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Zinc in PDB 1q3k: Crystal Structure of Creatinine Amidohydrolase (Creatininase)

Enzymatic activity of Crystal Structure of Creatinine Amidohydrolase (Creatininase)

All present enzymatic activity of Crystal Structure of Creatinine Amidohydrolase (Creatininase):
3.5.2.10;

Protein crystallography data

The structure of Crystal Structure of Creatinine Amidohydrolase (Creatininase), PDB code: 1q3k was solved by B.Beuth, K.Niefind, D.Schomburg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.392, 94.084, 114.746, 90.00, 104.62, 90.00
R / Rfree (%) 20.7 / 24.7

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Creatinine Amidohydrolase (Creatininase) (pdb code 1q3k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of Creatinine Amidohydrolase (Creatininase), PDB code: 1q3k:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 1q3k

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Zinc binding site 1 out of 12 in the Crystal Structure of Creatinine Amidohydrolase (Creatininase)


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 Creatinine Amidohydrolase (Creatininase) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn300

b:38.2
occ:1.00
OD2 A:ASP45 1.9 29.6 1.0
OE1 A:GLU34 2.0 29.3 1.0
ND1 A:HIS120 2.4 28.6 1.0
O A:HOH904 2.4 39.5 1.0
O A:HOH903 2.5 27.0 1.0
O A:HOH905 2.7 53.4 1.0
CD A:GLU34 3.1 28.0 1.0
CE1 A:HIS120 3.1 30.3 1.0
CG A:ASP45 3.2 31.4 1.0
OE2 A:GLU34 3.4 27.6 1.0
ZN A:ZN301 3.5 38.5 1.0
CG A:HIS120 3.6 33.0 1.0
OD1 A:ASP45 3.7 28.1 1.0
ND1 A:HIS178 4.0 36.4 1.0
CB A:HIS120 4.1 33.1 1.0
CA A:HIS120 4.1 34.4 1.0
OE1 A:GLU122 4.1 33.1 1.0
CE1 A:HIS178 4.2 38.6 1.0
CE1 A:HIS36 4.3 32.9 1.0
NE2 A:HIS120 4.3 33.0 1.0
CG A:GLU34 4.4 27.3 1.0
NE2 A:HIS36 4.4 31.4 1.0
CB A:ASP45 4.4 33.0 1.0
CD2 A:HIS120 4.6 29.8 1.0
N A:TYR121 4.6 34.6 1.0
CB A:GLU34 4.6 30.1 1.0
O A:GLY119 4.7 34.6 1.0
C A:HIS120 4.8 34.4 1.0

Zinc binding site 2 out of 12 in 1q3k

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Zinc binding site 2 out of 12 in the Crystal Structure of Creatinine Amidohydrolase (Creatininase)


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 Creatinine Amidohydrolase (Creatininase) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:38.5
occ:1.00
OE2 A:GLU183 1.9 35.7 1.0
O A:HOH903 1.9 27.0 1.0
OD1 A:ASP45 2.0 28.1 1.0
NE2 A:HIS36 2.1 31.4 1.0
CD A:GLU183 2.7 40.2 1.0
OE1 A:GLU183 2.8 36.4 1.0
CG A:ASP45 2.9 31.4 1.0
CE1 A:HIS36 3.0 32.9 1.0
OD2 A:ASP45 3.1 29.6 1.0
CD2 A:HIS36 3.2 31.5 1.0
ZN A:ZN300 3.5 38.2 1.0
O A:HOH905 3.6 53.4 1.0
ND1 A:HIS178 3.9 36.4 1.0
O A:HOH923 3.9 24.2 1.0
CG A:GLU183 4.1 42.8 1.0
ND1 A:HIS36 4.2 31.2 1.0
CG1 A:VAL44 4.2 36.3 1.0
OE1 A:GLU34 4.3 29.3 1.0
CB A:ASP45 4.3 33.0 1.0
CG A:HIS36 4.3 33.9 1.0
CE1 A:HIS178 4.3 38.6 1.0
O A:GLY119 4.5 34.6 1.0
N A:ASP45 4.5 34.3 1.0
O A:HOH1009 4.5 55.5 1.0
CA A:ASP45 4.6 33.9 1.0
CB A:VAL44 4.7 34.9 1.0

Zinc binding site 3 out of 12 in 1q3k

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Zinc binding site 3 out of 12 in the Crystal Structure of Creatinine Amidohydrolase (Creatininase)


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 Creatinine Amidohydrolase (Creatininase) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn300

b:42.5
occ:1.00
OD2 B:ASP45 1.9 32.6 1.0
OE1 B:GLU34 2.0 28.8 1.0
O B:HOH904 2.0 62.0 1.0
O B:HOH903 2.1 42.0 1.0
ND1 B:HIS120 2.4 35.9 1.0
O B:HOH902 2.8 35.0 1.0
CD B:GLU34 3.0 28.2 1.0
CE1 B:HIS120 3.1 35.2 1.0
CG B:ASP45 3.1 31.9 1.0
ZN B:ZN301 3.3 47.8 1.0
OE2 B:GLU34 3.5 28.0 1.0
CG B:HIS120 3.5 37.3 1.0
O B:HOH905 3.6 61.2 1.0
OD1 B:ASP45 3.7 37.8 1.0
CA B:HIS120 4.0 36.2 1.0
CB B:HIS120 4.0 37.0 1.0
ND1 B:HIS178 4.0 38.4 1.0
CE1 B:HIS178 4.2 39.1 1.0
OE1 B:GLU122 4.3 36.6 1.0
CE1 B:HIS36 4.3 34.2 1.0
NE2 B:HIS120 4.3 37.7 1.0
CB B:ASP45 4.3 33.0 1.0
CG B:GLU34 4.3 30.5 1.0
NE2 B:HIS36 4.4 34.4 1.0
N B:TYR121 4.5 36.6 1.0
CD2 B:HIS120 4.5 33.2 1.0
CB B:GLU34 4.6 31.7 1.0
O B:GLY119 4.6 38.2 1.0
C B:HIS120 4.7 36.7 1.0

Zinc binding site 4 out of 12 in 1q3k

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Zinc binding site 4 out of 12 in the Crystal Structure of Creatinine Amidohydrolase (Creatininase)


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 Creatinine Amidohydrolase (Creatininase) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:47.8
occ:1.00
O B:HOH902 1.9 35.0 1.0
OE2 B:GLU183 2.1 44.0 1.0
OD1 B:ASP45 2.1 37.8 1.0
NE2 B:HIS36 2.1 34.4 1.0
O B:HOH905 2.4 61.2 1.0
CD B:GLU183 2.8 43.6 1.0
OE1 B:GLU183 2.9 43.4 1.0
CG B:ASP45 2.9 31.9 1.0
OD2 B:ASP45 3.0 32.6 1.0
CE1 B:HIS36 3.0 34.2 1.0
CD2 B:HIS36 3.2 36.2 1.0
ZN B:ZN300 3.3 42.5 1.0
O B:HOH904 3.7 62.0 1.0
O B:HOH906 3.8 39.8 1.0
ND1 B:HIS178 3.8 38.4 1.0
OE1 B:GLU34 4.1 28.8 1.0
ND1 B:HIS36 4.2 37.5 1.0
CE1 B:HIS178 4.2 39.1 1.0
CB B:ASP45 4.3 33.0 1.0
CG B:HIS36 4.3 37.4 1.0
CG B:GLU183 4.3 42.8 1.0
CG1 B:VAL44 4.3 35.5 1.0
O B:GLY119 4.5 38.2 1.0
N B:ASP45 4.6 33.8 1.0
CA B:ASP45 4.7 33.4 1.0
CB B:VAL44 4.7 35.0 1.0
O B:HOH903 4.8 42.0 1.0
CG B:HIS178 5.0 41.3 1.0

Zinc binding site 5 out of 12 in 1q3k

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Zinc binding site 5 out of 12 in the Crystal Structure of Creatinine Amidohydrolase (Creatininase)


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 Creatinine Amidohydrolase (Creatininase) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn300

b:40.1
occ:1.00
O C:HOH907 2.0 38.2 1.0
OD2 C:ASP45 2.0 31.4 1.0
OE1 C:GLU34 2.1 30.4 1.0
O C:HOH906 2.3 41.5 1.0
ND1 C:HIS120 2.4 35.9 1.0
O C:HOH905 2.7 38.2 1.0
CE1 C:HIS120 3.0 32.8 1.0
CD C:GLU34 3.0 29.1 1.0
CG C:ASP45 3.2 33.4 1.0
OE2 C:GLU34 3.3 29.6 1.0
ZN C:ZN301 3.5 39.6 1.0
O C:HOH908 3.5 38.0 1.0
CG C:HIS120 3.6 34.5 1.0
OD1 C:ASP45 3.6 33.1 1.0
CA C:HIS120 4.1 34.4 1.0
CB C:HIS120 4.1 33.7 1.0
ND1 C:HIS178 4.1 38.1 1.0
OE1 C:GLU122 4.1 34.0 1.0
NE2 C:HIS120 4.2 35.5 1.0
CE1 C:HIS178 4.3 36.6 1.0
CE1 C:HIS36 4.3 29.3 1.0
CG C:GLU34 4.4 29.9 1.0
NE2 C:HIS36 4.4 26.7 1.0
CB C:ASP45 4.4 33.6 1.0
N C:TYR121 4.5 35.8 1.0
CD2 C:HIS120 4.5 35.2 1.0
O C:GLY119 4.6 35.6 1.0
CB C:GLU34 4.7 31.6 1.0
C C:HIS120 4.7 34.8 1.0

Zinc binding site 6 out of 12 in 1q3k

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Zinc binding site 6 out of 12 in the Crystal Structure of Creatinine Amidohydrolase (Creatininase)


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 Creatinine Amidohydrolase (Creatininase) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:39.6
occ:1.00
NE2 C:HIS36 2.0 26.7 1.0
OE2 C:GLU183 2.0 42.5 1.0
O C:HOH908 2.0 38.0 1.0
OD1 C:ASP45 2.2 33.1 1.0
CD C:GLU183 2.7 44.4 1.0
OE1 C:GLU183 2.7 38.5 1.0
O C:HOH905 2.7 38.2 1.0
CE1 C:HIS36 2.9 29.3 1.0
CD2 C:HIS36 3.0 31.6 1.0
CG C:ASP45 3.1 33.4 1.0
OD2 C:ASP45 3.3 31.4 1.0
ZN C:ZN300 3.5 40.1 1.0
ND1 C:HIS178 3.8 38.1 1.0
O C:HOH907 3.9 38.2 1.0
OE1 C:GLU34 4.0 30.4 1.0
ND1 C:HIS36 4.0 29.9 1.0
CG C:HIS36 4.1 32.3 1.0
CE1 C:HIS178 4.2 36.6 1.0
CG C:GLU183 4.2 42.5 1.0
CG1 C:VAL44 4.2 36.0 1.0
CB C:ASP45 4.4 33.6 1.0
N C:ASP45 4.6 35.4 1.0
O C:GLY119 4.7 35.6 1.0
CB C:VAL44 4.7 35.8 1.0
CA C:ASP45 4.7 33.6 1.0
N C:GLY179 5.0 41.5 1.0
CG C:HIS178 5.0 39.8 1.0

Zinc binding site 7 out of 12 in 1q3k

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Zinc binding site 7 out of 12 in the Crystal Structure of Creatinine Amidohydrolase (Creatininase)


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 Creatinine Amidohydrolase (Creatininase) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn300

b:41.9
occ:1.00
OD2 D:ASP45 1.9 29.7 1.0
OE1 D:GLU34 2.0 22.9 1.0
ND1 D:HIS120 2.4 32.3 1.0
O D:HOH303 2.4 34.6 1.0
O D:HOH302 2.5 34.6 1.0
CD D:GLU34 3.1 23.9 1.0
CE1 D:HIS120 3.1 33.7 1.0
CG D:ASP45 3.1 32.5 1.0
OE2 D:GLU34 3.4 29.6 1.0
CG D:HIS120 3.5 35.1 1.0
ZN D:ZN301 3.5 41.7 1.0
OD1 D:ASP45 3.7 31.6 1.0
CA D:HIS120 3.9 35.5 1.0
CB D:HIS120 3.9 35.0 1.0
OE1 D:GLU122 4.1 31.1 1.0
ND1 D:HIS178 4.2 38.6 1.0
N D:TYR121 4.3 35.8 1.0
CE1 D:HIS36 4.3 29.3 1.0
NE2 D:HIS120 4.3 36.5 1.0
NE2 D:HIS36 4.4 27.5 1.0
CB D:ASP45 4.4 33.6 1.0
CG D:GLU34 4.5 24.8 1.0
CD2 D:HIS120 4.5 34.1 1.0
CE1 D:HIS178 4.5 36.5 1.0
C D:HIS120 4.6 35.9 1.0
O D:GLY119 4.6 36.6 1.0
CB D:GLU34 4.8 30.0 1.0
CD D:GLU122 5.0 33.8 1.0

Zinc binding site 8 out of 12 in 1q3k

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Zinc binding site 8 out of 12 in the Crystal Structure of Creatinine Amidohydrolase (Creatininase)


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 Creatinine Amidohydrolase (Creatininase) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:41.7
occ:1.00
NE2 D:HIS36 2.0 27.5 1.0
OE2 D:GLU183 2.0 46.7 1.0
OD1 D:ASP45 2.1 31.6 1.0
O D:HOH302 2.2 34.6 1.0
CD D:GLU183 2.7 44.3 1.0
OE1 D:GLU183 2.8 42.8 1.0
CE1 D:HIS36 2.9 29.3 1.0
CG D:ASP45 3.0 32.5 1.0
CD2 D:HIS36 3.0 29.5 1.0
OD2 D:ASP45 3.1 29.7 1.0
ZN D:ZN300 3.5 41.9 1.0
ND1 D:HIS178 3.9 38.6 1.0
O D:HOH304 3.9 39.5 1.0
ND1 D:HIS36 4.1 28.4 1.0
OE1 D:GLU34 4.1 22.9 1.0
CG D:HIS36 4.1 30.8 1.0
CG D:GLU183 4.2 43.6 1.0
CE1 D:HIS178 4.3 36.5 1.0
CG1 D:VAL44 4.3 34.9 1.0
CB D:ASP45 4.3 33.6 1.0
O D:GLY119 4.6 36.6 1.0
N D:ASP45 4.6 34.2 1.0
CA D:ASP45 4.7 33.8 1.0
CB D:VAL44 4.7 34.5 1.0
N D:GLY179 5.0 43.5 1.0

Zinc binding site 9 out of 12 in 1q3k

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Zinc binding site 9 out of 12 in the Crystal Structure of Creatinine Amidohydrolase (Creatininase)


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 Creatinine Amidohydrolase (Creatininase) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn300

b:36.0
occ:1.00
OD2 E:ASP45 2.0 28.5 1.0
OE1 E:GLU34 2.0 21.9 1.0
O E:HOH905 2.3 32.3 1.0
O E:HOH907 2.3 46.8 1.0
ND1 E:HIS120 2.3 25.5 1.0
CE1 E:HIS120 3.0 29.6 1.0
CD E:GLU34 3.1 24.8 1.0
CG E:ASP45 3.1 31.8 1.0
O E:HOH904 3.2 58.2 1.0
OE2 E:GLU34 3.5 28.2 1.0
CG E:HIS120 3.5 30.0 1.0
ZN E:ZN301 3.5 36.5 1.0
OD1 E:ASP45 3.7 30.9 1.0
O E:HOH906 3.9 38.9 1.0
CA E:HIS120 4.0 33.1 1.0
OE1 E:GLU122 4.0 30.6 1.0
CB E:HIS120 4.0 33.4 1.0
ND1 E:HIS178 4.2 34.1 1.0
NE2 E:HIS120 4.3 33.5 1.0
CE1 E:HIS36 4.3 28.8 1.0
CB E:ASP45 4.4 31.8 1.0
CG E:GLU34 4.4 27.6 1.0
NE2 E:HIS36 4.5 23.6 1.0
N E:TYR121 4.5 34.0 1.0
CE1 E:HIS178 4.5 30.1 1.0
CD2 E:HIS120 4.5 29.4 1.0
O E:GLY119 4.6 32.7 1.0
C E:HIS120 4.7 33.8 1.0
CB E:GLU34 4.8 28.7 1.0
CD E:GLU122 4.9 34.2 1.0

Zinc binding site 10 out of 12 in 1q3k

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Zinc binding site 10 out of 12 in the Crystal Structure of Creatinine Amidohydrolase (Creatininase)


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 Creatinine Amidohydrolase (Creatininase) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:36.5
occ:1.00
OE2 E:GLU183 1.9 44.4 1.0
NE2 E:HIS36 2.0 23.6 1.0
OD1 E:ASP45 2.0 30.9 1.0
O E:HOH906 2.3 38.9 1.0
CD E:GLU183 2.7 42.4 1.0
CE1 E:HIS36 2.8 28.8 1.0
OE1 E:GLU183 2.9 43.4 1.0
CG E:ASP45 3.0 31.8 1.0
O E:HOH904 3.0 58.2 1.0
CD2 E:HIS36 3.1 26.1 1.0
OD2 E:ASP45 3.2 28.5 1.0
ZN E:ZN300 3.5 36.0 1.0
O E:HOH905 3.8 32.3 1.0
O E:HOH934 3.8 35.0 1.0
ND1 E:HIS178 3.9 34.1 1.0
CG1 E:VAL44 4.0 33.2 1.0
ND1 E:HIS36 4.0 30.0 1.0
OE1 E:GLU34 4.1 21.9 1.0
CG E:GLU183 4.2 41.2 1.0
CG E:HIS36 4.2 31.2 1.0
CE1 E:HIS178 4.3 30.1 1.0
CB E:ASP45 4.3 31.8 1.0
O E:GLY119 4.5 32.7 1.0
N E:ASP45 4.6 32.8 1.0
CB E:VAL44 4.6 33.4 1.0
CA E:ASP45 4.7 32.1 1.0
N E:GLY179 5.0 42.0 1.0

Reference:

B.Beuth, K.Niefind, D.Schomburg. Crystal Structure of Creatininase From Pseudomonas Putida: A Novel Fold and A Case of Convergent Evolution J.Mol.Biol. V. 332 287 2003.
ISSN: ISSN 0022-2836
PubMed: 12946365
DOI: 10.1016/S0022-2836(03)00860-X
Page generated: Wed Dec 16 03:01:33 2020

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