Magnesium 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:

Zinc (Zn) 8 atoms
Iron (Fe) 4 atoms
Chlorine (Cl) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3, PDB code: 6ai5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6ai5

Go back to Magnesium Binding Sites List in 6ai5
Magnesium binding site 1 out of 4 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 Magnesium with other atoms in the Mg 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:Mg205

b:33.5
occ:1.00
OE2 A:GLU8 2.2 40.1 1.0
OD2 A:ASP12 2.4 26.9 1.0
OD1 A:ASP12 3.0 24.9 1.0
CG A:ASP12 3.0 24.8 1.0
CD A:GLU8 3.1 33.6 1.0
CG A:GLU8 3.2 29.7 1.0
O A:HOH335 3.6 48.0 1.0
O A:HOH301 4.0 36.1 1.0
OE1 A:GLU8 4.3 33.7 1.0
CB A:ASP12 4.5 23.5 1.0
CB A:GLU8 4.7 25.1 1.0
O A:GLU8 4.9 19.0 1.0

Magnesium binding site 2 out of 4 in 6ai5

Go back to Magnesium Binding Sites List in 6ai5
Magnesium binding site 2 out of 4 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 Magnesium with other atoms in the Mg 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
C:Mg203

b:45.5
occ:1.00
O C:HOH342 2.8 39.2 1.0
O C:HOH318 2.8 32.8 1.0
ND2 C:ASN13 2.9 18.9 1.0
O C:HOH436 3.3 30.1 1.0
CD C:LYS32 3.7 24.8 1.0
CG2 C:THR9 3.9 17.5 1.0
O C:HOH302 3.9 26.5 1.0
CG C:ASN13 3.9 18.1 1.0
OD1 C:ASN13 4.1 18.0 1.0
CG C:LYS32 4.5 21.3 1.0
CB C:LYS32 4.5 20.3 1.0
CE C:LYS32 4.6 25.2 1.0
NZ C:LYS32 4.6 27.8 1.0
OG1 C:THR9 4.6 16.5 1.0
CB C:THR9 4.6 16.0 1.0
CA C:THR9 4.7 15.9 1.0
O C:THR9 4.8 14.8 1.0

Magnesium binding site 3 out of 4 in 6ai5

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Magnesium binding site 3 out of 4 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 Magnesium with other atoms in the Mg 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
E:Mg205

b:22.0
occ:1.00
OD2 E:ASP2 2.0 25.3 1.0
O E:HOH302 2.9 40.5 1.0
CG E:ASP2 2.9 23.2 1.0
OD1 E:ASP2 3.2 23.5 1.0
OD1 E:ASP5 3.6 21.6 1.0
CG E:ASP5 4.2 21.6 1.0
CB E:ASP2 4.3 22.7 1.0
OD2 E:ASP5 4.4 26.5 1.0
CB E:GLU4 4.7 26.5 1.0
O E:HOH356 4.8 26.5 1.0
OE1 E:GLU4 4.8 37.9 1.0
N E:ASP5 5.0 20.1 1.0

Magnesium binding site 4 out of 4 in 6ai5

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Magnesium binding site 4 out of 4 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 Magnesium with other atoms in the Mg 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
G:Mg203

b:35.2
occ:1.00
O C:HOH397 2.5 46.3 1.0
O A:HOH343 2.6 33.9 1.0
OE2 G:GLU81 2.7 26.1 1.0
CE1 C:HIS77 3.2 14.9 1.0
CD G:GLU81 3.5 25.6 1.0
OE1 G:GLU81 3.5 25.2 1.0
ND1 C:HIS77 3.6 14.9 1.0
O C:HOH381 3.7 27.7 1.0
ND2 C:ASN80 3.7 22.9 1.0
CD2 G:LEU78 3.8 19.9 1.0
NZ G:LYS83 4.0 32.8 1.0
CE G:LYS83 4.0 32.1 1.0
CD2 A:HIS63 4.0 15.7 1.0
O A:HOH347 4.2 38.1 1.0
CD G:LYS83 4.3 29.8 1.0
NE2 C:HIS77 4.4 14.7 1.0
CG A:HIS63 4.5 15.9 1.0
OD1 A:ASP60 4.5 30.5 1.0
NE2 A:HIS63 4.6 16.3 1.0
CB A:HIS63 4.9 16.2 1.0
CG C:HIS77 4.9 15.6 1.0
CG G:GLU81 4.9 25.1 1.0
CG C:ASN80 4.9 22.2 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 Dec 14 22:20:30 2020

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