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Zinc in PDB 8yye: Crystal Structure of Lipase Ctl (Caldibacillus Thermoamylovorans)

Enzymatic activity of Crystal Structure of Lipase Ctl (Caldibacillus Thermoamylovorans)

All present enzymatic activity of Crystal Structure of Lipase Ctl (Caldibacillus Thermoamylovorans):
3.1.1.3;

Protein crystallography data

The structure of Crystal Structure of Lipase Ctl (Caldibacillus Thermoamylovorans), PDB code: 8yye was solved by S.Y.Pan, D.M.Lan, Y.H.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.93 / 2.52
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.859, 148.965, 58.884, 90, 100.95, 90
R / Rfree (%) 19.9 / 25.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Lipase Ctl (Caldibacillus Thermoamylovorans) (pdb code 8yye). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Lipase Ctl (Caldibacillus Thermoamylovorans), PDB code: 8yye:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8yye

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Zinc binding site 1 out of 6 in the Crystal Structure of Lipase Ctl (Caldibacillus Thermoamylovorans)


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 Lipase Ctl (Caldibacillus Thermoamylovorans) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:32.2
occ:1.00
 OD2 A:ASP233 1.9 30.2 1.0
OD1 A:ASP59 2.0 25.6 1.0
NE2 A:HIS79 2.2 26.9 1.0
NE2 A:HIS85 2.3 26.2 1.0
CG A:ASP233 2.5 27.5 1.0
OD1 A:ASP233 2.6 27.9 1.0
CG A:ASP59 2.7 25.2 1.0
OD2 A:ASP59 2.8 25.1 1.0
CD2 A:HIS79 3.1 25.5 1.0
CD2 A:HIS85 3.1 27.3 1.0
CE1 A:HIS79 3.2 25.7 1.0
CE1 A:HIS85 3.3 27.0 1.0
OG A:SER56 3.9 25.2 1.0
CB A:ASP233 4.0 26.8 1.0
CB A:ASP59 4.2 27.5 1.0
CD1 A:TRP58 4.2 23.9 1.0
CG A:HIS85 4.2 28.0 1.0
CG A:HIS79 4.3 28.4 1.0
O A:HOH520 4.3 26.6 1.0
ND1 A:HIS79 4.3 33.5 1.0
ND1 A:HIS85 4.3 29.3 1.0
N A:ASP59 4.7 23.8 1.0
CA A:ASP59 4.7 26.3 1.0
CD1 A:TYR75 4.9 30.2 1.0
NE1 A:TRP58 4.9 25.5 1.0
O A:ASP233 4.9 26.6 1.0
CB A:HIS83 4.9 34.7 1.0
CA A:ASP233 5.0 28.6 1.0

Zinc binding site 2 out of 6 in 8yye

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Zinc binding site 2 out of 6 in the Crystal Structure of Lipase Ctl (Caldibacillus Thermoamylovorans)


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 Lipase Ctl (Caldibacillus Thermoamylovorans) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:37.6
occ:1.00
 CE1 B:HIS185 2.1 28.1 1.0
CE1 A:HIS185 2.1 30.1 1.0
OD1 B:ASP181 2.4 35.8 1.0
OD1 A:ASP181 2.6 36.6 1.0
OD2 A:ASP181 2.6 37.2 1.0
OD2 B:ASP181 2.9 33.3 1.0
CG A:ASP181 2.9 26.4 1.0
CG B:ASP181 3.0 29.7 1.0
NE2 B:HIS185 3.0 32.8 1.0
NE2 A:HIS185 3.1 32.6 1.0
ND1 B:HIS185 3.1 32.0 1.0
ND1 A:HIS185 3.1 29.4 1.0
CD2 B:HIS185 4.2 26.3 1.0
CG B:HIS185 4.2 31.6 1.0
CD2 A:HIS185 4.2 30.8 1.0
CG A:HIS185 4.3 34.9 1.0
CB A:ASP181 4.4 30.9 1.0
CB B:ASP181 4.5 33.1 1.0
CD1 B:LEU285 4.5 30.6 1.0
O B:ASP181 4.7 24.9 1.0
O A:ASP181 4.8 27.9 1.0
CD1 A:LEU285 4.9 29.3 1.0
CA A:ASP181 5.0 28.0 1.0

Zinc binding site 3 out of 6 in 8yye

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Zinc binding site 3 out of 6 in the Crystal Structure of Lipase Ctl (Caldibacillus Thermoamylovorans)


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 Lipase Ctl (Caldibacillus Thermoamylovorans) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:148.1
occ:1.00
 OD2 A:ASP351 1.8 38.4 1.0
OD1 A:ASP354 2.0 38.7 1.0
CG A:ASP354 2.9 33.2 1.0
CG A:ASP351 2.9 36.6 1.0
CE1 A:HIS283 2.9 45.0 1.0
OD2 A:ASP354 3.1 29.2 1.0
O A:THR281 3.4 36.4 1.0
OD1 A:ASP351 3.4 37.4 1.0
ND1 A:HIS283 3.4 43.4 1.0
O A:GLY360 3.5 49.8 1.0
NE2 A:HIS283 3.9 43.6 1.0
N A:ASN362 3.9 48.5 1.0
CB A:ASN362 3.9 51.8 1.0
CB A:ASP351 4.2 23.9 1.0
CB A:ASP354 4.3 34.7 1.0
C A:THR281 4.5 33.5 1.0
C A:SER361 4.5 54.3 1.0
CA A:SER361 4.5 61.9 1.0
CA A:ASN362 4.5 49.0 1.0
CG A:HIS283 4.6 43.2 1.0
C A:GLY360 4.6 55.1 1.0
CA A:ASP354 4.7 35.4 1.0
O A:ASN362 4.7 45.2 1.0
N A:ASP354 4.7 29.9 1.0
CD2 A:HIS283 4.8 43.5 1.0
N A:HIS283 4.8 39.3 1.0
CA A:MET282 5.0 29.4 1.0
CB A:THR281 5.0 36.0 1.0
N A:ASP351 5.0 24.6 1.0

Zinc binding site 4 out of 6 in 8yye

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Zinc binding site 4 out of 6 in the Crystal Structure of Lipase Ctl (Caldibacillus Thermoamylovorans)


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 Lipase Ctl (Caldibacillus Thermoamylovorans) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:33.5
occ:1.00
 OD2 B:ASP233 1.8 26.3 1.0
OD1 B:ASP59 2.1 32.4 1.0
CE1 B:HIS79 2.1 28.0 1.0
NE2 B:HIS85 2.3 34.6 1.0
NE2 B:HIS79 2.8 30.2 1.0
CG B:ASP233 2.8 27.9 1.0
CD2 B:HIS85 2.9 33.2 1.0
CG B:ASP59 2.9 29.5 1.0
OD2 B:ASP59 3.1 25.9 1.0
ND1 B:HIS79 3.2 28.9 1.0
OD1 B:ASP233 3.3 31.2 1.0
CE1 B:HIS85 3.4 34.4 1.0
OG B:SER56 3.9 27.8 1.0
CB B:ASP233 4.1 29.0 1.0
CD2 B:HIS79 4.1 31.9 1.0
CG B:HIS85 4.1 33.6 1.0
CG B:HIS79 4.3 28.4 1.0
ND1 B:HIS85 4.3 32.6 1.0
CB B:ASP59 4.3 28.7 1.0
CD1 B:TRP58 4.5 25.7 1.0
N B:ASP59 4.7 27.3 1.0
CB B:HIS83 4.8 30.8 1.0
CA B:ASP59 4.8 25.9 1.0
O B:ASP233 4.9 33.3 1.0
CZ2 B:TRP206 4.9 30.1 1.0
CD2 B:HIS83 5.0 38.6 1.0

Zinc binding site 5 out of 6 in 8yye

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Zinc binding site 5 out of 6 in the Crystal Structure of Lipase Ctl (Caldibacillus Thermoamylovorans)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Lipase Ctl (Caldibacillus Thermoamylovorans) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:63.7
occ:1.00
 OE2 B:GLU82 1.9 51.8 1.0
NE2 B:HIS83 2.3 33.2 1.0
CD B:GLU82 3.1 52.6 1.0
CE1 B:HIS83 3.1 37.7 1.0
CD2 B:HIS83 3.3 38.6 1.0
OE1 B:GLU82 3.9 59.3 1.0
CG B:GLU82 4.1 43.4 1.0
CD2 B:HIS79 4.3 31.9 1.0
ND1 B:HIS83 4.3 36.3 1.0
CG B:HIS83 4.4 34.6 1.0
NE2 B:HIS79 4.9 30.2 1.0

Zinc binding site 6 out of 6 in 8yye

Go back to Zinc Binding Sites List in 8yye
Zinc binding site 6 out of 6 in the Crystal Structure of Lipase Ctl (Caldibacillus Thermoamylovorans)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Lipase Ctl (Caldibacillus Thermoamylovorans) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:159.2
occ:1.00
 OD2 B:ASP351 2.2 35.4 1.0
CE1 B:HIS283 2.3 33.3 1.0
ND1 B:HIS283 2.3 40.7 1.0
O B:THR281 2.8 41.5 1.0
OD1 B:ASP354 2.8 33.9 1.0
CG B:ASP351 3.3 30.2 1.0
NE2 B:HIS283 3.4 33.2 1.0
OD1 B:ASN362 3.4 48.6 1.0
CG B:HIS283 3.4 36.6 1.0
N B:HIS283 3.6 32.5 1.0
O B:GLY360 3.6 39.3 1.0
CG B:ASP354 3.7 30.2 1.0
OD1 B:ASP351 3.8 30.9 1.0
OD2 B:ASP354 3.9 25.2 1.0
CD2 B:HIS283 3.9 31.8 1.0
O B:HOH515 3.9 38.0 1.0
C B:THR281 4.0 37.3 1.0
CG B:ASN362 4.1 46.1 1.0
CA B:SER361 4.1 29.4 1.0
C B:MET282 4.2 34.9 1.0
CA B:MET282 4.2 32.2 1.0
ND2 B:ASN362 4.3 43.3 1.0
CA B:HIS283 4.3 31.5 1.0
N B:ASN362 4.4 32.5 1.0
CB B:HIS283 4.4 32.1 1.0
C B:GLY360 4.5 33.8 1.0
CB B:ASP351 4.5 26.0 1.0
N B:MET282 4.6 38.7 1.0
C B:SER361 4.7 32.4 1.0
OG B:SER361 4.8 26.9 1.0
N B:SER361 4.8 28.9 1.0

Reference:

S.Y.Pan, D.M.Lan, Y.H.Wang. Crystal Structure of Lipase Ctl (Caldibacillus Thermoamylovorans) To Be Published.
Page generated: Fri Aug 22 16:01:15 2025

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