Atomistry » Calcium » PDB 3dcq-3dsw » 3de8
Atomistry »
  Calcium »
    PDB 3dcq-3dsw »
      3de8 »

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

Go back to Calcium Binding Sites List in 3de8
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

Go back to Calcium Binding Sites List in 3de8
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: Sat Jul 13 09:00:05 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy