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Zinc in PDB 2jg4: Substrate-Free Ide Structure in Its Closed Conformation

Enzymatic activity of Substrate-Free Ide Structure in Its Closed Conformation

All present enzymatic activity of Substrate-Free Ide Structure in Its Closed Conformation:
3.4.24.56;

Protein crystallography data

The structure of Substrate-Free Ide Structure in Its Closed Conformation, PDB code: 2jg4 was solved by E.Malito, W.J.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.80
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 263.211, 263.211, 90.408, 90.00, 90.00, 120.00
R / Rfree (%) 18.2 / 22.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Substrate-Free Ide Structure in Its Closed Conformation (pdb code 2jg4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Substrate-Free Ide Structure in Its Closed Conformation, PDB code: 2jg4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2jg4

Go back to Zinc Binding Sites List in 2jg4
Zinc binding site 1 out of 2 in the Substrate-Free Ide Structure in Its Closed Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Substrate-Free Ide Structure in Its Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2012

b:32.9
occ:0.75
OE1 A:GLU189 2.0 33.3 1.0
OE2 A:GLU189 2.0 34.6 1.0
NE2 A:HIS112 2.1 28.7 1.0
NE2 A:HIS108 2.1 28.6 1.0
CD A:GLU189 2.2 32.4 1.0
O A:HOH3242 2.3 1.0 0.5
CE1 A:HIS108 2.8 26.7 1.0
CE1 A:HIS112 3.0 27.0 1.0
CD2 A:HIS112 3.1 27.4 1.0
CD2 A:HIS108 3.3 28.2 1.0
CG A:GLU189 3.7 30.9 1.0
ND1 A:HIS108 4.0 27.1 1.0
ND1 A:HIS112 4.1 26.3 1.0
CG A:HIS112 4.2 26.9 1.0
CG A:HIS108 4.3 27.0 1.0
CE1 A:PHE831 4.3 28.4 1.0
OE1 A:GLU111 4.4 31.0 1.0
CB A:GLU189 4.6 31.2 1.0
OE2 A:GLU111 4.7 30.6 1.0
CD A:GLU111 4.9 30.1 1.0
CZ A:PHE831 4.9 27.0 1.0

Zinc binding site 2 out of 2 in 2jg4

Go back to Zinc Binding Sites List in 2jg4
Zinc binding site 2 out of 2 in the Substrate-Free Ide Structure in Its Closed Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Substrate-Free Ide Structure in Its Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2012

b:42.7
occ:0.75
OE1 B:GLU189 2.0 44.4 1.0
NE2 B:HIS112 2.1 41.3 1.0
NE2 B:HIS108 2.1 38.4 1.0
OE2 B:GLU189 2.3 46.7 1.0
CD B:GLU189 2.5 42.5 1.0
CE1 B:HIS108 2.9 37.8 1.0
CE1 B:HIS112 3.0 41.1 1.0
CD2 B:HIS112 3.1 41.0 1.0
CD2 B:HIS108 3.2 37.1 1.0
ND1 B:HIS108 4.0 37.6 1.0
CG B:GLU189 4.0 40.9 1.0
ND1 B:HIS112 4.1 40.4 1.0
CG B:HIS112 4.2 40.7 1.0
CG B:HIS108 4.2 36.0 1.0
OE1 B:GLU111 4.3 37.7 1.0
CE1 B:PHE831 4.3 47.1 1.0
OE2 B:GLU111 4.6 37.9 1.0
O B:HOH3022 4.7 35.9 1.0
CZ B:PHE831 4.8 46.4 1.0
CD B:GLU111 4.8 37.2 1.0
CB B:GLU189 4.8 40.5 1.0
CG2 B:VAL186 5.0 40.1 1.0

Reference:

H.Im, M.Manolopoulou, E.Malito, Y.Shen, J.Zhao, M.Neant-Fery, C.-Y.Sun, S.C.Meredith, S.S.Sisodia, M.A.Leissring, W.J.Tang. Structure of Substrate-Free Human Insulin Degrading Enzyme (Ide) and Biophysical Analysis of Atp-Induced Conformational Switch of Ide J.Biol.Chem. V. 282 25453 2007.
ISSN: ISSN 0021-9258
PubMed: 17613531
DOI: 10.1074/JBC.M701590200
Page generated: Wed Dec 16 03:32:00 2020

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