in the Palmitoyltransferase Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Palmitoyltransferase Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1001

b:63.3
occ:1.00
ND1 D:HIS132 2.1 66.3 1.0
SG D:CYS119 2.4 63.4 1.0
SG D:CYS122 2.4 63.0 1.0
SG D:CYS139 2.5 57.1 1.0
CE1 D:HIS132 3.1 52.6 1.0
CG D:HIS132 3.1 65.2 1.0
CB D:CYS122 3.2 60.0 1.0
N D:CYS139 3.3 59.0 1.0
CB D:CYS139 3.4 50.0 1.0
CB D:CYS119 3.4 62.8 1.0
CB D:HIS132 3.5 54.9 1.0
CA D:CYS139 3.6 56.5 1.0
C D:THR138 3.9 68.4 1.0
N D:CYS122 4.0 63.9 1.0
NE2 D:HIS132 4.2 61.5 1.0
CA D:HIS132 4.2 60.1 1.0
CD2 D:HIS132 4.2 53.5 1.0
CA D:CYS122 4.3 58.2 1.0
CA D:THR138 4.5 71.6 1.0
O D:THR138 4.5 63.2 1.0
CA D:CYS119 4.8 54.3 1.0
N D:HIS132 5.0 55.1 1.0

Zinc binding site 4 out of 4 in 6bms

Go back to Zinc Binding Sites List in 6bms
Zinc binding site 4 out of 4 in the Palmitoyltransferase Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Palmitoyltransferase Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1002

b:63.6
occ:1.00
CD2 D:HIS146 2.2 68.5 1.0
SG D:CYS133 2.3 58.4 1.0
SG D:CYS136 2.4 63.6 1.0
SG D:CYS153 2.4 60.0 1.0
CB D:CYS153 3.0 54.5 1.0
CG D:HIS146 3.2 62.7 1.0
NE2 D:HIS146 3.3 61.8 1.0
CB D:CYS133 3.3 58.3 1.0
CB D:CYS136 3.4 59.3 1.0
CA D:CYS153 3.5 59.1 1.0
CB D:HIS146 3.6 50.9 1.0
N D:CYS153 3.7 59.1 1.0
N D:CYS136 3.8 72.7 1.0
CA D:HIS146 4.1 51.8 1.0
CA D:CYS136 4.2 58.5 1.0
ND1 D:HIS146 4.3 63.8 1.0
CE1 D:HIS146 4.4 61.4 1.0
C D:ASN152 4.5 70.2 1.0
CB D:VAL135 4.7 63.3 1.0
CA D:CYS133 4.7 55.6 1.0
N D:HIS146 4.9 53.7 1.0
CE D:MET143 4.9 59.8 1.0
C D:VAL135 4.9 71.9 1.0
O D:ASN152 5.0 70.4 1.0
C D:CYS153 5.0 53.5 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 11:32:40 2020

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