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Zinc in PDB 3wle: Crystal Structure of (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with Nad

Enzymatic activity of Crystal Structure of (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with Nad

All present enzymatic activity of Crystal Structure of (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with Nad:
1.1.1.1;

Protein crystallography data

The structure of Crystal Structure of (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with Nad, PDB code: 3wle was solved by S.S.Wang, Y.Nie, Y.Xu, R.Z.Zhang, C.H.Huang, H.C.Chan, R.T.Guo, R.Xiao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.16
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.641, 106.105, 145.550, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with Nad (pdb code 3wle). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with Nad, PDB code: 3wle:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3wle

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Zinc binding site 1 out of 8 in the Crystal Structure of (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with Nad


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 (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:25.4
occ:1.00
 OD2 A:ASP154 2.0 23.5 1.0
NE2 A:HIS65 2.1 26.7 1.0
O A:HOH501 2.2 20.0 1.0
SG A:CYS44 2.3 27.9 1.0
CD2 A:HIS65 3.0 27.6 1.0
CG A:ASP154 3.1 25.6 1.0
CB A:CYS44 3.1 27.5 1.0
CE1 A:HIS65 3.1 28.1 1.0
C5N A:NAD401 3.3 26.3 1.0
OG A:SER46 3.5 32.3 1.0
OD1 A:ASP154 3.6 26.4 1.0
CB A:SER46 3.8 31.4 1.0
C6N A:NAD401 3.9 27.3 1.0
C4N A:NAD401 4.0 27.2 1.0
CG A:HIS65 4.2 27.8 1.0
ND1 A:HIS65 4.2 26.7 1.0
CB A:ASP154 4.3 24.4 1.0
CA A:CYS44 4.6 28.0 1.0
NH2 A:ARG331 4.8 24.8 1.0
N A:SER46 4.9 30.8 1.0
CA A:SER46 5.0 33.0 1.0

Zinc binding site 2 out of 8 in 3wle

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Zinc binding site 2 out of 8 in the Crystal Structure of (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with Nad


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 (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:27.5
occ:1.00
 SG A:CYS95 2.2 26.9 1.0
SG A:CYS98 2.2 28.0 1.0
SG A:CYS109 2.3 24.5 1.0
SG A:CYS101 2.4 32.5 1.0
CB A:CYS109 3.2 22.8 1.0
CB A:CYS98 3.4 29.8 1.0
CB A:CYS95 3.4 29.7 1.0
N A:CYS95 3.5 28.6 1.0
CB A:CYS101 3.5 31.3 1.0
N A:GLY96 3.7 32.6 1.0
N A:CYS98 3.8 34.3 1.0
CA A:CYS95 3.9 29.4 1.0
O A:HOH547 4.0 30.4 1.0
N A:CYS101 4.1 29.3 1.0
CA A:CYS98 4.2 30.3 1.0
CA A:CYS109 4.2 27.5 1.0
C A:CYS95 4.2 30.8 1.0
N A:GLY97 4.4 35.9 1.0
CA A:CYS101 4.4 30.9 1.0
ND2 A:ASN111 4.5 36.5 1.0
C A:GLY94 4.5 29.0 1.0
CA A:GLY96 4.7 34.1 1.0
CB A:ASN111 4.8 35.6 1.0
CA A:GLY94 4.8 26.6 1.0
C A:CYS98 4.8 31.4 1.0
C A:GLY96 4.9 36.4 1.0
C A:CYS109 4.9 28.9 1.0
C A:GLY97 4.9 34.8 1.0
O A:CYS98 5.0 30.8 1.0
CB A:TYR100 5.0 30.7 1.0

Zinc binding site 3 out of 8 in 3wle

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Zinc binding site 3 out of 8 in the Crystal Structure of (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with Nad


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 (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:26.2
occ:1.00
 OD2 B:ASP154 1.9 25.0 1.0
NE2 B:HIS65 2.1 24.3 1.0
SG B:CYS44 2.2 23.1 1.0
O B:HOH501 2.6 32.7 1.0
CD2 B:HIS65 2.8 23.1 1.0
CB B:CYS44 3.0 24.1 1.0
CG B:ASP154 3.1 25.2 1.0
CE1 B:HIS65 3.2 21.6 1.0
C5N B:NAD401 3.3 20.6 1.0
OG B:SER46 3.6 23.9 1.0
OD1 B:ASP154 3.7 21.4 1.0
CB B:SER46 3.8 21.8 1.0
C6N B:NAD401 3.9 21.2 1.0
CG B:HIS65 4.1 23.6 1.0
C4N B:NAD401 4.1 21.8 1.0
ND1 B:HIS65 4.2 22.6 1.0
CB B:ASP154 4.3 23.9 1.0
CA B:CYS44 4.5 23.5 1.0
NH2 B:ARG331 4.8 21.8 1.0
N B:SER46 4.8 23.0 1.0
CA B:SER46 4.9 22.2 1.0

Zinc binding site 4 out of 8 in 3wle

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Zinc binding site 4 out of 8 in the Crystal Structure of (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with Nad


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 (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:31.2
occ:1.00
 SG B:CYS98 2.2 25.8 1.0
SG B:CYS101 2.2 34.6 1.0
SG B:CYS109 2.3 33.9 1.0
SG B:CYS95 2.4 35.1 1.0
CB B:CYS109 3.2 28.1 1.0
CB B:CYS101 3.4 35.5 1.0
N B:CYS95 3.4 31.3 1.0
CB B:CYS95 3.4 33.0 1.0
CB B:CYS98 3.5 32.9 1.0
N B:GLY96 3.5 35.9 1.0
CA B:CYS95 3.8 32.9 1.0
N B:CYS98 3.8 37.6 1.0
N B:CYS101 4.0 34.7 1.0
O B:HOH544 4.1 28.9 1.0
C B:CYS95 4.1 34.6 1.0
CA B:CYS109 4.1 28.9 1.0
CA B:CYS98 4.2 34.1 1.0
CA B:CYS101 4.3 35.8 1.0
N B:GLY97 4.3 40.2 1.0
ND2 B:ASN111 4.4 28.1 1.0
C B:GLY94 4.4 30.4 1.0
CA B:GLY96 4.5 38.6 1.0
CA B:GLY94 4.7 28.7 1.0
CB B:ASN111 4.7 32.4 1.0
CB B:TYR100 4.8 34.6 1.0
C B:GLY96 4.8 39.5 1.0
C B:CYS109 4.9 30.6 1.0
C B:CYS98 4.9 33.1 1.0
C B:GLY97 4.9 39.1 1.0

Zinc binding site 5 out of 8 in 3wle

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Zinc binding site 5 out of 8 in the Crystal Structure of (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with Nad


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 (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:23.2
occ:1.00
 OD1 C:ASP154 1.9 20.3 1.0
NE2 C:HIS65 2.2 21.6 1.0
SG C:CYS44 2.4 18.9 1.0
O C:HOH501 2.9 31.6 1.0
CD2 C:HIS65 3.0 16.7 1.0
CG C:ASP154 3.1 20.1 1.0
CB C:CYS44 3.1 19.1 1.0
C5N C:NAD401 3.2 15.6 1.0
CE1 C:HIS65 3.3 18.0 1.0
OG C:SER46 3.4 21.5 1.0
OD2 C:ASP154 3.6 19.0 1.0
C6N C:NAD401 3.8 17.1 1.0
CB C:SER46 3.9 16.5 1.0
C4N C:NAD401 3.9 19.2 1.0
CG C:HIS65 4.2 18.7 1.0
ND1 C:HIS65 4.3 19.2 1.0
CB C:ASP154 4.3 17.4 1.0
NH2 C:ARG331 4.6 18.4 1.0
CA C:CYS44 4.6 19.4 1.0
N C:SER46 4.9 15.9 1.0
N1N C:NAD401 5.0 15.7 1.0

Zinc binding site 6 out of 8 in 3wle

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Zinc binding site 6 out of 8 in the Crystal Structure of (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with Nad


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 (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn403

b:22.3
occ:1.00
 SG C:CYS95 2.3 23.1 1.0
SG C:CYS109 2.3 19.8 1.0
SG C:CYS101 2.3 24.7 1.0
SG C:CYS98 2.4 19.9 1.0
CB C:CYS109 3.2 15.7 1.0
CB C:CYS98 3.4 23.5 1.0
CB C:CYS95 3.5 23.1 1.0
CB C:CYS101 3.5 23.2 1.0
N C:CYS95 3.5 21.9 1.0
N C:GLY96 3.6 25.1 1.0
N C:CYS98 3.8 26.8 1.0
CA C:CYS95 3.9 23.4 1.0
O C:HOH549 4.1 18.7 1.0
N C:CYS101 4.1 25.4 1.0
C C:CYS95 4.1 24.5 1.0
CA C:CYS98 4.2 25.9 1.0
CA C:CYS109 4.2 18.5 1.0
N C:GLY97 4.3 29.3 1.0
ND2 C:ASN111 4.4 21.9 1.0
CA C:CYS101 4.4 26.1 1.0
C C:GLY94 4.5 21.2 1.0
CA C:GLY96 4.5 28.0 1.0
C C:GLY96 4.8 29.7 1.0
CA C:GLY94 4.8 20.1 1.0
CB C:ASN111 4.8 21.6 1.0
C C:CYS98 4.8 26.4 1.0
C C:GLY97 4.9 29.8 1.0
C C:CYS109 4.9 20.0 1.0

Zinc binding site 7 out of 8 in 3wle

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Zinc binding site 7 out of 8 in the Crystal Structure of (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with Nad


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 (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:28.1
occ:1.00
 OD2 D:ASP154 1.9 30.2 1.0
NE2 D:HIS65 2.2 29.2 1.0
SG D:CYS44 2.3 25.5 1.0
O D:HOH502 2.6 27.6 1.0
CD2 D:HIS65 3.0 27.1 1.0
CB D:CYS44 3.0 25.1 1.0
CG D:ASP154 3.1 29.0 1.0
C5N D:NAD401 3.2 26.4 1.0
CE1 D:HIS65 3.2 27.1 1.0
OD1 D:ASP154 3.6 29.2 1.0
OG D:SER46 3.7 25.7 1.0
C6N D:NAD401 3.9 25.1 1.0
CB D:SER46 4.0 26.4 1.0
C4N D:NAD401 4.0 25.8 1.0
CG D:HIS65 4.2 27.0 1.0
CB D:ASP154 4.3 26.0 1.0
ND1 D:HIS65 4.3 28.0 1.0
CA D:CYS44 4.5 27.4 1.0
NH2 D:ARG331 4.6 28.9 1.0
N D:SER46 4.9 26.5 1.0

Zinc binding site 8 out of 8 in 3wle

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Zinc binding site 8 out of 8 in the Crystal Structure of (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with Nad


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 (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn403

b:34.2
occ:1.00
 SG D:CYS98 2.2 32.5 1.0
SG D:CYS101 2.2 41.6 1.0
SG D:CYS109 2.3 34.3 1.0
SG D:CYS95 2.3 32.3 1.0
CB D:CYS109 3.2 32.1 1.0
CB D:CYS98 3.3 38.0 1.0
CB D:CYS101 3.4 40.6 1.0
CB D:CYS95 3.5 34.9 1.0
N D:GLY96 3.6 40.4 1.0
N D:CYS95 3.7 34.8 1.0
N D:CYS98 3.8 40.8 1.0
CA D:CYS95 4.0 36.1 1.0
CA D:CYS98 4.1 38.5 1.0
N D:CYS101 4.1 40.8 1.0
O D:HOH504 4.1 43.4 1.0
CA D:CYS109 4.2 33.3 1.0
C D:CYS95 4.2 38.5 1.0
ND2 D:ASN111 4.3 40.2 1.0
CA D:CYS101 4.3 41.5 1.0
N D:GLY97 4.5 44.6 1.0
CA D:GLY96 4.6 43.2 1.0
C D:CYS98 4.7 38.5 1.0
C D:GLY96 4.7 44.9 1.0
C D:GLY94 4.7 34.3 1.0
CB D:ASN111 4.7 40.0 1.0
O D:CYS98 4.8 38.2 1.0
C D:GLY97 4.9 43.5 1.0
C D:CYS109 4.9 34.6 1.0
CG D:ASN111 4.9 41.4 1.0

Reference:

S.S.Wang, Y.Nie, Y.Xu, R.Z.Zhang, T.P.Ko, C.H.Huang, H.C.Chan, R.T.Guo, R.Xiao. Unconserved Substrate-Binding Sites Direct the Stereoselectivity of Medium-Chain Alcohol Dehydrogenase Chem.Commun.(Camb.) V. 50 7770 2014.
ISSN: ISSN 1359-7345
PubMed: 24834985
DOI: 10.1039/C4CC01752H
Page generated: Sat Oct 26 18:08:06 2024

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