Atomistry » Zinc » PDB 4yiw-4yye » 4ymk
Atomistry »
  Zinc »
    PDB 4yiw-4yye »
      4ymk »

Zinc in PDB 4ymk: Crystal Structure of Stearoyl-Coenzyme A Desaturase 1

Enzymatic activity of Crystal Structure of Stearoyl-Coenzyme A Desaturase 1

All present enzymatic activity of Crystal Structure of Stearoyl-Coenzyme A Desaturase 1:
1.14.19.1;

Protein crystallography data

The structure of Crystal Structure of Stearoyl-Coenzyme A Desaturase 1, PDB code: 4ymk was solved by Y.Bai, J.G.Mccoy, K.R.Rajashankar, M.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.41 / 2.61
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.061, 113.766, 141.698, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 23.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Stearoyl-Coenzyme A Desaturase 1 (pdb code 4ymk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Stearoyl-Coenzyme A Desaturase 1, PDB code: 4ymk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4ymk

Go back to Zinc Binding Sites List in 4ymk
Zinc binding site 1 out of 4 in the Crystal Structure of Stearoyl-Coenzyme A Desaturase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Stearoyl-Coenzyme A Desaturase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:34.9
occ:1.00
NE2 A:HIS297 2.0 31.5 1.0
NE2 A:HIS153 2.0 29.8 1.0
NE2 A:HIS121 2.2 22.1 1.0
NE2 A:HIS157 2.2 26.5 1.0
NE2 A:HIS116 2.4 23.4 1.0
CE1 A:HIS153 2.8 21.9 1.0
CE1 A:HIS297 2.9 31.8 1.0
CE1 A:HIS121 3.0 28.6 1.0
CD2 A:HIS297 3.0 24.3 1.0
CE1 A:HIS157 3.1 27.6 1.0
CD2 A:HIS153 3.1 28.5 1.0
CD2 A:HIS116 3.2 23.4 1.0
CD2 A:HIS157 3.2 26.3 1.0
CD2 A:HIS121 3.3 23.1 1.0
CE1 A:HIS116 3.5 21.9 1.0
ND1 A:HIS153 4.0 24.9 1.0
ND1 A:HIS297 4.1 23.1 1.0
CG A:HIS297 4.1 23.3 1.0
CG A:HIS153 4.2 21.9 1.0
ND1 A:HIS121 4.2 29.3 1.0
ND1 A:HIS157 4.2 24.5 1.0
CG A:HIS157 4.3 29.9 1.0
CG A:HIS121 4.3 22.4 1.0
CG A:HIS116 4.4 24.5 1.0
ND1 A:HIS116 4.5 24.8 1.0
C10 A:ST9403 4.7 45.9 1.0

Zinc binding site 2 out of 4 in 4ymk

Go back to Zinc Binding Sites List in 4ymk
Zinc binding site 2 out of 4 in the Crystal Structure of Stearoyl-Coenzyme A Desaturase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Stearoyl-Coenzyme A Desaturase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:31.8
occ:1.00
NE2 A:HIS294 2.0 36.3 1.0
NE2 A:HIS156 2.2 24.2 1.0
NE2 A:HIS265 2.2 34.3 1.0
O A:HOH542 2.2 50.1 1.0
NE2 A:HIS298 2.3 32.1 1.0
CE1 A:HIS294 2.9 33.1 1.0
CE1 A:HIS156 3.0 24.1 1.0
CD2 A:HIS294 3.0 27.5 1.0
CE1 A:HIS265 3.1 28.5 1.0
CD2 A:HIS298 3.2 30.6 1.0
CE1 A:HIS298 3.3 34.1 1.0
CD2 A:HIS265 3.3 36.9 1.0
CD2 A:HIS156 3.3 23.2 1.0
ND1 A:HIS294 4.0 25.9 1.0
CG A:HIS294 4.1 29.2 1.0
ND1 A:HIS156 4.2 30.8 1.0
ND1 A:HIS265 4.2 31.8 1.0
CG A:HIS298 4.3 29.2 1.0
CG A:HIS156 4.4 28.1 1.0
ND1 A:HIS298 4.4 32.0 1.0
CG A:HIS265 4.4 34.3 1.0
O A:VAL260 4.4 37.9 1.0
ND2 A:ASN261 4.5 26.9 1.0
OG A:SER278 4.9 63.2 1.0

Zinc binding site 3 out of 4 in 4ymk

Go back to Zinc Binding Sites List in 4ymk
Zinc binding site 3 out of 4 in the Crystal Structure of Stearoyl-Coenzyme A Desaturase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Stearoyl-Coenzyme A Desaturase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:38.4
occ:1.00
NE2 D:HIS297 2.0 36.3 1.0
NE2 D:HIS153 2.1 40.3 1.0
NE2 D:HIS121 2.2 37.5 1.0
NE2 D:HIS157 2.2 47.3 1.0
NE2 D:HIS116 2.3 30.9 1.0
CE1 D:HIS121 2.7 34.0 1.0
CE1 D:HIS297 2.9 31.7 1.0
CE1 D:HIS153 3.0 35.7 1.0
CD2 D:HIS157 3.1 42.2 1.0
CD2 D:HIS153 3.1 33.3 1.0
CD2 D:HIS297 3.1 34.3 1.0
CD2 D:HIS116 3.1 27.6 1.0
CE1 D:HIS157 3.1 40.6 1.0
CE1 D:HIS116 3.3 26.1 1.0
CD2 D:HIS121 3.4 43.9 1.0
ND1 D:HIS121 4.0 30.6 1.0
ND1 D:HIS297 4.1 33.4 1.0
ND1 D:HIS153 4.1 32.4 1.0
ND1 D:HIS157 4.2 39.9 1.0
CG D:HIS297 4.2 27.4 1.0
CG D:HIS157 4.2 37.7 1.0
CG D:HIS153 4.2 32.1 1.0
CG D:HIS121 4.3 28.4 1.0
CG D:HIS116 4.3 30.3 1.0
ND1 D:HIS116 4.4 36.5 1.0
C10 D:ST9403 4.7 41.6 1.0

Zinc binding site 4 out of 4 in 4ymk

Go back to Zinc Binding Sites List in 4ymk
Zinc binding site 4 out of 4 in the Crystal Structure of Stearoyl-Coenzyme A Desaturase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Stearoyl-Coenzyme A Desaturase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:38.6
occ:1.00
NE2 D:HIS294 2.0 38.3 1.0
NE2 D:HIS156 2.1 34.9 1.0
NE2 D:HIS298 2.2 38.1 1.0
NE2 D:HIS265 2.2 36.8 1.0
O D:HOH530 2.2 56.2 1.0
CD2 D:HIS294 2.8 33.1 1.0
CE1 D:HIS156 2.9 34.6 1.0
CE1 D:HIS265 3.0 40.6 1.0
CE1 D:HIS294 3.1 30.0 1.0
CE1 D:HIS298 3.1 37.5 1.0
CD2 D:HIS298 3.2 30.7 1.0
CD2 D:HIS156 3.3 34.0 1.0
CD2 D:HIS265 3.4 37.4 1.0
CG D:HIS294 4.0 31.8 1.0
ND1 D:HIS156 4.1 35.1 1.0
ND1 D:HIS294 4.1 29.9 1.0
ND1 D:HIS265 4.2 38.9 1.0
ND1 D:HIS298 4.2 37.3 1.0
CG D:HIS298 4.3 38.4 1.0
CG D:HIS156 4.3 33.1 1.0
CG D:HIS265 4.4 37.0 1.0
O D:VAL260 4.4 39.5 1.0
OG D:SER278 4.5 68.3 1.0
ND2 D:ASN261 4.5 44.2 1.0
O D:HOH504 4.9 31.4 1.0

Reference:

Y.Bai, J.G.Mccoy, E.J.Levin, P.Sobrado, K.R.Rajashankar, B.G.Fox, M.Zhou. X-Ray Structure of A Mammalian Stearoyl-Coa Desaturase. Nature V. 524 252 2015.
ISSN: ESSN 1476-4687
PubMed: 26098370
DOI: 10.1038/NATURE14549
Page generated: Wed Dec 16 05:57:35 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy