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Calcium in PDB 3c63: Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination

Protein crystallography data

The structure of Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination, PDB code: 3c63 was solved by F.A.Tezcan, E.N.Salgado, R.A.Lewis, J.Faraone-Mennella, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.24 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.966, 89.899, 49.688, 90.00, 110.30, 90.00
R / Rfree (%) 19.9 / 24.7

Other elements in 3c63:

The structure of Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination (pdb code 3c63). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination, PDB code: 3c63:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 3c63

Go back to Calcium Binding Sites List in 3c63
Calcium binding site 1 out of 5 in the Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca108

b:23.7
occ:1.00
 O2A A:HEM150 2.6 18.1 1.0
OE1 A:GLU4 2.6 10.4 1.0
O1A A:HEM150 2.7 14.7 1.0
CGA A:HEM150 3.0 16.9 1.0
O A:HOH222 3.2 28.8 1.0
CD A:GLU4 3.7 12.2 1.0
CG A:GLU4 4.2 9.9 1.0
CBA A:HEM150 4.5 15.3 1.0
CB A:GLU4 4.6 6.9 1.0
OE2 A:GLU4 4.6 16.2 1.0
O1D A:HEM150 5.0 17.2 1.0

Calcium binding site 2 out of 5 in 3c63

Go back to Calcium Binding Sites List in 3c63
Calcium binding site 2 out of 5 in the Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca108

b:21.9
occ:1.00
 O B:HOH264 2.4 45.7 1.0
OD2 B:ASP12 2.7 15.2 1.0
O B:HOH282 2.9 15.5 1.0
OD1 B:ASP12 2.9 11.5 1.0
CG B:ASP12 3.1 12.1 1.0
O B:HOH219 3.7 39.9 1.0
CB B:ASP12 4.5 8.7 1.0

Calcium binding site 3 out of 5 in 3c63

Go back to Calcium Binding Sites List in 3c63
Calcium binding site 3 out of 5 in the Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca109

b:5.3
occ:1.00
 OE2 B:GLU4 2.5 6.6 1.0
OD1 B:ASP2 2.6 11.2 1.0
OD2 B:ASP2 2.7 11.2 1.0
O B:HOH233 2.7 9.5 1.0
CG B:ASP2 3.0 12.8 1.0
CD B:GLU4 3.5 8.5 1.0
O B:HOH251 4.0 10.8 1.0
CG B:GLU4 4.1 6.8 1.0
O B:HOH350 4.2 15.4 1.0
O B:HOH257 4.4 7.3 1.0
CB B:ASP2 4.4 10.5 1.0
OE1 B:GLU4 4.4 8.3 1.0
O1D B:HEM150 4.5 8.4 1.0
CB B:GLU4 4.7 7.0 1.0
N B:GLU4 4.8 5.5 1.0
N B:LEU3 4.8 7.7 1.0

Calcium binding site 4 out of 5 in 3c63

Go back to Calcium Binding Sites List in 3c63
Calcium binding site 4 out of 5 in the Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca110

b:56.8
occ:1.00
 OD1 B:ASP28 3.5 19.8 1.0
CG B:ASP28 4.0 15.6 1.0
OD2 B:ASP28 4.4 20.5 1.0
CB B:ASP28 4.8 10.8 1.0
O B:HOH342 5.0 30.4 1.0

Calcium binding site 5 out of 5 in 3c63

Go back to Calcium Binding Sites List in 3c63
Calcium binding site 5 out of 5 in the Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Tetrameric Cytochrome CB562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca108

b:10.6
occ:1.00
 OD1 D:ASP5 2.5 6.6 1.0
OE1 D:GLU4 2.5 11.0 1.0
O D:HOH366 2.6 16.5 1.0
OE2 D:GLU4 2.8 6.1 1.0
O D:HOH259 2.9 16.8 1.0
CD D:GLU4 3.0 8.9 1.0
CG D:ASP5 3.5 9.2 1.0
OD2 D:ASP5 4.0 8.4 1.0
CG D:GLU8 4.4 11.7 1.0
CG D:GLU4 4.5 8.3 1.0
CA D:ASP5 4.5 5.6 1.0
CB D:ASP5 4.6 5.0 1.0
O D:HOH293 4.7 13.3 1.0
N D:ASP5 4.8 5.5 1.0

Reference:

E.N.Salgado, R.A.Lewis, J.Faraone-Mennella, F.A.Tezcan. Metal-Mediated Self-Assembly of Protein Superstructures: Influence of Secondary Interactions on Protein Oligomerization and Aggregation. J.Am.Chem.Soc. V. 130 6082 2008.
ISSN: ISSN 0002-7863
PubMed: 18422313
DOI: 10.1021/JA8012177
Page generated: Tue Jul 8 11:19:19 2025

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