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

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

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
Calcium	(Ca)	5 atoms

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 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 Zinc with other atoms in the Zn 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:Zn107 b:7.2 occ:1.00 NE2 A:HIS77 2.0 8.1 1.0 NE2 A:HIS73 2.0 2.9 1.0 NE2 B:HIS63 2.0 3.9 1.0 NE2 D:HIS59 2.1 5.8 1.0 CE1 A:HIS77 2.9 10.9 1.0 CE1 A:HIS73 2.9 6.7 1.0 CD2 A:HIS73 3.0 6.7 1.0 CD2 B:HIS63 3.0 5.5 1.0 CE1 D:HIS59 3.0 6.0 1.0 CE1 B:HIS63 3.0 5.8 1.0 CD2 A:HIS77 3.0 5.0 1.0 CD2 D:HIS59 3.1 7.3 1.0 O A:HOH188 4.0 12.6 1.0 ND1 A:HIS73 4.0 6.5 1.0 ND1 A:HIS77 4.0 9.7 1.0 O D:HOH282 4.1 9.9 1.0 CG A:HIS73 4.1 5.8 1.0 ND1 B:HIS63 4.1 4.3 1.0 CG A:HIS77 4.1 10.1 1.0 ND1 D:HIS59 4.1 7.8 1.0 CG B:HIS63 4.1 5.6 1.0 CG D:HIS59 4.2 7.4 1.0 CD1 B:ILE67 4.4 4.7 1.0 O D:HOH266 4.4 4.3 1.0 O A:HOH217 4.6 12.4 1.0 O B:HOH266 4.8 18.2 1.0

Zinc binding site 2 out of 4 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 Zinc with other atoms in the Zn 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:Zn107 b:10.2 occ:1.00 NE2 A:HIS63 2.0 5.5 1.0 NE2 B:HIS77 2.0 7.4 1.0 NE2 C:HIS59 2.0 5.2 1.0 NE2 B:HIS73 2.0 5.1 1.0 CE1 B:HIS73 2.9 8.3 1.0 CE1 C:HIS59 2.9 4.5 1.0 CD2 A:HIS63 3.0 5.5 1.0 CE1 B:HIS77 3.0 11.2 1.0 CE1 A:HIS63 3.0 5.0 1.0 CD2 B:HIS77 3.0 7.5 1.0 CD2 C:HIS59 3.1 8.5 1.0 CD2 B:HIS73 3.1 7.0 1.0 O C:HOH152 3.8 6.7 1.0 ND1 B:HIS73 4.1 5.4 1.0 ND1 A:HIS63 4.1 6.0 1.0 ND1 C:HIS59 4.1 8.3 1.0 ND1 B:HIS77 4.1 10.8 1.0 CG A:HIS63 4.1 7.2 1.0 O B:HOH254 4.1 7.1 1.0 CG B:HIS77 4.1 9.6 1.0 CG B:HIS73 4.2 5.6 1.0 CG C:HIS59 4.2 8.5 1.0 CD1 A:ILE67 4.4 5.6 1.0 O C:HOH155 4.5 7.3 1.0 O A:HOH207 4.7 10.7 1.0 O A:HOH215 5.0 16.0 1.0

Zinc binding site 3 out of 4 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 Zinc with other atoms in the Zn 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 C:Zn107 b:8.0 occ:1.00 NE2 C:HIS73 1.9 5.6 1.0 NE2 C:HIS77 2.0 8.6 1.0 NE2 B:HIS59 2.0 4.8 1.0 NE2 D:HIS63 2.1 6.8 1.0 CE1 C:HIS73 2.8 8.9 1.0 CE1 C:HIS77 2.9 11.7 1.0 CE1 B:HIS59 2.9 6.5 1.0 CD2 D:HIS63 3.0 5.3 1.0 CD2 C:HIS73 3.0 6.8 1.0 CD2 C:HIS77 3.1 8.8 1.0 CD2 B:HIS59 3.1 5.9 1.0 CE1 D:HIS63 3.1 7.3 1.0 O B:HOH346 3.9 13.2 1.0 O C:HOH177 3.9 12.0 1.0 ND1 C:HIS73 4.0 7.7 1.0 ND1 C:HIS77 4.0 12.1 1.0 ND1 B:HIS59 4.0 6.2 1.0 CG C:HIS73 4.1 5.2 1.0 CG C:HIS77 4.1 9.8 1.0 CG D:HIS63 4.2 5.9 1.0 CG B:HIS59 4.2 5.9 1.0 ND1 D:HIS63 4.2 5.6 1.0 CD1 D:ILE67 4.4 6.2 1.0 O B:HOH225 4.5 6.1 1.0 O D:HOH310 4.5 16.0 1.0 O C:HOH175 4.7 17.8 1.0 O D:HOH307 5.0 23.6 1.0

Zinc binding site 4 out of 4 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 Zinc with other atoms in the Zn 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 D:Zn107 b:9.4 occ:1.00 NE2 C:HIS63 2.0 6.0 1.0 NE2 D:HIS77 2.0 10.1 1.0 NE2 A:HIS59 2.1 9.5 1.0 NE2 D:HIS73 2.1 6.8 1.0 CE1 C:HIS63 2.9 5.8 1.0 CE1 D:HIS77 2.9 12.5 1.0 CD2 C:HIS63 2.9 4.1 1.0 CE1 A:HIS59 3.0 9.9 1.0 CD2 D:HIS77 3.0 10.3 1.0 CD2 D:HIS73 3.1 6.2 1.0 CE1 D:HIS73 3.1 9.8 1.0 CD2 A:HIS59 3.1 9.4 1.0 O A:HOH172 3.6 13.3 1.0 O D:HOH324 3.8 19.1 1.0 ND1 C:HIS63 4.0 5.1 1.0 CG C:HIS63 4.1 7.1 1.0 ND1 D:HIS77 4.1 12.9 1.0 ND1 A:HIS59 4.1 9.1 1.0 CG D:HIS77 4.1 8.9 1.0 ND1 D:HIS73 4.2 9.7 1.0 CG D:HIS73 4.2 8.3 1.0 CG A:HIS59 4.2 8.0 1.0 O C:HOH190 4.4 14.5 1.0 CD1 C:ILE67 4.4 8.0 1.0 O A:HOH184 4.5 10.4 1.0 O A:HOH164 5.0 9.6 1.0

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