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Zinc in PDB 4wjb: X-Ray Crystal Structure of A Putative Amidohydrolase/Peptidase From Burkholderia Cenocepacia

Enzymatic activity of X-Ray Crystal Structure of A Putative Amidohydrolase/Peptidase From Burkholderia Cenocepacia

All present enzymatic activity of X-Ray Crystal Structure of A Putative Amidohydrolase/Peptidase From Burkholderia Cenocepacia:
3.5.1.87;

Protein crystallography data

The structure of X-Ray Crystal Structure of A Putative Amidohydrolase/Peptidase From Burkholderia Cenocepacia, PDB code: 4wjb was solved by C.M.Lukacs, D.M.Dranow, T.E.Edwards, D.Lorimer, Seattle Structuralgenomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.72 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.660, 113.060, 126.670, 90.00, 95.50, 90.00
R / Rfree (%) 17.3 / 21.3

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Crystal Structure of A Putative Amidohydrolase/Peptidase From Burkholderia Cenocepacia (pdb code 4wjb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the X-Ray Crystal Structure of A Putative Amidohydrolase/Peptidase From Burkholderia Cenocepacia, PDB code: 4wjb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4wjb

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Zinc binding site 1 out of 8 in the X-Ray Crystal Structure of A Putative Amidohydrolase/Peptidase From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Crystal Structure of A Putative Amidohydrolase/Peptidase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:30.6
occ:0.72
 ZN A:ZN501 0.0 30.6 0.7
NE2 A:HIS88 2.1 24.6 1.0
O A:HOH667 2.1 26.1 1.0
OD1 A:ASP99 2.1 46.9 1.0
NE2 A:HIS195 2.2 19.2 1.0
CE1 A:HIS88 2.9 23.1 1.0
CE1 A:HIS195 3.0 19.6 1.0
CD2 A:HIS88 3.2 22.1 1.0
CD2 A:HIS195 3.3 18.5 1.0
CG A:ASP99 3.4 48.0 1.0
ZN A:ZN501 3.4 21.8 0.3
N A:GLY100 3.7 21.0 1.0
OE1 A:GLU133 4.0 26.4 1.0
CA A:GLY100 4.1 21.3 1.0
OD2 A:ASP99 4.1 49.6 1.0
ND1 A:HIS88 4.1 22.1 1.0
ND1 A:HIS195 4.2 21.3 1.0
C A:ASP99 4.2 22.1 1.0
OE2 A:GLU134 4.2 43.5 1.0
ND1 A:HIS363 4.2 27.5 1.0
NE2 A:GLN198 4.3 33.7 1.0
CG A:HIS88 4.3 21.5 1.0
CD A:GLU133 4.3 25.9 1.0
CG A:HIS195 4.3 19.6 1.0
O A:HOH669 4.4 25.3 1.0
CA A:ASP99 4.5 23.2 1.0
CB A:ASP99 4.5 24.9 1.0
CD A:GLU134 4.5 44.0 1.0
OE1 A:GLU134 4.6 45.0 1.0
CE1 A:HIS363 4.6 28.5 1.0
OE2 A:GLU133 4.6 25.1 1.0
NE2 A:HIS387 4.9 49.1 1.0
CD A:GLN198 4.9 29.1 1.0
O A:ASP99 4.9 22.6 1.0
OG A:SER87 5.0 22.7 1.0

Zinc binding site 2 out of 8 in 4wjb

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Zinc binding site 2 out of 8 in the X-Ray Crystal Structure of A Putative Amidohydrolase/Peptidase From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Crystal Structure of A Putative Amidohydrolase/Peptidase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:21.8
occ:0.28
 ZN A:ZN501 0.0 21.8 0.3
NE2 A:HIS387 1.9 49.1 1.0
OD2 A:ASP99 2.0 49.6 1.0
OE2 A:GLU134 2.1 43.5 1.0
OE1 A:GLU134 2.2 45.0 1.0
OD1 A:ASP99 2.3 46.9 1.0
CE1 A:HIS387 2.3 49.4 1.0
CG A:ASP99 2.4 48.0 1.0
CD A:GLU134 2.4 44.0 1.0
CD2 A:HIS387 3.0 49.5 1.0
NE2 A:GLN198 3.3 33.7 1.0
ZN A:ZN501 3.4 30.6 0.7
ND1 A:HIS387 3.4 51.9 1.0
CG A:HIS387 3.8 50.8 1.0
CB A:ASP99 4.0 24.9 1.0
CG A:GLU134 4.0 28.9 1.0
O A:HOH717 4.1 25.1 1.0
CE1 A:HIS88 4.2 23.1 1.0
OE1 A:GLU133 4.2 26.4 1.0
NE2 A:HIS88 4.4 24.6 1.0
CD A:GLN198 4.5 29.1 1.0
O A:HOH667 4.8 26.1 1.0
CG A:GLN92 4.9 32.3 1.0
OE1 A:GLN198 5.0 30.2 1.0
CB A:GLU134 5.0 27.4 1.0

Zinc binding site 3 out of 8 in 4wjb

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Zinc binding site 3 out of 8 in the X-Ray Crystal Structure of A Putative Amidohydrolase/Peptidase From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Crystal Structure of A Putative Amidohydrolase/Peptidase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:26.2
occ:0.72
 ZN B:ZN501 0.0 26.2 0.7
NE2 B:HIS88 2.1 20.1 1.0
O B:HOH790 2.1 16.2 1.0
OD1 B:ASP99 2.1 52.9 1.0
NE2 B:HIS195 2.2 17.9 1.0
CE1 B:HIS88 3.0 21.0 1.0
CE1 B:HIS195 3.1 17.5 1.0
CD2 B:HIS88 3.1 17.6 1.0
CD2 B:HIS195 3.3 17.0 1.0
CG B:ASP99 3.3 52.9 1.0
ZN B:ZN501 3.4 22.4 0.3
N B:GLY100 3.7 16.2 1.0
O B:HOH955 3.8 36.8 1.0
OE1 B:GLU133 3.9 25.3 1.0
OE2 B:GLU134 4.0 26.5 1.0
ND1 B:HIS363 4.0 26.6 1.0
OD2 B:ASP99 4.0 53.8 1.0
CA B:GLY100 4.1 17.1 1.0
ND1 B:HIS88 4.2 20.4 1.0
CD B:GLU133 4.2 25.0 1.0
C B:ASP99 4.2 16.5 1.0
CG B:HIS88 4.2 17.1 1.0
ND1 B:HIS195 4.2 19.2 1.0
CG B:HIS195 4.4 16.5 1.0
CE1 B:HIS363 4.4 26.3 1.0
O B:HOH678 4.5 19.5 1.0
CB B:ASP99 4.5 23.4 1.0
OE2 B:GLU133 4.5 26.9 1.0
CA B:ASP99 4.5 19.3 1.0
CD B:GLU134 4.6 27.2 1.0
NE2 B:GLN198 4.6 31.7 1.0
OE1 B:GLU134 4.8 27.6 1.0
CG B:GLU133 4.9 19.6 1.0
OE1 B:GLN198 5.0 25.3 1.0
OG B:SER87 5.0 16.8 1.0
CD B:GLN198 5.0 27.3 1.0
O B:ASP99 5.0 18.7 1.0

Zinc binding site 4 out of 8 in 4wjb

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Zinc binding site 4 out of 8 in the X-Ray Crystal Structure of A Putative Amidohydrolase/Peptidase From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Crystal Structure of A Putative Amidohydrolase/Peptidase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:22.4
occ:0.28
 ZN B:ZN501 0.0 22.4 0.3
NE2 B:HIS387 2.0 53.4 1.0
OE2 B:GLU134 2.0 26.5 1.0
OD2 B:ASP99 2.1 53.8 1.0
OE1 B:GLU134 2.2 27.6 1.0
OD1 B:ASP99 2.3 52.9 1.0
CD B:GLU134 2.4 27.2 1.0
CG B:ASP99 2.5 52.9 1.0
CE1 B:HIS387 2.9 55.2 1.0
CD2 B:HIS387 3.0 54.5 1.0
ZN B:ZN501 3.4 26.2 0.7
NE2 B:GLN198 3.6 31.7 1.0
O B:HOH955 3.8 36.8 1.0
O B:HOH821 4.0 22.4 1.0
CG B:GLU134 4.0 25.0 1.0
ND1 B:HIS387 4.0 58.4 1.0
CB B:ASP99 4.0 23.4 1.0
OE1 B:GLU133 4.0 25.3 1.0
CE1 B:HIS88 4.1 21.0 1.0
CG B:HIS387 4.1 59.2 1.0
NE2 B:HIS88 4.2 20.1 1.0
O B:HOH846 4.6 41.7 1.0
CG B:GLN92 4.6 24.9 1.0
CD B:GLN198 4.7 27.3 1.0
O B:HOH790 4.8 16.2 1.0
CD B:GLU133 4.9 25.0 1.0
CB B:GLU134 4.9 24.6 1.0

Zinc binding site 5 out of 8 in 4wjb

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Zinc binding site 5 out of 8 in the X-Ray Crystal Structure of A Putative Amidohydrolase/Peptidase From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of X-Ray Crystal Structure of A Putative Amidohydrolase/Peptidase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:71.6
occ:0.80
 ZN C:ZN501 0.0 71.6 0.8
O C:HOH658 2.1 30.6 1.0
NE2 C:HIS88 2.1 22.2 1.0
NE2 C:HIS195 2.2 25.4 1.0
OD2 C:ASP99 2.2 80.9 1.0
OD1 C:ASP99 2.2 80.6 1.0
CG C:ASP99 2.4 80.2 1.0
CE1 C:HIS195 2.9 27.2 1.0
CE1 C:HIS88 3.0 23.0 1.0
CD2 C:HIS88 3.3 19.4 1.0
CD2 C:HIS195 3.4 22.9 1.0
ZN C:ZN501 3.5 23.6 0.2
N C:GLY100 3.7 23.9 1.0
OE1 C:GLU133 3.8 31.0 1.0
CB C:ASP99 3.8 31.9 1.0
OE2 C:GLU134 4.0 46.2 1.0
C C:ASP99 4.1 25.7 1.0
OE1 C:GLN198 4.1 54.4 1.0
ND1 C:HIS195 4.1 27.7 1.0
CD C:GLU133 4.2 28.9 1.0
ND1 C:HIS88 4.2 23.2 1.0
CA C:ASP99 4.2 30.1 1.0
O C:HOH874 4.2 34.9 1.0
CA C:GLY100 4.2 24.6 1.0
ND1 C:HIS363 4.3 23.7 1.0
CG C:HIS88 4.3 21.1 1.0
OE2 C:GLU133 4.4 28.4 1.0
CG C:HIS195 4.4 23.3 1.0
CD C:GLU134 4.5 43.2 1.0
O C:HOH642 4.6 18.0 1.0
OE1 C:GLU134 4.7 44.2 1.0
CE1 C:HIS363 4.7 24.9 1.0
O C:ASP99 4.9 23.2 1.0

Zinc binding site 6 out of 8 in 4wjb

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Zinc binding site 6 out of 8 in the X-Ray Crystal Structure of A Putative Amidohydrolase/Peptidase From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of X-Ray Crystal Structure of A Putative Amidohydrolase/Peptidase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:23.6
occ:0.20
 ZN C:ZN501 0.0 23.6 0.2
OE2 C:GLU134 2.0 46.2 1.0
NE2 C:HIS387 2.0 50.6 1.0
OE1 C:GLU134 2.1 44.2 1.0
OD2 C:ASP99 2.3 80.9 1.0
OD1 C:ASP99 2.3 80.6 1.0
CD C:GLU134 2.4 43.2 1.0
CG C:ASP99 2.4 80.2 1.0
CD2 C:HIS387 2.8 51.6 1.0
CE1 C:HIS387 3.2 51.4 1.0
ZN C:ZN501 3.5 71.6 0.8
CB C:ASP99 3.6 31.9 1.0
O C:HOH674 3.8 30.9 1.0
CG C:GLU134 3.9 38.8 1.0
CG C:HIS387 4.0 51.7 1.0
ND1 C:HIS387 4.2 51.4 1.0
OE1 C:GLU133 4.2 31.0 1.0
CE1 C:HIS88 4.3 23.0 1.0
O C:HOH874 4.3 34.9 1.0
NE2 C:HIS88 4.5 22.2 1.0
CG C:GLN92 4.6 36.4 1.0
OE1 C:GLN198 4.7 54.4 1.0
CB C:GLU134 4.9 32.6 1.0
NE2 C:GLN198 4.9 53.8 1.0
CD C:GLN198 4.9 49.0 1.0
CA C:ASP99 5.0 30.1 1.0

Zinc binding site 7 out of 8 in 4wjb

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Zinc binding site 7 out of 8 in the X-Ray Crystal Structure of A Putative Amidohydrolase/Peptidase From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of X-Ray Crystal Structure of A Putative Amidohydrolase/Peptidase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:26.5
occ:0.66
 ZN D:ZN501 0.0 26.5 0.7
O D:HOH670 2.1 25.9 1.0
OD1 D:ASP99 2.1 55.7 1.0
NE2 D:HIS195 2.1 26.2 1.0
NE2 D:HIS88 2.1 23.4 1.0
CE1 D:HIS195 3.0 26.7 1.0
CE1 D:HIS88 3.0 23.7 1.0
CD2 D:HIS88 3.2 22.4 1.0
CD2 D:HIS195 3.2 25.1 1.0
ZN D:ZN501 3.3 73.0 0.3
CG D:ASP99 3.3 56.8 1.0
N D:GLY100 3.6 22.6 1.0
CA D:GLY100 4.0 21.6 1.0
OE1 D:GLU133 4.0 24.7 1.0
OD2 D:ASP99 4.0 57.2 1.0
ND1 D:HIS195 4.1 26.8 1.0
O D:HOH858 4.1 37.3 1.0
ND1 D:HIS363 4.1 28.6 1.0
C D:ASP99 4.1 21.7 1.0
ND1 D:HIS88 4.2 22.1 1.0
OE2 D:GLU134 4.2 39.8 1.0
NE2 D:GLN198 4.2 29.4 1.0
CG D:HIS195 4.3 25.7 1.0
CG D:HIS88 4.3 21.1 1.0
CD D:GLU133 4.3 25.8 1.0
O D:HOH646 4.4 25.6 1.0
CA D:ASP99 4.4 24.1 1.0
CB D:ASP99 4.5 23.2 1.0
CE1 D:HIS363 4.5 29.6 1.0
OE2 D:GLU133 4.6 25.4 1.0
CD D:GLU134 4.7 36.5 1.0
OE1 D:GLU134 4.8 41.0 1.0
CD D:GLN198 4.8 27.9 1.0
O D:ASP99 4.9 22.6 1.0
OG D:SER87 4.9 21.0 1.0
OE1 D:GLN198 4.9 28.6 1.0

Zinc binding site 8 out of 8 in 4wjb

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Zinc binding site 8 out of 8 in the X-Ray Crystal Structure of A Putative Amidohydrolase/Peptidase From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of X-Ray Crystal Structure of A Putative Amidohydrolase/Peptidase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:73.0
occ:0.34
 ZN D:ZN501 0.0 73.0 0.3
OE2 D:GLU134 2.0 39.8 1.0
OD2 D:ASP99 2.0 57.2 1.0
OE1 D:GLU134 2.2 41.0 1.0
OD1 D:ASP99 2.3 55.7 1.0
CD D:GLU134 2.4 36.5 1.0
CG D:ASP99 2.5 56.8 1.0
ZN D:ZN501 3.3 26.5 0.7
NE2 D:GLN198 3.4 29.4 1.0
CG D:GLU134 3.9 29.2 1.0
OE1 D:GLU133 3.9 24.7 1.0
CE1 D:HIS88 3.9 23.7 1.0
CB D:ASP99 4.0 23.2 1.0
O D:HOH707 4.1 28.1 1.0
NE2 D:HIS88 4.1 23.4 1.0
O D:HOH858 4.1 37.3 1.0
CD D:GLN198 4.6 27.9 1.0
O D:HOH670 4.7 25.9 1.0
CG D:GLN92 4.7 28.3 1.0
CD D:GLU133 4.8 25.8 1.0
CB D:GLU134 4.9 23.7 1.0
OE2 D:GLU133 5.0 25.4 1.0

Reference:

C.M.Lukacs, D.M.Dranow, T.E.Edwards, D.Lorimer. X-Ray Crystal Structure of A Putative Amidohydrolase/Peptidase From Burkholderia Cenocepacia To Be Published.
Page generated: Sun Oct 27 09:55:36 2024

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