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Zinc in PDB 4c4o: Structure of Carbonyl Reductase CPCR2 From Candida Parapsilosis in Complex with Nadh

Enzymatic activity of Structure of Carbonyl Reductase CPCR2 From Candida Parapsilosis in Complex with Nadh

All present enzymatic activity of Structure of Carbonyl Reductase CPCR2 From Candida Parapsilosis in Complex with Nadh:
1.1.1.1;

Protein crystallography data

The structure of Structure of Carbonyl Reductase CPCR2 From Candida Parapsilosis in Complex with Nadh, PDB code: 4c4o was solved by H.Man, C.Loderer, M.Ansorge-Schumacher, G.Grogan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.13 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 66.720, 88.840, 118.200, 90.00, 100.40, 90.00
R / Rfree (%) 20.482 / 24.073

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Carbonyl Reductase CPCR2 From Candida Parapsilosis in Complex with Nadh (pdb code 4c4o). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Structure of Carbonyl Reductase CPCR2 From Candida Parapsilosis in Complex with Nadh, PDB code: 4c4o:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 4c4o

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Zinc binding site 1 out of 9 in the Structure of Carbonyl Reductase CPCR2 From Candida Parapsilosis in Complex with Nadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Carbonyl Reductase CPCR2 From Candida Parapsilosis in Complex with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn500

b:45.0
occ:0.75
 OD2 A:ASP154 2.0 57.3 1.0
OE2 A:GLU66 2.0 51.1 1.0
NE2 A:HIS65 2.1 54.4 1.0
O A:HOH2003 2.4 34.0 1.0
CE1 A:HIS65 2.9 47.5 1.0
CD2 A:HIS65 3.1 44.4 1.0
CD A:GLU66 3.1 47.9 1.0
CG A:ASP154 3.1 53.9 1.0
CG A:GLU66 3.6 43.7 1.0
CB A:ASP154 3.6 50.2 1.0
O A:HOH2006 3.8 55.4 1.0
O A:HOH2028 4.0 52.5 1.0
ND1 A:HIS65 4.0 51.2 1.0
CG A:HIS65 4.1 44.8 1.0
OE1 A:GLU66 4.2 45.0 1.0
OD1 A:ASP154 4.3 49.2 1.0
CB A:SER46 4.9 58.7 1.0
O A:HOH2002 5.0 41.8 1.0

Zinc binding site 2 out of 9 in 4c4o

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Zinc binding site 2 out of 9 in the Structure of Carbonyl Reductase CPCR2 From Candida Parapsilosis in Complex with Nadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Carbonyl Reductase CPCR2 From Candida Parapsilosis in Complex with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn600

b:38.7
occ:0.80
 SG A:CYS109 2.3 46.7 1.0
SG A:CYS101 2.3 45.1 1.0
SG A:CYS98 2.3 43.2 1.0
SG A:CYS95 2.4 48.2 1.0
CB A:CYS109 3.3 45.9 1.0
CB A:CYS101 3.4 46.5 1.0
CB A:CYS98 3.4 49.1 1.0
CB A:CYS95 3.4 52.1 1.0
N A:CYS95 3.5 42.9 1.0
N A:GLY96 3.7 43.1 1.0
O A:HOH2015 3.9 53.1 1.0
N A:CYS98 3.9 51.8 1.0
CA A:CYS95 3.9 46.1 1.0
N A:CYS101 4.1 48.0 1.0
CA A:CYS109 4.1 46.8 1.0
C A:CYS95 4.2 47.0 1.0
CA A:CYS98 4.2 50.3 1.0
CA A:CYS101 4.4 49.2 1.0
N A:GLY97 4.4 49.9 1.0
C A:GLY94 4.5 42.0 1.0
ND2 A:ASN111 4.5 52.0 1.0
CA A:GLY94 4.8 39.5 1.0
CA A:GLY96 4.8 49.1 1.0
C A:CYS98 4.8 54.4 1.0
CB A:ASN111 4.8 55.3 1.0
O A:CYS98 4.9 47.5 1.0
C A:CYS109 4.9 50.0 1.0
C A:GLY97 5.0 55.6 1.0
C A:GLY96 5.0 49.9 1.0

Zinc binding site 3 out of 9 in 4c4o

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Zinc binding site 3 out of 9 in the Structure of Carbonyl Reductase CPCR2 From Candida Parapsilosis in Complex with Nadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Carbonyl Reductase CPCR2 From Candida Parapsilosis in Complex with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn499

b:37.4
occ:0.50
 OE2 B:GLU66 2.0 37.5 0.5
NE2 B:HIS65 2.0 32.8 1.0
OD2 B:ASP154 2.1 35.4 1.0
CB B:CYS44 2.2 39.8 1.0
ZN B:ZN500 2.3 28.7 0.5
SG B:CYS44 2.3 38.3 1.0
CE1 B:HIS65 2.6 34.2 1.0
CD B:GLU66 2.9 35.5 0.5
CD2 B:HIS65 3.0 28.4 1.0
CA B:CYS44 3.3 34.2 1.0
CG B:GLU66 3.3 36.2 0.5
CG B:ASP154 3.4 30.8 1.0
NH2 B:ARG331 3.6 29.9 1.0
CG B:GLU66 3.6 35.5 0.5
ND1 B:HIS65 3.6 33.2 1.0
CG B:HIS65 3.8 32.4 1.0
N B:CYS44 3.9 35.0 1.0
CB B:ASP154 4.0 32.9 1.0
OE1 B:GLU66 4.1 35.6 0.5
CD B:GLU66 4.1 34.7 0.5
O B:HOH2010 4.2 27.5 1.0
O B:HOH2012 4.3 35.9 1.0
C B:CYS44 4.4 34.0 1.0
OE1 B:GLU66 4.4 33.6 0.5
OD1 B:ASP154 4.4 32.1 1.0
CZ B:ARG331 4.4 29.1 1.0
C B:LEU43 4.5 31.3 1.0
NE B:ARG331 4.7 27.7 1.0
CB B:GLU66 4.8 32.8 0.5
CB B:GLU66 4.8 32.0 0.5
O B:CYS44 4.8 31.9 1.0
OE2 B:GLU66 4.8 28.7 0.5
O B:LEU43 4.9 38.4 1.0
N B:HIS45 4.9 39.5 1.0
CB B:SER46 5.0 44.4 1.0

Zinc binding site 4 out of 9 in 4c4o

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Zinc binding site 4 out of 9 in the Structure of Carbonyl Reductase CPCR2 From Candida Parapsilosis in Complex with Nadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Carbonyl Reductase CPCR2 From Candida Parapsilosis in Complex with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:28.7
occ:0.50
 OD2 B:ASP154 1.8 35.4 1.0
O B:HOH2012 2.0 35.9 1.0
NE2 B:HIS65 2.1 32.8 1.0
ZN B:ZN499 2.3 37.4 0.5
SG B:CYS44 2.3 38.3 1.0
CG B:ASP154 2.7 30.8 1.0
CE1 B:HIS65 3.1 34.2 1.0
CD2 B:HIS65 3.1 28.4 1.0
OD1 B:ASP154 3.2 32.1 1.0
C5N B:NAD1000 3.4 31.5 1.0
CB B:CYS44 3.5 39.8 1.0
CB B:SER46 3.8 44.4 1.0
OE2 B:GLU66 4.0 37.5 0.5
OG B:SER46 4.0 39.5 1.0
CB B:ASP154 4.1 32.9 1.0
ND1 B:HIS65 4.2 33.2 1.0
C6N B:NAD1000 4.2 29.7 1.0
CG B:HIS65 4.2 32.4 1.0
C4N B:NAD1000 4.2 29.0 1.0
NH2 B:ARG331 4.5 29.9 1.0
CA B:CYS44 4.9 34.2 1.0
N B:SER46 4.9 39.7 1.0
CD B:GLU66 4.9 35.5 0.5
CA B:SER46 5.0 39.6 1.0
CG B:GLU66 5.0 36.2 0.5

Zinc binding site 5 out of 9 in 4c4o

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Zinc binding site 5 out of 9 in the Structure of Carbonyl Reductase CPCR2 From Candida Parapsilosis in Complex with Nadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Carbonyl Reductase CPCR2 From Candida Parapsilosis in Complex with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn600

b:36.2
occ:1.00
 SG B:CYS109 2.3 36.5 1.0
SG B:CYS98 2.3 35.1 1.0
SG B:CYS101 2.3 34.2 1.0
SG B:CYS95 2.4 35.1 1.0
CB B:CYS109 3.3 38.7 1.0
CB B:CYS98 3.4 34.8 1.0
CB B:CYS101 3.4 33.5 1.0
CB B:CYS95 3.5 38.6 1.0
N B:CYS95 3.5 36.0 1.0
N B:GLY96 3.8 32.7 1.0
N B:CYS98 3.9 35.9 1.0
CA B:CYS95 3.9 33.5 1.0
CA B:CYS109 4.0 39.3 1.0
N B:CYS101 4.2 34.4 1.0
CA B:CYS98 4.2 34.9 1.0
C B:CYS95 4.2 31.2 1.0
CA B:CYS101 4.4 34.5 1.0
ND2 B:ASN111 4.4 35.5 1.0
N B:GLY97 4.4 44.2 1.0
C B:GLY94 4.5 34.2 1.0
CA B:GLY94 4.8 32.7 1.0
C B:CYS98 4.8 33.9 1.0
C B:CYS109 4.8 36.9 1.0
CB B:ASN111 4.8 39.5 1.0
CA B:GLY96 4.8 38.6 1.0
O B:CYS98 4.9 33.9 1.0
C B:GLY96 5.0 39.9 1.0
C B:GLY97 5.0 42.7 1.0

Zinc binding site 6 out of 9 in 4c4o

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Zinc binding site 6 out of 9 in the Structure of Carbonyl Reductase CPCR2 From Candida Parapsilosis in Complex with Nadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Carbonyl Reductase CPCR2 From Candida Parapsilosis in Complex with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn500

b:60.7
occ:0.80
 OE2 C:GLU66 2.0 65.7 1.0
OD2 C:ASP154 2.0 72.2 1.0
NE2 C:HIS65 2.1 69.1 1.0
O C:HOH2003 2.5 44.5 1.0
CE1 C:HIS65 3.0 71.5 1.0
CD2 C:HIS65 3.0 64.1 1.0
CD C:GLU66 3.0 55.9 1.0
CG C:ASP154 3.1 61.1 1.0
CB C:ASP154 3.5 53.0 1.0
CG C:GLU66 3.5 55.7 1.0
ND1 C:HIS65 4.0 65.6 1.0
CG C:HIS65 4.1 70.3 1.0
OE1 C:GLU66 4.1 63.0 1.0
OD1 C:ASP154 4.2 70.2 1.0
CA C:ASP154 5.0 41.5 1.0
C C:LEU43 5.0 56.5 1.0

Zinc binding site 7 out of 9 in 4c4o

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Zinc binding site 7 out of 9 in the Structure of Carbonyl Reductase CPCR2 From Candida Parapsilosis in Complex with Nadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Carbonyl Reductase CPCR2 From Candida Parapsilosis in Complex with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn600

b:49.9
occ:1.00
 SG C:CYS109 2.3 47.2 1.0
SG C:CYS98 2.3 49.3 1.0
SG C:CYS101 2.3 47.4 1.0
SG C:CYS95 2.4 51.5 1.0
CB C:CYS109 3.3 48.5 1.0
CB C:CYS101 3.4 54.8 1.0
N C:CYS95 3.4 56.6 1.0
CB C:CYS98 3.4 55.6 1.0
CB C:CYS95 3.5 49.5 1.0
O C:HOH2009 3.7 49.4 1.0
N C:GLY96 3.7 53.5 1.0
CA C:CYS95 3.8 53.3 1.0
N C:CYS98 3.9 65.3 1.0
CA C:CYS109 4.1 49.6 1.0
N C:CYS101 4.1 49.1 1.0
C C:CYS95 4.2 57.5 1.0
CA C:CYS98 4.2 55.5 1.0
CA C:CYS101 4.3 55.7 1.0
N C:GLY97 4.4 63.9 1.0
C C:GLY94 4.4 62.7 1.0
ND2 C:ASN111 4.5 60.8 1.0
CA C:GLY94 4.7 59.2 1.0
CA C:GLY96 4.8 53.8 1.0
C C:CYS98 4.8 48.9 1.0
C C:CYS109 4.8 49.6 1.0
O C:CYS98 4.9 43.5 1.0
CB C:ASN111 4.9 58.6 1.0
C C:GLY96 5.0 60.9 1.0

Zinc binding site 8 out of 9 in 4c4o

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Zinc binding site 8 out of 9 in the Structure of Carbonyl Reductase CPCR2 From Candida Parapsilosis in Complex with Nadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Carbonyl Reductase CPCR2 From Candida Parapsilosis in Complex with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn500

b:92.9
occ:1.00
 OE2 D:GLU66 2.0 73.2 1.0
OD2 D:ASP154 2.0 77.4 1.0
NE2 D:HIS65 2.1 83.4 1.0
O D:HOH2001 2.4 54.6 1.0
CE1 D:HIS65 3.0 71.7 1.0
CD2 D:HIS65 3.0 70.1 1.0
CG D:ASP154 3.1 53.6 1.0
CD D:GLU66 3.1 62.8 1.0
CB D:ASP154 3.5 53.5 1.0
CG D:GLU66 3.5 58.0 1.0
O D:HOH2003 3.9 59.8 1.0
ND1 D:HIS65 4.0 73.4 1.0
CG D:HIS65 4.1 74.0 1.0
OD1 D:ASP154 4.2 59.6 1.0
OE1 D:GLU66 4.2 63.3 1.0
C D:LEU43 4.9 66.6 1.0
CA D:ASP154 5.0 40.4 1.0

Zinc binding site 9 out of 9 in 4c4o

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Zinc binding site 9 out of 9 in the Structure of Carbonyl Reductase CPCR2 From Candida Parapsilosis in Complex with Nadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Carbonyl Reductase CPCR2 From Candida Parapsilosis in Complex with Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn600

b:50.5
occ:1.00
 SG D:CYS98 2.3 50.5 1.0
SG D:CYS109 2.3 56.3 1.0
SG D:CYS101 2.4 50.4 1.0
SG D:CYS95 2.4 54.1 1.0
CB D:CYS109 3.3 50.7 1.0
CB D:CYS101 3.4 50.9 1.0
CB D:CYS98 3.4 51.9 1.0
CB D:CYS95 3.5 60.4 1.0
N D:CYS95 3.5 63.6 1.0
O D:HOH2005 3.6 48.4 1.0
N D:GLY96 3.8 68.8 1.0
N D:CYS98 3.8 58.4 1.0
CA D:CYS95 3.9 62.8 1.0
CA D:CYS109 4.1 54.0 1.0
N D:CYS101 4.1 53.5 1.0
CA D:CYS98 4.2 52.2 1.0
C D:CYS95 4.2 63.3 1.0
CA D:CYS101 4.4 55.5 1.0
N D:GLY97 4.4 61.1 1.0
ND2 D:ASN111 4.5 52.9 1.0
C D:GLY94 4.5 54.4 1.0
C D:CYS98 4.8 46.6 1.0
CA D:GLY96 4.8 69.5 1.0
CA D:GLY94 4.8 53.8 1.0
O D:CYS98 4.9 45.7 1.0
CB D:ASN111 4.9 51.3 1.0
C D:CYS109 4.9 55.0 1.0
C D:GLY97 4.9 62.3 1.0
C D:GLY96 5.0 65.8 1.0

Reference:

H.Man, C.Loderer, M.B.Ansorge-Schumacher, G.Grogan. Structure of Nadh-Dependent Carbonyl Reductase (CPCR2) From Candida Parapsilosis Provides Insight Into Mutations That Improve Catalytic Properties Chemcatchem V. 6 1103 2014.
ISSN: ISSN 1867-3880
DOI: 10.1002/CCTC.201300788
Page generated: Wed Dec 16 05:07:45 2020

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