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Zinc in PDB 1lcp: Bovine Lens Leucine Aminopeptidase Complexed with L-Leucine Phosphonic Acid

Enzymatic activity of Bovine Lens Leucine Aminopeptidase Complexed with L-Leucine Phosphonic Acid

All present enzymatic activity of Bovine Lens Leucine Aminopeptidase Complexed with L-Leucine Phosphonic Acid:
3.4.11.1;

Protein crystallography data

The structure of Bovine Lens Leucine Aminopeptidase Complexed with L-Leucine Phosphonic Acid, PDB code: 1lcp was solved by N.Straeter, W.N.Lipscomb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.00 / 1.65
Space group P 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 130.400, 130.400, 125.400, 90.00, 90.00, 120.00
R / Rfree (%) 16 / 19.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Bovine Lens Leucine Aminopeptidase Complexed with L-Leucine Phosphonic Acid (pdb code 1lcp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Bovine Lens Leucine Aminopeptidase Complexed with L-Leucine Phosphonic Acid, PDB code: 1lcp:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1lcp

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Zinc binding site 1 out of 6 in the Bovine Lens Leucine Aminopeptidase Complexed with L-Leucine Phosphonic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Bovine Lens Leucine Aminopeptidase Complexed with L-Leucine Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn488

b:10.7
occ:1.00
 OE1 A:GLU334 2.0 5.1 1.0
OD1 A:ASP332 2.0 6.8 1.0
O2 A:PLU500 2.1 9.2 1.0
OD2 A:ASP255 2.1 5.4 1.0
O A:ASP332 2.2 7.0 1.0
O1 A:PLU500 2.5 8.0 1.0
P A:PLU500 2.8 9.7 1.0
CD A:GLU334 3.0 5.1 1.0
CG A:ASP255 3.0 7.8 1.0
CG A:ASP332 3.0 6.4 1.0
C A:ASP332 3.1 7.0 1.0
OD1 A:ASP255 3.1 6.1 1.0
OE2 A:GLU334 3.3 7.4 1.0
ZN A:ZN489 3.4 9.6 1.0
CA A:ASP332 3.5 7.0 1.0
NZ A:LYS262 3.7 8.6 1.0
CB A:ASP332 3.8 6.6 1.0
OD2 A:ASP332 3.8 7.4 1.0
O3 A:PLU500 3.9 10.0 1.0
N A:PLU500 4.0 8.6 1.0
CE A:LYS262 4.1 10.4 1.0
CA A:PLU500 4.1 10.2 1.0
N A:ALA333 4.3 6.7 1.0
N A:GLU334 4.3 6.2 1.0
CG A:GLU334 4.3 6.5 1.0
CB A:ASP255 4.4 5.8 1.0
OD1 A:ASN305 4.5 8.1 1.0
CA A:ALA333 4.7 6.4 1.0
CA A:GLY257 4.7 6.0 1.0
OD2 A:ASP273 4.8 7.7 1.0
CB A:GLU334 4.9 6.4 1.0
O A:HOH989 4.9 26.8 1.0
N A:ASP332 4.9 6.1 1.0
CB A:PLU500 5.0 11.7 1.0

Zinc binding site 2 out of 6 in 1lcp

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Zinc binding site 2 out of 6 in the Bovine Lens Leucine Aminopeptidase Complexed with L-Leucine Phosphonic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Bovine Lens Leucine Aminopeptidase Complexed with L-Leucine Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn489

b:9.6
occ:1.00
 OE2 A:GLU334 2.1 7.4 1.0
OD2 A:ASP273 2.1 7.7 1.0
NZ A:LYS250 2.1 5.4 1.0
O1 A:PLU500 2.3 8.0 1.0
N A:PLU500 2.3 8.6 1.0
OD2 A:ASP255 2.7 5.4 1.0
CG A:ASP273 2.9 7.7 1.0
CE A:LYS250 3.0 4.7 1.0
OD1 A:ASP273 3.0 5.5 1.0
CA A:PLU500 3.1 10.2 1.0
CD A:GLU334 3.1 5.1 1.0
P A:PLU500 3.2 9.7 1.0
ZN A:ZN488 3.4 10.7 1.0
OE1 A:GLU334 3.5 5.1 1.0
CG A:ASP255 3.6 7.8 1.0
O A:HOH989 3.8 26.8 1.0
O2 A:PLU500 3.8 9.2 1.0
CB A:ASP255 4.1 5.8 1.0
O A:THR359 4.3 6.8 1.0
CB A:ASP273 4.4 7.3 1.0
CG A:GLU334 4.4 6.5 1.0
CD A:LYS250 4.5 5.4 1.0
CB A:PLU500 4.5 11.7 1.0
O3 A:PLU500 4.5 10.0 1.0
OD1 A:ASP255 4.5 6.1 1.0
N A:GLY335 4.6 5.8 1.0
CG1 A:ILE252 4.7 5.3 1.0
CB A:ILE252 4.9 5.7 1.0
O A:ASP332 4.9 7.0 1.0
CA A:GLY335 4.9 5.2 1.0
CG2 A:ILE252 5.0 5.5 1.0

Zinc binding site 3 out of 6 in 1lcp

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Zinc binding site 3 out of 6 in the Bovine Lens Leucine Aminopeptidase Complexed with L-Leucine Phosphonic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Bovine Lens Leucine Aminopeptidase Complexed with L-Leucine Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn490

b:18.6
occ:1.00
 O A:THR173 2.7 5.8 1.0
O A:ARG271 2.7 5.3 1.0
O A:HOH525 2.7 5.6 1.0
O A:LEU170 2.8 5.5 1.0
O A:MET171 2.9 5.5 1.0
C A:MET171 3.5 4.8 1.0
SD A:MET274 3.5 7.2 1.0
C A:ARG271 3.6 6.2 1.0
C A:THR173 3.8 6.2 1.0
CA A:MET171 3.9 4.9 1.0
CG A:MET178 3.9 7.0 1.0
C A:LEU170 3.9 6.5 1.0
CB A:MET178 4.0 8.0 1.0
N A:THR173 4.1 6.2 1.0
CB A:ARG271 4.1 6.4 1.0
CG A:MET274 4.3 8.1 1.0
CG A:ARG271 4.3 6.8 1.0
CE A:MET274 4.4 7.1 1.0
N A:MET171 4.4 4.4 1.0
CA A:THR173 4.4 6.0 1.0
CA A:ARG271 4.4 6.1 1.0
N A:GLU172 4.4 4.7 1.0
C A:GLU172 4.4 5.7 1.0
N A:ALA272 4.5 5.5 1.0
CB A:THR173 4.6 5.7 1.0
CA A:ALA272 4.7 5.8 1.0
CD A:ARG271 4.8 8.0 1.0
C A:PRO174 4.8 7.0 1.0
O A:THR253 4.9 5.3 1.0
N A:ALA175 4.9 7.6 1.0
O A:GLU172 4.9 5.8 1.0
CA A:GLU172 4.9 5.3 1.0
N A:PRO174 4.9 6.0 1.0

Zinc binding site 4 out of 6 in 1lcp

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Zinc binding site 4 out of 6 in the Bovine Lens Leucine Aminopeptidase Complexed with L-Leucine Phosphonic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Bovine Lens Leucine Aminopeptidase Complexed with L-Leucine Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn488

b:10.8
occ:1.00
 OD1 B:ASP332 2.0 7.2 1.0
OE1 B:GLU334 2.0 7.0 1.0
O2 B:PLU500 2.1 7.5 1.0
OD2 B:ASP255 2.1 8.1 1.0
O B:ASP332 2.2 6.5 1.0
O1 B:PLU500 2.5 9.2 1.0
P B:PLU500 2.8 10.5 1.0
CG B:ASP255 3.0 8.6 1.0
CG B:ASP332 3.0 7.1 1.0
CD B:GLU334 3.0 6.5 1.0
C B:ASP332 3.1 7.7 1.0
OD1 B:ASP255 3.1 6.9 1.0
OE2 B:GLU334 3.3 7.0 1.0
ZN B:ZN489 3.4 9.8 1.0
CA B:ASP332 3.5 7.4 1.0
NZ B:LYS262 3.8 7.6 1.0
CB B:ASP332 3.8 7.0 1.0
OD2 B:ASP332 3.8 8.9 1.0
N B:PLU500 4.0 9.5 1.0
O3 B:PLU500 4.0 10.2 1.0
CE B:LYS262 4.0 9.2 1.0
CA B:PLU500 4.1 10.3 1.0
N B:ALA333 4.3 8.1 1.0
N B:GLU334 4.3 7.0 1.0
CG B:GLU334 4.4 5.0 1.0
CB B:ASP255 4.4 7.5 1.0
OD1 B:ASN305 4.5 9.2 1.0
CA B:GLY257 4.7 6.8 1.0
CA B:ALA333 4.8 7.3 1.0
OD2 B:ASP273 4.8 6.6 1.0
O B:HOH985 4.9 22.4 1.0
CB B:PLU500 4.9 12.5 1.0
CB B:GLU334 4.9 7.4 1.0
N B:ASP332 4.9 6.4 1.0

Zinc binding site 5 out of 6 in 1lcp

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Zinc binding site 5 out of 6 in the Bovine Lens Leucine Aminopeptidase Complexed with L-Leucine Phosphonic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Bovine Lens Leucine Aminopeptidase Complexed with L-Leucine Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn489

b:9.8
occ:1.00
 OE2 B:GLU334 2.1 7.0 1.0
OD2 B:ASP273 2.1 6.6 1.0
NZ B:LYS250 2.2 5.4 1.0
O1 B:PLU500 2.2 9.2 1.0
N B:PLU500 2.2 9.5 1.0
OD2 B:ASP255 2.7 8.1 1.0
CG B:ASP273 2.9 6.5 1.0
OD1 B:ASP273 3.0 7.2 1.0
CA B:PLU500 3.0 10.3 1.0
CE B:LYS250 3.1 6.5 1.0
P B:PLU500 3.1 10.5 1.0
CD B:GLU334 3.1 6.5 1.0
ZN B:ZN488 3.4 10.8 1.0
OE1 B:GLU334 3.5 7.0 1.0
CG B:ASP255 3.6 8.6 1.0
O2 B:PLU500 3.8 7.5 1.0
O B:HOH985 3.9 22.4 1.0
CB B:ASP255 4.1 7.5 1.0
O B:THR359 4.3 7.0 1.0
CB B:ASP273 4.4 6.3 1.0
CB B:PLU500 4.4 12.5 1.0
CG B:GLU334 4.5 5.0 1.0
O3 B:PLU500 4.5 10.2 1.0
CD B:LYS250 4.5 4.8 1.0
OD1 B:ASP255 4.5 6.9 1.0
N B:GLY335 4.6 6.6 1.0
CG1 B:ILE252 4.7 7.5 1.0
O B:ASP332 4.8 6.5 1.0
CB B:ILE252 4.9 6.2 1.0
CA B:GLY335 5.0 7.1 1.0

Zinc binding site 6 out of 6 in 1lcp

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Zinc binding site 6 out of 6 in the Bovine Lens Leucine Aminopeptidase Complexed with L-Leucine Phosphonic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Bovine Lens Leucine Aminopeptidase Complexed with L-Leucine Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn490

b:20.0
occ:1.00
 O B:THR173 2.7 5.4 1.0
O B:ARG271 2.7 6.4 1.0
O B:HOH588 2.8 7.0 1.0
O B:LEU170 2.8 6.5 1.0
O B:MET171 2.8 6.6 1.0
C B:MET171 3.4 6.4 1.0
SD B:MET274 3.5 7.9 1.0
C B:ARG271 3.6 5.9 1.0
C B:THR173 3.8 5.8 1.0
CA B:MET171 3.8 6.0 1.0
CG B:MET178 3.9 7.5 1.0
C B:LEU170 3.9 6.5 1.0
CB B:MET178 4.0 6.7 1.0
N B:THR173 4.1 5.0 1.0
CB B:ARG271 4.2 7.8 1.0
CG B:ARG271 4.3 6.5 1.0
CG B:MET274 4.3 6.8 1.0
CE B:MET274 4.3 9.0 1.0
N B:MET171 4.3 6.2 1.0
N B:GLU172 4.4 5.6 1.0
CA B:THR173 4.4 6.0 1.0
CA B:ARG271 4.4 6.2 1.0
C B:GLU172 4.4 6.6 1.0
N B:ALA272 4.5 5.6 1.0
CA B:ALA272 4.6 6.5 1.0
CB B:THR173 4.6 5.0 1.0
CD B:ARG271 4.8 9.1 1.0
C B:PRO174 4.8 7.6 1.0
O B:THR253 4.9 6.5 1.0
O B:GLU172 4.9 5.5 1.0
CA B:GLU172 4.9 6.1 1.0
N B:ALA175 4.9 8.0 1.0
N B:PRO174 5.0 7.1 1.0

Reference:

N.Strater, W.N.Lipscomb. Transition State Analogue L-Leucinephosphonic Acid Bound to Bovine Lens Leucine Aminopeptidase: X-Ray Structure at 1.65 A Resolution in A New Crystal Form. Biochemistry V. 34 9200 1995.
ISSN: ISSN 0006-2960
PubMed: 7619821
DOI: 10.1021/BI00028A033
Page generated: Sun Oct 13 04:57:06 2024

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