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Cadmium in PDB 3kxu: Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant

Protein crystallography data

The structure of Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant, PDB code: 3kxu was solved by T.Granier, B.Gallois, B.Langlois D'estaintot, P.Arosio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.78 / 1.85
Space group I 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 151.355, 151.355, 151.355, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 21.1

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant (pdb code 3kxu). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 12 binding sites of Cadmium where determined in the Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant, PDB code: 3kxu:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12;

Cadmium binding site 1 out of 12 in 3kxu

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Cadmium binding site 1 out of 12 in the Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:22.9
occ:1.00
NE2 A:HIS115 2.2 23.1 1.0
O A:HOH192 2.3 32.6 1.0
O A:HOH193 2.3 21.8 1.0
O A:HOH194 2.4 30.6 1.0
SG A:CYS127 2.5 20.2 1.0
CE1 A:HIS115 3.2 22.1 1.0
CD2 A:HIS115 3.3 24.9 1.0
CB A:CYS127 3.5 21.6 1.0
O A:HOH215 3.9 11.2 0.3
ND1 A:HIS115 4.3 23.4 1.0
CD A:CD313 4.3 18.9 0.5
CG A:HIS115 4.4 21.5 1.0
OE2 A:GLU131 4.5 34.4 1.0
O A:HOH269 4.5 29.2 1.0
CA A:CYS127 4.6 19.8 1.0
OG A:SER119 4.7 34.8 1.0
CB A:SER119 4.9 25.7 1.0

Cadmium binding site 2 out of 12 in 3kxu

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Cadmium binding site 2 out of 12 in the Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:48.9
occ:0.25
CE1 A:HIS50 2.1 25.3 0.5
NE2 A:HIS50 2.3 34.7 0.5
CE1 A:HIS50 2.3 31.6 0.5
O A:HOH220 2.4 48.2 0.2
CD A:CD304 2.7 39.9 0.2
OE2 A:GLU54 2.9 40.7 1.0
NE2 A:HIS50 2.9 27.8 0.5
ND1 A:HIS50 3.2 27.6 0.5
CD A:GLU54 3.3 35.5 1.0
O A:HOH223 3.4 41.6 0.5
ND1 A:HIS50 3.6 31.7 0.5
CD2 A:HIS50 3.6 31.4 0.5
CG A:GLU54 3.7 29.7 1.0
OE1 A:GLU54 4.0 42.8 1.0
CD A:CD305 4.2 40.7 0.5
CD2 A:HIS50 4.2 29.0 0.5
CG A:HIS50 4.2 28.5 0.5
O A:HOH221 4.3 37.3 0.5
CG A:HIS50 4.3 26.9 0.5
O A:HOH372 4.6 33.6 0.5

Cadmium binding site 3 out of 12 in 3kxu

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Cadmium binding site 3 out of 12 in the Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:39.9
occ:0.25
NE2 A:HIS50 2.2 27.8 0.5
CE1 A:HIS50 2.6 31.6 0.5
CD A:CD302 2.7 48.9 0.2
CE1 A:HIS50 2.8 25.3 0.5
ND1 A:HIS50 3.3 31.7 0.5
CD2 A:HIS50 3.4 29.0 0.5
NE2 A:HIS50 3.7 34.7 0.5
ND1 A:HIS50 4.0 27.6 0.5
CG A:HIS50 4.3 26.9 0.5
CG A:GLU54 4.4 29.7 1.0
CG A:HIS50 4.6 28.5 0.5
CD A:GLU54 4.7 35.5 1.0
O A:HOH223 4.7 41.6 0.5
CD2 A:HIS50 4.7 31.4 0.5
OE2 A:GLU54 5.0 40.7 1.0
O A:HOH396 5.0 53.1 1.0

Cadmium binding site 4 out of 12 in 3kxu

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Cadmium binding site 4 out of 12 in the Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd305

b:40.7
occ:0.50
OE1 A:GLU54 2.3 42.8 1.0
O A:HOH221 2.3 37.3 0.5
O A:HOH222 2.3 36.3 0.5
O A:HOH223 2.4 41.6 0.5
OE1 A:GLU57 2.4 35.7 1.0
OE2 A:GLU54 2.6 40.7 1.0
CD A:GLU54 2.7 35.5 1.0
CD A:GLU57 3.2 29.9 1.0
OE2 A:GLU57 3.3 44.9 1.0
O A:HOH268 4.0 36.9 1.0
O A:HOH220 4.0 48.2 0.2
CD A:CD302 4.2 48.9 0.2
CG A:GLU54 4.3 29.7 1.0
CG A:GLU57 4.6 25.0 1.0
O A:HOH225 4.7 29.8 0.5
CB A:GLU57 5.0 20.0 1.0

Cadmium binding site 5 out of 12 in 3kxu

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Cadmium binding site 5 out of 12 in the Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd306

b:39.9
occ:0.50
OE2 A:GLU58 2.2 40.1 1.0
OE1 A:GLU61 2.2 29.2 1.0
O A:HOH225 2.3 29.8 0.5
O A:HOH224 2.3 34.8 0.5
CD A:GLU61 2.9 25.0 1.0
OE2 A:GLU61 2.9 31.8 1.0
CD A:GLU58 2.9 32.0 1.0
OE1 A:GLU58 3.0 38.0 1.0
O A:HOH210 3.8 16.0 0.5
O A:HOH418 4.0 55.0 1.0
CG A:GLU61 4.4 25.3 1.0
CG A:GLU58 4.4 25.4 1.0
O A:HOH268 4.4 36.9 1.0

Cadmium binding site 6 out of 12 in 3kxu

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Cadmium binding site 6 out of 12 in the Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd308

b:34.3
occ:0.25
O A:HOH226 2.3 26.9 0.2
O A:HOH227 2.3 32.0 0.2
OE2 A:GLU89 2.5 36.2 1.0
OE1 A:GLU89 2.6 38.5 1.0
CD A:GLU89 2.8 29.9 1.0
O A:HOH343 3.3 41.5 1.0
O A:HOH416 4.2 51.9 1.0
CG A:GLU89 4.3 27.1 1.0
NH1 A:ARG40 4.5 30.7 1.0
NH2 A:ARG40 4.5 29.1 1.0
CB A:GLU89 4.9 25.7 1.0

Cadmium binding site 7 out of 12 in 3kxu

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Cadmium binding site 7 out of 12 in the Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd309

b:26.4
occ:1.00
O A:HOH230 2.2 31.6 1.0
O A:HOH229 2.3 32.8 1.0
NE2 A:HIS133 2.3 26.3 1.0
O A:HOH232 2.3 27.4 1.0
O A:HOH228 2.3 29.0 1.0
O A:HOH231 2.3 20.9 1.0
CD2 A:HIS133 3.3 25.5 1.0
CE1 A:HIS133 3.3 26.4 1.0
NH1 A:ARG65 4.1 39.0 1.0
O A:HOH394 4.3 32.1 1.0
ND1 A:HIS133 4.4 23.1 1.0
CG A:HIS133 4.4 25.7 1.0
O A:HOH200 4.7 33.8 1.0
O A:HOH356 4.7 32.3 1.0
CD1 A:PHE129 4.9 17.3 1.0
O A:HOH379 4.9 25.3 1.0

Cadmium binding site 8 out of 12 in 3kxu

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Cadmium binding site 8 out of 12 in the Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd312

b:30.3
occ:0.50
OE2 A:GLU87 2.2 25.2 0.5
O A:HOH233 2.3 26.5 0.5
O A:HOH234 2.4 19.3 0.5
O A:HOH235 2.4 29.5 0.5
OE1 A:GLU87 2.5 24.8 0.5
CD A:GLU87 2.7 23.7 0.5
CG A:GLU87 4.2 23.4 0.5
CG A:GLU87 4.2 24.0 0.5
OE2 A:GLU87 4.4 26.5 0.5
O A:TRP90 4.4 23.9 1.0
CD A:GLU87 4.5 24.1 0.5
O A:ASP95 4.5 22.8 1.0
CE3 A:TRP90 4.6 21.6 1.0
O A:HOH377 4.6 30.9 1.0
CB A:ASP95 4.6 27.1 1.0
C A:TRP90 4.7 23.0 1.0
O A:HOH212 4.8 59.9 1.0
CB A:ALA99 4.8 22.2 1.0
CA A:TRP90 4.9 22.0 1.0
C A:ASP95 4.9 22.8 1.0

Cadmium binding site 9 out of 12 in 3kxu

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Cadmium binding site 9 out of 12 in the Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd313

b:18.9
occ:0.50
OE1 A:GLU131 2.2 31.6 1.0
SG A:CYS127 2.5 20.2 1.0
CD A:GLU131 3.0 25.9 1.0
OE2 A:GLU131 3.4 34.4 1.0
CB A:CYS127 3.5 21.6 1.0
N A:ASP128 3.7 19.4 1.0
C A:CYS127 3.8 19.4 1.0
CA A:ASP128 4.0 21.4 1.0
O A:CYS127 4.1 18.4 1.0
CG A:GLU131 4.2 27.7 1.0
CA A:CYS127 4.3 19.8 1.0
CD A:CD301 4.3 22.9 1.0
O A:HOH194 4.4 30.6 1.0
O A:HOH215 4.5 11.2 0.3
CB A:ASP128 4.6 20.9 1.0
O A:HOH192 4.7 32.6 1.0
O A:PRO124 4.8 18.7 1.0
CB A:GLU131 4.9 22.7 1.0

Cadmium binding site 10 out of 12 in 3kxu

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Cadmium binding site 10 out of 12 in the Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd314

b:28.5
occ:0.33
OD1 A:ASP128 3.1 26.4 1.0
OG1 A:THR132 4.1 24.6 1.0
CG A:ASP128 4.3 25.3 1.0
OE1 A:GLU131 4.5 31.6 1.0

Cadmium binding site 11 out of 12 in 3kxu

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Cadmium binding site 11 out of 12 in the Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 11 of Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd315

b:17.5
occ:0.50
OD1 A:ASP12 2.2 15.7 1.0
O A:HOH236 2.3 24.9 0.5
OD2 A:ASP12 2.4 24.6 1.0
O A:HOH237 2.5 16.1 0.5
CG A:ASP12 2.6 17.7 1.0
O A:HOH361 3.9 49.4 1.0
CB A:ASP12 4.1 19.0 1.0
NH2 A:ARG121 4.7 26.3 1.0
OG1 A:THR11 4.7 23.6 1.0
O A:HOH421 4.7 43.8 1.0
O4 A:SO4317 4.8 37.5 1.0
CA A:ASP12 4.9 18.9 1.0
N A:ASP12 5.0 18.4 1.0

Cadmium binding site 12 out of 12 in 3kxu

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Cadmium binding site 12 out of 12 in the Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 12 of Crystal Structure of Human Ferritin FTL498INSTC Pathogenic Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd316

b:60.4
occ:0.25
NE2 A:HIS153 2.3 52.9 1.0
O A:HOH239 2.4 59.2 0.2
O A:HOH238 2.4 59.3 0.2
CE1 A:HIS153 3.0 51.7 1.0
CD2 A:HIS153 3.4 51.8 1.0
ND1 A:HIS153 4.2 52.8 1.0
CG A:HIS153 4.4 49.7 1.0

Reference:

S.Luscieti, P.Santambrogio, B.Langlois D'estaintot, T.Granier, A.Cozzi, M.Poli, B.Gallois, D.Finazzi, A.Cattaneo, S.Levi, P.Arosio. Mutant Ferritin L-Chains That Cause Neurodegeneration Act in A Dominant-Negative Manner to Reduce Ferritin Iron Incorporation. J.Biol.Chem. V. 285 11948 2010.
ISSN: ISSN 0021-9258
PubMed: 20159981
DOI: 10.1074/JBC.M109.096404
Page generated: Fri Aug 28 13:47:12 2020
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