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Zinc in PDB 1v51: The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation

Enzymatic activity of The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation

All present enzymatic activity of The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation:
3.5.1.81;

Protein crystallography data

The structure of The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation, PDB code: 1v51 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) 25.40 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.134, 77.384, 134.522, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 20.8

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Zinc atom in the The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation (pdb code 1v51). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation, PDB code: 1v51:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in 1v51

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Zinc binding site 1 out of 11 in the The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:7.7
occ:1.00
ND1 A:HIS220 2.0 7.0 1.0
NE2 A:HIS250 2.1 6.0 1.0
O A:ACT901 2.1 6.6 1.0
SG A:CYS96 2.3 7.7 1.0
OXT A:ACT901 2.5 6.7 1.0
C A:ACT901 2.6 7.7 1.0
CE1 A:HIS220 3.0 8.0 1.0
CG A:HIS220 3.0 5.5 1.0
CE1 A:HIS250 3.0 5.4 1.0
CD2 A:HIS250 3.1 6.3 1.0
CB A:CYS96 3.3 7.7 1.0
CB A:HIS220 3.4 7.1 1.0
ZN A:ZN602 3.8 10.9 1.0
NE2 A:HIS220 4.0 8.9 1.0
CH3 A:ACT901 4.1 7.1 1.0
CD2 A:HIS220 4.1 6.7 1.0
CH3 A:ACT902 4.1 8.2 1.0
ND1 A:HIS250 4.2 6.2 1.0
CG A:HIS250 4.2 5.3 1.0
OH A:TYR192 4.2 11.1 1.0
CE2 A:TYR192 4.3 8.8 1.0
NE2 A:HIS67 4.4 6.3 1.0
CA A:HIS220 4.4 5.8 1.0
CE1 A:HIS67 4.4 5.8 1.0
CA A:CYS96 4.5 6.6 1.0
CZ A:TYR192 4.8 9.9 1.0
NE2 A:HIS69 4.9 7.4 1.0
OD2 A:ASP366 5.0 9.4 1.0

Zinc binding site 2 out of 11 in 1v51

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Zinc binding site 2 out of 11 in the The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:10.9
occ:1.00
OXT A:ACT901 1.9 6.7 1.0
OD1 A:ASP366 2.0 6.7 1.0
NE2 A:HIS67 2.0 6.3 1.0
NE2 A:HIS69 2.1 7.4 1.0
CG A:ASP366 2.8 8.0 1.0
CD2 A:HIS67 2.8 6.8 1.0
CD2 A:HIS69 2.9 8.2 1.0
C A:ACT901 2.9 7.7 1.0
OD2 A:ASP366 3.1 9.4 1.0
CE1 A:HIS69 3.1 8.3 1.0
CE1 A:HIS67 3.2 5.8 1.0
CH3 A:ACT901 3.4 7.1 1.0
SG A:CYS96 3.5 7.7 1.0
ZN A:ZN601 3.8 7.7 1.0
CD2 A:HIS250 3.8 6.3 1.0
O A:ACT901 4.0 6.6 1.0
CG A:HIS67 4.1 4.4 1.0
CG A:HIS69 4.1 5.2 1.0
CB A:ASP366 4.1 6.8 1.0
ND1 A:HIS67 4.2 5.4 1.0
ND1 A:HIS69 4.2 6.1 1.0
NE2 A:HIS250 4.3 6.0 1.0
CA A:ASP366 4.4 6.5 1.0
CB A:ASN95 4.8 5.0 1.0
CB A:CYS96 4.9 7.7 1.0

Zinc binding site 3 out of 11 in 1v51

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Zinc binding site 3 out of 11 in the The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:23.1
occ:1.00
ND1 A:HIS388 2.1 14.5 1.0
CE1 A:HIS388 2.9 17.2 1.0
CG A:HIS388 3.2 14.1 1.0
CB A:HIS388 3.7 11.0 1.0
OD2 A:ASP392 3.7 18.1 1.0
CA A:HIS388 3.9 10.1 1.0
O A:HOH1082 4.0 23.4 1.0
NE2 A:HIS388 4.0 15.6 1.0
CB A:ASP392 4.1 13.0 1.0
CD2 A:HIS388 4.2 14.2 1.0
CG A:ASP392 4.4 16.3 1.0
O A:HIS388 4.6 10.8 1.0
C A:HIS388 4.7 10.8 1.0
N A:HIS388 5.0 8.8 1.0

Zinc binding site 4 out of 11 in 1v51

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Zinc binding site 4 out of 11 in the The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn604

b:58.7
occ:1.00
OE1 A:GLU325 2.0 17.7 1.0
OE2 A:GLU325 2.2 19.1 1.0
OE2 A:GLU321 2.4 18.5 1.0
CD A:GLU325 2.4 17.8 1.0
CD A:GLU321 3.2 16.1 1.0
CG A:GLU321 3.5 14.3 1.0
CG A:GLU325 3.9 17.5 1.0
NH1 A:ARG317 4.1 15.4 1.0
O A:HOH1050 4.1 18.6 1.0
OE1 A:GLU321 4.3 14.6 1.0
O A:HOH1149 4.7 25.3 1.0
CB A:GLU325 4.8 14.9 1.0

Zinc binding site 5 out of 11 in 1v51

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Zinc binding site 5 out of 11 in the The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn605

b:67.5
occ:1.00
O A:HOH1039 3.2 17.3 1.0
OD2 A:ASP332 4.7 11.4 1.0

Zinc binding site 6 out of 11 in 1v51

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Zinc binding site 6 out of 11 in the The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn606

b:26.1
occ:1.00
O A:HOH960 3.8 14.4 1.0
O A:ALA300 3.9 13.9 1.0
CB A:ALA300 4.1 11.8 1.0
C A:ALA300 4.5 12.1 1.0
CB A:LYS256 4.7 12.0 1.0
CA A:ALA300 4.8 11.9 1.0

Zinc binding site 7 out of 11 in 1v51

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Zinc binding site 7 out of 11 in the The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn607

b:22.9
occ:1.00
OE1 A:GLU201 1.9 10.8 1.0
OE2 A:GLU201 2.1 12.8 1.0
OE2 A:GLU205 2.2 10.4 1.0
CD A:GLU201 2.3 11.5 1.0
CD A:GLU205 3.1 9.8 1.0
CG A:GLU205 3.4 9.0 1.0
CG A:GLU201 3.8 10.7 1.0
OE1 A:GLU205 4.2 12.2 1.0
NH2 A:ARG208 4.4 13.0 1.0
CB A:GLU201 4.5 11.0 1.0
O A:GLU201 4.6 9.1 1.0
CA A:GLU201 4.9 9.8 1.0
O A:HOH1006 4.9 15.3 1.0
CB A:GLU205 4.9 8.9 1.0

Zinc binding site 8 out of 11 in 1v51

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Zinc binding site 8 out of 11 in the The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn608

b:24.4
occ:1.00
OD2 A:ASP243 2.1 22.0 1.0
OD1 A:ASP243 2.3 17.0 1.0
O A:HOH1091 2.3 22.8 1.0
CG A:ASP243 2.5 15.7 1.0
CB A:ASP243 4.0 14.3 1.0
O A:HOH953 4.2 14.3 1.0
CA A:ASP243 4.8 11.9 1.0

Zinc binding site 9 out of 11 in 1v51

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Zinc binding site 9 out of 11 in the The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn609

b:30.7
occ:1.00
NE2 A:HIS213 2.1 25.5 1.0
OD1 A:ASP176 2.2 21.8 1.0
OD2 A:ASP176 2.4 17.4 1.0
CG A:ASP176 2.6 15.3 1.0
CE1 A:HIS213 2.8 24.7 1.0
CD2 A:HIS213 3.2 21.3 1.0
ND1 A:HIS213 4.0 24.3 1.0
O A:ASP176 4.1 12.5 1.0
CB A:ASP176 4.1 12.5 1.0
CG A:HIS213 4.3 22.9 1.0
CB A:ALA180 4.5 12.4 1.0
C A:ASP176 4.6 12.2 1.0
CA A:ASP176 4.7 12.4 1.0

Zinc binding site 10 out of 11 in 1v51

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Zinc binding site 10 out of 11 in the The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The Functional Role of the Binuclear Metal Center in D- Aminoacylase. One-Metal Activation and Second-Metal Attenuation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn610

b:23.1
occ:1.00
ND1 A:HIS473 1.9 12.9 1.0
CE1 A:HIS473 2.8 16.7 1.0
CG A:HIS473 3.1 14.2 1.0
CB A:HIS473 3.5 10.5 1.0
O A:GLY471 3.7 14.7 1.0
NE2 A:HIS473 3.9 14.7 1.0
NH2 A:ARG78 4.0 12.5 1.0
CD2 A:HIS473 4.1 15.1 1.0
N A:HIS473 4.3 9.9 1.0
NH1 A:ARG78 4.3 19.6 1.0
CZ A:ARG78 4.4 15.2 1.0
CA A:HIS473 4.6 9.3 1.0
C A:GLY471 4.8 11.7 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: Wed Dec 16 03:07:40 2020

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