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Zinc in PDB 6ai5: Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3

Protein crystallography data

The structure of Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3, PDB code: 6ai5 was solved by W.J.Song, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.60 / 1.81
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 57.562, 76.871, 96.425, 90.00, 105.84, 90.00
R / Rfree (%) 17.5 / 20.9

Other elements in 6ai5:

The structure of Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3 also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Iron (Fe) 4 atoms
Chlorine (Cl) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3 (pdb code 6ai5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3, PDB code: 6ai5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6ai5

Go back to Zinc Binding Sites List in 6ai5
Zinc binding site 1 out of 8 in the Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:16.9
occ:1.00
 NE2 A:HIS73 2.0 20.1 1.0
NE2 C:HIS63 2.0 17.8 1.0
OD1 E:ASP74 2.0 21.2 1.0
NE2 A:HIS77 2.0 16.2 1.0
CG E:ASP74 2.7 19.0 1.0
OD2 E:ASP74 2.8 21.3 1.0
CE1 A:HIS73 2.9 20.0 1.0
CD2 C:HIS63 3.0 18.6 1.0
CD2 A:HIS77 3.0 16.6 1.0
CD2 A:HIS73 3.0 19.0 1.0
CE1 A:HIS77 3.0 17.1 1.0
CE1 C:HIS63 3.0 18.6 1.0
ND1 A:HIS73 4.0 19.2 1.0
CG C:HIS63 4.1 18.5 1.0
ND1 C:HIS63 4.1 19.3 1.0
CG A:HIS73 4.1 19.1 1.0
ND1 A:HIS77 4.1 16.8 1.0
CG A:HIS77 4.1 16.6 1.0
CB E:ASP74 4.2 18.8 1.0
O E:HOH352 4.4 32.3 1.0
O A:HOH364 4.6 31.5 1.0
CA E:ASP74 4.8 17.8 1.0
O E:ASP74 4.8 17.6 1.0
O E:HOH393 4.8 24.3 1.0
CD1 C:ILE67 4.8 17.9 1.0
O A:HOH303 4.8 33.4 1.0

Zinc binding site 2 out of 8 in 6ai5

Go back to Zinc Binding Sites List in 6ai5
Zinc binding site 2 out of 8 in the Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:30.9
occ:1.00
 ND1 A:HIS89 2.0 26.8 1.0
NE2 G:HIS100 2.1 22.5 1.0
OE1 A:GLU86 2.1 29.6 1.0
CL A:CL204 2.2 54.8 1.0
OE2 A:GLU86 2.6 35.3 1.0
CD A:GLU86 2.7 30.2 1.0
CE1 G:HIS100 3.0 25.0 1.0
CE1 A:HIS89 3.0 26.9 1.0
CD2 G:HIS100 3.1 22.4 1.0
CG A:HIS89 3.1 24.4 1.0
CB A:HIS89 3.4 22.4 1.0
ND1 G:HIS100 4.1 22.5 1.0
O G:HOH352 4.1 32.2 1.0
NE2 A:HIS89 4.1 26.9 1.0
CG G:HIS100 4.2 20.7 1.0
CD2 A:HIS89 4.2 26.5 1.0
CG A:GLU86 4.2 28.4 1.0
O G:HOH305 4.4 38.2 1.0
CA A:GLU86 4.6 22.0 1.0
CB A:GLU86 4.9 25.4 1.0
CA A:HIS89 4.9 20.8 1.0

Zinc binding site 3 out of 8 in 6ai5

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Zinc binding site 3 out of 8 in the Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn206

b:16.5
occ:1.00
 OD1 G:ASP74 1.9 18.2 1.0
NE2 A:HIS63 2.0 16.3 1.0
NE2 C:HIS73 2.0 17.4 1.0
NE2 C:HIS77 2.0 14.7 1.0
CG G:ASP74 2.8 17.8 1.0
CD2 A:HIS63 2.9 15.7 1.0
CE1 C:HIS73 3.0 18.0 1.0
CE1 A:HIS63 3.0 16.1 1.0
CE1 C:HIS77 3.0 14.9 1.0
CD2 C:HIS77 3.0 15.5 1.0
CD2 C:HIS73 3.0 17.1 1.0
OD2 G:ASP74 3.1 19.2 1.0
CG A:HIS63 4.1 15.9 1.0
ND1 A:HIS63 4.1 15.8 1.0
O G:HOH348 4.1 24.8 1.0
ND1 C:HIS73 4.1 17.1 1.0
ND1 C:HIS77 4.1 14.9 1.0
CG C:HIS73 4.2 16.8 1.0
CG C:HIS77 4.2 15.6 1.0
CB G:ASP74 4.2 18.5 1.0
CD1 A:ILE67 4.4 17.4 1.0
O C:HOH357 4.7 18.8 1.0
CA G:ASP74 4.8 17.9 1.0
O G:ASP74 4.9 18.0 1.0

Zinc binding site 4 out of 8 in 6ai5

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Zinc binding site 4 out of 8 in the Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn207

b:16.4
occ:1.00
 OD1 A:ASP74 2.0 22.8 1.0
NE2 E:HIS73 2.0 18.1 1.0
NE2 E:HIS77 2.0 14.3 1.0
NE2 G:HIS63 2.0 16.0 1.0
CG A:ASP74 2.7 20.5 1.0
OD2 A:ASP74 2.9 25.8 1.0
CD2 G:HIS63 2.9 17.2 1.0
CE1 E:HIS73 2.9 18.1 1.0
CD2 E:HIS77 3.0 14.4 1.0
CE1 E:HIS77 3.0 14.7 1.0
CD2 E:HIS73 3.0 17.7 1.0
CE1 G:HIS63 3.1 16.7 1.0
O A:HOH303 3.8 33.4 1.0
ND1 E:HIS73 4.1 17.1 1.0
ND1 E:HIS77 4.1 14.7 1.0
CG G:HIS63 4.1 17.5 1.0
CG E:HIS77 4.1 15.8 1.0
CG E:HIS73 4.1 17.7 1.0
ND1 G:HIS63 4.2 17.0 1.0
CB A:ASP74 4.2 19.1 1.0
O E:HOH352 4.4 32.3 1.0
O E:HOH366 4.7 27.9 1.0
CD1 G:ILE67 4.7 17.0 1.0
CA A:ASP74 4.8 17.8 1.0
O A:ASP74 4.9 16.1 1.0
O A:HOH398 5.0 24.7 1.0
O A:HOH302 5.0 38.5 1.0

Zinc binding site 5 out of 8 in 6ai5

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Zinc binding site 5 out of 8 in the Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn208

b:48.6
occ:1.00
 ND1 G:HIS89 1.8 35.1 1.0
NE2 A:HIS100 2.2 30.0 1.0
OE1 G:GLU86 2.3 44.2 1.0
OE2 G:GLU86 2.5 40.6 1.0
O G:HOH384 2.6 33.6 1.0
CD G:GLU86 2.7 41.2 1.0
CE1 G:HIS89 2.8 34.2 1.0
CG G:HIS89 2.9 32.0 1.0
CD2 A:HIS100 3.1 29.7 1.0
CE1 A:HIS100 3.3 32.5 1.0
CB G:HIS89 3.3 30.4 1.0
O G:HOH307 3.5 38.2 1.0
NE2 G:HIS89 3.9 35.2 1.0
CD2 G:HIS89 3.9 35.1 1.0
CG A:HIS100 4.2 26.9 1.0
CG G:GLU86 4.3 39.5 1.0
ND1 A:HIS100 4.3 30.9 1.0
CA G:GLU86 4.5 30.6 1.0
O G:HOH359 4.8 29.0 1.0
O G:LYS85 4.8 32.1 1.0
CA G:HIS89 4.8 28.0 1.0
CB G:GLU86 4.9 35.0 1.0

Zinc binding site 6 out of 8 in 6ai5

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Zinc binding site 6 out of 8 in the Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:23.3
occ:0.50
 ND1 E:HIS100 1.9 32.8 1.0
O E:HOH316 2.0 37.8 1.0
NE2 C:HIS89 2.1 41.5 1.0
CE1 E:HIS100 2.6 36.9 1.0
CD2 C:HIS89 2.7 40.9 1.0
CG E:HIS100 3.1 31.0 1.0
CE1 C:HIS89 3.2 44.5 1.0
CB E:HIS100 3.7 25.9 1.0
CA E:HIS100 3.7 22.9 1.0
O E:HOH395 3.8 44.9 1.0
NE2 E:HIS100 3.9 37.6 1.0
CG C:HIS89 3.9 38.1 1.0
ND1 C:HIS89 4.1 40.6 1.0
O E:HIS100 4.1 21.2 1.0
CD2 E:HIS100 4.1 34.8 1.0
OE1 E:GLN103 4.3 26.3 1.0
C E:HIS100 4.4 22.7 1.0
CB E:GLN103 4.5 24.9 1.0
OE1 C:GLN93 4.6 41.5 1.0
CG E:GLN103 4.7 28.0 1.0
CD E:GLN103 4.8 27.6 1.0
N E:HIS100 4.8 21.6 1.0
CL E:CL202 4.8 65.3 1.0

Zinc binding site 7 out of 8 in 6ai5

Go back to Zinc Binding Sites List in 6ai5
Zinc binding site 7 out of 8 in the Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn204

b:75.5
occ:1.00
 NE2 C:HIS100 1.8 31.4 1.0
ND1 E:HIS89 1.9 31.9 0.5
OE2 E:GLU86 2.4 36.2 1.0
OE1 E:GLU86 2.4 31.5 1.0
CE1 E:HIS89 2.6 32.1 0.5
CD E:GLU86 2.7 31.9 1.0
CE1 C:HIS100 2.7 29.9 1.0
O E:HOH371 2.8 38.0 1.0
CD2 C:HIS100 2.9 29.6 1.0
CG E:HIS89 3.2 33.2 0.5
NE2 E:HIS89 3.8 33.3 0.5
CB E:HIS89 3.8 32.6 0.5
ND1 C:HIS100 3.9 32.8 1.0
O C:HOH322 3.9 38.2 1.0
CB E:HIS89 3.9 29.7 0.5
CG C:HIS100 4.0 27.9 1.0
CD2 E:HIS89 4.1 33.8 0.5
CG E:HIS89 4.1 28.5 0.5
CG E:GLU86 4.2 29.7 1.0
CA E:GLU86 4.5 25.7 1.0
O E:HOH362 4.5 32.0 1.0
CD2 E:HIS89 4.6 28.8 0.5
ND1 E:HIS89 4.7 29.6 0.5
O E:HOH310 4.8 36.8 1.0
CB E:GLU86 4.8 26.8 1.0
O E:LYS85 5.0 26.7 1.0

Zinc binding site 8 out of 8 in 6ai5

Go back to Zinc Binding Sites List in 6ai5
Zinc binding site 8 out of 8 in the Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn205

b:17.0
occ:1.00
 OD1 C:ASP74 2.0 19.1 1.0
NE2 G:HIS73 2.0 17.4 1.0
NE2 E:HIS63 2.0 17.1 1.0
NE2 G:HIS77 2.0 14.8 1.0
CG C:ASP74 2.9 17.8 1.0
CE1 G:HIS73 2.9 17.2 1.0
CD2 E:HIS63 3.0 17.3 1.0
CD2 G:HIS77 3.0 15.6 1.0
CD2 G:HIS73 3.0 17.6 1.0
CE1 G:HIS77 3.1 15.6 1.0
CE1 E:HIS63 3.1 17.4 1.0
OD2 C:ASP74 3.1 18.3 1.0
ND1 G:HIS73 4.1 17.2 1.0
O C:HOH357 4.1 18.8 1.0
CG E:HIS63 4.1 16.6 1.0
CG G:HIS73 4.1 17.9 1.0
ND1 E:HIS63 4.2 16.8 1.0
ND1 G:HIS77 4.2 15.1 1.0
CG G:HIS77 4.2 15.7 1.0
CB C:ASP74 4.2 17.3 1.0
O G:HOH382 4.6 41.0 1.0
CD1 E:ILE67 4.6 16.4 1.0
O G:HOH348 4.6 24.8 1.0
CA C:ASP74 4.8 16.3 1.0
O C:ASP74 4.9 16.4 1.0

Reference:

W.J.Song, F.A.Tezcan. Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3 To Be Published.
Page generated: Mon Oct 28 17:31:38 2024

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