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

Go back to Zinc Binding Sites List in 6ai5
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

Go back to Zinc Binding Sites List in 6ai5
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

Go back to Zinc Binding Sites List in 6ai5
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

Go back to Zinc Binding Sites List in 6ai5
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: Wed Dec 16 11:29:49 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy