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Cadmium in PDB 1mfm: Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution

Enzymatic activity of Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution

All present enzymatic activity of Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution:
1.15.1.1;

Protein crystallography data

The structure of Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution, PDB code: 1mfm was solved by M.Ferraroni, W.Rypniewski, K.S.Wilson, P.L.Orioli, M.S.Viezzoli, L.Banci, I.Bertini, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.02
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 34.990, 48.110, 81.080, 90.00, 90.00, 90.00
R / Rfree (%) 11.8 / n/a

Other elements in 1mfm:

The structure of Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution also contains other interesting chemical elements:

Copper (Cu) 1 atom
Chlorine (Cl) 2 atoms
Zinc (Zn) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution (pdb code 1mfm). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution, PDB code: 1mfm:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 1mfm

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Cadmium binding site 1 out of 9 in the Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd156

b:10.9
occ:0.83
 OE2 A:GLU51 2.2 13.6 0.7
O A:HOH178 2.3 13.5 1.0
OE2 A:GLU51 2.3 14.1 0.3
OE1 A:GLU51 2.7 14.6 0.7
CD A:GLU51 2.8 10.9 0.7
CD A:GLU51 3.2 13.2 0.3
CG A:GLU51 3.4 13.7 0.3
OD1 A:ASP52 3.9 14.4 1.0
CG A:GLU51 4.3 12.6 0.7
O A:HOH333 4.3 39.0 1.0
OE1 A:GLU51 4.3 11.7 0.3
O A:HOH381 4.4 44.0 1.0
OD2 A:ASP52 4.4 12.9 1.0
CG A:ASP52 4.5 11.4 1.0
CB A:GLU51 4.9 10.4 0.3

Cadmium binding site 2 out of 9 in 1mfm

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Cadmium binding site 2 out of 9 in the Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd157

b:15.6
occ:0.58
 OE1 A:GLU121 2.3 27.4 1.0
O A:HOH257 2.4 28.8 1.0
OG A:SER142 2.4 25.2 1.0
CL A:CL165 2.4 27.5 1.0
CL A:CL166 2.5 23.3 1.0
O A:HOH275 2.5 31.2 1.0
CD A:GLU121 3.2 29.1 1.0
CB A:SER142 3.5 19.9 1.0
OE2 A:GLU121 3.5 50.4 1.0
O A:HOH272 4.1 30.6 1.0
N A:SER142 4.4 14.1 1.0
O A:HOH443 4.5 64.2 1.0
CG A:GLU121 4.5 24.4 1.0
CA A:SER142 4.6 15.7 1.0
CB A:GLU121 4.8 17.0 1.0

Cadmium binding site 3 out of 9 in 1mfm

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Cadmium binding site 3 out of 9 in the Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd158

b:12.4
occ:0.73
 OE1 A:GLU50 2.1 9.7 0.3
OD2 A:ASP52 2.3 12.9 1.0
OE2 A:GLU50 2.4 16.1 0.7
OE1 A:GLU50 2.6 16.3 0.7
CD A:GLU50 2.8 11.2 0.3
CD A:GLU50 2.8 14.7 0.7
OE2 A:GLU50 2.9 14.1 0.3
CG A:ASP52 3.2 11.4 1.0
CB A:ASP52 3.5 12.3 1.0
O A:HOH333 3.8 39.0 1.0
O A:HOH268 4.0 30.3 1.0
OG A:SER59 4.1 29.8 1.0
O A:HOH178 4.1 13.5 1.0
N A:ASP52 4.2 12.5 1.0
CG A:GLU50 4.3 11.4 0.3
CG A:GLU50 4.3 15.4 0.7
OD1 A:ASP52 4.3 14.4 1.0
O A:HOH327 4.4 38.0 1.0
CA A:ASP52 4.5 12.4 1.0
O A:HOH298 4.5 33.5 1.0
CG2 A:THR54 4.7 54.9 1.0
CB A:GLU50 4.9 12.7 0.3
N A:GLU51 4.9 12.0 1.0
O A:SER59 5.0 79.7 1.0
CA A:GLU50 5.0 11.3 1.0

Cadmium binding site 4 out of 9 in 1mfm

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Cadmium binding site 4 out of 9 in the Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd159

b:16.2
occ:0.59
 CE1 A:HIS110 2.2 17.7 0.4
NE2 A:HIS110 2.2 13.4 0.6
O A:HOH396 2.3 46.4 1.0
O A:HOH244 2.5 26.1 1.0
O A:HOH210 2.5 20.5 1.0
NE2 A:HIS110 3.0 17.0 0.4
CD2 A:HIS110 3.1 11.7 0.6
CE1 A:HIS110 3.2 16.8 0.6
ND1 A:HIS110 3.3 16.8 0.4
CD A:CD162 3.6 8.8 0.3
O A:HOH187 3.7 16.1 1.0
O A:HOH385 3.9 45.2 1.0
CD2 A:HIS110 4.2 15.7 0.4
ND1 A:HIS110 4.3 12.0 0.6
CG A:HIS110 4.3 12.0 0.6
O A:HOH376 4.3 43.0 1.0
CG A:HIS110 4.4 13.6 0.4
O A:PRO66 4.5 22.9 1.0
CB A:PRO66 4.9 14.3 1.0
O A:HOH295 5.0 33.1 1.0

Cadmium binding site 5 out of 9 in 1mfm

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Cadmium binding site 5 out of 9 in the Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd160

b:10.3
occ:0.33
 OE1 A:GLU24 2.3 17.6 0.5
O A:HOH319 2.4 36.9 1.0
OE2 A:GLU24 2.4 18.2 0.5
O A:HOH179 2.5 13.5 1.0
O A:HOH435 2.6 57.5 1.0
CD A:GLU24 2.7 13.9 0.5
OE2 A:GLU24 3.3 52.5 0.5
O A:HOH387 3.7 45.3 1.0
CG A:GLU24 4.2 14.9 0.5
CG A:GLU24 4.2 27.1 0.5
CD A:GLU24 4.2 35.0 0.5
O A:LYS23 4.4 13.4 1.0
O A:HOH254 4.6 27.4 1.0
O A:HOH346 4.6 40.2 1.0
CB A:GLU24 4.9 18.6 0.5

Cadmium binding site 6 out of 9 in 1mfm

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Cadmium binding site 6 out of 9 in the Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd161

b:15.1
occ:0.22
 OD1 A:ASP76 2.4 39.9 1.0
O A:HOH234 2.6 24.9 1.0
O A:HOH206 2.6 19.4 1.0
O A:HOH384 2.6 45.1 1.0
CG A:ASP76 3.3 38.6 1.0
CB A:ASP76 3.8 22.7 1.0
O A:HOH287 3.9 32.6 1.0
CA A:ASP76 4.2 22.4 1.0
OD2 A:ASP76 4.3 25.6 1.0
O A:HOH368 4.3 42.0 1.0
O A:HOH357 4.3 41.2 1.0
O A:HOH246 4.6 26.5 1.0
N A:GLU77 4.6 29.5 1.0
CE A:LYS128 4.6 56.5 0.8
O A:HOH440 4.9 60.8 1.0
C A:ASP76 5.0 26.2 1.0
NZ A:LYS128 5.0 44.3 0.8

Cadmium binding site 7 out of 9 in 1mfm

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Cadmium binding site 7 out of 9 in the Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd162

b:8.8
occ:0.31
 O A:HOH182 2.4 15.3 1.0
O A:ASP109 2.5 12.0 1.0
ND1 A:HIS110 2.5 16.8 0.4
CD2 A:HIS110 2.5 11.7 0.6
O A:HOH339 2.8 40.0 1.0
CE1 A:HIS110 3.1 17.7 0.4
O A:HOH244 3.2 26.1 1.0
NE2 A:HIS110 3.3 13.4 0.6
C A:ASP109 3.4 9.9 1.0
O A:HOH401 3.6 47.0 1.0
CG A:HIS110 3.6 12.0 0.6
CD A:CD159 3.6 16.2 0.6
CG A:HIS110 3.7 13.6 0.4
O A:HOH232 3.7 24.6 1.0
CA A:HIS110 3.9 9.3 1.0
O A:HOH430 4.0 54.2 1.0
N A:HIS110 4.0 9.0 1.0
CB A:HIS110 4.3 11.5 0.6
CB A:HIS110 4.3 12.8 0.4
CB A:ASP109 4.3 13.9 1.0
NE2 A:HIS110 4.4 17.0 0.4
CA A:ASP109 4.4 10.4 1.0
CE1 A:HIS110 4.5 16.8 0.6
CB A:PRO66 4.5 14.3 1.0
ND1 A:HIS110 4.6 12.0 0.6
CD2 A:HIS110 4.6 15.7 0.4

Cadmium binding site 8 out of 9 in 1mfm

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Cadmium binding site 8 out of 9 in the Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd163

b:16.8
occ:0.23
 OD2 A:ASP109 2.3 36.0 1.0
O A:HOH419 2.4 51.1 1.0
O A:HOH343 2.4 40.0 1.0
O A:HOH295 2.5 33.1 1.0
O A:HOH209 2.6 20.5 1.0
O A:HOH376 2.6 43.0 1.0
O A:HOH306 2.9 35.5 1.0
O A:HOH421 3.0 52.0 1.0
CG A:ASP109 3.3 16.2 1.0
CB A:ASP109 3.7 13.9 1.0
OD1 A:ASP109 4.4 20.0 1.0
N A:ASP109 4.4 10.0 1.0
O A:HOH396 4.6 46.4 1.0
CA A:ASP109 4.7 10.4 1.0
O A:HOH273 4.9 30.9 1.0
NE2 A:HIS110 5.0 17.0 0.4

Cadmium binding site 9 out of 9 in 1mfm

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Cadmium binding site 9 out of 9 in the Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd164

b:90.8
occ:0.45
 CU A:CU155 1.6 10.0 0.4
NE2 A:HIS63 2.3 11.7 1.0
NE2 A:HIS120 2.3 13.4 1.0
O A:HOH176 2.4 13.0 1.0
NE2 A:HIS48 2.4 13.2 1.0
ND1 A:HIS46 2.5 12.3 1.0
O A:HOH224 2.6 23.1 1.0
CE1 A:HIS48 3.0 17.5 1.0
CE1 A:HIS120 3.0 13.8 1.0
CD2 A:HIS63 3.0 11.6 1.0
CE1 A:HIS46 3.2 11.6 1.0
CD2 A:HIS120 3.3 11.7 1.0
CE1 A:HIS63 3.3 10.5 1.0
CG A:HIS46 3.5 11.2 1.0
CD2 A:HIS48 3.6 14.7 1.0
CB A:HIS46 4.0 15.2 1.0
ND1 A:HIS120 4.1 13.0 1.0
O A:HOH184 4.1 15.7 1.0
CG A:HIS63 4.2 10.5 1.0
ND1 A:HIS48 4.2 18.1 1.0
CG A:HIS120 4.3 10.7 1.0
ND1 A:HIS63 4.3 9.8 1.0
NE2 A:HIS46 4.4 10.4 1.0
O A:HOH300 4.5 34.0 1.0
CD2 A:HIS46 4.6 12.4 1.0
CG A:HIS48 4.6 10.0 1.0
O A:HOH270 4.6 30.5 1.0
O A:THR137 4.7 11.0 1.0

Reference:

M.Ferraroni, W.Rypniewski, K.S.Wilson, M.S.Viezzoli, L.Banci, I.Bertini, S.Mangani. The Crystal Structure of the Monomeric Human Sod Mutant F50E/G51E/E133Q at Atomic Resolution. the Enzyme Mechanism Revisited. J.Mol.Biol. V. 288 413 1999.
ISSN: ISSN 0022-2836
PubMed: 10329151
DOI: 10.1006/JMBI.1999.2681
Page generated: Fri Jul 19 13:51:56 2024

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