Nickel in PDB 7lsl: Cu-Bound Crystal Structure of the Engineered Cyt CB562 Variant, DICYT2 - H63A, Crystallized in the Presence of Ni(II)

The structure of Cu-Bound Crystal Structure of the Engineered Cyt CB562 Variant, DICYT2 - H63A, Crystallized in the Presence of Ni(II), PDB code: 7lsl was solved by T.S.Choi, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.14 / 1.64
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.63, 60.87, 64.11, 90, 90, 90
R / Rfree (%)	20.6 / 24.4

The structure of Cu-Bound Crystal Structure of the Engineered Cyt CB562 Variant, DICYT2 - H63A, Crystallized in the Presence of Ni(II) also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Nickel atom in the Cu-Bound Crystal Structure of the Engineered Cyt CB562 Variant, DICYT2 - H63A, Crystallized in the Presence of Ni(II) (pdb code 7lsl). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Cu-Bound Crystal Structure of the Engineered Cyt CB562 Variant, DICYT2 - H63A, Crystallized in the Presence of Ni(II), PDB code: 7lsl:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Cu-Bound Crystal Structure of the Engineered Cyt CB562 Variant, DICYT2 - H63A, Crystallized in the Presence of Ni(II)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Cu-Bound Crystal Structure of the Engineered Cyt CB562 Variant, DICYT2 - H63A, Crystallized in the Presence of Ni(II) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni202 b:15.8 occ:1.00 NE2 C:HIS100 2.0 16.5 1.0 NE2 C:HIS104 2.1 13.5 1.0 NE2 A:HIS67 2.1 15.0 1.0 O C:HOH347 2.2 16.6 1.0 NE2 A:HIS71 2.2 16.9 1.0 NE2 C:HIS60 2.2 15.3 1.0 CE1 C:HIS100 2.9 15.9 1.0 CD2 C:HIS104 3.1 18.7 1.0 CE1 A:HIS67 3.1 15.3 1.0 CD2 C:HIS100 3.1 15.6 1.0 CE1 A:HIS71 3.1 18.3 1.0 CE1 C:HIS60 3.1 14.1 1.0 CE1 C:HIS104 3.1 14.7 1.0 CD2 A:HIS67 3.1 15.4 1.0 CD2 A:HIS71 3.2 17.1 1.0 CD2 C:HIS60 3.3 15.8 1.0 ND1 C:HIS100 4.1 13.4 1.0 CG C:HIS100 4.2 14.3 1.0 ND1 A:HIS67 4.2 16.8 1.0 ND1 C:HIS104 4.2 17.4 1.0 CG C:HIS104 4.2 16.7 1.0 ND1 A:HIS71 4.2 18.4 1.0 ND1 C:HIS60 4.3 14.0 1.0 CG A:HIS67 4.3 16.0 1.0 O A:HOH352 4.3 22.8 1.0 CG A:HIS71 4.3 18.5 1.0 CG C:HIS60 4.4 13.9 1.0 O C:HOH383 4.4 23.7 1.0

Nickel binding site 2 out of 2 in the Cu-Bound Crystal Structure of the Engineered Cyt CB562 Variant, DICYT2 - H63A, Crystallized in the Presence of Ni(II)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Cu-Bound Crystal Structure of the Engineered Cyt CB562 Variant, DICYT2 - H63A, Crystallized in the Presence of Ni(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni202 b:15.8 occ:1.00 NE2 A:HIS100 2.0 18.3 1.0 NE2 C:HIS67 2.1 12.7 1.0 O A:HOH331 2.1 17.0 1.0 NE2 A:HIS104 2.2 15.3 1.0 NE2 C:HIS71 2.2 14.6 1.0 NE2 A:HIS60 2.3 16.9 1.0 CE1 A:HIS100 3.0 17.4 1.0 CD2 A:HIS100 3.0 14.6 1.0 CD2 A:HIS104 3.1 20.0 1.0 CE1 C:HIS67 3.1 14.2 1.0 CD2 C:HIS67 3.1 15.5 1.0 CE1 C:HIS71 3.1 16.4 1.0 CE1 A:HIS60 3.2 15.8 1.0 CD2 C:HIS71 3.2 17.7 1.0 CE1 A:HIS104 3.2 19.9 1.0 CD2 A:HIS60 3.3 19.1 1.0 ND1 A:HIS100 4.1 15.6 1.0 CG A:HIS100 4.2 17.3 1.0 ND1 C:HIS67 4.2 15.5 1.0 CG C:HIS67 4.2 16.0 1.0 ND1 C:HIS71 4.2 19.8 1.0 CG A:HIS104 4.3 15.6 1.0 ND1 A:HIS60 4.3 14.2 1.0 CG C:HIS71 4.3 20.5 1.0 ND1 A:HIS104 4.3 17.5 1.0 O C:HOH338 4.3 21.3 1.0 CG A:HIS60 4.4 16.6 1.0 O A:HOH321 4.9 20.9 1.0

T.S.Choi, F.A.Tezcan. Structure-Guided Metal Selectivity in Malleable Protein Interface Mediated By Single Disulfide Bond To Be Published.