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Zinc 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

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Tetrameric Cytochrome CB562 (H59/D62/H63/H73/A74/H77) Assembly Stabilized By Interprotein Zinc Coordination, PDB code: 3c62:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3c62

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Zinc binding site 1 out of 4 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 Zinc with other atoms in the Zn 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:Zn107

b:7.5
occ:1.00
NE2 B:HIS63 2.0 2.7 1.0
NE2 A:HIS77 2.0 3.7 1.0
NE2 A:HIS73 2.0 2.1 1.0
NE2 D:HIS59 2.2 4.6 1.0
CE1 A:HIS73 3.0 5.6 1.0
CD2 B:HIS63 3.0 2.0 1.0
CD2 A:HIS77 3.0 4.3 1.0
CE1 B:HIS63 3.0 3.7 1.0
CD2 A:HIS73 3.0 4.0 1.0
CE1 A:HIS77 3.1 6.2 1.0
CD2 D:HIS59 3.1 5.3 1.0
CE1 D:HIS59 3.2 5.6 1.0
ND1 A:HIS73 4.0 5.5 1.0
ND1 B:HIS63 4.1 4.0 1.0
CG A:HIS73 4.1 4.6 1.0
CG B:HIS63 4.1 4.8 1.0
CG A:HIS77 4.2 4.7 1.0
ND1 A:HIS77 4.2 4.4 1.0
O B:HOH416 4.2 23.0 1.0
ND1 D:HIS59 4.3 5.2 1.0
CG D:HIS59 4.3 6.5 1.0
O C:HOH288 4.3 4.5 1.0
O A:HOH229 4.3 3.3 1.0
O D:HOH208 4.5 2.6 1.0
O C:HOH313 4.8 20.8 1.0
CD1 B:ILE67 4.8 10.5 1.0
O B:HOH360 4.8 26.7 1.0

Zinc binding site 2 out of 4 in 3c62

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Zinc binding site 2 out of 4 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 Zinc with other atoms in the Zn 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:Zn107

b:8.6
occ:1.00
NE2 B:HIS77 2.0 2.0 1.0
NE2 C:HIS59 2.0 9.4 1.0
NE2 A:HIS63 2.0 4.5 1.0
NE2 B:HIS73 2.1 8.7 1.0
CE1 B:HIS77 2.9 6.1 1.0
CD2 A:HIS63 2.9 4.7 1.0
CE1 C:HIS59 2.9 11.7 1.0
CE1 B:HIS73 3.0 9.4 1.0
CD2 B:HIS77 3.0 2.1 1.0
CE1 A:HIS63 3.1 6.7 1.0
CD2 C:HIS59 3.1 12.0 1.0
CD2 B:HIS73 3.1 9.1 1.0
O A:HOH244 3.7 25.0 1.0
ND1 B:HIS77 4.0 3.5 1.0
ND1 C:HIS59 4.1 9.4 1.0
CG A:HIS63 4.1 6.4 1.0
CG B:HIS77 4.1 3.5 1.0
ND1 B:HIS73 4.1 9.3 1.0
ND1 A:HIS63 4.2 5.0 1.0
CG C:HIS59 4.2 11.7 1.0
CG B:HIS73 4.2 7.9 1.0
O B:HOH309 4.2 3.9 1.0
O C:HOH270 4.3 7.6 1.0
CD1 A:ILE67 4.5 5.5 1.0

Zinc binding site 3 out of 4 in 3c62

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Zinc binding site 3 out of 4 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 Zinc with other atoms in the Zn 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
C:Zn107

b:7.9
occ:1.00
NE2 C:HIS73 2.1 5.8 1.0
NE2 C:HIS77 2.1 10.2 1.0
NE2 D:HIS63 2.1 4.3 1.0
NE2 B:HIS59 2.1 2.0 1.0
CE1 C:HIS77 2.8 10.8 1.0
CE1 C:HIS73 3.0 7.7 1.0
CD2 D:HIS63 3.0 2.0 1.0
CD2 C:HIS73 3.1 5.8 1.0
CD2 B:HIS59 3.1 5.6 1.0
CE1 D:HIS63 3.1 4.1 1.0
CE1 B:HIS59 3.1 5.3 1.0
CD2 C:HIS77 3.2 9.7 1.0
ND1 C:HIS77 4.0 11.4 1.0
ND1 C:HIS73 4.1 6.4 1.0
O C:HOH239 4.1 18.6 1.0
CG D:HIS63 4.1 2.9 1.0
ND1 D:HIS63 4.1 2.0 1.0
CG C:HIS73 4.1 5.9 1.0
ND1 B:HIS59 4.2 4.9 1.0
CG B:HIS59 4.2 5.4 1.0
CG C:HIS77 4.2 8.8 1.0
O B:HOH343 4.5 7.3 1.0
CD1 D:ILE67 4.6 7.5 1.0
O C:HOH285 4.6 8.5 1.0
O D:HOH175 4.7 29.6 1.0

Zinc binding site 4 out of 4 in 3c62

Go back to Zinc Binding Sites List in 3c62
Zinc binding site 4 out of 4 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 Zinc with other atoms in the Zn 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
D:Zn107

b:8.6
occ:1.00
NE2 C:HIS63 1.9 7.0 1.0
NE2 D:HIS77 2.1 5.1 1.0
NE2 D:HIS73 2.1 4.3 1.0
NE2 A:HIS59 2.1 4.8 1.0
CE1 A:HIS59 2.8 6.0 1.0
CD2 C:HIS63 2.9 6.1 1.0
CE1 C:HIS63 3.0 6.2 1.0
CD2 D:HIS73 3.0 5.1 1.0
CE1 D:HIS77 3.0 6.3 1.0
CD2 D:HIS77 3.1 5.9 1.0
CE1 D:HIS73 3.1 5.0 1.0
CD2 A:HIS59 3.3 5.8 1.0
ND1 A:HIS59 4.0 5.8 1.0
ND1 C:HIS63 4.0 2.8 1.0
CG C:HIS63 4.0 6.4 1.0
O C:HOH284 4.1 9.4 1.0
ND1 D:HIS77 4.1 4.2 1.0
ND1 D:HIS73 4.2 5.3 1.0
CG D:HIS73 4.2 5.2 1.0
CG D:HIS77 4.2 5.2 1.0
CG A:HIS59 4.3 5.6 1.0
O D:HOH231 4.5 2.0 1.0
O A:HOH201 4.7 2.0 1.0
CD1 C:ILE67 4.8 8.2 1.0
O C:HOH258 5.0 10.8 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 Sep 26 05:45:31 2020
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