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Zinc in PDB 3lub: Crystal Structure of Putative Creatinine Amidohydrolase (YP_211512.1) From Bacteroides Fragilis Nctc 9343 at 2.11 A Resolution

Protein crystallography data

The structure of Crystal Structure of Putative Creatinine Amidohydrolase (YP_211512.1) From Bacteroides Fragilis Nctc 9343 at 2.11 A Resolution, PDB code: 3lub was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.03 / 2.11
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.906, 156.790, 170.161, 90.00, 95.29, 90.00
R / Rfree (%) 15.1 / 19.3

Other elements in 3lub:

The structure of Crystal Structure of Putative Creatinine Amidohydrolase (YP_211512.1) From Bacteroides Fragilis Nctc 9343 at 2.11 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 13 atoms
Calcium (Ca) 12 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Putative Creatinine Amidohydrolase (YP_211512.1) From Bacteroides Fragilis Nctc 9343 at 2.11 A Resolution (pdb code 3lub). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the Crystal Structure of Putative Creatinine Amidohydrolase (YP_211512.1) From Bacteroides Fragilis Nctc 9343 at 2.11 A Resolution, PDB code: 3lub:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in 3lub

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Zinc binding site 1 out of 24 in the Crystal Structure of Putative Creatinine Amidohydrolase (YP_211512.1) From Bacteroides Fragilis Nctc 9343 at 2.11 A Resolution


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 Putative Creatinine Amidohydrolase (YP_211512.1) From Bacteroides Fragilis Nctc 9343 at 2.11 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:40.0
occ:1.00
 OD2 A:ASP42 2.2 19.9 1.0
OE1 A:GLU31 2.2 23.1 1.0
ND1 A:HIS119 2.4 25.6 1.0
O A:HOH775 2.5 27.4 1.0
O A:HOH454 2.8 22.6 1.0
O A:HOH1149 3.1 36.4 1.0
CD A:GLU31 3.1 23.7 1.0
CE1 A:HIS119 3.1 24.3 1.0
CG A:ASP42 3.3 17.2 1.0
OE2 A:GLU31 3.3 27.8 1.0
ZN A:ZN302 3.4 23.2 1.0
CG A:HIS119 3.5 20.8 1.0
OD1 A:ASP42 3.7 25.6 1.0
ND1 A:HIS162 3.8 24.9 1.0
CE1 A:HIS162 3.8 27.5 1.0
CB A:HIS119 3.9 20.3 1.0
CA A:HIS119 4.0 21.2 1.0
NE2 A:HIS33 4.1 20.4 1.0
CE1 A:HIS33 4.3 20.2 1.0
NE2 A:HIS119 4.3 25.1 1.0
CD2 A:HIS119 4.5 23.0 1.0
CG A:GLU31 4.5 22.0 1.0
CB A:ASP42 4.5 19.8 1.0
O A:GLY118 4.5 21.3 1.0
CB A:ALA29 4.8 16.1 1.0
N A:GLY120 4.8 22.9 1.0
CB A:GLU31 4.9 18.9 1.0
C A:HIS119 4.9 22.7 1.0

Zinc binding site 2 out of 24 in 3lub

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Zinc binding site 2 out of 24 in the Crystal Structure of Putative Creatinine Amidohydrolase (YP_211512.1) From Bacteroides Fragilis Nctc 9343 at 2.11 A Resolution


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 Putative Creatinine Amidohydrolase (YP_211512.1) From Bacteroides Fragilis Nctc 9343 at 2.11 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:23.2
occ:1.00
 OE2 A:GLU167 1.9 25.5 1.0
O A:HOH775 2.0 27.4 1.0
OD1 A:ASP42 2.0 25.6 1.0
NE2 A:HIS33 2.2 20.4 1.0
CD A:GLU167 2.7 25.9 1.0
OE1 A:GLU167 2.8 23.6 1.0
CG A:ASP42 2.9 17.2 1.0
CD2 A:HIS33 3.0 19.7 1.0
OD2 A:ASP42 3.2 19.9 1.0
CE1 A:HIS33 3.3 20.2 1.0
ZN A:ZN301 3.4 40.0 1.0
O A:HOH363 3.8 22.7 1.0
ND1 A:HIS162 3.9 24.9 1.0
CG2 A:THR41 4.0 14.6 1.0
CE1 A:HIS162 4.0 27.5 1.0
CG A:GLU167 4.1 26.9 1.0
O A:GLY118 4.1 21.3 1.0
O A:HOH1149 4.1 36.4 1.0
CG A:HIS33 4.2 19.1 1.0
CB A:ASP42 4.3 19.8 1.0
ND1 A:HIS33 4.3 19.8 1.0
OE1 A:GLU31 4.3 23.1 1.0
CB A:THR41 4.6 18.6 1.0
N A:ASP42 4.6 19.3 1.0
CA A:ASP42 4.6 17.9 1.0

Zinc binding site 3 out of 24 in 3lub

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Zinc binding site 3 out of 24 in the Crystal Structure of Putative Creatinine Amidohydrolase (YP_211512.1) From Bacteroides Fragilis Nctc 9343 at 2.11 A Resolution


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 Putative Creatinine Amidohydrolase (YP_211512.1) From Bacteroides Fragilis Nctc 9343 at 2.11 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:39.7
occ:1.00
 OD2 B:ASP42 2.0 22.0 1.0
OE1 B:GLU31 2.2 20.1 1.0
ND1 B:HIS119 2.3 19.6 1.0
O B:HOH262 2.6 19.1 1.0
O B:HOH1005 2.8 30.2 1.0
CG B:ASP42 3.1 20.4 1.0
CE1 B:HIS119 3.2 24.6 1.0
CD B:GLU31 3.3 25.7 1.0
O B:HOH1063 3.3 33.0 1.0
CG B:HIS119 3.3 20.9 1.0
ZN B:ZN302 3.5 20.2 1.0
OD1 B:ASP42 3.6 20.7 1.0
OE2 B:GLU31 3.7 22.4 1.0
CB B:HIS119 3.7 20.6 1.0
CA B:HIS119 3.9 21.2 1.0
ND1 B:HIS162 4.0 23.4 1.0
CE1 B:HIS162 4.1 26.2 1.0
NE2 B:HIS33 4.1 21.7 1.0
CE1 B:HIS33 4.3 20.3 1.0
O B:GLY118 4.3 21.7 1.0
NE2 B:HIS119 4.3 25.1 1.0
CB B:ASP42 4.4 18.8 1.0
CD2 B:HIS119 4.4 22.3 1.0
CG B:GLU31 4.6 18.8 1.0
N B:GLY120 4.6 22.7 1.0
CB B:ALA29 4.7 13.6 1.0
C B:HIS119 4.7 22.5 1.0
CB B:GLU31 4.9 22.0 1.0
N B:HIS119 4.9 20.0 1.0

Zinc binding site 4 out of 24 in 3lub

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Zinc binding site 4 out of 24 in the Crystal Structure of Putative Creatinine Amidohydrolase (YP_211512.1) From Bacteroides Fragilis Nctc 9343 at 2.11 A Resolution


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 Putative Creatinine Amidohydrolase (YP_211512.1) From Bacteroides Fragilis Nctc 9343 at 2.11 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:20.2
occ:1.00
 O B:HOH262 1.9 19.1 1.0
OD1 B:ASP42 2.0 20.7 1.0
NE2 B:HIS33 2.1 21.7 1.0
OE2 B:GLU167 2.1 23.7 1.0
OE1 B:GLU167 2.7 22.6 1.0
CD B:GLU167 2.7 25.6 1.0
CG B:ASP42 2.9 20.4 1.0
CD2 B:HIS33 2.9 19.1 1.0
CE1 B:HIS33 3.2 20.3 1.0
OD2 B:ASP42 3.2 22.0 1.0
ZN B:ZN301 3.5 39.7 1.0
ND1 B:HIS162 3.9 23.4 1.0
O B:HOH1063 3.9 33.0 1.0
O B:HOH273 4.1 20.9 1.0
CG2 B:THR41 4.1 14.1 1.0
O B:GLY118 4.1 21.7 1.0
CE1 B:HIS162 4.1 26.2 1.0
CG B:HIS33 4.2 18.3 1.0
CG B:GLU167 4.2 25.3 1.0
ND1 B:HIS33 4.2 19.0 1.0
CB B:ASP42 4.3 18.8 1.0
OE1 B:GLU31 4.4 20.1 1.0
CB B:THR41 4.6 19.9 1.0
N B:ASP42 4.6 19.1 1.0
CA B:ASP42 4.6 17.8 1.0
N B:ALA163 4.9 20.9 1.0

Zinc binding site 5 out of 24 in 3lub

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Zinc binding site 5 out of 24 in the Crystal Structure of Putative Creatinine Amidohydrolase (YP_211512.1) From Bacteroides Fragilis Nctc 9343 at 2.11 A Resolution


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 Putative Creatinine Amidohydrolase (YP_211512.1) From Bacteroides Fragilis Nctc 9343 at 2.11 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:32.1
occ:1.00
 OD2 C:ASP42 2.1 20.5 1.0
OE1 C:GLU31 2.2 22.1 1.0
ND1 C:HIS119 2.4 21.6 1.0
O C:HOH332 2.4 22.0 1.0
O C:HOH478 2.7 24.7 1.0
CD C:GLU31 3.1 24.0 1.0
CG C:ASP42 3.2 18.1 1.0
CE1 C:HIS119 3.3 22.9 1.0
OE2 C:GLU31 3.3 23.8 1.0
O C:HOH687 3.3 27.2 1.0
CG C:HIS119 3.4 18.0 1.0
ZN C:ZN302 3.4 17.4 1.0
CB C:HIS119 3.7 21.1 1.0
OD1 C:ASP42 3.7 17.0 1.0
ND1 C:HIS162 3.9 18.6 1.0
CA C:HIS119 3.9 21.0 1.0
NE2 C:HIS33 4.0 20.4 1.0
CE1 C:HIS33 4.1 21.4 1.0
CE1 C:HIS162 4.1 25.9 1.0
NE2 C:HIS119 4.4 18.6 1.0
O C:GLY118 4.4 21.0 1.0
CD2 C:HIS119 4.5 22.4 1.0
O C:HOH2053 4.5 44.0 1.0
CB C:ASP42 4.5 20.0 1.0
CG C:GLU31 4.5 21.8 1.0
CB C:ALA29 4.7 14.2 1.0
N C:GLY120 4.7 22.9 1.0
C C:HIS119 4.8 22.6 1.0
CB C:GLU31 4.9 18.8 1.0
N C:HIS119 5.0 19.6 1.0

Zinc binding site 6 out of 24 in 3lub

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Zinc binding site 6 out of 24 in the Crystal Structure of Putative Creatinine Amidohydrolase (YP_211512.1) From Bacteroides Fragilis Nctc 9343 at 2.11 A Resolution


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 Putative Creatinine Amidohydrolase (YP_211512.1) From Bacteroides Fragilis Nctc 9343 at 2.11 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:17.4
occ:1.00
 O C:HOH332 2.1 22.0 1.0
OE2 C:GLU167 2.1 22.4 1.0
OD1 C:ASP42 2.1 17.0 1.0
NE2 C:HIS33 2.1 20.4 1.0
CD C:GLU167 2.8 27.2 1.0
OE1 C:GLU167 2.8 22.8 1.0
CG C:ASP42 2.9 18.1 1.0
CD2 C:HIS33 3.0 20.9 1.0
CE1 C:HIS33 3.1 21.4 1.0
OD2 C:ASP42 3.2 20.5 1.0
ZN C:ZN301 3.4 32.1 1.0
O C:HOH268 4.0 18.5 1.0
O C:GLY118 4.0 21.0 1.0
ND1 C:HIS162 4.0 18.6 1.0
O C:HOH687 4.1 27.2 1.0
CG2 C:THR41 4.1 13.9 1.0
CG C:HIS33 4.2 18.5 1.0
ND1 C:HIS33 4.2 16.5 1.0
CG C:GLU167 4.2 23.2 1.0
CB C:ASP42 4.3 20.0 1.0
CE1 C:HIS162 4.3 25.9 1.0
OE1 C:GLU31 4.3 22.1 1.0
N C:ASP42 4.6 18.8 1.0
CB C:THR41 4.6 18.1 1.0
CA C:ASP42 4.6 18.1 1.0
N C:ALA163 4.9 21.0 1.0

Zinc binding site 7 out of 24 in 3lub

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Zinc binding site 7 out of 24 in the Crystal Structure of Putative Creatinine Amidohydrolase (YP_211512.1) From Bacteroides Fragilis Nctc 9343 at 2.11 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Putative Creatinine Amidohydrolase (YP_211512.1) From Bacteroides Fragilis Nctc 9343 at 2.11 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:28.8
occ:1.00
 OD2 D:ASP42 2.1 18.9 1.0
OE1 D:GLU31 2.3 21.5 1.0
ND1 D:HIS119 2.4 18.8 1.0
O D:HOH289 2.4 18.4 1.0
O D:HOH292 2.5 23.9 1.0
O D:HOH295 2.9 21.3 1.0
CG D:ASP42 3.2 19.4 1.0
CE1 D:HIS119 3.2 21.5 1.0
CD D:GLU31 3.3 25.3 1.0
ZN D:ZN302 3.4 18.4 1.0
CG D:HIS119 3.5 20.6 1.0
OD1 D:ASP42 3.6 17.8 1.0
OE2 D:GLU31 3.7 26.1 1.0
CE1 D:HIS162 3.8 27.6 1.0
ND1 D:HIS162 3.8 22.8 1.0
CB D:HIS119 3.8 21.3 1.0
CA D:HIS119 3.9 21.2 1.0
NE2 D:HIS33 4.0 17.1 1.0
CE1 D:HIS33 4.1 19.1 1.0
NE2 D:HIS119 4.4 18.6 1.0
CB D:ASP42 4.4 18.9 1.0
O D:GLY118 4.4 21.1 1.0
CD2 D:HIS119 4.5 20.4 1.0
CG D:GLU31 4.7 20.1 1.0
N D:GLY120 4.7 22.8 1.0
C D:HIS119 4.8 22.4 1.0
CB D:ALA29 4.8 13.7 1.0
N D:HIS119 4.9 19.5 1.0
CB D:GLU31 5.0 20.0 1.0

Zinc binding site 8 out of 24 in 3lub

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Zinc binding site 8 out of 24 in the Crystal Structure of Putative Creatinine Amidohydrolase (YP_211512.1) From Bacteroides Fragilis Nctc 9343 at 2.11 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Putative Creatinine Amidohydrolase (YP_211512.1) From Bacteroides Fragilis Nctc 9343 at 2.11 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:18.4
occ:1.00
 O D:HOH289 2.0 18.4 1.0
OD1 D:ASP42 2.0 17.8 1.0
NE2 D:HIS33 2.0 17.1 1.0
OE2 D:GLU167 2.0 22.2 1.0
CD D:GLU167 2.7 26.5 1.0
OE1 D:GLU167 2.7 21.4 1.0
CD2 D:HIS33 2.9 18.0 1.0
CG D:ASP42 2.9 19.4 1.0
CE1 D:HIS33 3.1 19.1 1.0
OD2 D:ASP42 3.3 18.9 1.0
ZN D:ZN301 3.4 28.8 1.0
ND1 D:HIS162 3.9 22.8 1.0
CE1 D:HIS162 4.0 27.6 1.0
O D:HOH295 4.0 21.3 1.0
CG2 D:THR41 4.1 14.5 1.0
O D:HOH288 4.1 20.7 1.0
O D:GLY118 4.1 21.1 1.0
CG D:HIS33 4.1 15.5 1.0
ND1 D:HIS33 4.1 14.0 1.0
CG D:GLU167 4.2 19.9 1.0
CB D:ASP42 4.3 18.9 1.0
N D:ASP42 4.6 18.9 1.0
OE1 D:GLU31 4.6 21.5 1.0
CB D:THR41 4.6 19.2 1.0
CA D:ASP42 4.6 18.1 1.0
N D:ALA163 4.9 20.7 1.0
O D:HOH292 5.0 23.9 1.0

Zinc binding site 9 out of 24 in 3lub

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Zinc binding site 9 out of 24 in the Crystal Structure of Putative Creatinine Amidohydrolase (YP_211512.1) From Bacteroides Fragilis Nctc 9343 at 2.11 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Putative Creatinine Amidohydrolase (YP_211512.1) From Bacteroides Fragilis Nctc 9343 at 2.11 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:32.7
occ:1.00
 OD2 E:ASP42 2.2 21.6 1.0
OE1 E:GLU31 2.3 22.0 1.0
ND1 E:HIS119 2.4 19.0 1.0
O E:HOH445 2.5 22.9 1.0
O E:HOH1163 2.8 32.1 1.0
O E:HOH333 2.9 22.2 1.0
CG E:ASP42 3.2 17.0 1.0
CE1 E:HIS119 3.2 21.9 1.0
CD E:GLU31 3.4 24.1 1.0
ZN E:ZN302 3.4 20.3 1.0
CG E:HIS119 3.4 19.3 1.0
OD1 E:ASP42 3.6 21.6 1.0
OE2 E:GLU31 3.7 27.9 1.0
CB E:HIS119 3.8 19.3 1.0
ND1 E:HIS162 3.9 18.4 1.0
CA E:HIS119 3.9 21.0 1.0
NE2 E:HIS33 4.0 18.0 1.0
CE1 E:HIS162 4.0 24.6 1.0
CE1 E:HIS33 4.1 21.8 1.0
NE2 E:HIS119 4.4 18.4 1.0
O E:GLY118 4.4 20.4 1.0
CB E:ASP42 4.5 19.6 1.0
CD2 E:HIS119 4.5 22.6 1.0
N E:GLY120 4.6 22.6 1.0
CG E:GLU31 4.7 19.7 1.0
C E:HIS119 4.8 22.1 1.0
CB E:ALA29 4.8 14.6 1.0
CB E:GLU31 4.9 19.6 1.0
N E:HIS119 5.0 19.5 1.0

Zinc binding site 10 out of 24 in 3lub

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Zinc binding site 10 out of 24 in the Crystal Structure of Putative Creatinine Amidohydrolase (YP_211512.1) From Bacteroides Fragilis Nctc 9343 at 2.11 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Putative Creatinine Amidohydrolase (YP_211512.1) From Bacteroides Fragilis Nctc 9343 at 2.11 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn302

b:20.3
occ:1.00
 O E:HOH445 1.7 22.9 1.0
OE2 E:GLU167 1.9 22.6 1.0
OD1 E:ASP42 2.0 21.6 1.0
NE2 E:HIS33 2.0 18.0 1.0
CD E:GLU167 2.7 23.4 1.0
OE1 E:GLU167 2.8 21.0 1.0
CD2 E:HIS33 2.9 19.7 1.0
CG E:ASP42 2.9 17.0 1.0
CE1 E:HIS33 3.1 21.8 1.0
OD2 E:ASP42 3.2 21.6 1.0
ZN E:ZN301 3.4 32.7 1.0
O E:HOH563 3.7 27.4 1.0
ND1 E:HIS162 3.9 18.4 1.0
O E:HOH333 4.0 22.2 1.0
O E:GLY118 4.0 20.4 1.0
CG E:HIS33 4.1 17.1 1.0
CG E:GLU167 4.1 22.8 1.0
ND1 E:HIS33 4.1 16.0 1.0
CG2 E:THR41 4.1 18.1 1.0
CE1 E:HIS162 4.2 24.6 1.0
CB E:ASP42 4.3 19.6 1.0
N E:ASP42 4.5 19.1 1.0
CB E:THR41 4.6 19.9 1.0
OE1 E:GLU31 4.6 22.0 1.0
CA E:ASP42 4.6 17.9 1.0
N E:ALA163 4.9 21.1 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Sat Oct 26 08:53:55 2024

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