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Zinc in PDB 3wlf: Crystal Structure of (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with (R)-1-Phenyl-1,2-Ethanediol

Enzymatic activity of Crystal Structure of (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with (R)-1-Phenyl-1,2-Ethanediol

All present enzymatic activity of Crystal Structure of (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with (R)-1-Phenyl-1,2-Ethanediol:
1.1.1.1;

Protein crystallography data

The structure of Crystal Structure of (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with (R)-1-Phenyl-1,2-Ethanediol, PDB code: 3wlf 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 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.493, 103.722, 141.941, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 25

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of (R)-Carbonyl Reductase From Candida Parapsilosis in Complex with (R)-1-Phenyl-1,2-Ethanediol (pdb code 3wlf). 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 (R)-1-Phenyl-1,2-Ethanediol, PDB code: 3wlf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3wlf

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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 (R)-1-Phenyl-1,2-Ethanediol


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 (R)-1-Phenyl-1,2-Ethanediol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:24.5
occ:1.00
 NE2 A:HIS65 2.1 19.4 1.0
OD2 A:ASP154 2.2 25.7 1.0
OE2 A:GLU66 2.3 28.5 1.0
SG A:CYS44 2.4 26.1 1.0
CD2 A:HIS65 2.9 18.3 1.0
CE1 A:HIS65 3.1 21.0 1.0
CG A:ASP154 3.2 25.1 1.0
CD A:GLU66 3.2 27.0 1.0
CB A:CYS44 3.4 26.4 1.0
CB A:ASP154 3.6 23.4 1.0
CG A:GLU66 3.6 24.7 1.0
NH2 A:ARG331 3.8 64.8 1.0
CG A:HIS65 4.0 19.0 1.0
ND1 A:HIS65 4.1 18.3 1.0
O1 A:FEH401 4.2 46.0 1.0
OD1 A:ASP154 4.2 27.9 1.0
OE1 A:GLU66 4.3 25.3 1.0
NE A:ARG331 4.4 63.6 1.0
OG A:SER46 4.5 31.1 1.0
CZ A:ARG331 4.6 64.1 1.0
CB A:SER46 4.6 31.6 1.0
CA A:CYS44 4.6 28.2 1.0
N A:CYS44 4.7 29.7 1.0
O A:HOH736 4.8 23.1 1.0

Zinc binding site 2 out of 8 in 3wlf

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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 (R)-1-Phenyl-1,2-Ethanediol


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 (R)-1-Phenyl-1,2-Ethanediol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:20.1
occ:1.00
 SG A:CYS98 2.2 17.9 1.0
SG A:CYS101 2.3 19.3 1.0
SG A:CYS109 2.4 18.3 1.0
SG A:CYS95 2.4 16.4 1.0
CB A:CYS109 3.3 17.2 1.0
CB A:CYS101 3.3 20.0 1.0
CB A:CYS98 3.5 17.5 1.0
CB A:CYS95 3.5 17.2 1.0
N A:CYS95 3.6 17.0 1.0
N A:GLY96 3.6 19.9 1.0
N A:CYS98 3.7 18.8 1.0
CA A:CYS95 3.9 18.4 1.0
N A:CYS101 4.0 18.6 1.0
O A:HOH669 4.1 20.0 1.0
N A:GLY97 4.1 20.5 1.0
CA A:CYS98 4.2 18.6 1.0
CA A:CYS109 4.2 17.8 1.0
C A:CYS95 4.2 18.9 1.0
CA A:CYS101 4.2 22.1 1.0
C A:GLY94 4.5 16.7 1.0
CA A:GLY96 4.5 20.1 1.0
ND2 A:ASN111 4.5 19.5 1.0
C A:GLY96 4.8 21.8 1.0
CA A:GLY94 4.8 15.5 1.0
C A:CYS98 4.8 19.4 1.0
C A:GLY97 4.8 19.8 1.0
O A:CYS98 4.8 19.3 1.0
C A:CYS109 4.9 18.1 1.0
CB A:ASN111 5.0 22.0 1.0
CA A:GLY97 5.0 19.9 1.0

Zinc binding site 3 out of 8 in 3wlf

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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 (R)-1-Phenyl-1,2-Ethanediol


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 (R)-1-Phenyl-1,2-Ethanediol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:18.3
occ:1.00
 CE1 B:HIS65 2.1 17.9 1.0
OE2 B:GLU66 2.1 22.4 1.0
OD2 B:ASP154 2.2 21.7 1.0
SG B:CYS44 2.3 18.4 1.0
ND1 B:HIS65 3.0 17.6 1.0
NE2 B:HIS65 3.0 17.9 1.0
CD B:GLU66 3.2 22.7 1.0
CG B:ASP154 3.2 19.5 1.0
CB B:CYS44 3.4 19.6 1.0
CB B:ASP154 3.6 15.2 1.0
CG B:GLU66 3.7 20.0 1.0
O B:HOH559 4.1 31.2 1.0
O1 B:FEH401 4.1 40.4 1.0
CD2 B:HIS65 4.2 17.3 1.0
CG B:HIS65 4.2 16.3 1.0
OE1 B:GLU66 4.2 23.5 1.0
OD1 B:ASP154 4.3 23.1 1.0
OG B:SER46 4.4 24.7 1.0
CB B:SER46 4.5 25.0 1.0
CA B:CYS44 4.6 21.9 1.0
N B:CYS44 4.6 21.4 1.0
NH1 B:ARG331 4.8 57.1 1.0
O B:HOH516 4.9 15.5 1.0

Zinc binding site 4 out of 8 in 3wlf

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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 (R)-1-Phenyl-1,2-Ethanediol


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 (R)-1-Phenyl-1,2-Ethanediol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:18.4
occ:1.00
 SG B:CYS98 2.2 21.1 1.0
SG B:CYS109 2.3 18.3 1.0
SG B:CYS95 2.3 18.2 1.0
SG B:CYS101 2.3 18.3 1.0
CB B:CYS109 3.2 17.4 1.0
CB B:CYS101 3.4 19.3 1.0
CB B:CYS98 3.5 24.9 1.0
CB B:CYS95 3.5 16.8 1.0
N B:CYS95 3.5 13.8 1.0
N B:GLY96 3.7 19.9 1.0
N B:CYS98 3.8 22.9 1.0
CA B:CYS95 3.9 17.2 1.0
O B:HOH706 4.1 23.9 1.0
N B:CYS101 4.1 19.0 1.0
CA B:CYS109 4.2 17.1 1.0
CA B:CYS98 4.2 22.2 1.0
C B:CYS95 4.3 17.5 1.0
N B:GLY97 4.3 20.6 1.0
CA B:CYS101 4.4 20.1 1.0
ND2 B:ASN111 4.4 22.4 1.0
C B:GLY94 4.5 12.8 1.0
CA B:GLY96 4.6 19.1 1.0
CA B:GLY94 4.8 13.4 1.0
C B:CYS98 4.8 22.3 1.0
O B:CYS98 4.8 23.0 1.0
CB B:ASN111 4.9 24.2 1.0
C B:CYS109 4.9 18.6 1.0
C B:GLY96 4.9 21.2 1.0
C B:GLY97 4.9 23.0 1.0

Zinc binding site 5 out of 8 in 3wlf

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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 (R)-1-Phenyl-1,2-Ethanediol


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 (R)-1-Phenyl-1,2-Ethanediol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:22.7
occ:1.00
 SG C:CYS98 2.2 25.4 1.0
SG C:CYS101 2.3 23.4 1.0
SG C:CYS109 2.4 27.6 1.0
SG C:CYS95 2.4 26.6 1.0
CB C:CYS109 3.3 28.4 1.0
CB C:CYS101 3.3 22.7 1.0
CB C:CYS98 3.4 29.3 1.0
N C:CYS95 3.6 22.7 1.0
CB C:CYS95 3.6 24.1 1.0
N C:GLY96 3.7 27.9 1.0
N C:CYS98 3.7 31.4 1.0
O C:HOH696 3.8 25.6 1.0
CA C:CYS95 4.0 25.9 1.0
CA C:CYS98 4.1 29.6 1.0
N C:CYS101 4.1 22.6 1.0
CA C:CYS109 4.2 31.2 1.0
N C:GLY97 4.2 30.9 1.0
ND2 C:ASN111 4.2 36.5 1.0
C C:CYS95 4.2 26.4 1.0
CA C:CYS101 4.3 24.2 1.0
CA C:GLY96 4.6 29.0 1.0
C C:GLY94 4.6 22.8 1.0
C C:CYS98 4.8 29.3 1.0
CA C:GLY94 4.8 19.8 1.0
C C:GLY97 4.8 32.9 1.0
O C:CYS98 4.8 28.1 1.0
C C:GLY96 4.9 30.7 1.0
C C:CYS109 5.0 31.9 1.0

Zinc binding site 6 out of 8 in 3wlf

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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 (R)-1-Phenyl-1,2-Ethanediol


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 (R)-1-Phenyl-1,2-Ethanediol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn403

b:26.1
occ:1.00
 OD2 C:ASP154 2.1 25.4 1.0
CE1 C:HIS65 2.1 22.5 1.0
OE2 C:GLU66 2.3 28.3 1.0
SG C:CYS44 2.4 27.9 1.0
ND1 C:HIS65 3.0 22.4 1.0
CG C:ASP154 3.1 23.6 1.0
NE2 C:HIS65 3.1 23.4 1.0
CD C:GLU66 3.2 29.9 1.0
CB C:CYS44 3.4 29.2 1.0
CG C:GLU66 3.5 26.9 1.0
CB C:ASP154 3.6 20.3 1.0
O1 C:FEH401 3.8 42.8 1.0
OD1 C:ASP154 4.2 23.7 1.0
OE1 C:GLU66 4.2 29.8 1.0
CG C:HIS65 4.2 22.5 1.0
CD2 C:HIS65 4.2 20.1 1.0
O C:HOH687 4.3 46.1 1.0
OG C:SER46 4.3 44.5 1.0
CB C:SER46 4.5 41.8 1.0
CA C:CYS44 4.5 31.7 1.0
N C:CYS44 4.6 29.2 1.0
NH2 C:ARG331 4.9 72.9 1.0
O C:HOH703 4.9 20.1 1.0
C1 C:FEH401 4.9 44.8 1.0

Zinc binding site 7 out of 8 in 3wlf

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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 (R)-1-Phenyl-1,2-Ethanediol


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 (R)-1-Phenyl-1,2-Ethanediol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:18.2
occ:1.00
 NE2 D:HIS65 2.0 15.7 1.0
OE2 D:GLU66 2.1 22.5 1.0
OD2 D:ASP154 2.1 22.8 1.0
SG D:CYS44 2.3 19.3 1.0
CD2 D:HIS65 2.9 16.9 1.0
CE1 D:HIS65 2.9 18.8 1.0
CG D:ASP154 3.0 20.2 1.0
CD D:GLU66 3.1 18.0 1.0
CB D:CYS44 3.4 21.3 1.0
CB D:ASP154 3.5 16.7 1.0
CG D:GLU66 3.5 17.9 1.0
O D:HOH724 3.7 44.1 1.0
O1 D:FEH401 3.9 26.1 1.0
ND1 D:HIS65 4.0 15.8 1.0
CG D:HIS65 4.0 16.9 1.0
OD1 D:ASP154 4.1 22.9 1.0
OE1 D:GLU66 4.2 20.4 1.0
OG D:SER46 4.4 25.1 1.0
CB D:SER46 4.5 23.4 1.0
CA D:CYS44 4.6 22.8 1.0
N D:CYS44 4.7 23.5 1.0
NH1 D:ARG331 4.7 55.3 1.0
O D:HOH549 4.9 22.8 1.0
CB D:GLU66 4.9 17.3 1.0
NH2 D:ARG331 5.0 56.3 1.0
CA D:ASP154 5.0 16.1 1.0

Zinc binding site 8 out of 8 in 3wlf

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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 (R)-1-Phenyl-1,2-Ethanediol


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 (R)-1-Phenyl-1,2-Ethanediol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn403

b:18.8
occ:1.00
 SG D:CYS109 2.3 18.7 1.0
SG D:CYS98 2.3 20.3 1.0
SG D:CYS95 2.3 20.8 1.0
SG D:CYS101 2.4 18.6 1.0
CB D:CYS109 3.3 13.8 1.0
CB D:CYS101 3.4 19.7 1.0
CB D:CYS98 3.4 25.1 1.0
CB D:CYS95 3.4 21.5 1.0
N D:CYS95 3.4 21.4 1.0
N D:GLY96 3.6 25.7 1.0
CA D:CYS95 3.9 23.2 1.0
N D:CYS98 3.9 25.9 1.0
O D:HOH523 4.0 28.0 1.0
ND2 D:ASN111 4.1 23.9 1.0
N D:CYS101 4.1 19.4 1.0
CA D:CYS109 4.2 14.3 1.0
C D:CYS95 4.2 24.6 1.0
CA D:CYS98 4.3 25.2 1.0
N D:GLY97 4.3 26.0 1.0
CA D:CYS101 4.3 19.8 1.0
C D:GLY94 4.5 21.4 1.0
CA D:GLY96 4.6 25.7 1.0
CA D:GLY94 4.7 20.4 1.0
C D:GLY97 4.8 27.5 1.0
CB D:ASN111 4.8 21.7 1.0
C D:CYS109 4.9 14.4 1.0
C D:GLY96 4.9 26.9 1.0
C D:CYS98 4.9 25.6 1.0
CG D:ASN111 4.9 23.5 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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