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Zinc in PDB 4mcm: Human SOD1 C57S Mutant, As-Isolated

Enzymatic activity of Human SOD1 C57S Mutant, As-Isolated

All present enzymatic activity of Human SOD1 C57S Mutant, As-Isolated:
1.15.1.1;

Protein crystallography data

The structure of Human SOD1 C57S Mutant, As-Isolated, PDB code: 4mcm was solved by K.Sea, S.H.Sohn, A.Durazo, Y.Sheng, B.Shaw, X.Cao, A.B.Taylor, L.J.Whitson, S.P.Holloway, P.J.Hart, D.E.Cabelli, E.B.Gralla, J.S.Valentine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.84 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.530, 163.883, 174.140, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 26.2

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc atom in the Human SOD1 C57S Mutant, As-Isolated (pdb code 4mcm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the Human SOD1 C57S Mutant, As-Isolated, PDB code: 4mcm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in 4mcm

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Zinc binding site 1 out of 24 in the Human SOD1 C57S Mutant, As-Isolated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human SOD1 C57S Mutant, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:22.5
occ:0.85
NE2 A:HIS120 2.0 12.9 1.0
NE2 A:HIS48 2.0 14.5 1.0
O4 A:SO4203 2.2 15.5 0.7
ND1 A:HIS46 2.2 16.6 1.0
CE1 A:HIS48 2.8 14.9 1.0
CE1 A:HIS120 2.9 14.7 1.0
CD2 A:HIS120 3.0 10.9 1.0
CD2 A:HIS48 3.1 10.4 1.0
CG A:HIS46 3.1 12.0 1.0
NE2 A:HIS63 3.2 14.0 1.0
CE1 A:HIS46 3.2 16.0 1.0
CB A:HIS46 3.4 11.4 1.0
S A:SO4203 3.4 16.1 0.7
CD2 A:HIS63 3.6 13.2 1.0
O3 A:SO4203 3.6 19.0 0.7
ND1 A:HIS48 4.0 15.9 1.0
ND1 A:HIS120 4.0 15.0 1.0
CG A:HIS120 4.1 13.4 1.0
CG A:HIS48 4.2 10.5 1.0
O2 A:SO4203 4.3 22.8 0.7
CE1 A:HIS63 4.3 15.7 1.0
CD2 A:HIS46 4.3 14.1 1.0
NE2 A:HIS46 4.3 12.6 1.0
O1 A:SO4203 4.4 21.0 0.7
CB A:VAL118 4.5 12.2 1.0
CG1 A:VAL118 4.5 10.6 1.0
CA A:HIS46 4.8 9.3 1.0
CG A:HIS63 4.8 14.1 1.0

Zinc binding site 2 out of 24 in 4mcm

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Zinc binding site 2 out of 24 in the Human SOD1 C57S Mutant, As-Isolated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human SOD1 C57S Mutant, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:13.9
occ:1.00
OD1 A:ASP83 1.9 9.1 1.0
ND1 A:HIS80 2.0 12.0 1.0
ND1 A:HIS71 2.1 11.2 1.0
ND1 A:HIS63 2.1 13.7 1.0
CG A:ASP83 2.7 12.5 1.0
CE1 A:HIS80 2.9 14.2 1.0
OD2 A:ASP83 2.9 12.2 1.0
CG A:HIS80 3.0 11.9 1.0
CE1 A:HIS71 3.1 11.8 1.0
CE1 A:HIS63 3.1 15.7 1.0
CG A:HIS71 3.1 14.9 1.0
CG A:HIS63 3.2 14.1 1.0
CB A:HIS80 3.4 12.0 1.0
CB A:HIS71 3.5 14.5 1.0
CB A:HIS63 3.5 13.2 1.0
O A:LYS136 3.7 21.3 1.0
CA A:HIS71 3.8 14.4 1.0
NE2 A:HIS80 4.0 17.0 1.0
CD2 A:HIS80 4.1 12.7 1.0
CB A:ASP83 4.2 10.2 1.0
NE2 A:HIS71 4.2 11.3 1.0
NE2 A:HIS63 4.2 14.0 1.0
CD2 A:HIS71 4.2 15.1 1.0
CD2 A:HIS63 4.3 13.2 1.0
N A:HIS80 4.6 12.1 1.0
N A:GLY72 4.7 13.9 1.0
CA A:HIS80 4.7 11.8 1.0
CA A:ASP83 4.7 10.3 1.0
O A:HOH306 4.7 12.8 1.0
C A:LYS136 4.8 21.2 1.0
C A:HIS71 4.8 13.9 1.0
N A:HIS71 4.9 11.6 1.0
O A:GLY72 4.9 11.8 1.0
N A:ASP83 4.9 9.3 1.0

Zinc binding site 3 out of 24 in 4mcm

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Zinc binding site 3 out of 24 in the Human SOD1 C57S Mutant, As-Isolated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human SOD1 C57S Mutant, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:21.8
occ:0.67
NE2 B:HIS120 2.0 10.4 1.0
NE2 B:HIS48 2.1 11.7 1.0
O2 B:SO4203 2.3 14.9 0.7
ND1 B:HIS46 2.5 13.5 1.0
CE1 B:HIS48 2.8 12.9 1.0
CE1 B:HIS120 2.9 11.8 1.0
CD2 B:HIS120 2.9 9.9 1.0
NE2 B:HIS63 3.2 16.7 1.0
CD2 B:HIS48 3.2 10.0 1.0
CE1 B:HIS46 3.4 14.2 1.0
O B:HOH353 3.5 20.7 1.0
CG B:HIS46 3.5 13.1 1.0
CD2 B:HIS63 3.5 16.3 1.0
S B:SO4203 3.5 23.2 0.7
CB B:HIS46 3.8 9.1 1.0
O1 B:SO4203 3.8 23.2 0.7
ND1 B:HIS120 3.9 12.6 1.0
ND1 B:HIS48 4.0 12.7 1.0
CG B:HIS120 4.0 13.3 1.0
CG B:HIS48 4.2 10.8 1.0
O4 B:SO4203 4.3 22.9 0.7
CE1 B:HIS63 4.3 15.0 1.0
NE2 B:HIS46 4.5 10.5 1.0
CB B:VAL118 4.5 10.2 1.0
CG1 B:VAL118 4.5 10.0 1.0
O3 B:SO4203 4.6 26.5 0.7
CD2 B:HIS46 4.6 11.5 1.0
CG B:HIS63 4.7 16.9 1.0
NE B:ARG143 5.0 20.9 1.0
CA B:HIS46 5.0 11.2 1.0

Zinc binding site 4 out of 24 in 4mcm

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Zinc binding site 4 out of 24 in the Human SOD1 C57S Mutant, As-Isolated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human SOD1 C57S Mutant, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:13.1
occ:1.00
OD1 B:ASP83 1.8 7.7 1.0
ND1 B:HIS63 2.0 14.8 1.0
ND1 B:HIS71 2.0 11.1 1.0
ND1 B:HIS80 2.1 12.1 1.0
CG B:ASP83 2.6 11.5 1.0
OD2 B:ASP83 2.8 11.4 1.0
CE1 B:HIS63 2.9 15.0 1.0
CE1 B:HIS71 3.0 14.9 1.0
CE1 B:HIS80 3.0 13.8 1.0
CG B:HIS63 3.1 16.9 1.0
CG B:HIS80 3.1 13.1 1.0
CG B:HIS71 3.1 11.7 1.0
CB B:HIS80 3.4 12.1 1.0
CB B:HIS63 3.4 12.9 1.0
CB B:HIS71 3.5 14.5 1.0
CA B:HIS71 3.9 13.0 1.0
O B:LYS136 4.0 15.2 1.0
CB B:ASP83 4.1 8.6 1.0
NE2 B:HIS63 4.1 16.7 1.0
NE2 B:HIS80 4.1 17.0 1.0
NE2 B:HIS71 4.1 13.5 1.0
CD2 B:HIS80 4.2 13.1 1.0
CD2 B:HIS63 4.2 16.3 1.0
CD2 B:HIS71 4.2 11.9 1.0
CA B:ASP83 4.6 9.5 1.0
N B:HIS80 4.6 16.2 1.0
CA B:HIS80 4.6 12.6 1.0
O B:HOH316 4.7 20.7 1.0
N B:GLY72 4.8 10.5 1.0
N B:ASP83 4.8 10.6 1.0
C B:HIS71 4.9 15.2 1.0
N B:HIS71 4.9 15.7 1.0
CA B:HIS63 5.0 14.2 1.0
C B:LYS136 5.0 19.0 1.0

Zinc binding site 5 out of 24 in 4mcm

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Zinc binding site 5 out of 24 in the Human SOD1 C57S Mutant, As-Isolated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human SOD1 C57S Mutant, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:62.4
occ:0.88
O3 C:SO4203 2.0 54.7 0.8
NE2 C:HIS120 2.0 59.0 1.0
ND1 C:HIS46 2.3 59.0 1.0
CE1 C:HIS120 2.5 61.2 1.0
NE2 C:HIS48 2.6 55.6 1.0
NE2 C:HIS63 3.1 58.3 1.0
CE1 C:HIS46 3.2 58.7 1.0
S C:SO4203 3.2 63.5 0.8
CE1 C:HIS48 3.2 54.1 1.0
CG C:HIS46 3.2 59.9 1.0
CD2 C:HIS120 3.3 58.4 1.0
O1 C:SO4203 3.5 56.6 0.8
CB C:HIS46 3.5 53.4 1.0
CD2 C:HIS63 3.6 58.5 1.0
ND1 C:HIS120 3.7 58.5 1.0
CG2 C:VAL118 3.7 56.4 1.0
CD2 C:HIS48 3.7 51.1 1.0
O4 C:SO4203 3.8 69.4 0.8
CE1 C:HIS63 4.0 59.5 1.0
CG C:HIS120 4.1 58.3 1.0
NE2 C:HIS46 4.3 59.2 1.0
CD2 C:HIS46 4.3 55.1 1.0
O2 C:SO4203 4.3 56.3 0.8
ND1 C:HIS48 4.4 54.0 1.0
CG C:HIS48 4.7 51.6 1.0
CG C:HIS63 4.7 53.8 1.0
CA C:HIS46 4.8 50.8 1.0
ND1 C:HIS63 4.9 54.6 1.0
N C:HIS46 4.9 50.1 1.0

Zinc binding site 6 out of 24 in 4mcm

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Zinc binding site 6 out of 24 in the Human SOD1 C57S Mutant, As-Isolated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human SOD1 C57S Mutant, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:49.1
occ:0.88
OD1 C:ASP83 2.1 42.9 1.0
ND1 C:HIS80 2.2 47.5 1.0
ND1 C:HIS63 2.3 54.6 1.0
OD2 C:ASP83 2.5 45.9 1.0
ND1 C:HIS71 2.5 60.3 1.0
CG C:ASP83 2.6 41.5 1.0
CG C:HIS80 2.9 51.5 1.0
CB C:HIS80 3.1 47.0 1.0
CG C:HIS63 3.1 53.8 1.0
CE1 C:HIS80 3.2 51.7 1.0
CE1 C:HIS63 3.3 59.5 1.0
CB C:HIS63 3.3 49.9 1.0
CG C:HIS71 3.4 59.1 1.0
CB C:HIS71 3.5 57.9 1.0
CE1 C:HIS71 3.6 58.6 1.0
O C:LYS136 3.6 68.5 1.0
CA C:HIS71 3.7 58.2 1.0
CD2 C:HIS80 4.0 56.4 1.0
CB C:ASP83 4.1 37.3 1.0
NE2 C:HIS80 4.2 58.1 1.0
CA C:HIS80 4.3 50.9 1.0
N C:HIS80 4.3 53.7 1.0
CD2 C:HIS63 4.3 58.5 1.0
NE2 C:HIS63 4.3 58.3 1.0
N C:GLY72 4.5 59.3 1.0
CD2 C:HIS71 4.6 63.3 1.0
N C:HIS71 4.6 56.6 1.0
NE2 C:HIS71 4.6 59.2 1.0
C C:HIS71 4.6 63.1 1.0
C C:LYS136 4.7 67.0 1.0
CA C:ASP83 4.8 45.4 1.0
N C:ASP83 4.8 45.6 1.0
CA C:HIS63 4.9 50.5 1.0
O C:HIS80 4.9 46.8 1.0
C C:HIS80 5.0 48.9 1.0

Zinc binding site 7 out of 24 in 4mcm

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Zinc binding site 7 out of 24 in the Human SOD1 C57S Mutant, As-Isolated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human SOD1 C57S Mutant, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:32.2
occ:0.62
NE2 D:HIS120 1.9 22.6 1.0
NE2 D:HIS48 2.1 22.7 1.0
ND1 D:HIS46 2.5 17.4 1.0
CE1 D:HIS120 2.8 24.8 1.0
O4 D:SO4203 2.8 27.1 0.6
CD2 D:HIS120 2.8 19.6 1.0
CE1 D:HIS48 2.9 21.9 1.0
NE2 D:HIS63 3.1 20.8 1.0
CD2 D:HIS48 3.2 18.0 1.0
CG D:HIS46 3.3 17.2 1.0
CB D:HIS46 3.4 18.0 1.0
CD2 D:HIS63 3.5 20.8 1.0
CE1 D:HIS46 3.5 18.2 1.0
ND1 D:HIS120 3.8 22.2 1.0
CG D:HIS120 3.9 21.8 1.0
S D:SO4203 4.1 38.6 0.6
ND1 D:HIS48 4.1 23.4 1.0
CE1 D:HIS63 4.1 20.2 1.0
CG D:HIS48 4.2 19.9 1.0
O3 D:SO4203 4.4 33.5 0.6
CB D:VAL118 4.4 18.4 1.0
CD2 D:HIS46 4.5 17.3 1.0
CG1 D:VAL118 4.5 19.2 1.0
NE2 D:HIS46 4.5 19.1 1.0
O1 D:SO4203 4.6 34.6 0.6
CG D:HIS63 4.7 19.2 1.0
CA D:HIS46 4.7 18.6 1.0
N D:HIS46 4.9 20.7 1.0
ND1 D:HIS63 5.0 14.8 1.0

Zinc binding site 8 out of 24 in 4mcm

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Zinc binding site 8 out of 24 in the Human SOD1 C57S Mutant, As-Isolated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Human SOD1 C57S Mutant, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn202

b:15.0
occ:1.00
OD1 D:ASP83 1.9 11.3 1.0
ND1 D:HIS80 2.1 18.9 1.0
ND1 D:HIS71 2.1 15.6 1.0
ND1 D:HIS63 2.2 14.8 1.0
CG D:ASP83 2.7 14.9 1.0
OD2 D:ASP83 2.8 11.3 1.0
CE1 D:HIS71 2.9 14.4 1.0
CE1 D:HIS80 3.0 15.8 1.0
CG D:HIS80 3.1 14.0 1.0
CG D:HIS63 3.1 19.2 1.0
CE1 D:HIS63 3.2 20.2 1.0
CG D:HIS71 3.2 15.3 1.0
CB D:HIS63 3.4 14.8 1.0
CB D:HIS80 3.4 10.6 1.0
CB D:HIS71 3.6 13.0 1.0
O D:LYS136 3.8 18.0 1.0
CA D:HIS71 3.9 17.3 1.0
NE2 D:HIS80 4.1 17.3 1.0
CB D:ASP83 4.1 11.8 1.0
NE2 D:HIS71 4.1 15.1 1.0
CD2 D:HIS80 4.1 17.5 1.0
CD2 D:HIS63 4.3 20.8 1.0
CD2 D:HIS71 4.3 14.1 1.0
NE2 D:HIS63 4.3 20.8 1.0
CA D:ASP83 4.6 13.3 1.0
N D:HIS80 4.7 14.4 1.0
CA D:HIS80 4.7 15.9 1.0
N D:GLY72 4.7 15.6 1.0
C D:HIS71 4.9 16.9 1.0
C D:LYS136 4.9 19.6 1.0
CA D:HIS63 4.9 20.9 1.0
N D:ASP83 4.9 11.6 1.0
N D:HIS71 4.9 17.4 1.0
O D:HOH352 4.9 23.7 1.0
O D:GLY72 5.0 15.6 1.0
CD2 D:HIS46 5.0 17.3 1.0

Zinc binding site 9 out of 24 in 4mcm

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Zinc binding site 9 out of 24 in the Human SOD1 C57S Mutant, As-Isolated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Human SOD1 C57S Mutant, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:36.1
occ:0.78
NE2 E:HIS120 1.9 41.9 1.0
O2 E:SO4203 2.1 37.0 0.7
NE2 E:HIS48 2.2 32.7 1.0
ND1 E:HIS46 2.3 39.2 1.0
CE1 E:HIS120 2.5 40.0 1.0
CE1 E:HIS48 3.1 27.2 1.0
CD2 E:HIS120 3.1 38.6 1.0
CG E:HIS46 3.2 38.2 1.0
S E:SO4203 3.2 35.4 0.7
O4 E:SO4203 3.3 24.7 0.7
CD2 E:HIS48 3.3 30.4 1.0
CB E:HIS46 3.3 36.0 1.0
NE2 E:HIS63 3.3 34.7 1.0
CE1 E:HIS46 3.4 38.4 1.0
ND1 E:HIS120 3.7 43.1 1.0
CD2 E:HIS63 3.8 30.5 1.0
O3 E:SO4203 3.9 34.3 0.7
CG E:HIS120 4.0 43.3 1.0
ND1 E:HIS48 4.3 32.5 1.0
O1 E:SO4203 4.3 38.0 0.7
CD2 E:HIS46 4.4 39.6 1.0
CE1 E:HIS63 4.4 33.6 1.0
CG E:HIS48 4.4 35.3 1.0
NE2 E:HIS46 4.4 37.5 1.0
CB E:VAL118 4.5 36.7 1.0
CG1 E:VAL118 4.5 29.4 1.0
O E:HOH333 4.5 37.8 1.0
NE E:ARG143 4.6 35.0 1.0
CA E:HIS46 4.7 36.4 1.0

Zinc binding site 10 out of 24 in 4mcm

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Zinc binding site 10 out of 24 in the Human SOD1 C57S Mutant, As-Isolated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Human SOD1 C57S Mutant, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn202

b:28.5
occ:1.00
ND1 E:HIS80 2.0 24.5 1.0
ND1 E:HIS63 2.1 30.6 1.0
OD1 E:ASP83 2.1 30.3 1.0
ND1 E:HIS71 2.3 37.5 1.0
CG E:ASP83 2.7 31.9 1.0
OD2 E:ASP83 2.7 28.6 1.0
CE1 E:HIS80 3.0 26.4 1.0
CG E:HIS80 3.0 29.9 1.0
CE1 E:HIS63 3.0 33.6 1.0
CG E:HIS63 3.1 33.4 1.0
CE1 E:HIS71 3.3 33.3 1.0
CG E:HIS71 3.3 32.4 1.0
CB E:HIS80 3.4 28.6 1.0
CB E:HIS63 3.4 25.5 1.0
CB E:HIS71 3.6 32.2 1.0
CA E:HIS71 3.9 31.9 1.0
O E:LYS136 4.0 33.8 1.0
NE2 E:HIS80 4.1 27.2 1.0
CD2 E:HIS80 4.1 29.0 1.0
NE2 E:HIS63 4.1 34.7 1.0
CD2 E:HIS63 4.2 30.5 1.0
CB E:ASP83 4.2 31.9 1.0
NE2 E:HIS71 4.4 36.5 1.0
CD2 E:HIS71 4.4 33.3 1.0
N E:HIS80 4.5 34.2 1.0
N E:GLY72 4.5 36.1 1.0
CA E:HIS80 4.5 34.0 1.0
C E:HIS71 4.8 32.8 1.0
CA E:ASP83 4.8 35.0 1.0
N E:HIS71 4.9 28.9 1.0
CA E:HIS63 4.9 27.1 1.0
C E:LYS136 5.0 31.6 1.0
N E:ASP83 5.0 29.5 1.0

Reference:

K.Sea, S.H.Sohn, A.Durazo, Y.Sheng, B.Shaw, X.Cao, A.B.Taylor, L.J.Whitson, S.P.Holloway, P.J.Hart, D.E.Cabelli, E.B.Gralla, J.S.Valentine. Intrasubunit Disulfide Bond Is Not Essential For the Activity of Copper-Zinc Superoxide Dismutase To Be Published.
Page generated: Wed Dec 16 05:34:26 2020

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