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Zinc in PDB 1xx4: Crystal Structure of Rat Mitochondrial 3,2-Enoyl-Coa

Enzymatic activity of Crystal Structure of Rat Mitochondrial 3,2-Enoyl-Coa

All present enzymatic activity of Crystal Structure of Rat Mitochondrial 3,2-Enoyl-Coa:
5.3.3.8;

Protein crystallography data

The structure of Crystal Structure of Rat Mitochondrial 3,2-Enoyl-Coa, PDB code: 1xx4 was solved by P.A.Hubbard, W.Yu, H.Schulz, J.-J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.15 / 2.20
Space group I 41 3 2
Cell size a, b, c (Å), α, β, γ (°) 169.918, 169.918, 169.918, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 26.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rat Mitochondrial 3,2-Enoyl-Coa (pdb code 1xx4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Rat Mitochondrial 3,2-Enoyl-Coa, PDB code: 1xx4:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 1xx4

Go back to Zinc Binding Sites List in 1xx4
Zinc binding site 1 out of 3 in the Crystal Structure of Rat Mitochondrial 3,2-Enoyl-Coa


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 Rat Mitochondrial 3,2-Enoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:47.8
occ:1.00
ND1 A:HIS107 2.1 39.9 1.0
O4 A:PO4300 2.1 50.3 1.0
OE1 A:GLU110 2.3 51.6 1.0
CE1 A:HIS107 3.0 40.8 1.0
O3 A:PO4300 3.1 50.5 1.0
CG A:HIS107 3.1 41.6 1.0
P A:PO4300 3.1 49.8 1.0
CD A:GLU110 3.4 50.2 1.0
CB A:HIS107 3.5 41.9 1.0
CA A:HIS107 3.8 42.2 1.0
OE2 A:GLU110 3.8 52.2 1.0
O2 A:PO4300 4.0 54.3 1.0
NE2 A:HIS107 4.2 42.1 1.0
CD2 A:HIS107 4.2 42.1 1.0
O1 A:PO4300 4.3 52.5 1.0
NH1 A:ARG103 4.3 58.1 1.0
CG A:GLU110 4.6 47.4 1.0
O A:HIS107 4.6 42.9 1.0
C A:HIS107 4.7 42.6 1.0
CD2 A:LEU59 4.7 44.3 1.0
N A:HIS107 4.8 41.6 1.0
CB A:GLU110 4.9 43.2 1.0

Zinc binding site 2 out of 3 in 1xx4

Go back to Zinc Binding Sites List in 1xx4
Zinc binding site 2 out of 3 in the Crystal Structure of Rat Mitochondrial 3,2-Enoyl-Coa


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 Rat Mitochondrial 3,2-Enoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:63.8
occ:1.00
ND1 A:HIS220 2.4 59.4 1.0
O3 A:PO4302 2.6 48.9 1.0
O1 A:PO4301 2.7 49.6 1.0
O1 A:PO4302 2.9 48.4 1.0
O4 A:PO4302 3.0 47.4 1.0
P A:PO4302 3.0 54.4 1.0
CE1 A:HIS220 3.1 59.5 1.0
CG A:HIS220 3.3 57.1 1.0
ZN A:ZN402 3.3 65.7 1.0
P A:PO4301 3.4 53.7 1.0
O3 A:PO4301 3.4 48.3 1.0
O4 A:PO4301 3.5 48.4 1.0
CB A:HIS220 3.7 50.6 1.0
NE2 A:HIS220 4.2 58.9 1.0
CD2 A:HIS220 4.3 57.9 1.0
O2 A:PO4302 4.5 48.9 1.0
O2 A:PO4301 4.8 49.3 1.0

Zinc binding site 3 out of 3 in 1xx4

Go back to Zinc Binding Sites List in 1xx4
Zinc binding site 3 out of 3 in the Crystal Structure of Rat Mitochondrial 3,2-Enoyl-Coa


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 Rat Mitochondrial 3,2-Enoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:65.7
occ:1.00
O1 A:PO4302 2.6 48.4 1.0
O4 A:PO4302 2.7 47.4 1.0
O4 A:PO4301 2.7 48.4 1.0
O3 A:PO4301 2.7 48.3 1.0
P A:PO4302 3.2 54.4 1.0
P A:PO4301 3.3 53.7 1.0
ZN A:ZN401 3.3 63.8 1.0
O1 A:PO4301 4.1 49.6 1.0
O2 A:PO4302 4.3 48.9 1.0
O3 A:PO4302 4.4 48.9 1.0
O2 A:PO4301 4.5 49.3 1.0

Reference:

P.A.Hubbard, W.Yu, H.Schulz, J.J.Kim. Domain Swapping in the Low-Similarity Isomerase/Hydratase Superfamily: the Crystal Structure of Rat Mitochondrial DELTA3, DELTA2-Enoyl-Coa Isomerase. Protein Sci. V. 14 1545 2005.
ISSN: ISSN 0961-8368
PubMed: 15883186
DOI: 10.1110/PS.041303705
Page generated: Sat Sep 26 00:25:07 2020
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