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Zinc in PDB 3m79: A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II)

Protein crystallography data

The structure of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II), PDB code: 3m79 was solved by J.D.Brodin, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.87 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.547, 78.068, 178.339, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 27.1

Other elements in 3m79:

The structure of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II) also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II) (pdb code 3m79). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II), PDB code: 3m79:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3m79

Go back to Zinc Binding Sites List in 3m79
Zinc binding site 1 out of 8 in the A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn107

b:17.0
occ:1.00
 NE2 A:HIS73 2.0 22.7 1.0
NE2 D:HIS63 2.0 18.1 1.0
NE2 A:HIS77 2.0 21.4 1.0
OD1 C:ASP74 2.1 21.8 1.0
OD2 C:ASP74 2.2 21.7 1.0
CG C:ASP74 2.4 20.5 1.0
CE1 A:HIS73 2.9 24.1 1.0
CD2 D:HIS63 3.0 19.1 1.0
CE1 D:HIS63 3.0 18.1 1.0
CE1 A:HIS77 3.0 21.7 1.0
CD2 A:HIS77 3.1 19.0 1.0
CD2 A:HIS73 3.1 23.3 1.0
CB C:ASP74 3.9 20.4 1.0
ND1 A:HIS73 4.0 23.7 1.0
ND1 D:HIS63 4.1 16.9 1.0
CG D:HIS63 4.1 19.8 1.0
ND1 A:HIS77 4.1 20.8 1.0
CG A:HIS73 4.1 21.9 1.0
CG A:HIS77 4.2 20.2 1.0
O A:HOH340 4.4 29.8 1.0
CD1 D:ILE67 4.6 20.4 1.0
CA C:ASP74 4.7 20.6 1.0
O C:ASP74 4.7 20.5 1.0
O C:HOH394 4.8 26.2 1.0
CD2 C:LEU78 4.9 21.1 1.0

Zinc binding site 2 out of 8 in 3m79

Go back to Zinc Binding Sites List in 3m79
Zinc binding site 2 out of 8 in the A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn107

b:19.5
occ:1.00
 OD2 D:ASP74 1.9 22.7 1.0
NE2 B:HIS77 1.9 18.0 1.0
NE2 C:HIS63 2.0 19.7 1.0
NE2 B:HIS73 2.2 21.4 1.0
CG D:ASP74 2.7 20.6 1.0
OD1 D:ASP74 2.7 24.0 1.0
CD2 C:HIS63 2.9 19.9 1.0
CE1 B:HIS77 2.9 19.2 1.0
CD2 B:HIS77 3.0 18.5 1.0
CE1 B:HIS73 3.0 24.3 1.0
CE1 C:HIS63 3.1 19.2 1.0
CD2 B:HIS73 3.3 21.3 1.0
ND1 B:HIS77 4.0 18.3 1.0
CG C:HIS63 4.1 20.8 1.0
CG B:HIS77 4.1 18.9 1.0
CB D:ASP74 4.1 20.9 1.0
ND1 C:HIS63 4.1 20.9 1.0
ND1 B:HIS73 4.2 21.9 1.0
O D:HOH384 4.3 43.6 1.0
CG B:HIS73 4.4 21.5 1.0
O B:HOH322 4.6 34.1 1.0
CA D:ASP74 4.7 20.7 1.0
O D:ASP74 4.8 20.5 1.0

Zinc binding site 3 out of 8 in 3m79

Go back to Zinc Binding Sites List in 3m79
Zinc binding site 3 out of 8 in the A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn107

b:20.2
occ:1.00
 NE2 C:HIS73 1.9 22.4 1.0
NE2 C:HIS77 2.0 16.1 1.0
OD2 A:ASP74 2.0 24.2 1.0
NE2 B:HIS63 2.0 19.8 1.0
OD1 A:ASP74 2.6 24.9 1.0
CE1 C:HIS73 2.6 25.6 1.0
CG A:ASP74 2.6 23.2 1.0
CD2 B:HIS63 3.0 21.1 1.0
CD2 C:HIS77 3.0 18.3 1.0
CE1 C:HIS77 3.0 16.8 1.0
CE1 B:HIS63 3.0 21.0 1.0
CD2 C:HIS73 3.1 22.6 1.0
ND1 C:HIS73 3.8 25.1 1.0
CG C:HIS73 4.0 22.1 1.0
CB A:ASP74 4.1 21.7 1.0
ND1 C:HIS77 4.1 16.0 1.0
ND1 B:HIS63 4.1 19.9 1.0
CG B:HIS63 4.1 21.4 1.0
CG C:HIS77 4.1 18.6 1.0
O A:HOH128 4.6 30.0 1.0
O A:ASP74 4.7 20.5 1.0
CA A:ASP74 4.7 20.7 1.0
O A:HOH369 4.8 32.4 1.0
CD1 B:ILE67 4.9 19.4 1.0

Zinc binding site 4 out of 8 in 3m79

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Zinc binding site 4 out of 8 in the A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn107

b:17.5
occ:1.00
 NE2 D:HIS73 1.9 16.3 1.0
OD1 B:ASP74 1.9 22.3 1.0
NE2 A:HIS63 2.0 18.9 1.0
NE2 D:HIS77 2.0 20.2 1.0
CE1 D:HIS73 2.8 19.4 1.0
CG B:ASP74 2.9 21.9 1.0
CD2 D:HIS77 2.9 18.1 1.0
CD2 A:HIS63 2.9 18.8 1.0
CE1 A:HIS63 3.0 18.9 1.0
CD2 D:HIS73 3.0 18.0 1.0
CE1 D:HIS77 3.1 19.4 1.0
OD2 B:ASP74 3.3 23.4 1.0
ND1 D:HIS73 3.9 20.3 1.0
ND1 A:HIS63 4.1 17.7 1.0
CG A:HIS63 4.1 19.1 1.0
O B:HOH322 4.1 34.1 1.0
CG D:HIS73 4.1 19.7 1.0
CG D:HIS77 4.1 19.4 1.0
ND1 D:HIS77 4.2 18.4 1.0
CD1 A:ILE67 4.3 20.1 1.0
CB B:ASP74 4.3 21.0 1.0
O D:HOH384 4.8 43.6 1.0
CA B:ASP74 4.9 20.6 1.0
O B:ASP74 4.9 20.3 1.0
O B:HOH372 5.0 24.2 1.0

Zinc binding site 5 out of 8 in 3m79

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Zinc binding site 5 out of 8 in the A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn107

b:17.7
occ:1.00
 NE2 E:HIS77 2.0 20.3 1.0
NE2 H:HIS63 2.0 19.1 1.0
NE2 E:HIS73 2.1 21.2 1.0
OD1 G:ASP74 2.2 26.1 1.0
OD2 G:ASP74 2.4 25.0 1.0
CG G:ASP74 2.6 23.1 1.0
CE1 E:HIS77 3.0 20.0 1.0
CD2 E:HIS77 3.0 18.8 1.0
CD2 H:HIS63 3.0 19.4 1.0
CE1 E:HIS73 3.0 20.1 1.0
CE1 H:HIS63 3.0 18.8 1.0
CD2 E:HIS73 3.1 20.8 1.0
ND1 E:HIS77 4.1 19.4 1.0
CB G:ASP74 4.1 21.4 1.0
ND1 H:HIS63 4.1 19.0 1.0
CG E:HIS77 4.1 19.6 1.0
ND1 E:HIS73 4.1 19.9 1.0
CG H:HIS63 4.1 19.8 1.0
CG E:HIS73 4.2 20.3 1.0
CD1 H:ILE67 4.6 19.6 1.0
O G:ASP74 4.7 20.4 1.0
CA G:ASP74 4.8 20.8 1.0

Zinc binding site 6 out of 8 in 3m79

Go back to Zinc Binding Sites List in 3m79
Zinc binding site 6 out of 8 in the A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn107

b:19.1
occ:1.00
 NE2 G:HIS63 2.0 19.4 1.0
NE2 F:HIS73 2.1 24.3 1.0
NE2 F:HIS77 2.1 20.4 1.0
OD2 H:ASP74 2.1 23.7 1.0
OD1 H:ASP74 2.6 23.0 1.0
CG H:ASP74 2.7 21.4 1.0
CE1 F:HIS73 2.9 26.5 1.0
CE1 G:HIS63 2.9 19.6 1.0
CD2 G:HIS63 3.0 19.9 1.0
CE1 F:HIS77 3.1 20.6 1.0
CD2 F:HIS77 3.1 19.9 1.0
CD2 F:HIS73 3.1 23.2 1.0
ND1 G:HIS63 4.1 20.2 1.0
ND1 F:HIS73 4.1 24.2 1.0
CG G:HIS63 4.1 20.6 1.0
CB H:ASP74 4.1 20.5 1.0
ND1 F:HIS77 4.2 20.6 1.0
CG F:HIS73 4.2 23.1 1.0
CG F:HIS77 4.2 20.7 1.0
CD1 G:ILE67 4.8 20.4 1.0
O H:ASP74 4.8 20.5 1.0
CA H:ASP74 4.8 20.6 1.0
O F:HOH117 4.9 24.6 1.0

Zinc binding site 7 out of 8 in 3m79

Go back to Zinc Binding Sites List in 3m79
Zinc binding site 7 out of 8 in the A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn107

b:16.8
occ:1.00
 NE2 G:HIS73 1.8 20.1 1.0
OD1 E:ASP74 2.0 22.2 1.0
NE2 G:HIS77 2.0 16.8 1.0
NE2 F:HIS63 2.1 21.0 1.0
OD2 E:ASP74 2.5 23.5 1.0
CE1 G:HIS73 2.6 23.8 1.0
CG E:ASP74 2.6 21.8 1.0
CD2 F:HIS63 3.0 20.0 1.0
CD2 G:HIS77 3.0 17.4 1.0
CD2 G:HIS73 3.0 19.9 1.0
CE1 G:HIS77 3.1 15.9 1.0
CE1 F:HIS63 3.1 20.9 1.0
ND1 G:HIS73 3.8 24.5 1.0
CG G:HIS73 4.0 21.9 1.0
CB E:ASP74 4.1 21.3 1.0
CG F:HIS63 4.1 21.7 1.0
ND1 G:HIS77 4.1 16.1 1.0
CG G:HIS77 4.1 18.1 1.0
ND1 F:HIS63 4.2 21.2 1.0
CD1 F:TRP66 4.3 30.8 1.0
O E:HOH210 4.6 26.9 1.0
O E:ASP74 4.7 20.3 1.0
NE1 F:TRP66 4.7 32.8 1.0
CA E:ASP74 4.8 20.6 1.0

Zinc binding site 8 out of 8 in 3m79

Go back to Zinc Binding Sites List in 3m79
Zinc binding site 8 out of 8 in the A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces Crystallized in the Presence of Cu(II) and Zn(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn107

b:17.5
occ:1.00
 OD1 F:ASP74 1.9 18.7 1.0
NE2 H:HIS77 2.0 20.9 1.0
NE2 H:HIS73 2.1 17.7 1.0
NE2 E:HIS63 2.1 16.5 1.0
CG F:ASP74 2.9 20.4 1.0
CE1 H:HIS77 2.9 21.3 1.0
CE1 H:HIS73 3.0 20.4 1.0
CD2 H:HIS77 3.0 19.9 1.0
CD2 E:HIS63 3.1 16.7 1.0
CE1 E:HIS63 3.1 16.8 1.0
CD2 H:HIS73 3.1 19.9 1.0
OD2 F:ASP74 3.3 20.4 1.0
O F:HOH117 4.0 24.6 1.0
ND1 H:HIS77 4.1 20.7 1.0
ND1 H:HIS73 4.1 19.1 1.0
CG H:HIS77 4.1 20.8 1.0
ND1 E:HIS63 4.2 16.9 1.0
CG E:HIS63 4.2 18.5 1.0
CG H:HIS73 4.2 20.5 1.0
CB F:ASP74 4.2 20.0 1.0
O H:HOH286 4.6 22.1 1.0
CA F:ASP74 4.8 20.4 1.0
CG1 E:ILE67 4.9 20.6 1.0

Reference:

J.D.Brodin, A.Medina-Morales, T.Ni, E.N.Salgado, X.I.Ambroggio, F.A.Tezcan. Evolution of Metal Selectivity in Templated Protein Interfaces. J.Am.Chem.Soc. V. 132 8610 2010.
ISSN: ISSN 0002-7863
PubMed: 20515031
DOI: 10.1021/JA910844N
Page generated: Sat Oct 26 09:15:38 2024

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