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

The structure of Ni-Bound Crystal Structure of the Engineered Cyt CB562 Variant, DICYT2, Crystallized in the Presence of Ni(II), PDB code: 7lrv 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)	41.61 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.91, 60.72, 63.77, 90, 90, 90
R / Rfree (%)	19 / 21.6

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

Nickel binding site 1 out of 2 in the Ni-Bound Crystal Structure of the Engineered Cyt CB562 Variant, DICYT2, 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 Ni-Bound Crystal Structure of the Engineered Cyt CB562 Variant, DICYT2, Crystallized in the Presence of Ni(II) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni202 b:15.3 occ:1.00 NE2 C:HIS100 2.1 14.0 1.0 O A:HOH360 2.1 16.1 1.0 NE2 C:HIS104 2.1 15.6 1.0 NE2 A:HIS71 2.1 14.5 1.0 NE2 A:HIS67 2.1 14.5 1.0 NE2 C:HIS60 2.2 14.9 1.0 CE1 A:HIS71 3.0 15.8 1.0 CE1 C:HIS100 3.0 14.8 1.0 CD2 C:HIS104 3.1 15.2 1.0 CE1 A:HIS67 3.1 15.5 1.0 CD2 C:HIS100 3.1 14.8 1.0 CE1 C:HIS104 3.1 18.2 1.0 CD2 A:HIS67 3.1 14.3 1.0 CE1 C:HIS60 3.1 15.3 1.0 CD2 A:HIS71 3.2 14.4 1.0 CD2 C:HIS60 3.2 16.2 1.0 ND1 C:HIS100 4.1 14.6 1.0 ND1 A:HIS71 4.2 15.5 1.0 ND1 A:HIS67 4.2 16.9 1.0 CG C:HIS100 4.2 14.9 1.0 ND1 C:HIS104 4.2 17.3 1.0 CG C:HIS104 4.2 17.3 1.0 CG A:HIS67 4.3 14.5 1.0 CG A:HIS71 4.3 14.7 1.0 ND1 C:HIS60 4.3 15.9 1.0 O A:HOH356 4.3 22.9 0.9 CG C:HIS60 4.3 15.7 1.0 O C:HOH418 4.4 27.2 0.9

Nickel binding site 2 out of 2 in the Ni-Bound Crystal Structure of the Engineered Cyt CB562 Variant, DICYT2, 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 Ni-Bound Crystal Structure of the Engineered Cyt CB562 Variant, DICYT2, Crystallized in the Presence of Ni(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni202 b:15.1 occ:1.00 NE2 A:HIS100 2.1 14.4 1.0 NE2 C:HIS67 2.1 14.5 1.0 NE2 C:HIS71 2.1 15.6 1.0 NE2 A:HIS104 2.2 14.6 1.0 O A:HOH366 2.2 15.9 1.0 NE2 A:HIS60 2.2 16.0 1.0 CE1 C:HIS71 3.1 15.4 1.0 CE1 A:HIS100 3.1 14.6 1.0 CE1 C:HIS67 3.1 15.6 1.0 CD2 A:HIS104 3.1 18.2 1.0 CD2 A:HIS100 3.1 15.7 1.0 CD2 C:HIS67 3.1 13.6 1.0 CE1 A:HIS60 3.1 17.0 1.0 CD2 C:HIS71 3.2 14.2 1.0 CE1 A:HIS104 3.2 18.4 1.0 CD2 A:HIS60 3.2 15.6 1.0 ND1 A:HIS100 4.2 14.1 1.0 ND1 C:HIS71 4.2 18.9 1.0 ND1 C:HIS67 4.2 16.1 1.0 CG A:HIS100 4.2 15.4 1.0 ND1 A:HIS60 4.2 17.0 1.0 CG C:HIS67 4.2 15.2 1.0 CG A:HIS104 4.3 16.3 1.0 O C:HOH360 4.3 18.9 1.0 ND1 A:HIS104 4.3 19.5 1.0 CG C:HIS71 4.3 15.0 1.0 CG A:HIS60 4.3 17.0 1.0 O A:HOH388 4.3 25.7 0.9 O A:HOH390 4.5 24.2 0.9 O A:HOH358 4.9 21.0 0.9

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