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Zinc in PDB 3km8: Crystal Structuore of Adenosine Deaminase From Mus Musculus Complexed with 9-Deazainosine

Enzymatic activity of Crystal Structuore of Adenosine Deaminase From Mus Musculus Complexed with 9-Deazainosine

All present enzymatic activity of Crystal Structuore of Adenosine Deaminase From Mus Musculus Complexed with 9-Deazainosine:
3.5.4.4;

Protein crystallography data

The structure of Crystal Structuore of Adenosine Deaminase From Mus Musculus Complexed with 9-Deazainosine, PDB code: 3km8 was solved by X.Fan, Y.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.48 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.337, 93.616, 85.416, 90.00, 97.35, 90.00
R / Rfree (%) 20.2 / 22.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structuore of Adenosine Deaminase From Mus Musculus Complexed with 9-Deazainosine (pdb code 3km8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structuore of Adenosine Deaminase From Mus Musculus Complexed with 9-Deazainosine, PDB code: 3km8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3km8

Go back to Zinc Binding Sites List in 3km8
Zinc binding site 1 out of 2 in the Crystal Structuore of Adenosine Deaminase From Mus Musculus Complexed with 9-Deazainosine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structuore of Adenosine Deaminase From Mus Musculus Complexed with 9-Deazainosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:23.6
occ:1.00
O A:HOH526 2.0 31.4 1.0
NE2 A:HIS17 2.1 16.5 1.0
NE2 A:HIS15 2.1 25.9 1.0
NE2 A:HIS214 2.2 17.4 1.0
OD1 A:ASP295 2.5 24.0 1.0
CD2 A:HIS17 2.9 14.6 1.0
CD2 A:HIS214 3.1 21.9 1.0
CE1 A:HIS15 3.1 23.1 1.0
CD2 A:HIS15 3.1 22.6 1.0
CE1 A:HIS214 3.1 17.6 1.0
CE1 A:HIS17 3.2 15.0 1.0
CG A:ASP295 3.4 23.2 1.0
OD2 A:ASP295 3.6 25.6 1.0
NE2 A:HIS238 3.8 21.6 1.0
C5 A:9DI353 3.9 16.5 1.0
C6 A:9DI353 4.0 21.1 1.0
N7 A:9DI353 4.1 18.4 1.0
CG A:HIS17 4.1 16.3 1.0
ND1 A:HIS17 4.2 11.7 1.0
ND1 A:HIS15 4.2 17.7 1.0
ND1 A:HIS214 4.2 17.8 1.0
CG A:HIS214 4.2 17.5 1.0
CG A:HIS15 4.3 20.7 1.0
O6 A:9DI353 4.3 22.7 1.0
C4 A:9DI353 4.4 18.8 1.0
N1 A:9DI353 4.4 20.2 1.0
CE1 A:HIS238 4.6 20.4 1.0
CD2 A:HIS238 4.7 18.1 1.0
C9 A:9DI353 4.7 15.4 1.0
CB A:ASP295 4.7 19.9 1.0
C8 A:9DI353 4.7 19.7 1.0
N3 A:9DI353 4.8 21.4 1.0
C2 A:9DI353 4.8 21.6 1.0
CD A:ARG101 4.8 15.6 1.0
OD2 A:ASP296 4.9 28.3 1.0

Zinc binding site 2 out of 2 in 3km8

Go back to Zinc Binding Sites List in 3km8
Zinc binding site 2 out of 2 in the Crystal Structuore of Adenosine Deaminase From Mus Musculus Complexed with 9-Deazainosine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structuore of Adenosine Deaminase From Mus Musculus Complexed with 9-Deazainosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn400

b:21.9
occ:1.00
O B:HOH366 1.9 23.1 1.0
NE2 B:HIS17 2.0 24.5 1.0
NE2 B:HIS15 2.0 14.2 1.0
OD1 B:ASP295 2.3 15.6 1.0
NE2 B:HIS214 2.3 14.7 1.0
CE1 B:HIS17 3.0 18.6 1.0
CE1 B:HIS15 3.0 16.5 1.0
CD2 B:HIS17 3.0 14.8 1.0
CD2 B:HIS214 3.1 12.3 1.0
CD2 B:HIS15 3.1 19.6 1.0
CE1 B:HIS214 3.3 18.0 1.0
CG B:ASP295 3.4 23.0 1.0
OD2 B:ASP295 3.7 19.5 1.0
NE2 B:HIS238 3.8 19.6 1.0
C5 B:9DI353 3.9 17.8 1.0
C6 B:9DI353 4.0 19.5 1.0
ND1 B:HIS17 4.1 14.8 1.0
N7 B:9DI353 4.1 19.0 1.0
ND1 B:HIS15 4.1 15.1 1.0
CG B:HIS17 4.1 17.8 1.0
CG B:HIS15 4.2 17.5 1.0
O6 B:9DI353 4.2 26.2 1.0
CG B:HIS214 4.3 19.3 1.0
ND1 B:HIS214 4.4 18.8 1.0
C4 B:9DI353 4.4 20.0 1.0
N1 B:9DI353 4.4 18.9 1.0
CE1 B:HIS238 4.5 20.3 1.0
CB B:ASP295 4.7 17.5 1.0
C8 B:9DI353 4.7 20.4 1.0
OD2 B:ASP296 4.8 20.4 1.0
CD2 B:HIS238 4.8 18.2 1.0
C9 B:9DI353 4.8 15.9 1.0
CD B:ARG101 4.8 17.4 1.0
N3 B:9DI353 4.9 17.1 1.0
C2 B:9DI353 4.9 16.8 1.0

Reference:

X.Wu, X.Fan, Y.Gao, X.Su, H.Zhang, Y.Wu. The Catalytic Mechanism of Adenosine Deaminase From Mouse: An Experimental and Theoretical Study To Be Published.
Page generated: Sat Sep 26 11:11:25 2020
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