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Calcium in PDB 3de8: Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination

Protein crystallography data

The structure of Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination, PDB code: 3de8 was solved by E.N.Salgado, R.A.Lewis, A.L.Rheingold, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.92 / 1.72
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.566, 89.504, 52.019, 90.00, 111.01, 90.00
R / Rfree (%) 19.4 / 24.4

Other elements in 3de8:

The structure of Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Copper (Cu) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination (pdb code 3de8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination, PDB code: 3de8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3de8

Go back to Calcium Binding Sites List in 3de8
Calcium binding site 1 out of 6 in the Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca109

b:12.5
occ:1.00
 O C:HOH314 2.3 26.0 1.0
O A:HOH151 2.3 20.6 1.0
O C:HOH313 2.4 17.1 1.0
OD2 A:ASP74 2.5 20.8 1.0
OD1 A:ASP74 2.5 21.6 1.0
OD2 C:ASP74 2.5 20.4 1.0
O A:HOH152 2.5 16.3 1.0
OD1 C:ASP74 2.5 22.7 1.0
CG A:ASP74 2.8 18.3 1.0
CG C:ASP74 2.9 20.2 1.0
O A:GLY70 4.0 22.4 1.0
O C:GLY70 4.0 21.6 1.0
ND1 C:HIS73 4.3 18.9 1.0
ND1 A:HIS73 4.3 21.6 1.0
CB A:ASP74 4.4 18.1 1.0
CB C:ASP74 4.4 19.4 1.0
O A:HOH289 4.4 24.8 1.0
O C:HOH384 4.5 28.7 1.0
O A:HOH314 4.7 36.5 1.0
C C:GLY70 4.7 21.2 1.0
C A:GLY70 4.7 22.7 1.0
O A:HOH316 4.8 24.6 1.0
CE1 C:HIS73 4.8 20.6 1.0
O A:HOH162 4.8 10.8 1.0
CE1 A:HIS73 4.9 22.4 1.0
O C:HOH355 4.9 24.2 1.0
O A:HOH239 4.9 28.5 1.0
O C:HOH332 5.0 26.8 1.0

Calcium binding site 2 out of 6 in 3de8

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Calcium binding site 2 out of 6 in the Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca110

b:19.0
occ:1.00
 OE2 A:GLU8 2.2 26.0 1.0
O A:HOH155 2.3 18.4 1.0
O A:HOH154 2.3 20.7 1.0
OD2 A:ASP12 2.3 20.2 1.0
OD1 A:ASP12 2.6 22.9 1.0
O A:HOH153 2.6 23.3 1.0
CG A:ASP12 2.8 21.7 1.0
CD A:GLU8 3.4 25.4 1.0
CG A:GLU8 4.1 20.3 1.0
CB A:ASP12 4.3 20.0 1.0
O A:HOH188 4.3 18.5 1.0
OE1 A:GLU8 4.3 26.1 1.0
O A:HOH245 4.3 33.5 1.0
O A:HOH298 4.4 35.2 1.0
O A:HOH194 4.6 23.4 1.0
O A:HOH189 4.6 24.3 1.0
O A:HOH297 4.7 32.8 1.0
O A:HOH242 4.8 31.5 1.0

Calcium binding site 3 out of 6 in 3de8

Go back to Calcium Binding Sites List in 3de8
Calcium binding site 3 out of 6 in the Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca111

b:22.0
occ:1.00
 O A:HOH278 2.2 23.8 1.0
O A:HOH292 2.4 21.4 1.0
O A:HOH217 2.5 23.2 1.0
O A:HOH200 2.5 27.1 1.0
O A:HOH228 2.6 17.5 1.0
OE2 A:GLU92 4.0 29.1 1.0
O A:HOH277 4.2 19.2 1.0
OE1 A:GLU92 4.3 28.8 1.0
O A:HOH210 4.4 17.4 1.0
CD A:GLU92 4.4 28.3 1.0
NZ A:LYS95 4.5 27.6 1.0
OE1 A:GLU18 4.7 29.2 1.0

Calcium binding site 4 out of 6 in 3de8

Go back to Calcium Binding Sites List in 3de8
Calcium binding site 4 out of 6 in the Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca109

b:14.1
occ:1.00
 OD1 B:ASP5 2.3 22.9 1.0
O B:HOH255 2.4 30.6 1.0
O B:HOH254 2.5 16.5 1.0
OE1 B:GLU4 2.5 20.9 1.0
OE2 B:GLU4 2.7 22.0 1.0
CD B:GLU4 3.0 20.3 1.0
CG B:ASP5 3.5 23.1 1.0
CA B:CA110 3.9 16.8 1.0
OD2 B:ASP5 4.1 27.3 1.0
CA B:ASP5 4.3 20.5 1.0
CG B:GLU4 4.5 20.6 1.0
CB B:ASP5 4.5 20.0 1.0
N B:ASP5 4.5 20.5 1.0
CG B:GLU8 4.7 18.8 1.0
C B:GLU4 4.9 20.5 1.0
O B:HOH276 4.9 15.8 1.0
O B:HOH282 5.0 19.6 1.0
O B:GLU4 5.0 21.1 1.0

Calcium binding site 5 out of 6 in 3de8

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Calcium binding site 5 out of 6 in the Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca110

b:16.8
occ:1.00
 OE2 B:GLU4 2.2 22.0 1.0
O B:HOH257 2.3 32.3 1.0
OD2 B:ASP2 2.4 23.3 1.0
OD2 B:ASP5 2.5 27.3 1.0
O B:HOH256 2.5 17.1 1.0
OD1 B:ASP2 2.6 28.5 1.0
CG B:ASP2 2.8 26.4 1.0
CG B:ASP5 3.1 23.1 1.0
CD B:GLU4 3.3 20.3 1.0
OD1 B:ASP5 3.4 22.9 1.0
O B:HOH361 3.9 21.8 1.0
CA B:CA109 3.9 14.1 1.0
CG B:GLU4 4.0 20.6 1.0
O B:HOH317 4.2 38.4 1.0
CB B:ASP5 4.3 20.0 1.0
OE1 B:GLU4 4.3 20.9 1.0
CB B:ASP2 4.3 26.0 1.0
O B:HOH261 4.3 26.2 1.0
N B:ASP5 4.6 20.5 1.0
O B:HOH333 4.6 28.9 1.0
CA B:ASP5 4.9 20.5 1.0

Calcium binding site 6 out of 6 in 3de8

Go back to Calcium Binding Sites List in 3de8
Calcium binding site 6 out of 6 in the Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca107

b:16.6
occ:1.00
 OD2 C:ASP21 2.3 20.4 1.0
O C:LYS19 2.4 18.0 1.0
O C:HOH315 2.4 20.6 1.0
O C:HOH316 2.6 28.1 1.0
CG C:ASP21 3.2 21.1 1.0
OD1 C:ASP21 3.5 23.5 1.0
C C:LYS19 3.6 19.0 1.0
CA C:LYS19 4.4 19.3 1.0
C C:ALA20 4.4 19.2 1.0
CB C:LYS19 4.5 19.4 1.0
N C:ASP21 4.5 18.5 1.0
O C:HOH368 4.5 29.3 1.0
CB C:ASP21 4.6 18.9 1.0
N C:ALA20 4.6 18.9 1.0
O C:HOH350 4.7 25.7 1.0
O C:ALA20 4.7 19.1 1.0
CA C:ALA20 4.7 18.6 1.0
CA C:ASP21 4.8 18.9 1.0
O C:HOH343 4.9 22.6 1.0

Reference:

E.N.Salgado, R.A.Lewis, S.Mossin, A.L.Rheingold, F.A.Tezcan. Control of Protein Oligomerization Symmetry By Metal Coordination: C2 and C3 Symmetrical Assemblies Through Cu(II) and Ni(II) Coordination. Inorg.Chem. V. 48 2726 2009.
ISSN: ISSN 0020-1669
PubMed: 19267481
DOI: 10.1021/IC9001237
Page generated: Tue Jul 8 11:36:37 2025

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