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Calcium in PDB 3c62: Tetrameric Cytochrome CB562 (H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination

Protein crystallography data

The structure of Tetrameric Cytochrome CB562 (H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination, PDB code: 3c62 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) 25.23 / 1.87
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.968, 90.133, 49.357, 90.00, 109.64, 90.00
R / Rfree (%) 23.1 / 27.3

Other elements in 3c62:

The structure of Tetrameric Cytochrome CB562 (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 (H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination (pdb code 3c62). 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 (H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination, PDB code: 3c62:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 3c62

Go back to Calcium Binding Sites List in 3c62
Calcium binding site 1 out of 5 in the Tetrameric Cytochrome CB562 (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 (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 2.7 6.5 1.0
OE1 A:GLU4 2.8 21.7 1.0
O1A A:HEM150 2.8 10.8 1.0
O A:HOH180 2.9 8.2 1.0
CGA A:HEM150 3.1 9.3 1.0
CD A:GLU4 3.1 19.5 1.0
OE2 A:GLU4 3.2 22.0 1.0
CG A:GLU4 4.2 17.6 1.0
CBA A:HEM150 4.6 6.6 1.0
O A:HOH234 4.8 7.0 1.0
CB A:GLU4 4.9 12.8 1.0

Calcium binding site 2 out of 5 in 3c62

Go back to Calcium Binding Sites List in 3c62
Calcium binding site 2 out of 5 in the Tetrameric Cytochrome CB562 (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 (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:27.5
occ:1.00
 OD1 B:ASP12 2.9 14.4 1.0
O B:HOH349 2.9 17.6 1.0
CG B:ASP12 3.5 12.1 1.0
OD2 B:ASP12 3.6 15.8 1.0
O B:HOH402 4.2 13.0 1.0
CB B:ASP12 4.6 7.0 1.0
OE2 B:GLU8 4.7 14.5 1.0

Calcium binding site 3 out of 5 in 3c62

Go back to Calcium Binding Sites List in 3c62
Calcium binding site 3 out of 5 in the Tetrameric Cytochrome CB562 (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 (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:9.6
occ:1.00
 OD1 B:ASP2 2.6 12.2 1.0
OE2 B:GLU4 2.7 11.7 1.0
OD2 B:ASP2 2.8 14.1 1.0
CG B:ASP2 3.1 14.0 1.0
CD B:GLU4 3.6 12.4 1.0
O B:HOH341 4.0 2.6 1.0
O1D B:HEM150 4.2 6.1 1.0
CG B:GLU4 4.3 11.5 1.0
O B:HOH351 4.3 9.9 1.0
OE1 B:GLU4 4.3 11.4 1.0
CB B:ASP2 4.6 11.8 1.0
N B:GLU4 4.9 10.5 1.0
N B:LEU3 4.9 11.0 1.0
CB B:GLU4 4.9 11.9 1.0

Calcium binding site 4 out of 5 in 3c62

Go back to Calcium Binding Sites List in 3c62
Calcium binding site 4 out of 5 in the Tetrameric Cytochrome CB562 (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 (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:5.8
occ:1.00
 OD1 B:ASP28 2.5 7.5 1.0
O B:HOH278 3.0 21.2 1.0
CG B:ASP28 3.5 6.5 1.0
OD2 B:ASP28 4.0 8.9 1.0
NZ B:LYS32 4.1 11.1 1.0
O B:HOH362 4.2 10.2 1.0
CB B:ASP28 4.7 5.7 1.0
O B:HOH304 4.8 4.4 1.0

Calcium binding site 5 out of 5 in 3c62

Go back to Calcium Binding Sites List in 3c62
Calcium binding site 5 out of 5 in the Tetrameric Cytochrome CB562 (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 (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:8.6
occ:1.00
 O D:HOH277 2.3 31.4 1.0
OD1 D:ASP5 2.6 6.3 1.0
OE2 D:GLU8 2.9 17.1 1.0
O D:HOH273 2.9 9.4 1.0
O D:HOH209 3.0 12.2 1.0
O D:HOH181 3.1 20.4 1.0
CD D:GLU8 3.5 16.0 1.0
CG D:ASP5 3.5 7.3 1.0
OE1 D:GLU8 3.6 15.7 1.0
OD2 D:ASP5 4.0 8.0 1.0
CA D:ASP5 4.5 5.7 1.0
CB D:ASP5 4.6 5.6 1.0
CG D:GLU8 4.6 13.6 1.0
N D:ASP5 4.8 6.2 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 11:19:12 2025

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