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Zinc in PDB 1nw2: The Crystal Structure of the Mutant R82E of Thioredoxin From Alicyclobacillus Acidocaldarius

Enzymatic activity of The Crystal Structure of the Mutant R82E of Thioredoxin From Alicyclobacillus Acidocaldarius

All present enzymatic activity of The Crystal Structure of the Mutant R82E of Thioredoxin From Alicyclobacillus Acidocaldarius:
1.8.1.9;

Protein crystallography data

The structure of The Crystal Structure of the Mutant R82E of Thioredoxin From Alicyclobacillus Acidocaldarius, PDB code: 1nw2 was solved by S.Bartolucci, G.De Simone, S.Galdiero, R.Improta, V.Menchise, C.Pedone, E.Pedone, M.Saviano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.610, 60.210, 82.950, 90.00, 93.30, 90.00
R / Rfree (%) 21.2 / 25.5

Other elements in 1nw2:

The structure of The Crystal Structure of the Mutant R82E of Thioredoxin From Alicyclobacillus Acidocaldarius also contains other interesting chemical elements:

Arsenic (As) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystal Structure of the Mutant R82E of Thioredoxin From Alicyclobacillus Acidocaldarius (pdb code 1nw2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the The Crystal Structure of the Mutant R82E of Thioredoxin From Alicyclobacillus Acidocaldarius, PDB code: 1nw2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 1nw2

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Zinc binding site 1 out of 9 in the The Crystal Structure of the Mutant R82E of Thioredoxin From Alicyclobacillus Acidocaldarius


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of the Mutant R82E of Thioredoxin From Alicyclobacillus Acidocaldarius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn6001

b:34.4
occ:1.00
 NE2 A:HIS46 2.3 32.0 1.0
OE2 A:GLU97 2.3 30.7 1.0
OXT A:ACT7001 2.8 14.5 1.0
CD A:GLU97 3.0 30.2 1.0
O A:ACT7002 3.0 22.5 1.0
OE1 A:GLU97 3.0 28.8 1.0
CE1 A:HIS46 3.1 31.7 1.0
CD2 A:HIS46 3.4 32.3 1.0
C A:ACT7002 3.6 20.8 1.0
O A:HOH7074 3.8 17.3 1.0
OXT A:ACT7002 3.9 27.2 1.0
C A:ACT7001 4.0 17.2 1.0
ND1 A:HIS46 4.2 31.5 1.0
CE A:LYS93 4.3 35.7 1.0
CB A:ALA45 4.3 32.8 1.0
CG A:GLU97 4.4 29.1 1.0
CG A:HIS46 4.4 31.9 1.0
CH3 A:ACT7002 4.7 24.2 1.0
NZ A:LYS93 4.7 36.0 1.0
CE1 A:PHE42 4.7 31.5 1.0
O A:ACT7001 4.8 22.9 1.0
CD1 A:PHE42 4.8 30.4 1.0

Zinc binding site 2 out of 9 in 1nw2

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Zinc binding site 2 out of 9 in the The Crystal Structure of the Mutant R82E of Thioredoxin From Alicyclobacillus Acidocaldarius


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of the Mutant R82E of Thioredoxin From Alicyclobacillus Acidocaldarius within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn6002

b:17.0
occ:1.00
 OE1 B:GLU97 2.0 14.2 1.0
OE1 H:GLU94 2.1 18.0 1.0
O B:ACT7003 2.1 17.4 1.0
NE2 B:HIS46 2.2 15.3 1.0
OE2 B:GLU97 2.6 13.3 1.0
CD B:GLU97 2.6 16.1 1.0
CD H:GLU94 3.0 18.8 1.0
C B:ACT7003 3.0 18.7 1.0
CD2 B:HIS46 3.0 16.9 1.0
OXT B:ACT7003 3.2 20.7 1.0
OE2 H:GLU94 3.2 18.2 1.0
CE1 B:HIS46 3.2 16.3 1.0
NZ B:LYS49 4.0 27.4 1.0
O B:HOH7044 4.1 32.0 1.0
CG B:GLU97 4.1 14.0 1.0
CG B:HIS46 4.2 15.9 1.0
ND1 B:HIS46 4.3 15.3 1.0
N H:GLU94 4.3 16.9 1.0
CB H:LYS93 4.3 18.5 1.0
CG H:GLU94 4.4 18.2 1.0
CH3 B:ACT7003 4.4 16.5 1.0
CE B:LYS49 4.5 31.0 1.0
N H:LYS93 4.5 15.9 1.0
CE1 B:PHE42 4.7 14.8 1.0
CB H:GLU94 4.7 18.1 1.0
CB H:PRO92 4.7 15.3 1.0
CB B:GLU97 4.7 15.2 1.0
O B:HOH7041 4.7 23.4 1.0
CA H:LYS93 4.9 17.1 1.0

Zinc binding site 3 out of 9 in 1nw2

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Zinc binding site 3 out of 9 in the The Crystal Structure of the Mutant R82E of Thioredoxin From Alicyclobacillus Acidocaldarius


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of the Mutant R82E of Thioredoxin From Alicyclobacillus Acidocaldarius within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn6003

b:66.8
occ:1.00
 NE2 C:HIS46 2.3 32.6 1.0
OE1 C:GLU97 2.6 38.2 1.0
O C:ACT7004 2.9 64.3 1.0
O C:HOH7019 3.0 39.0 1.0
OE2 C:GLU97 3.1 37.9 1.0
CD C:GLU97 3.1 37.1 1.0
CD2 C:HIS46 3.2 31.9 1.0
C C:ACT7004 3.3 64.7 1.0
CE1 C:HIS46 3.3 32.0 1.0
OXT C:ACT7004 3.6 64.8 1.0
CD1 C:LEU104 3.9 45.7 1.0
CH3 C:ACT7004 4.1 64.6 1.0
CG C:HIS46 4.3 31.6 1.0
ND1 C:HIS46 4.4 32.2 1.0
CG C:GLU97 4.4 35.1 1.0
CB C:GLU97 4.8 31.0 1.0
CG C:LEU104 4.8 45.8 1.0
CB C:LEU104 4.9 45.5 1.0
CD2 C:LEU104 4.9 45.7 1.0

Zinc binding site 4 out of 9 in 1nw2

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Zinc binding site 4 out of 9 in the The Crystal Structure of the Mutant R82E of Thioredoxin From Alicyclobacillus Acidocaldarius


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of the Mutant R82E of Thioredoxin From Alicyclobacillus Acidocaldarius within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn6004

b:19.1
occ:1.00
 O2 D:CAC5001 2.0 24.2 1.0
O2 D:CAC5002 2.0 23.0 1.0
OE2 D:GLU97 2.0 11.0 1.0
NE2 D:HIS46 2.1 15.9 1.0
OE1 D:GLU97 2.7 11.9 1.0
CD D:GLU97 2.7 12.4 1.0
CE1 D:HIS46 3.1 15.3 1.0
CD2 D:HIS46 3.1 14.1 1.0
AS D:CAC5002 3.2 23.6 1.0
AS D:CAC5001 3.3 22.0 1.0
C1 D:CAC5001 3.4 23.0 1.0
C1 D:CAC5002 3.7 24.4 1.0
O1 D:CAC5002 3.8 24.8 1.0
CB D:ALA101 3.9 16.2 1.0
O D:HOH6027 4.2 20.5 1.0
ND1 D:HIS46 4.2 13.0 1.0
CG D:GLU97 4.2 12.1 1.0
CG D:HIS46 4.2 14.2 1.0
O D:HOH6040 4.2 26.3 1.0
C2 D:CAC5001 4.4 23.4 1.0
O D:HOH6092 4.4 27.0 1.0
O1 D:CAC5001 4.6 23.3 1.0
O D:HOH6042 4.9 21.3 1.0
C2 D:CAC5002 4.9 24.3 1.0
ZN D:ZN6009 4.9 19.7 1.0

Zinc binding site 5 out of 9 in 1nw2

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Zinc binding site 5 out of 9 in the The Crystal Structure of the Mutant R82E of Thioredoxin From Alicyclobacillus Acidocaldarius


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Crystal Structure of the Mutant R82E of Thioredoxin From Alicyclobacillus Acidocaldarius within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn6009

b:19.7
occ:1.00
 O1 D:CAC5002 2.0 24.8 1.0
O1 D:CAC5001 2.1 23.3 1.0
AS D:CAC5002 3.2 23.6 1.0
C1 D:CAC5002 3.3 24.4 1.0
AS D:CAC5001 3.4 22.0 1.0
O2 D:CAC5001 3.8 24.2 1.0
C1 D:CAC5001 3.9 23.0 1.0
C2 D:CAC5002 4.3 24.3 1.0
O2 D:CAC5002 4.6 23.0 1.0
ZN D:ZN6004 4.9 19.1 1.0

Zinc binding site 6 out of 9 in 1nw2

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Zinc binding site 6 out of 9 in the The Crystal Structure of the Mutant R82E of Thioredoxin From Alicyclobacillus Acidocaldarius


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Crystal Structure of the Mutant R82E of Thioredoxin From Alicyclobacillus Acidocaldarius within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn6005

b:20.6
occ:1.00
 NE2 E:HIS46 2.2 17.1 1.0
OE1 E:GLU97 2.2 20.9 1.0
O E:ACT7005 2.2 31.8 1.0
OE2 E:GLU97 2.7 25.3 1.0
CD E:GLU97 2.8 23.4 1.0
O E:HOH7052 3.0 48.0 1.0
CD2 E:HIS46 3.0 16.8 1.0
C E:ACT7005 3.1 33.1 1.0
CE1 E:HIS46 3.2 16.3 1.0
OXT E:ACT7005 3.3 33.4 1.0
CG E:HIS46 4.2 16.5 1.0
ND1 E:HIS46 4.2 15.7 1.0
CG E:GLU97 4.3 21.7 1.0
O E:HOH7095 4.3 41.2 1.0
CH3 E:ACT7005 4.6 31.9 1.0
NZ E:LYS49 4.6 27.2 1.0
CE1 E:PHE42 4.9 18.7 1.0
CB E:GLU97 5.0 20.1 1.0

Zinc binding site 7 out of 9 in 1nw2

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Zinc binding site 7 out of 9 in the The Crystal Structure of the Mutant R82E of Thioredoxin From Alicyclobacillus Acidocaldarius


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Crystal Structure of the Mutant R82E of Thioredoxin From Alicyclobacillus Acidocaldarius within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn6006

b:13.3
occ:1.00
 OE1 D:GLU94 2.0 12.9 1.0
OE1 F:GLU97 2.0 14.3 1.0
OXT F:ACT7006 2.1 13.8 1.0
NE2 F:HIS46 2.1 20.2 1.0
OE2 F:GLU97 2.6 14.0 1.0
CD F:GLU97 2.6 16.0 1.0
CD D:GLU94 2.8 16.5 1.0
CD2 F:HIS46 3.0 20.5 1.0
C F:ACT7006 3.0 14.7 1.0
OE2 D:GLU94 3.1 13.0 1.0
CE1 F:HIS46 3.2 21.1 1.0
CH3 F:ACT7006 3.3 13.4 1.0
O F:HOH7041 3.9 16.5 1.0
CG F:GLU97 4.1 13.5 1.0
O F:HOH7031 4.2 17.9 1.0
CG F:HIS46 4.2 21.3 1.0
O F:ACT7006 4.2 15.4 1.0
ND1 F:HIS46 4.3 20.8 1.0
CG D:GLU94 4.3 14.0 1.0
N D:GLU94 4.3 13.3 1.0
N D:LYS93 4.3 12.5 1.0
CB D:LYS93 4.5 14.7 1.0
CE1 F:PHE42 4.7 22.9 1.0
CB D:PRO92 4.7 13.1 1.0
O F:HOH7014 4.7 24.0 1.0
CB D:GLU94 4.7 14.3 1.0
CB F:GLU97 4.8 14.3 1.0
CA D:LYS93 4.8 13.3 1.0
CA F:GLU97 5.0 14.5 1.0

Zinc binding site 8 out of 9 in 1nw2

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Zinc binding site 8 out of 9 in the The Crystal Structure of the Mutant R82E of Thioredoxin From Alicyclobacillus Acidocaldarius


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Crystal Structure of the Mutant R82E of Thioredoxin From Alicyclobacillus Acidocaldarius within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn6007

b:67.6
occ:1.00
 OE2 G:GLU97 2.4 41.8 1.0
O G:HOH7008 2.6 13.3 1.0
NE2 G:HIS46 2.7 46.2 1.0
CD G:GLU97 3.0 40.7 1.0
OE1 G:GLU97 3.0 39.9 1.0
OXT G:ACT7007 3.4 64.8 1.0
CE1 G:HIS46 3.6 46.2 1.0
CD2 G:HIS46 3.6 45.9 1.0
CD1 G:PHE42 4.1 35.8 1.0
CB G:ALA45 4.2 45.1 1.0
CG G:GLU97 4.3 38.4 1.0
C G:ACT7007 4.3 64.7 1.0
CE1 G:PHE42 4.4 36.2 1.0
CH3 G:ACT7007 4.6 64.6 1.0
ND1 G:HIS46 4.7 45.9 1.0
CG G:HIS46 4.8 45.8 1.0

Zinc binding site 9 out of 9 in 1nw2

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Zinc binding site 9 out of 9 in the The Crystal Structure of the Mutant R82E of Thioredoxin From Alicyclobacillus Acidocaldarius


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Crystal Structure of the Mutant R82E of Thioredoxin From Alicyclobacillus Acidocaldarius within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn6008

b:33.6
occ:1.00
 NE2 H:HIS46 2.3 29.9 1.0
OE1 H:GLU97 2.3 27.8 1.0
OXT H:ACT7008 2.6 45.7 1.0
O B:ACT7009 2.9 43.3 1.0
CD2 H:HIS46 3.1 29.4 1.0
CD H:GLU97 3.1 28.4 1.0
O H:ACT7008 3.1 44.2 1.0
OE2 H:GLU97 3.1 29.5 1.0
C H:ACT7008 3.2 44.8 1.0
C B:ACT7009 3.3 42.7 1.0
CE1 H:HIS46 3.4 29.8 1.0
OXT B:ACT7009 3.4 43.5 1.0
CG H:HIS46 4.3 29.0 1.0
CH3 B:ACT7009 4.3 43.6 1.0
ND1 H:HIS46 4.4 29.8 1.0
CG H:GLU97 4.6 26.0 1.0
CH3 H:ACT7008 4.6 44.2 1.0
CE1 H:PHE42 4.7 22.8 1.0

Reference:

S.Bartolucci, G.De Simone, S.Galdiero, R.Improta, V.Menchise, C.Pedone, E.Pedone, M.Saviano. An Integrated Structural and Computational Study of the Thermostability of Two Thioredoxin Mutants From Alicyclobacillus Acidocaldarius J.Bacteriol. V. 185 4285 2003.
ISSN: ISSN 0021-9193
PubMed: 12837806
DOI: 10.1128/JB.185.14.4285-4289.2003
Page generated: Wed Oct 16 17:25:53 2024

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