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Zinc in PDB 3jru: Crystal Structure of Leucyl Aminopeptidase (Pepa) From XOO0834, Xanthomonas Oryzae Pv. Oryzae KACC10331

Enzymatic activity of Crystal Structure of Leucyl Aminopeptidase (Pepa) From XOO0834, Xanthomonas Oryzae Pv. Oryzae KACC10331

All present enzymatic activity of Crystal Structure of Leucyl Aminopeptidase (Pepa) From XOO0834, Xanthomonas Oryzae Pv. Oryzae KACC10331:
3.4.11.1;

Protein crystallography data

The structure of Crystal Structure of Leucyl Aminopeptidase (Pepa) From XOO0834, Xanthomonas Oryzae Pv. Oryzae KACC10331, PDB code: 3jru was solved by S.Natarajan, K.-H.Huynh, L.W.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.02 / 2.60
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 152.126, 152.126, 152.126, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 21.5

Other elements in 3jru:

The structure of Crystal Structure of Leucyl Aminopeptidase (Pepa) From XOO0834, Xanthomonas Oryzae Pv. Oryzae KACC10331 also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Leucyl Aminopeptidase (Pepa) From XOO0834, Xanthomonas Oryzae Pv. Oryzae KACC10331 (pdb code 3jru). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Leucyl Aminopeptidase (Pepa) From XOO0834, Xanthomonas Oryzae Pv. Oryzae KACC10331, PDB code: 3jru:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3jru

Go back to Zinc Binding Sites List in 3jru
Zinc binding site 1 out of 4 in the Crystal Structure of Leucyl Aminopeptidase (Pepa) From XOO0834, Xanthomonas Oryzae Pv. Oryzae KACC10331


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 Leucyl Aminopeptidase (Pepa) From XOO0834, Xanthomonas Oryzae Pv. Oryzae KACC10331 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn631

b:66.2
occ:1.00
 OD1 B:ASP285 2.1 34.8 1.0
OE2 B:GLU346 2.4 26.1 1.0
NZ B:LYS262 2.6 27.3 1.0
OD2 B:ASP267 3.0 19.7 1.0
ZN B:ZN632 3.1 39.9 1.0
CE B:LYS262 3.2 23.8 1.0
CG B:ASP285 3.2 26.7 1.0
CD B:GLU346 3.2 25.3 1.0
OE1 B:GLU346 3.3 29.1 1.0
OD2 B:ASP285 3.7 31.6 1.0
CG B:ASP267 3.7 18.4 1.0
O B:HOH534 3.8 36.4 1.0
CB B:ASP267 4.1 15.8 1.0
O2 B:CO3491 4.1 28.7 1.0
CG1 B:ILE264 4.3 13.0 1.0
CB B:ASP285 4.4 21.8 1.0
N B:GLY347 4.4 16.9 1.0
CG2 B:ILE264 4.4 14.2 1.0
CB B:ILE264 4.5 15.3 1.0
CD B:LYS262 4.6 19.5 1.0
O B:THR371 4.6 19.2 1.0
OD1 B:ASP267 4.6 21.1 1.0
CA B:GLY347 4.7 17.0 1.0
CG B:GLU346 4.7 21.2 1.0
O B:ASP344 4.9 19.5 1.0

Zinc binding site 2 out of 4 in 3jru

Go back to Zinc Binding Sites List in 3jru
Zinc binding site 2 out of 4 in the Crystal Structure of Leucyl Aminopeptidase (Pepa) From XOO0834, Xanthomonas Oryzae Pv. Oryzae KACC10331


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 Leucyl Aminopeptidase (Pepa) From XOO0834, Xanthomonas Oryzae Pv. Oryzae KACC10331 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn632

b:39.9
occ:1.00
 OD1 B:ASP344 2.1 22.0 1.0
OD2 B:ASP267 2.2 19.7 1.0
O B:ASP344 2.4 19.5 1.0
OE1 B:GLU346 2.5 29.1 1.0
O B:HOH534 2.6 36.4 1.0
ZN B:ZN631 3.1 66.2 1.0
CG B:ASP344 3.2 20.2 1.0
C B:ASP344 3.2 19.1 1.0
CG B:ASP267 3.3 18.4 1.0
CD B:GLU346 3.4 25.3 1.0
OE2 B:GLU346 3.6 26.1 1.0
CA B:ASP344 3.6 18.9 1.0
NZ B:LYS274 3.7 15.8 1.0
OD1 B:ASP267 3.7 21.1 1.0
CB B:ASP344 4.0 19.2 1.0
OD2 B:ASP344 4.1 19.0 1.0
N B:ALA345 4.3 19.1 1.0
CE B:LYS274 4.4 18.0 1.0
O2 B:CO3491 4.4 28.7 1.0
CB B:ASP267 4.5 15.8 1.0
N B:GLU346 4.5 18.1 1.0
OD1 B:ASP285 4.6 34.8 1.0
CA B:ALA345 4.8 18.8 1.0
CG B:GLU346 4.8 21.2 1.0
ND2 B:ASN317 4.8 17.0 1.0
CA B:GLY269 5.0 16.4 1.0
N B:ASP344 5.0 18.7 1.0

Zinc binding site 3 out of 4 in 3jru

Go back to Zinc Binding Sites List in 3jru
Zinc binding site 3 out of 4 in the Crystal Structure of Leucyl Aminopeptidase (Pepa) From XOO0834, Xanthomonas Oryzae Pv. Oryzae KACC10331


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 Leucyl Aminopeptidase (Pepa) From XOO0834, Xanthomonas Oryzae Pv. Oryzae KACC10331 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn629

b:44.7
occ:1.00
 OD1 A:ASP344 2.2 25.2 1.0
OD2 A:ASP267 2.2 26.3 1.0
O A:ASP344 2.2 20.5 1.0
OE1 A:GLU346 2.3 32.0 1.0
ZN A:ZN630 3.1 72.9 1.0
C A:ASP344 3.2 20.7 1.0
CG A:ASP344 3.3 23.9 1.0
CG A:ASP267 3.3 22.5 1.0
CD A:GLU346 3.3 28.8 1.0
OE2 A:GLU346 3.6 31.4 1.0
CA A:ASP344 3.7 20.9 1.0
OD1 A:ASP267 3.8 21.4 1.0
NZ A:LYS274 4.0 25.9 1.0
CB A:ASP344 4.0 20.6 1.0
OD2 A:ASP344 4.1 27.6 1.0
N A:GLU346 4.3 19.8 1.0
CE A:LYS274 4.3 24.8 1.0
N A:ALA345 4.3 20.4 1.0
OD1 A:ASP285 4.5 34.8 1.0
CB A:ASP267 4.6 19.8 1.0
CA A:ALA345 4.7 20.3 1.0
O1 A:CO3491 4.7 35.8 1.0
O A:HOH635 4.7 37.9 1.0
CG A:GLU346 4.7 22.7 1.0
CE A:MET282 4.7 30.7 1.0
ND2 A:ASN317 4.9 16.4 1.0

Zinc binding site 4 out of 4 in 3jru

Go back to Zinc Binding Sites List in 3jru
Zinc binding site 4 out of 4 in the Crystal Structure of Leucyl Aminopeptidase (Pepa) From XOO0834, Xanthomonas Oryzae Pv. Oryzae KACC10331


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Leucyl Aminopeptidase (Pepa) From XOO0834, Xanthomonas Oryzae Pv. Oryzae KACC10331 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn630

b:72.9
occ:1.00
 OD1 A:ASP285 2.2 34.8 1.0
OE2 A:GLU346 2.4 31.4 1.0
NZ A:LYS262 2.6 23.8 1.0
OD2 A:ASP267 3.0 26.3 1.0
ZN A:ZN629 3.1 44.7 1.0
CG A:ASP285 3.1 29.7 1.0
CE A:LYS262 3.2 21.1 1.0
CD A:GLU346 3.3 28.8 1.0
OE1 A:GLU346 3.5 32.0 1.0
OD2 A:ASP285 3.5 34.8 1.0
CG A:ASP267 3.8 22.5 1.0
O A:HOH635 4.0 37.9 1.0
O1 A:CO3491 4.1 35.8 1.0
N A:GLY347 4.2 19.6 1.0
CB A:ASP267 4.2 19.8 1.0
CE A:MET282 4.3 30.7 1.0
CG2 A:ILE264 4.3 21.1 1.0
CB A:ASP285 4.4 27.0 1.0
CG1 A:ILE264 4.4 20.4 1.0
O A:THR371 4.5 23.0 1.0
CB A:ILE264 4.5 21.7 1.0
CA A:GLY347 4.5 19.0 1.0
CD A:LYS262 4.6 22.6 1.0
OD1 A:ASP267 4.7 21.4 1.0
CG A:GLU346 4.8 22.7 1.0
O A:ASP344 4.9 20.5 1.0

Reference:

S.Natarajan, K.-H.Huynh, L.W.Kang. Crystal Structure of Leucyl Aminopeptidase (Pepa) From XOO0834,Xanthomonas Oryzae Pv. Oryzae KACC10331 To Be Published.
Page generated: Sat Oct 26 07:29:53 2024

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