Atomistry » Calcium » PDB 3bxl-3cfw » 3c63
Atomistry »
  Calcium »
    PDB 3bxl-3cfw »
      3c63 »

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: Sat Jul 13 08:34:40 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