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Copper in PDB 4tm7: Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4

Enzymatic activity of Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4

All present enzymatic activity of Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4:
3.1.1.31;

Protein crystallography data

The structure of Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4, PDB code: 4tm7 was solved by N.Fujieda, E.Stuttfeld, T.Maier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.23 / 1.39
Space group P 32 1 2
Cell size a, b, c (Å), α, β, γ (°) 42.520, 42.520, 222.700, 90.00, 90.00, 120.00
R / Rfree (%) 14.9 / 17.8

Other elements in 4tm7:

The structure of Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Copper atom in the Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4 (pdb code 4tm7). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 16 binding sites of Copper where determined in the Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4, PDB code: 4tm7:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 16 in 4tm7

Go back to Copper Binding Sites List in 4tm7
Copper binding site 1 out of 16 in the Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu305

b:22.1
occ:0.99
 NE2 A:HIS104 1.9 18.8 1.0
ND1 A:HIS67 2.0 23.0 1.0
O A:HOH428 2.8 37.3 1.0
CD2 A:HIS104 2.9 16.9 1.0
CE1 A:HIS104 2.9 19.6 1.0
CE1 A:HIS67 3.0 22.7 1.0
CG A:HIS67 3.0 19.2 1.0
CB A:HIS67 3.4 17.8 1.0
O A:ASN102 3.5 19.2 1.0
CA A:ASN102 3.6 19.4 1.0
C A:ASN102 3.8 18.2 1.0
O A:VAL101 3.8 27.6 1.0
O2 A:EDO301 3.9 50.4 1.0
ND1 A:HIS104 4.0 18.9 1.0
CG A:HIS104 4.0 16.9 1.0
NE2 A:HIS67 4.1 22.6 1.0
CD2 A:HIS67 4.1 23.4 1.0
CA A:HIS67 4.2 15.8 1.0
OH A:TYR69 4.3 30.0 1.0
CB A:ASN102 4.5 21.1 1.0
C2 A:EDO301 4.6 44.1 1.0
N A:ASN102 4.6 22.0 1.0
C A:VAL101 4.6 26.8 1.0
CZ A:TYR69 4.7 23.4 1.0
CG A:ASN102 4.8 22.5 1.0
N A:VAL103 4.8 20.9 1.0
OD1 A:ASN102 4.8 26.3 1.0
N A:ILE68 4.9 14.8 1.0
CE1 A:TYR69 4.9 21.4 1.0
C A:HIS67 4.9 14.4 1.0

Copper binding site 2 out of 16 in 4tm7

Go back to Copper Binding Sites List in 4tm7
Copper binding site 2 out of 16 in the Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu306

b:27.0
occ:0.94
 O A:HOH425 1.9 41.7 1.0
ND1 A:HIS9 2.0 22.6 1.0
CE1 A:HIS9 3.0 20.8 1.0
CG A:HIS9 3.1 20.2 1.0
CB A:HIS9 3.5 17.6 1.0
CA A:HIS9 4.0 15.4 1.0
NE2 A:HIS9 4.1 22.9 1.0
CD2 A:HIS9 4.2 19.8 1.0
O A:HOH459 4.3 46.1 1.0
CB A:ALA14 4.6 21.4 1.0
N A:ALA10 4.8 18.1 1.0
O A:ARG8 4.9 18.4 1.0
O A:ALA14 5.0 16.7 1.0
C A:HIS9 5.0 16.5 1.0

Copper binding site 3 out of 16 in 4tm7

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Copper binding site 3 out of 16 in the Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu307

b:24.3
occ:0.98
 ND1 A:HIS95 2.0 21.4 1.0
O A:HOH451 2.4 35.5 1.0
CE1 A:HIS95 2.9 20.2 1.0
CG A:HIS95 3.1 20.2 1.0
CB A:HIS95 3.5 18.2 1.0
NE2 A:HIS95 4.0 21.6 1.0
CA A:HIS95 4.1 18.6 1.0
CD2 A:HIS95 4.1 20.7 1.0
CD A:ARG55 4.7 28.2 1.0

Copper binding site 4 out of 16 in 4tm7

Go back to Copper Binding Sites List in 4tm7
Copper binding site 4 out of 16 in the Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu308

b:37.9
occ:0.44
 OD2 A:ASP25 2.2 31.6 1.0
O A:HOH515 2.3 55.3 1.0
O A:HOH557 2.6 50.6 1.0
CG A:ASP25 3.0 30.3 1.0
OD1 A:ASP25 3.1 28.9 1.0
NH1 A:ARG57 3.3 36.2 1.0
O A:ASP21 3.9 19.2 1.0
NH2 A:ARG57 4.0 34.8 1.0
CZ A:ARG57 4.1 35.0 1.0
CB A:ASP21 4.1 22.2 1.0
C A:ASP21 4.4 19.5 1.0
CB A:ASP25 4.4 24.4 1.0
CA A:ASP21 4.7 19.0 1.0
CG A:ASP21 4.8 27.5 1.0

Copper binding site 5 out of 16 in 4tm7

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Copper binding site 5 out of 16 in the Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu309

b:23.2
occ:0.17
 OD2 A:ASP116 1.7 36.5 1.0
O A:HOH448 2.6 56.1 1.0
CG A:ASP116 2.8 29.7 1.0
CU A:CU318 3.4 29.2 0.2
OD1 A:ASP116 3.4 28.2 1.0
CB A:ASP116 4.0 28.6 1.0
O A:HOH436 4.2 42.8 1.0
CB A:ALA119 4.6 23.1 1.0

Copper binding site 6 out of 16 in 4tm7

Go back to Copper Binding Sites List in 4tm7
Copper binding site 6 out of 16 in the Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu310

b:60.7
occ:0.44
 OD2 A:ASP207 1.9 41.6 1.0
O A:HOH558 2.4 59.4 1.0
CG A:ASP207 2.9 37.0 1.0
OD1 A:ASP207 3.2 37.0 1.0
NZ A:LYS243 3.7 52.8 1.0
CB A:ASP207 4.2 27.7 1.0
O A:HOH410 4.3 28.2 1.0
O A:HOH449 4.4 50.4 1.0

Copper binding site 7 out of 16 in 4tm7

Go back to Copper Binding Sites List in 4tm7
Copper binding site 7 out of 16 in the Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu311

b:39.8
occ:0.35
 O1 A:SO4304 1.8 43.5 0.8
NE2 A:HIS151 2.1 18.9 1.0
S A:SO4304 2.7 37.3 0.8
CD2 A:HIS151 2.9 17.4 1.0
O4 A:SO4304 2.9 48.0 0.8
O3 A:SO4304 2.9 37.6 0.8
O A:ASN153 3.0 11.5 1.0
CE1 A:HIS151 3.3 20.7 1.0
NH1 A:ARG182 3.8 24.9 1.0
O2 A:SO4304 4.0 46.5 0.8
CG A:HIS151 4.1 19.7 1.0
C A:ASN153 4.1 10.8 1.0
O A:HOH531 4.2 36.4 1.0
OD2 A:ASP72 4.3 15.2 1.0
ND1 A:HIS151 4.3 19.3 1.0
CZ A:PHE156 4.5 22.4 1.0
O A:HOH472 4.6 23.2 1.0
O A:HOH500 4.7 52.3 1.0
OG A:SER154 4.7 14.3 1.0
O A:HOH506 4.7 27.6 1.0
CA A:SER154 4.9 13.3 1.0
CZ A:ARG182 4.9 25.5 1.0
N A:SER154 5.0 11.2 1.0

Copper binding site 8 out of 16 in 4tm7

Go back to Copper Binding Sites List in 4tm7
Copper binding site 8 out of 16 in the Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu312

b:49.4
occ:0.32
 O A:HOH555 1.9 53.1 1.0
OD2 A:ASP160 2.0 33.1 1.0
CG A:ASP160 2.7 26.4 1.0
OD1 A:ASP160 2.8 28.5 1.0
CB A:ASP160 4.1 20.7 1.0

Copper binding site 9 out of 16 in 4tm7

Go back to Copper Binding Sites List in 4tm7
Copper binding site 9 out of 16 in the Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu313

b:49.5
occ:0.18
 OE2 A:GLU112 2.7 41.2 1.0
O A:HOH455 2.9 56.6 0.5
O2 A:EDO302 3.3 56.3 1.0
OE1 A:GLU112 3.4 31.7 1.0
CD A:GLU112 3.4 31.9 1.0
C2 A:EDO302 4.2 48.2 1.0
C1 A:EDO302 4.4 43.3 1.0
CG A:GLU112 4.9 28.9 1.0

Copper binding site 10 out of 16 in 4tm7

Go back to Copper Binding Sites List in 4tm7
Copper binding site 10 out of 16 in the Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Crystal Structure of 6-Phosphogluconolactonase From Mycobacterium Smegmatis N131D Mutant Soaked with CUSO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu314

b:56.8
occ:0.43
 OE1 A:GLU238 2.0 37.2 1.0
O A:HOH560 2.4 47.2 1.0
CD A:GLU238 2.8 36.1 1.0
OE2 A:GLU238 3.0 37.3 1.0
CG A:GLU238 4.2 28.1 1.0
CB A:GLU238 4.7 21.9 1.0

Reference:

N.Fujieda, J.Schatti, E.Stuttfeld, K.Ohkubo, T.Maier, S.Fukuzumi, T.R.Ward. Enzyme Repurposing of A Hydrolase As An Emergent Peroxidase Upon Metal Binding. Chem Sci V. 6 4060 2015.
ISSN: ISSN 2041-6520
PubMed: 29218172
DOI: 10.1039/C5SC01065A
Page generated: Sun Dec 13 11:15:59 2020

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