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Zinc in PDB 1rjr: The Crystal Structure of the D-Aminoacylase D366A Mutant in Complex with 100MM ZNCL2

Enzymatic activity of The Crystal Structure of the D-Aminoacylase D366A Mutant in Complex with 100MM ZNCL2

All present enzymatic activity of The Crystal Structure of the D-Aminoacylase D366A Mutant in Complex with 100MM ZNCL2:
3.5.1.81;

Protein crystallography data

The structure of The Crystal Structure of the D-Aminoacylase D366A Mutant in Complex with 100MM ZNCL2, PDB code: 1rjr was solved by W.L.Lai, L.Y.Chou, C.Y.Ting, Y.C.Tsai, S.H.Liaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.517, 77.815, 136.647, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 22.5

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystal Structure of the D-Aminoacylase D366A Mutant in Complex with 100MM ZNCL2 (pdb code 1rjr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The Crystal Structure of the D-Aminoacylase D366A Mutant in Complex with 100MM ZNCL2, PDB code: 1rjr:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1rjr

Go back to Zinc Binding Sites List in 1rjr
Zinc binding site 1 out of 2 in the The Crystal Structure of the D-Aminoacylase D366A Mutant in Complex with 100MM ZNCL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of the D-Aminoacylase D366A Mutant in Complex with 100MM ZNCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:22.0
occ:1.00
ND1 A:HIS220 2.0 20.1 1.0
O A:ACT901 2.0 21.2 1.0
NE2 A:HIS250 2.2 22.0 1.0
SG A:CYS96 2.3 19.0 1.0
C A:ACT901 2.7 24.2 1.0
CE1 A:HIS220 2.8 19.8 1.0
OXT A:ACT901 2.8 22.7 1.0
CG A:HIS220 3.0 19.1 1.0
CE1 A:HIS250 3.1 21.8 1.0
CD2 A:HIS250 3.2 22.4 1.0
ZN A:ZN602 3.2 51.7 1.0
CB A:CYS96 3.4 18.8 1.0
CB A:HIS220 3.5 17.2 1.0
NE2 A:HIS220 3.9 21.4 1.0
OH A:TYR192 4.0 23.6 1.0
CD2 A:HIS220 4.0 18.8 1.0
CH3 A:ACT901 4.1 24.2 1.0
CH3 A:ACT902 4.2 20.1 1.0
ND1 A:HIS250 4.2 23.8 1.0
CG A:HIS250 4.3 21.7 1.0
CE2 A:TYR192 4.4 24.1 1.0
NE2 A:HIS67 4.4 14.3 1.0
CA A:HIS220 4.6 18.9 1.0
CA A:CYS96 4.6 18.9 1.0
CZ A:TYR192 4.7 24.2 1.0
CE1 A:HIS67 4.8 15.7 1.0
NE2 A:HIS69 4.9 21.0 1.0

Zinc binding site 2 out of 2 in 1rjr

Go back to Zinc Binding Sites List in 1rjr
Zinc binding site 2 out of 2 in the The Crystal Structure of the D-Aminoacylase D366A Mutant in Complex with 100MM ZNCL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of the D-Aminoacylase D366A Mutant in Complex with 100MM ZNCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:51.7
occ:1.00
NE2 A:HIS69 2.1 21.0 1.0
NE2 A:HIS67 2.3 14.3 1.0
OXT A:ACT901 2.3 22.7 1.0
SG A:CYS96 2.5 19.0 1.0
CE1 A:HIS69 2.8 20.9 1.0
C A:ACT901 2.9 24.2 1.0
ZN A:ZN601 3.2 22.0 1.0
CD2 A:HIS67 3.2 16.1 1.0
CD2 A:HIS69 3.3 19.7 1.0
CE1 A:HIS67 3.3 15.7 1.0
O A:ACT901 3.4 21.2 1.0
CH3 A:ACT901 3.8 24.2 1.0
CB A:CYS96 3.8 18.8 1.0
ND1 A:HIS69 4.0 21.9 1.0
CD2 A:HIS250 4.0 22.4 1.0
NE2 A:HIS250 4.1 22.0 1.0
CB A:ASN95 4.2 15.2 1.0
CG A:HIS69 4.2 20.9 1.0
ND1 A:HIS67 4.4 16.4 1.0
CG A:HIS67 4.4 19.3 1.0
N A:CYS96 4.7 18.1 1.0
C A:ASN95 4.7 17.2 1.0
CB A:ALA366 4.8 17.1 1.0
CA A:CYS96 4.9 18.9 1.0
O A:ASN95 4.9 16.9 1.0

Reference:

W.L.Lai, L.Y.Chou, C.Y.Ting, R.Kirby, Y.C.Tsai, A.H.Wang, S.H.Liaw. The Functional Role of the Binuclear Metal Center in D-Aminoacylase: One-Metal Activation and Second-Metal Attenuation. J.Biol.Chem. V. 279 13962 2004.
ISSN: ISSN 0021-9258
PubMed: 14736882
DOI: 10.1074/JBC.M308849200
Page generated: Mon Jan 25 16:12:44 2021

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