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Copper in PDB 2gbv: C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase

Enzymatic activity of C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase

All present enzymatic activity of C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase:
1.15.1.1;

Protein crystallography data

The structure of C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase, PDB code: 2gbv was solved by A.Hornberg, D.T.Logan, S.L.Marklund, M.Oliveberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.88 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 166.800, 202.370, 143.640, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 20.7

Other elements in 2gbv:

The structure of C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase also contains other interesting chemical elements:

Zinc (Zn) 10 atoms

Copper Binding Sites:

The binding sites of Copper atom in the C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase (pdb code 2gbv). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 10 binding sites of Copper where determined in the C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase, PDB code: 2gbv:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 10 in 2gbv

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Copper binding site 1 out of 10 in the C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu154

b:28.2
occ:0.47
 NE2 A:HIS120 1.9 30.3 1.0
NE2 A:HIS48 2.0 29.2 1.0
ND1 A:HIS46 2.3 29.9 1.0
CD2 A:HIS120 2.8 29.6 1.0
CE1 A:HIS120 2.9 30.2 1.0
CE1 A:HIS48 3.0 29.3 1.0
CD2 A:HIS48 3.0 28.6 1.0
NE2 A:HIS63 3.1 29.1 1.0
CG A:HIS46 3.1 29.9 1.0
CB A:HIS46 3.3 29.7 1.0
CE1 A:HIS46 3.3 29.9 1.0
CD2 A:HIS63 3.4 29.6 1.0
O A:HOH1453 3.5 34.0 1.0
CG A:HIS120 3.9 29.6 1.0
ND1 A:HIS120 4.0 30.4 1.0
ND1 A:HIS48 4.1 29.6 1.0
O A:HOH1436 4.1 26.7 1.0
CB A:VAL118 4.1 29.3 1.0
CG A:HIS48 4.1 29.1 1.0
CG1 A:VAL118 4.2 29.1 1.0
CE1 A:HIS63 4.2 28.7 1.0
CD2 A:HIS46 4.3 30.8 1.0
NE2 A:HIS46 4.3 30.4 1.0
CA A:HIS46 4.4 29.4 1.0
N A:HIS46 4.4 29.2 1.0
CG A:HIS63 4.6 28.6 1.0
O A:VAL118 4.6 29.3 1.0
O A:HIS46 4.7 29.8 1.0
C A:HIS46 4.8 29.4 1.0
CG2 A:VAL118 4.9 29.9 1.0
ND1 A:HIS63 5.0 28.3 1.0

Copper binding site 2 out of 10 in 2gbv

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Copper binding site 2 out of 10 in the C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu154

b:41.5
occ:0.47
 NE2 B:HIS120 1.9 29.6 1.0
NE2 B:HIS48 2.0 28.1 1.0
ND1 B:HIS46 2.2 28.3 1.0
CD2 B:HIS120 2.8 30.0 1.0
CE1 B:HIS48 2.9 28.4 1.0
CE1 B:HIS120 2.9 29.5 1.0
NE2 B:HIS63 3.0 27.3 1.0
CD2 B:HIS48 3.1 29.1 1.0
CG B:HIS46 3.1 28.5 1.0
CB B:HIS46 3.3 28.3 1.0
CE1 B:HIS46 3.3 28.7 1.0
CD2 B:HIS63 3.5 27.9 1.0
O B:HOH1266 3.6 37.5 1.0
CE1 B:HIS63 3.9 27.5 1.0
ND1 B:HIS120 3.9 29.4 1.0
CG B:HIS120 3.9 29.4 1.0
ND1 B:HIS48 4.0 28.8 1.0
CG B:HIS48 4.1 28.8 1.0
CD2 B:HIS46 4.3 28.6 1.0
CB B:VAL118 4.3 28.5 1.0
NE2 B:HIS46 4.4 29.4 1.0
CA B:HIS46 4.4 28.2 1.0
CG1 B:VAL118 4.5 28.7 1.0
CG B:HIS63 4.5 27.9 1.0
N B:HIS46 4.6 28.0 1.0
ND1 B:HIS63 4.7 27.5 1.0
O B:VAL118 4.8 27.7 1.0
O B:HIS46 4.9 28.4 1.0
C B:HIS46 4.9 28.4 1.0

Copper binding site 3 out of 10 in 2gbv

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Copper binding site 3 out of 10 in the C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu154

b:26.4
occ:0.49
 NE2 C:HIS120 2.0 30.8 1.0
NE2 C:HIS48 2.1 29.1 1.0
ND1 C:HIS46 2.2 30.2 1.0
CD2 C:HIS120 2.7 30.1 1.0
CG C:HIS46 3.0 30.6 1.0
CD2 C:HIS48 3.0 29.2 1.0
CE1 C:HIS120 3.0 30.9 1.0
CB C:HIS46 3.1 30.2 1.0
CE1 C:HIS48 3.1 29.6 1.0
NE2 C:HIS63 3.2 28.9 1.0
CE1 C:HIS46 3.3 29.8 1.0
CD2 C:HIS63 3.6 30.2 1.0
CG C:HIS120 3.9 29.6 1.0
ND1 C:HIS120 4.0 31.2 1.0
CB C:VAL118 4.1 28.7 1.0
ND1 C:HIS48 4.2 29.6 1.0
CA C:HIS46 4.2 30.0 1.0
CE1 C:HIS63 4.2 29.8 1.0
CG C:HIS48 4.2 29.1 1.0
CD2 C:HIS46 4.2 30.5 1.0
N C:HIS46 4.3 30.1 1.0
NE2 C:HIS46 4.3 30.5 1.0
O C:HOH1175 4.4 33.4 1.0
CG1 C:VAL118 4.4 28.2 1.0
O C:VAL118 4.5 28.0 1.0
O C:HIS46 4.6 29.7 1.0
C C:HIS46 4.6 30.0 1.0
CG C:HIS63 4.7 29.3 1.0
CG2 C:VAL118 4.8 28.5 1.0
ND1 C:HIS63 5.0 28.5 1.0

Copper binding site 4 out of 10 in 2gbv

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Copper binding site 4 out of 10 in the C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu154

b:31.8
occ:0.50
 NE2 D:HIS120 2.0 31.9 1.0
NE2 D:HIS48 2.1 29.2 1.0
ND1 D:HIS46 2.2 30.4 1.0
CD2 D:HIS120 2.8 31.4 1.0
CG D:HIS46 3.0 30.2 1.0
CE1 D:HIS120 3.0 31.8 1.0
CD2 D:HIS48 3.0 30.0 1.0
CE1 D:HIS48 3.1 30.4 1.0
NE2 D:HIS63 3.2 27.4 1.0
CE1 D:HIS46 3.2 31.0 1.0
CB D:HIS46 3.2 30.3 1.0
CD2 D:HIS63 3.4 28.2 1.0
O D:HOH1000 3.6 34.1 1.0
CG D:HIS120 4.0 31.2 1.0
ND1 D:HIS120 4.0 31.9 1.0
CD2 D:HIS46 4.2 30.4 1.0
ND1 D:HIS48 4.2 29.4 1.0
CG D:HIS48 4.2 29.3 1.0
CB D:VAL118 4.2 29.3 1.0
NE2 D:HIS46 4.2 31.2 1.0
O D:HOH1593 4.3 28.4 1.0
CG1 D:VAL118 4.3 29.0 1.0
CE1 D:HIS63 4.3 28.1 1.0
CA D:HIS46 4.3 29.8 1.0
N D:HIS46 4.4 29.8 1.0
O D:VAL118 4.6 29.4 1.0
CG D:HIS63 4.6 28.0 1.0
O D:HIS46 4.7 29.8 1.0
C D:HIS46 4.8 29.7 1.0
CG2 D:VAL118 5.0 29.1 1.0

Copper binding site 5 out of 10 in 2gbv

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Copper binding site 5 out of 10 in the C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu154

b:46.5
occ:0.46
 NE2 E:HIS120 1.8 31.3 1.0
NE2 E:HIS48 2.0 29.6 1.0
ND1 E:HIS46 2.3 30.1 1.0
CD2 E:HIS120 2.7 31.0 1.0
CE1 E:HIS120 2.9 31.4 1.0
CE1 E:HIS48 2.9 29.7 1.0
CD2 E:HIS48 3.0 29.4 1.0
CG E:HIS46 3.0 29.8 1.0
CB E:HIS46 3.1 29.7 1.0
NE2 E:HIS63 3.2 29.8 1.0
CE1 E:HIS46 3.4 30.6 1.0
CD2 E:HIS63 3.4 30.0 1.0
CG E:HIS120 3.8 30.4 1.0
ND1 E:HIS120 3.9 32.1 1.0
ND1 E:HIS48 4.0 29.4 1.0
CG E:HIS48 4.1 29.4 1.0
CB E:VAL118 4.2 29.5 1.0
CA E:HIS46 4.2 29.5 1.0
CD2 E:HIS46 4.2 30.0 1.0
N E:HIS46 4.3 29.3 1.0
O E:HOH236 4.3 35.0 1.0
NE2 E:HIS46 4.3 30.2 1.0
CE1 E:HIS63 4.4 30.6 1.0
CG1 E:VAL118 4.4 29.8 1.0
O E:HIS46 4.6 29.4 1.0
CG E:HIS63 4.6 29.9 1.0
C E:HIS46 4.7 29.4 1.0
O E:VAL118 4.7 29.4 1.0
CG2 E:VAL118 4.9 29.4 1.0

Copper binding site 6 out of 10 in 2gbv

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Copper binding site 6 out of 10 in the C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu154

b:27.9
occ:0.48
 NE2 F:HIS120 1.9 31.4 1.0
NE2 F:HIS48 2.0 28.6 1.0
ND1 F:HIS46 2.3 31.2 1.0
CD2 F:HIS120 2.8 31.6 1.0
CE1 F:HIS48 2.9 29.3 1.0
CE1 F:HIS120 2.9 31.8 1.0
CD2 F:HIS48 3.0 29.1 1.0
CG F:HIS46 3.1 30.7 1.0
CB F:HIS46 3.2 30.5 1.0
NE2 F:HIS63 3.2 30.9 1.0
CE1 F:HIS46 3.4 31.4 1.0
CD2 F:HIS63 3.5 30.8 1.0
O F:HOH760 3.5 30.4 1.0
CG F:HIS120 3.9 30.4 1.0
ND1 F:HIS120 4.0 31.5 1.0
ND1 F:HIS48 4.0 28.7 1.0
O F:HOH774 4.1 16.4 0.5
CB F:VAL118 4.1 29.2 1.0
CG F:HIS48 4.1 28.4 1.0
CG1 F:VAL118 4.2 29.7 1.0
CE1 F:HIS63 4.3 30.3 1.0
CD2 F:HIS46 4.3 30.6 1.0
CA F:HIS46 4.3 30.1 1.0
NE2 F:HIS46 4.4 31.7 1.0
N F:HIS46 4.4 29.7 1.0
O F:VAL118 4.6 29.0 1.0
CG F:HIS63 4.6 30.5 1.0
O F:HIS46 4.7 29.4 1.0
C F:HIS46 4.7 29.6 1.0
CG2 F:VAL118 4.8 29.2 1.0

Copper binding site 7 out of 10 in 2gbv

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Copper binding site 7 out of 10 in the C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cu154

b:24.6
occ:0.44
 NE2 G:HIS120 1.9 31.7 1.0
NE2 G:HIS48 2.1 30.0 1.0
ND1 G:HIS46 2.3 30.3 1.0
CD2 G:HIS120 2.7 31.3 1.0
CE1 G:HIS120 2.9 31.3 1.0
CE1 G:HIS48 3.0 30.2 1.0
CD2 G:HIS48 3.1 30.4 1.0
CG G:HIS46 3.1 30.1 1.0
NE2 G:HIS63 3.1 29.6 1.0
CB G:HIS46 3.2 30.4 1.0
CE1 G:HIS46 3.4 30.8 1.0
O G:HOH593 3.4 35.2 1.0
CD2 G:HIS63 3.6 29.6 1.0
CG G:HIS120 3.8 29.9 1.0
ND1 G:HIS120 3.9 30.9 1.0
O G:HOH600 4.0 37.1 1.0
CE1 G:HIS63 4.1 29.9 1.0
CB G:VAL118 4.1 29.4 1.0
ND1 G:HIS48 4.2 29.7 1.0
CG G:HIS48 4.2 30.0 1.0
CG1 G:VAL118 4.2 30.2 1.0
CA G:HIS46 4.2 30.0 1.0
CD2 G:HIS46 4.3 30.6 1.0
N G:HIS46 4.3 29.8 1.0
NE2 G:HIS46 4.4 30.7 1.0
O G:VAL118 4.6 29.0 1.0
CG G:HIS63 4.6 29.4 1.0
O G:HIS46 4.7 30.1 1.0
C G:HIS46 4.7 30.1 1.0
ND1 G:HIS63 4.9 29.3 1.0
CG2 G:VAL118 4.9 29.1 1.0

Copper binding site 8 out of 10 in 2gbv

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Copper binding site 8 out of 10 in the C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cu154

b:26.7
occ:0.48
 NE2 H:HIS120 2.0 31.5 1.0
NE2 H:HIS48 2.0 29.1 1.0
ND1 H:HIS46 2.3 30.5 1.0
CD2 H:HIS120 2.8 30.8 1.0
CD2 H:HIS48 3.0 29.6 1.0
CE1 H:HIS48 3.0 29.4 1.0
CE1 H:HIS120 3.0 31.6 1.0
CG H:HIS46 3.1 30.6 1.0
NE2 H:HIS63 3.2 30.5 1.0
CB H:HIS46 3.2 30.2 1.0
CE1 H:HIS46 3.3 31.2 1.0
O H:HOH415 3.4 35.2 1.0
CD2 H:HIS63 3.5 30.7 1.0
CG H:HIS120 3.9 30.1 1.0
ND1 H:HIS120 4.0 31.0 1.0
ND1 H:HIS48 4.1 28.7 1.0
CG H:HIS48 4.1 29.2 1.0
CE1 H:HIS63 4.2 29.9 1.0
CB H:VAL118 4.2 28.1 1.0
CD2 H:HIS46 4.3 30.4 1.0
CA H:HIS46 4.3 29.8 1.0
NE2 H:HIS46 4.4 31.4 1.0
N H:HIS46 4.4 29.5 1.0
CG1 H:VAL118 4.4 28.2 1.0
O H:VAL118 4.6 28.1 1.0
CG H:HIS63 4.6 29.9 1.0
O H:HIS46 4.7 30.0 1.0
C H:HIS46 4.7 29.6 1.0
CG2 H:VAL118 4.9 27.7 1.0
ND1 H:HIS63 4.9 30.0 1.0

Copper binding site 9 out of 10 in 2gbv

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Copper binding site 9 out of 10 in the C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu154

b:36.4
occ:0.51
 NE2 I:HIS120 1.9 31.8 1.0
NE2 I:HIS48 2.0 29.4 1.0
ND1 I:HIS46 2.3 29.8 1.0
CD2 I:HIS120 2.7 31.4 1.0
CE1 I:HIS48 2.9 29.5 1.0
CE1 I:HIS120 3.0 31.7 1.0
CD2 I:HIS48 3.0 29.9 1.0
CG I:HIS46 3.0 29.8 1.0
NE2 I:HIS63 3.1 29.5 1.0
CB I:HIS46 3.1 29.6 1.0
CD2 I:HIS63 3.4 29.6 1.0
CE1 I:HIS46 3.4 30.7 1.0
O I:HOH274 3.7 28.3 1.0
CG I:HIS120 3.9 30.0 1.0
ND1 I:HIS120 4.0 32.0 1.0
CB I:VAL118 4.1 29.0 1.0
ND1 I:HIS48 4.1 29.3 1.0
CG I:HIS48 4.1 29.3 1.0
O I:HOH287 4.2 30.8 1.0
CE1 I:HIS63 4.2 29.7 1.0
CA I:HIS46 4.2 29.3 1.0
CD2 I:HIS46 4.2 30.3 1.0
CG1 I:VAL118 4.3 28.8 1.0
N I:HIS46 4.3 29.4 1.0
NE2 I:HIS46 4.4 30.4 1.0
CG I:HIS63 4.5 29.8 1.0
O I:VAL118 4.6 28.6 1.0
O I:HIS46 4.6 29.2 1.0
C I:HIS46 4.7 29.0 1.0
CG2 I:VAL118 4.8 29.0 1.0
ND1 I:HIS63 4.9 29.2 1.0

Copper binding site 10 out of 10 in 2gbv

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Copper binding site 10 out of 10 in the C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of C6A/C111A/C57A/C146A Holo Cuzn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cu154

b:31.3
occ:0.44
 NE2 J:HIS120 1.9 31.1 1.0
NE2 J:HIS48 2.0 28.6 1.0
ND1 J:HIS46 2.3 29.9 1.0
CD2 J:HIS120 2.7 30.6 1.0
CE1 J:HIS48 3.0 28.9 1.0
CD2 J:HIS48 3.0 29.4 1.0
CE1 J:HIS120 3.0 30.4 1.0
CG J:HIS46 3.1 29.5 1.0
CB J:HIS46 3.2 29.6 1.0
NE2 J:HIS63 3.2 28.6 1.0
CE1 J:HIS46 3.3 29.9 1.0
CD2 J:HIS63 3.5 29.1 1.0
O J:HOH283 3.8 32.3 1.0
CG J:HIS120 3.9 29.8 1.0
ND1 J:HIS120 4.0 30.1 1.0
ND1 J:HIS48 4.1 28.5 1.0
CB J:VAL118 4.1 29.6 1.0
CG J:HIS48 4.1 28.9 1.0
CA J:HIS46 4.2 29.5 1.0
O J:HOH194 4.2 33.5 1.0
CD2 J:HIS46 4.3 29.5 1.0
CE1 J:HIS63 4.3 29.0 1.0
N J:HIS46 4.3 29.6 1.0
CG1 J:VAL118 4.3 30.1 1.0
NE2 J:HIS46 4.4 29.8 1.0
CG J:HIS63 4.6 29.0 1.0
O J:VAL118 4.6 29.0 1.0
O J:HIS46 4.6 29.5 1.0
C J:HIS46 4.7 29.4 1.0
CG2 J:VAL118 4.8 29.4 1.0
ND1 J:HIS63 5.0 28.9 1.0

Reference:

A.Hornberg, D.T.Logan, S.L.Marklund, M.Oliveberg. The Coupling Between Disulphide Status, Metallation and Dimer Interface Strength in Cu/Zn Superoxide Dismutase J.Mol.Biol. V. 365 333 2007.
ISSN: ISSN 0022-2836
PubMed: 17070542
DOI: 10.1016/J.JMB.2006.09.048
Page generated: Tue Jul 30 23:36:50 2024

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