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Copper in PDB 1odb: The Crystal Structure of Human S100A12 - Copper Complex

Protein crystallography data

The structure of The Crystal Structure of Human S100A12 - Copper Complex, PDB code: 1odb was solved by O.V.Moroz, A.A.Antson, S.J.Grist, N.J.Maitland, G.G.Dodson, K.S.Wilson, E.M.Lukanidin, I.B.Bronstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.19
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 70.569, 118.957, 90.185, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22.6

Other elements in 1odb:

The structure of The Crystal Structure of Human S100A12 - Copper Complex also contains other interesting chemical elements:

Calcium (Ca) 12 atoms

Copper Binding Sites:

The binding sites of Copper atom in the The Crystal Structure of Human S100A12 - Copper Complex (pdb code 1odb). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the The Crystal Structure of Human S100A12 - Copper Complex, PDB code: 1odb:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 1odb

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Copper binding site 1 out of 6 in the The Crystal Structure of Human S100A12 - Copper Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of The Crystal Structure of Human S100A12 - Copper Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1091

b:23.6
occ:0.80
NE2 B:HIS89 2.0 12.9 1.0
NE2 A:HIS15 2.1 17.5 1.0
NE2 B:HIS85 2.3 19.0 1.0
CD2 B:HIS89 2.9 14.4 1.0
CE1 B:HIS89 3.0 15.8 1.0
CE1 A:HIS15 3.0 18.3 1.0
CD2 A:HIS15 3.1 17.8 1.0
CD2 B:HIS85 3.1 19.0 1.0
CE1 B:HIS85 3.5 20.0 1.0
O A:HOH2025 3.9 59.3 1.0
ND1 B:HIS89 4.1 17.6 1.0
CG B:HIS89 4.1 18.4 1.0
ND1 A:HIS15 4.1 19.8 1.0
CG A:HIS15 4.2 19.1 1.0
OG1 B:THR88 4.2 21.4 1.0
CG B:HIS85 4.3 18.7 1.0
ND1 B:HIS85 4.5 19.3 1.0

Copper binding site 2 out of 6 in 1odb

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Copper binding site 2 out of 6 in the The Crystal Structure of Human S100A12 - Copper Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of The Crystal Structure of Human S100A12 - Copper Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1091

b:22.9
occ:0.80
NE2 A:HIS85 2.0 15.3 1.0
OD1 B:ASP25 2.0 25.5 1.0
NE2 B:HIS15 2.1 20.0 1.0
NE2 A:HIS89 2.2 17.7 1.0
CG B:ASP25 2.9 22.6 1.0
OD2 B:ASP25 3.0 28.2 1.0
CD2 A:HIS85 3.0 17.3 1.0
CE1 A:HIS85 3.0 18.2 1.0
CE1 B:HIS15 3.1 19.3 1.0
CE1 A:HIS89 3.1 19.0 1.0
CD2 B:HIS15 3.1 18.1 1.0
CD2 A:HIS89 3.2 18.4 1.0
ND1 A:HIS85 4.1 17.1 1.0
CG A:HIS85 4.1 17.0 1.0
ND1 B:HIS15 4.2 18.7 1.0
ND1 A:HIS89 4.2 18.6 1.0
CG B:HIS15 4.2 18.7 1.0
CG A:HIS89 4.3 19.9 1.0
CB B:ASP25 4.3 21.4 1.0
CE2 B:PHE14 4.5 21.1 1.0
CD2 B:PHE14 4.8 19.4 1.0
CA B:ASP25 4.9 21.0 1.0
OG1 A:THR88 4.9 24.5 1.0

Copper binding site 3 out of 6 in 1odb

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Copper binding site 3 out of 6 in the The Crystal Structure of Human S100A12 - Copper Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of The Crystal Structure of Human S100A12 - Copper Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu1091

b:22.7
occ:0.80
NE2 C:HIS15 2.1 15.7 1.0
OD1 C:ASP25 2.1 19.9 1.0
NE2 D:HIS85 2.1 17.6 1.0
NE2 D:HIS89 2.3 17.6 1.0
OD2 C:ASP25 2.8 26.1 1.0
CG C:ASP25 2.8 20.0 1.0
CD2 D:HIS85 3.0 18.9 1.0
CE1 C:HIS15 3.0 14.9 1.0
CD2 C:HIS15 3.1 14.6 1.0
CE1 D:HIS85 3.1 18.7 1.0
CD2 D:HIS89 3.2 19.0 1.0
CE1 D:HIS89 3.3 18.0 1.0
CG D:HIS85 4.1 16.5 1.0
ND1 C:HIS15 4.1 16.5 1.0
ND1 D:HIS85 4.2 16.2 1.0
CG C:HIS15 4.2 16.0 1.0
CB C:ASP25 4.3 19.6 1.0
CG D:HIS89 4.4 17.9 1.0
ND1 D:HIS89 4.4 15.2 1.0
CE2 C:PHE14 4.5 21.5 1.0
CD2 C:PHE14 4.8 20.6 1.0
CA C:ASP25 4.8 19.6 1.0
OG1 D:THR88 4.9 18.9 1.0

Copper binding site 4 out of 6 in 1odb

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Copper binding site 4 out of 6 in the The Crystal Structure of Human S100A12 - Copper Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of The Crystal Structure of Human S100A12 - Copper Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu1091

b:26.2
occ:0.80
NE2 D:HIS15 2.0 19.0 1.0
NE2 C:HIS85 2.0 19.1 1.0
OD1 D:ASP25 2.1 21.9 1.0
NE2 C:HIS89 2.2 23.4 1.0
CG D:ASP25 2.9 20.7 1.0
CE1 D:HIS15 3.0 17.6 1.0
CD2 C:HIS85 3.0 17.8 1.0
CD2 D:HIS15 3.0 18.3 1.0
OD2 D:ASP25 3.0 23.8 1.0
CE1 C:HIS85 3.0 16.7 1.0
CE1 C:HIS89 3.1 23.4 1.0
CD2 C:HIS89 3.2 22.3 1.0
ND1 D:HIS15 4.1 16.2 1.0
ND1 C:HIS85 4.1 18.4 1.0
CG C:HIS85 4.1 17.5 1.0
CG D:HIS15 4.1 19.0 1.0
ND1 C:HIS89 4.3 21.4 1.0
CB D:ASP25 4.3 19.8 1.0
CG C:HIS89 4.3 21.4 1.0
CE2 D:PHE14 4.5 18.0 1.0
O D:HOH2023 4.6 54.1 1.0
CD2 D:PHE14 4.8 18.3 1.0
CA D:ASP25 4.8 19.3 1.0
CE2 D:PHE24 4.9 23.6 1.0

Copper binding site 5 out of 6 in 1odb

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Copper binding site 5 out of 6 in the The Crystal Structure of Human S100A12 - Copper Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of The Crystal Structure of Human S100A12 - Copper Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu1091

b:26.0
occ:0.80
NE2 F:HIS85 2.0 21.1 1.0
OD1 E:ASP25 2.0 26.1 1.0
NE2 E:HIS15 2.1 19.7 1.0
NE2 F:HIS89 2.2 16.5 1.0
OD2 E:ASP25 2.7 26.9 1.0
CG E:ASP25 2.8 23.1 1.0
CD2 F:HIS85 2.9 19.8 1.0
CE1 F:HIS85 3.0 20.1 1.0
CE1 E:HIS15 3.0 16.6 1.0
CD2 E:HIS15 3.1 16.4 1.0
CE1 F:HIS89 3.1 19.1 1.0
CD2 F:HIS89 3.2 17.4 1.0
ND1 F:HIS85 4.0 19.9 1.0
CG F:HIS85 4.0 19.8 1.0
ND1 E:HIS15 4.1 18.6 1.0
CG E:HIS15 4.2 20.0 1.0
CB E:ASP25 4.2 20.8 1.0
ND1 F:HIS89 4.3 15.3 1.0
CG F:HIS89 4.4 18.0 1.0
CE2 E:PHE14 4.6 21.3 1.0
CA E:ASP25 4.8 20.8 1.0
CD2 E:PHE14 4.9 20.4 1.0
OG1 F:THR88 4.9 21.6 1.0

Copper binding site 6 out of 6 in 1odb

Go back to Copper Binding Sites List in 1odb
Copper binding site 6 out of 6 in the The Crystal Structure of Human S100A12 - Copper Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of The Crystal Structure of Human S100A12 - Copper Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu1091

b:22.9
occ:0.80
NE2 E:HIS85 2.0 16.1 1.0
NE2 F:HIS15 2.1 21.8 1.0
OD1 F:ASP25 2.1 21.1 1.0
NE2 E:HIS89 2.2 19.7 1.0
CE1 F:HIS15 2.8 22.4 1.0
CD2 E:HIS85 2.8 16.3 1.0
CE1 E:HIS85 3.0 15.8 1.0
CG F:ASP25 3.1 21.6 1.0
CD2 E:HIS89 3.1 20.1 1.0
CD2 F:HIS15 3.2 22.4 1.0
CE1 E:HIS89 3.2 19.4 1.0
OD2 F:ASP25 3.3 24.0 1.0
CG E:HIS85 4.0 18.1 1.0
ND1 F:HIS15 4.0 22.0 1.0
ND1 E:HIS85 4.0 17.0 1.0
O F:HOH2009 4.2 50.0 1.0
CG F:HIS15 4.2 20.3 1.0
CG E:HIS89 4.3 21.2 1.0
ND1 E:HIS89 4.3 19.5 1.0
CB F:ASP25 4.4 20.0 1.0
CE2 F:PHE14 4.5 22.4 1.0
O F:ASP25 4.5 19.7 1.0
CA F:ASP25 4.8 20.2 1.0
CD2 F:PHE14 4.8 22.9 1.0

Reference:

O.V.Moroz, A.A.Antson, S.J.Grist, N.J.Maitland, G.G.Dodson, K.S.Wilson, E.M.Lukanidin, I.B.Bronstein. Structure of the Human S100A12-Copper Complex: Implications For Host-Parasite Defence Acta Crystallogr.,Sect.D V. 59 859 2003.
ISSN: ISSN 0907-4449
PubMed: 12777802
DOI: 10.1107/S0907444903004700
Page generated: Wed Oct 28 14:16:23 2020
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