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Copper in PDB 1fun: Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S)

Enzymatic activity of Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S)

All present enzymatic activity of Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S):
1.15.1.1;

Protein crystallography data

The structure of Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S), PDB code: 1fun was solved by T.P.Lo, J.A.Tainer, E.D.Getzoff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.85
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 205.200, 167.000, 145.500, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / n/a

Copper Binding Sites:

The binding sites of Copper atom in the Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S) (pdb code 1fun). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 10 binding sites of Copper where determined in the Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S), PDB code: 1fun:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 10 in 1fun

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Copper binding site 1 out of 10 in the Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu154

b:42.4
occ:1.00
NE2 A:HIS120 2.1 30.1 1.0
NE2 A:HIS48 2.1 24.0 1.0
ND1 A:HIS46 2.2 30.1 1.0
NE2 A:HIS63 2.6 37.2 1.0
CE1 A:HIS48 2.8 19.8 1.0
CE1 A:HIS120 2.9 27.2 1.0
CD2 A:HIS120 3.1 27.3 1.0
CG A:HIS46 3.1 27.2 1.0
CD2 A:HIS63 3.1 34.1 1.0
CE1 A:HIS46 3.1 32.1 1.0
CD2 A:HIS48 3.2 21.3 1.0
CB A:HIS46 3.4 23.6 1.0
CE1 A:HIS63 3.7 35.9 1.0
O A:HOH356 4.0 39.3 1.0
ND1 A:HIS48 4.0 19.6 1.0
ND1 A:HIS120 4.0 25.0 1.0
CG A:HIS120 4.1 25.7 1.0
NE2 A:HIS46 4.2 34.4 1.0
CD2 A:HIS46 4.2 30.5 1.0
CG A:HIS48 4.2 20.0 1.0
CG A:HIS63 4.3 29.9 1.0
CA A:HIS46 4.4 23.4 1.0
N A:HIS46 4.4 23.3 1.0
ND1 A:HIS63 4.5 35.7 1.0
CB A:VAL118 4.6 12.5 1.0
C A:HIS46 4.8 23.8 1.0
O A:HIS46 4.8 27.6 1.0
CG1 A:VAL118 4.8 12.7 1.0

Copper binding site 2 out of 10 in 1fun

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Copper binding site 2 out of 10 in the Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu154

b:18.4
occ:1.00
ND1 F:HIS46 2.1 6.5 1.0
NE2 F:HIS48 2.1 2.5 1.0
NE2 F:HIS120 2.1 10.5 1.0
CE1 F:HIS48 2.9 2.0 1.0
CG F:HIS46 3.0 2.9 1.0
CD2 F:HIS120 3.0 9.8 1.0
CE1 F:HIS120 3.1 7.6 1.0
CE1 F:HIS46 3.1 8.8 1.0
NE2 F:HIS63 3.2 14.4 1.0
CD2 F:HIS48 3.2 3.0 1.0
CB F:HIS46 3.2 2.0 1.0
CD2 F:HIS63 3.6 5.0 1.0
ND1 F:HIS48 4.0 2.0 1.0
ND1 F:HIS120 4.1 5.7 1.0
CG F:HIS120 4.1 6.6 1.0
CD2 F:HIS46 4.2 4.5 1.0
NE2 F:HIS46 4.2 5.2 1.0
CG F:HIS48 4.3 2.4 1.0
CE1 F:HIS63 4.3 16.1 1.0
CA F:HIS46 4.5 2.0 1.0
CG1 F:VAL118 4.6 2.0 1.0
CB F:VAL118 4.6 2.0 1.0
N F:HIS46 4.7 4.7 1.0
CG F:HIS63 4.8 8.9 1.0
O F:HOH342 5.0 37.7 1.0

Copper binding site 3 out of 10 in 1fun

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Copper binding site 3 out of 10 in the Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu154

b:23.6
occ:1.00
NE2 B:HIS120 1.9 20.7 1.0
ND1 B:HIS46 2.1 21.1 1.0
NE2 B:HIS48 2.1 10.1 1.0
NE2 B:HIS63 2.4 29.2 1.0
CE1 B:HIS120 2.8 17.8 1.0
CG B:HIS46 2.9 20.4 1.0
CE1 B:HIS48 3.0 10.6 1.0
CD2 B:HIS120 3.0 19.9 1.0
CD2 B:HIS63 3.0 26.6 1.0
CB B:HIS46 3.1 18.7 1.0
CE1 B:HIS46 3.2 22.9 1.0
CD2 B:HIS48 3.2 13.7 1.0
CE1 B:HIS63 3.6 28.1 1.0
ND1 B:HIS120 3.9 14.4 1.0
CG B:HIS120 4.0 17.4 1.0
ND1 B:HIS48 4.1 11.7 1.0
CD2 B:HIS46 4.1 22.3 1.0
NE2 B:HIS46 4.2 22.2 1.0
CG B:HIS63 4.3 22.3 1.0
CG B:HIS48 4.3 10.6 1.0
CA B:HIS46 4.4 15.4 1.0
ND1 B:HIS63 4.5 26.0 1.0
CG1 B:VAL118 4.5 2.0 1.0
CB B:VAL118 4.7 2.0 1.0
N B:HIS46 4.7 17.8 1.0
C B:HIS46 5.0 14.8 1.0

Copper binding site 4 out of 10 in 1fun

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Copper binding site 4 out of 10 in the Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cu154

b:18.2
occ:1.00
NE2 G:HIS120 2.1 11.1 1.0
NE2 G:HIS48 2.2 6.6 1.0
ND1 G:HIS46 2.2 10.8 1.0
NE2 G:HIS63 2.4 15.8 1.0
CE1 G:HIS120 2.9 6.1 1.0
CE1 G:HIS48 2.9 4.8 1.0
CG G:HIS46 3.0 6.8 1.0
CD2 G:HIS63 3.1 15.6 1.0
CD2 G:HIS120 3.1 8.8 1.0
CB G:HIS46 3.2 6.3 1.0
CE1 G:HIS46 3.3 10.1 1.0
CD2 G:HIS48 3.3 2.6 1.0
CE1 G:HIS63 3.5 16.6 1.0
ND1 G:HIS120 4.0 5.4 1.0
ND1 G:HIS48 4.1 2.0 1.0
CG G:HIS120 4.2 4.6 1.0
CD2 G:HIS46 4.2 7.1 1.0
CG G:HIS48 4.3 3.2 1.0
CG G:HIS63 4.3 11.3 1.0
NE2 G:HIS46 4.3 11.2 1.0
ND1 G:HIS63 4.4 12.4 1.0
CA G:HIS46 4.5 5.2 1.0
CG1 G:VAL118 4.6 2.0 1.0
N G:HIS46 4.6 8.3 1.0
CB G:VAL118 4.7 2.0 1.0

Copper binding site 5 out of 10 in 1fun

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Copper binding site 5 out of 10 in the Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu154

b:30.2
occ:1.00
ND1 C:HIS46 1.9 11.8 1.0
NE2 C:HIS120 2.0 14.0 1.0
NE2 C:HIS48 2.1 12.5 1.0
NE2 C:HIS63 2.4 20.3 1.0
CG C:HIS46 2.8 13.9 1.0
CE1 C:HIS120 2.9 11.1 1.0
CE1 C:HIS46 3.0 14.2 1.0
CD2 C:HIS120 3.0 11.4 1.0
CE1 C:HIS48 3.0 14.0 1.0
CB C:HIS46 3.1 14.1 1.0
CD2 C:HIS48 3.1 10.5 1.0
CD2 C:HIS63 3.2 19.3 1.0
CE1 C:HIS63 3.4 17.8 1.0
ND1 C:HIS120 4.0 8.1 1.0
CD2 C:HIS46 4.0 14.4 1.0
NE2 C:HIS46 4.0 18.8 1.0
CG C:HIS120 4.1 9.2 1.0
ND1 C:HIS48 4.1 8.1 1.0
CG C:HIS48 4.2 11.8 1.0
CG C:HIS63 4.3 16.4 1.0
ND1 C:HIS63 4.4 19.5 1.0
CA C:HIS46 4.4 11.5 1.0
N C:HIS46 4.7 12.4 1.0
CB C:VAL118 4.8 11.8 1.0
CG1 C:VAL118 4.9 14.2 1.0

Copper binding site 6 out of 10 in 1fun

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Copper binding site 6 out of 10 in the Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cu154

b:18.6
occ:1.00
ND1 H:HIS46 2.0 7.3 1.0
NE2 H:HIS120 2.0 9.9 1.0
NE2 H:HIS48 2.1 2.0 1.0
NE2 H:HIS63 2.5 11.5 1.0
CE1 H:HIS48 2.8 2.0 1.0
CE1 H:HIS120 2.8 3.9 1.0
CE1 H:HIS46 2.9 10.7 1.0
CG H:HIS46 3.0 5.8 1.0
CD2 H:HIS120 3.1 7.8 1.0
CD2 H:HIS63 3.1 7.7 1.0
CD2 H:HIS48 3.3 4.2 1.0
CB H:HIS46 3.4 5.7 1.0
CE1 H:HIS63 3.6 14.0 1.0
ND1 H:HIS120 4.0 2.0 1.0
ND1 H:HIS48 4.0 2.0 1.0
NE2 H:HIS46 4.0 8.6 1.0
CD2 H:HIS46 4.1 5.3 1.0
CG H:HIS120 4.1 4.7 1.0
CG H:HIS48 4.2 2.4 1.0
CG H:HIS63 4.3 6.9 1.0
ND1 H:HIS63 4.5 10.4 1.0
CA H:HIS46 4.6 2.8 1.0
CG1 H:VAL118 4.6 2.5 1.0
CB H:VAL118 4.7 3.0 1.0
N H:HIS46 4.8 4.8 1.0

Copper binding site 7 out of 10 in 1fun

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Copper binding site 7 out of 10 in the Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu154

b:47.0
occ:1.00
NE2 D:HIS120 2.0 38.6 1.0
NE2 D:HIS48 2.2 25.8 1.0
ND1 D:HIS46 2.3 41.5 1.0
NE2 D:HIS63 2.6 39.6 1.0
CB D:HIS46 2.8 31.0 1.0
CE1 D:HIS120 2.9 36.7 1.0
CG D:HIS46 2.9 37.5 1.0
CD2 D:HIS120 3.0 37.6 1.0
CD2 D:HIS63 3.1 40.7 1.0
CD2 D:HIS48 3.1 21.2 1.0
CE1 D:HIS48 3.1 24.5 1.0
CE1 D:HIS63 3.5 39.2 1.0
CE1 D:HIS46 3.5 42.4 1.0
ND1 D:HIS120 4.0 33.1 1.0
CA D:HIS46 4.0 29.0 1.0
CG D:HIS120 4.1 34.0 1.0
CD2 D:HIS46 4.2 42.1 1.0
CG D:HIS63 4.2 38.3 1.0
ND1 D:HIS48 4.2 25.1 1.0
CG D:HIS48 4.2 23.5 1.0
CG1 D:VAL118 4.2 14.4 1.0
N D:HIS46 4.3 31.0 1.0
ND1 D:HIS63 4.3 41.4 1.0
NE2 D:HIS46 4.4 42.8 1.0
CB D:VAL118 4.5 15.6 1.0
C D:HIS46 4.6 27.4 1.0
O D:VAL118 4.7 16.8 1.0
O D:HIS46 4.8 29.7 1.0

Copper binding site 8 out of 10 in 1fun

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Copper binding site 8 out of 10 in the Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu154

b:24.2
occ:1.00
ND1 I:HIS46 1.9 12.5 1.0
NE2 I:HIS48 1.9 10.9 1.0
NE2 I:HIS120 2.0 18.6 1.0
CE1 I:HIS48 2.7 9.9 1.0
CG I:HIS46 2.8 10.6 1.0
NE2 I:HIS63 2.8 22.3 1.0
CE1 I:HIS120 2.9 16.5 1.0
CE1 I:HIS46 2.9 18.1 1.0
CB I:HIS46 3.0 10.9 1.0
CD2 I:HIS48 3.0 13.6 1.0
CD2 I:HIS120 3.1 18.2 1.0
CD2 I:HIS63 3.3 17.9 1.0
CE1 I:HIS63 3.9 21.8 1.0
ND1 I:HIS48 3.9 13.7 1.0
CD2 I:HIS46 3.9 12.9 1.0
NE2 I:HIS46 4.0 14.8 1.0
ND1 I:HIS120 4.1 12.4 1.0
CG I:HIS48 4.1 13.9 1.0
CG I:HIS120 4.2 17.3 1.0
CA I:HIS46 4.4 8.6 1.0
CG I:HIS63 4.5 14.2 1.0
N I:HIS46 4.6 6.4 1.0
CG1 I:VAL118 4.7 7.4 1.0
CB I:VAL118 4.7 6.7 1.0
ND1 I:HIS63 4.7 17.6 1.0
C I:HIS46 4.9 13.1 1.0

Copper binding site 9 out of 10 in 1fun

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Copper binding site 9 out of 10 in the Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu154

b:51.6
occ:1.00
NE2 E:HIS120 1.9 44.7 1.0
ND1 E:HIS46 2.3 51.8 1.0
NE2 E:HIS48 2.4 54.9 1.0
CE1 E:HIS120 2.6 44.7 1.0
NE2 E:HIS63 3.0 51.1 1.0
CD2 E:HIS120 3.0 45.7 1.0
CG E:HIS46 3.1 52.4 1.0
CD2 E:HIS63 3.1 51.3 1.0
CB E:HIS46 3.2 50.9 1.0
CE1 E:HIS48 3.3 57.0 1.0
CD2 E:HIS48 3.4 56.5 1.0
CE1 E:HIS46 3.4 52.1 1.0
ND1 E:HIS120 3.8 44.7 1.0
CG E:HIS120 4.0 44.7 1.0
CE1 E:HIS63 4.2 49.6 1.0
CA E:HIS46 4.3 50.7 1.0
CD2 E:HIS46 4.3 52.0 1.0
CG E:HIS63 4.4 49.8 1.0
N E:HIS46 4.4 48.8 1.0
ND1 E:HIS48 4.4 55.1 1.0
NE2 E:HIS46 4.5 52.3 1.0
CB E:VAL118 4.5 46.1 1.0
CG E:HIS48 4.5 55.8 1.0
CG1 E:VAL118 4.6 43.5 1.0
C E:HIS46 4.8 51.0 1.0
O E:HIS46 4.8 52.8 1.0
ND1 E:HIS63 4.9 50.3 1.0
O E:VAL118 4.9 47.8 1.0

Copper binding site 10 out of 10 in 1fun

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Copper binding site 10 out of 10 in the Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Superoxide Dismutase Mutant with Lys 136 Replaced By Glu, Cys 6 Replaced By Ala and Cys 111 Replaced By Ser (K136E, C6A, C111S) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cu154

b:41.8
occ:1.00
NE2 J:HIS120 2.1 30.4 1.0
ND1 J:HIS46 2.1 37.5 1.0
NE2 J:HIS63 2.3 38.9 1.0
NE2 J:HIS48 2.4 32.2 1.0
CE1 J:HIS46 2.5 38.4 1.0
CE1 J:HIS120 2.7 28.5 1.0
CD2 J:HIS63 2.9 38.1 1.0
CE1 J:HIS48 3.0 31.3 1.0
CD2 J:HIS120 3.2 28.7 1.0
CG J:HIS46 3.3 36.9 1.0
CD2 J:HIS48 3.4 28.0 1.0
CE1 J:HIS63 3.5 38.8 1.0
NE2 J:HIS46 3.7 36.2 1.0
ND1 J:HIS120 3.9 26.6 1.0
CB J:HIS46 4.0 35.4 1.0
ND1 J:HIS48 4.1 27.3 1.0
CD2 J:HIS46 4.1 38.2 1.0
CG J:HIS120 4.1 27.8 1.0
CG J:HIS63 4.2 36.8 1.0
CG J:HIS48 4.3 28.4 1.0
ND1 J:HIS63 4.4 37.6 1.0
N J:HIS46 4.6 29.0 1.0
CB J:VAL118 4.7 30.2 1.0
CG1 J:VAL118 4.7 31.4 1.0
CA J:HIS46 4.8 33.1 1.0
O J:HIS46 5.0 35.0 1.0

Reference:

C.L.Fisher, D.E.Cabelli, R.A.Hallewell, P.Beroza, T.P.Lo, E.D.Getzoff, J.A.Tainer. Computational, Pulse-Radiolytic, and Structural Investigations of Lysine-136 and Its Role in the Electrostatic Triad of Human Cu,Zn Superoxide Dismutase. Proteins V. 29 103 1997.
ISSN: ISSN 0887-3585
PubMed: 9294870
DOI: 10.1002/(SICI)1097-0134(199709)29:1<103::AID-PROT8>3.0.CO;2-G
Page generated: Wed Sep 2 21:43:23 2020
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