Nickel in PDB 2isz: Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I

The structure of Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I, PDB code: 2isz was solved by G.Wisedchaisri, C.J.Chou, M.Wu, C.Roach, A.E.Rice, R.K.Holmes, C.Beeson, W.G.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	53.832, 69.739, 76.461, 106.57, 104.85, 99.66
R / Rfree (%)	19.9 / 23.9

The structure of Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Nickel atom in the Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I (pdb code 2isz). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 12 binding sites of Nickel where determined in the Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I, PDB code: 2isz:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Nickel binding site 1 out of 12 in the Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1001 b:49.2 occ:1.00 OE2 A:GLU83 2.0 43.4 1.0 NE2 A:HIS79 2.0 37.0 1.0 ND1 A:HIS98 2.0 39.5 1.0 O A:HOH2030 2.6 48.9 1.0 CE1 A:HIS98 2.9 37.2 1.0 CD2 A:HIS79 2.9 34.2 1.0 CD A:GLU83 3.1 39.0 1.0 CE1 A:HIS79 3.1 34.1 1.0 CG A:HIS98 3.2 36.9 1.0 CB A:HIS98 3.6 35.7 1.0 OE1 A:GLU83 3.6 39.1 1.0 CA A:HIS98 4.0 34.6 1.0 NE2 A:HIS98 4.1 36.8 1.0 CG A:HIS79 4.1 33.6 1.0 ND1 A:HIS79 4.2 33.4 1.0 CD2 A:HIS98 4.2 36.2 1.0 CG A:GLU83 4.3 38.1 1.0 O A:HIS98 4.8 32.9 1.0 C A:HIS98 4.9 33.0 1.0

Nickel binding site 2 out of 12 in the Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1002 b:28.5 occ:1.00 OE2 A:GLU105 1.9 26.4 1.0 O A:CYS102 2.0 30.8 1.0 O A:HOH2013 2.0 29.5 1.0 NE2 A:HIS106 2.0 26.4 1.0 SD A:MET10 2.4 29.4 1.0 SG A:CYS102 2.8 31.8 1.0 CE1 A:HIS106 2.9 25.6 1.0 C A:CYS102 3.0 28.6 1.0 CD A:GLU105 3.0 24.5 1.0 CD2 A:HIS106 3.1 25.9 1.0 CG A:MET10 3.5 29.8 1.0 CA A:CYS102 3.5 29.0 1.0 CG A:GLU105 3.5 24.0 1.0 CE A:MET10 3.6 31.0 1.0 CB A:CYS102 3.7 30.4 1.0 ND1 A:HIS106 4.1 25.7 1.0 OE1 A:GLU105 4.1 23.9 1.0 N A:ARG103 4.2 26.2 1.0 CG A:HIS106 4.2 24.8 1.0 O A:HOH2023 4.2 33.7 1.0 O A:LEU4 4.3 37.4 1.0 CA A:ARG103 4.7 26.7 1.0 CB A:MET10 4.9 28.8 1.0 N A:CYS102 4.9 28.3 1.0 NH2 A:ARG13 5.0 37.5 1.0

Nickel binding site 3 out of 12 in the Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1003 b:45.6 occ:1.00 ND1 A:HIS61 2.0 37.9 1.0 CG A:HIS61 3.0 35.4 1.0 CE1 A:HIS61 3.0 35.8 1.0 CB A:HIS61 3.3 33.2 1.0 OD2 A:ASP59 3.8 36.5 1.0 OD1 A:ASP59 3.9 38.0 1.0 CD2 A:HIS61 4.1 34.7 1.0 NE2 A:HIS61 4.1 34.4 1.0 CG A:ASP59 4.3 37.3 1.0 CA A:HIS61 4.8 32.3 1.0

Nickel binding site 4 out of 12 in the Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1001 b:49.5 occ:1.00 OE2 B:GLU83 2.0 37.6 1.0 NE2 B:HIS79 2.0 40.4 1.0 ND1 B:HIS98 2.0 45.3 1.0 O B:HOH1028 2.6 47.9 1.0 CE1 B:HIS98 2.8 44.8 1.0 CE1 B:HIS79 2.9 37.6 1.0 CD B:GLU83 3.0 33.8 1.0 CD2 B:HIS79 3.1 36.9 1.0 O B:HOH1018 3.2 51.5 1.0 CG B:HIS98 3.2 43.8 1.0 OE1 B:GLU83 3.4 34.1 1.0 CB B:HIS98 3.8 42.2 1.0 NE2 B:HIS98 4.0 44.3 1.0 ND1 B:HIS79 4.1 37.2 1.0 CG B:HIS79 4.2 35.5 1.0 CD2 B:HIS98 4.2 44.0 1.0 CG B:GLU83 4.3 32.4 1.0 CA B:HIS98 4.3 40.8 1.0 CE1 B:PHE128 4.6 44.6 1.0 CD1 B:PHE128 4.7 43.9 1.0 O B:HIS98 5.0 37.9 1.0

Nickel binding site 5 out of 12 in the Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1002 b:29.8 occ:1.00 OE2 B:GLU105 1.9 33.3 1.0 O B:CYS102 2.0 29.4 1.0 NE2 B:HIS106 2.0 27.1 1.0 SD B:MET10 2.3 28.1 1.0 SG B:CYS102 2.6 34.4 1.0 O B:HOH1026 3.0 41.0 1.0 CD2 B:HIS106 3.0 25.5 1.0 CE1 B:HIS106 3.0 26.3 1.0 C B:CYS102 3.0 29.8 1.0 CD B:GLU105 3.1 31.6 1.0 CG B:MET10 3.4 29.2 1.0 CA B:CYS102 3.5 30.5 1.0 CE B:MET10 3.6 26.5 1.0 CB B:CYS102 3.7 30.9 1.0 CG B:GLU105 3.7 30.3 1.0 O B:HOH1029 3.7 53.1 1.0 O B:LEU4 4.1 36.4 1.0 ND1 B:HIS106 4.1 24.6 1.0 OE1 B:GLU105 4.1 32.6 1.0 CG B:HIS106 4.1 24.6 1.0 N B:ARG103 4.2 27.5 1.0 NH2 B:ARG13 4.3 36.7 1.0 CA B:ARG103 4.7 26.7 1.0 CB B:MET10 4.8 28.9 1.0 N B:CYS102 5.0 31.1 1.0

Nickel binding site 6 out of 12 in the Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1003 b:52.4 occ:1.00 O B:HOH1030 1.8 25.6 1.0 ND1 B:HIS61 2.0 46.0 1.0 O B:HOH1019 2.3 34.3 1.0 O B:HOH1009 2.3 34.8 1.0 CE1 B:HIS61 3.0 44.9 1.0 CG B:HIS61 3.1 44.7 1.0 CB B:HIS61 3.5 43.9 1.0 OD1 B:ASP59 3.8 51.5 1.0 OD2 B:ASP59 3.9 51.6 1.0 NE2 B:HIS61 4.1 44.6 1.0 CD2 B:HIS61 4.2 44.2 1.0 CG B:ASP59 4.3 51.6 1.0 CA B:HIS61 4.9 42.9 1.0

Nickel binding site 7 out of 12 in the Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni1001 b:55.8 occ:1.00 OE2 C:GLU83 2.0 52.7 1.0 ND1 C:HIS98 2.0 49.8 1.0 NE2 C:HIS79 2.0 42.4 1.0 CE1 C:HIS79 2.9 38.4 1.0 O C:HOH2021 3.0 40.3 1.0 CG C:HIS98 3.0 47.8 1.0 CE1 C:HIS98 3.0 48.7 1.0 CD C:GLU83 3.1 50.2 1.0 CD2 C:HIS79 3.1 38.3 1.0 CB C:HIS98 3.3 46.7 1.0 OE1 C:GLU83 3.7 50.2 1.0 CA C:HIS98 3.8 45.4 1.0 ND1 C:HIS79 4.1 37.7 1.0 NE2 C:HIS98 4.1 48.1 1.0 CD2 C:HIS98 4.2 47.6 1.0 CG C:HIS79 4.2 37.4 1.0 CG C:GLU83 4.2 48.6 1.0 C C:HIS98 4.8 43.6 1.0 O C:HIS98 4.8 42.7 1.0 N C:HIS98 4.8 47.4 1.0

Nickel binding site 8 out of 12 in the Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni1002 b:36.7 occ:1.00 O C:CYS102 2.0 35.7 1.0 OE2 C:GLU105 2.0 38.5 1.0 NE2 C:HIS106 2.0 34.1 1.0 O C:HOH2020 2.3 48.9 1.0 SD C:MET10 2.4 35.5 1.0 SG C:CYS102 2.9 39.4 1.0 CD2 C:HIS106 3.0 33.8 1.0 C C:CYS102 3.0 34.9 1.0 CE1 C:HIS106 3.0 34.2 1.0 CD C:GLU105 3.0 37.7 1.0 CE C:MET10 3.4 33.6 1.0 CA C:CYS102 3.5 35.5 1.0 CG C:GLU105 3.6 36.5 1.0 CG C:MET10 3.6 32.9 1.0 CB C:CYS102 3.8 36.4 1.0 ND1 C:HIS106 4.1 33.8 1.0 OE1 C:GLU105 4.1 37.4 1.0 CG C:HIS106 4.1 33.5 1.0 N C:ARG103 4.1 34.4 1.0 NH2 C:ARG13 4.2 46.5 1.0 O C:LEU4 4.2 39.9 1.0 CA C:ARG103 4.6 34.1 1.0 CB C:MET10 4.9 32.8 1.0 N C:CYS102 4.9 35.0 1.0

Nickel binding site 9 out of 12 in the Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni1003 b:53.1 occ:1.00 ND1 C:HIS61 2.0 50.3 1.0 O C:HOH2023 2.1 18.9 1.0 O C:HOH2024 2.4 32.3 1.0 O C:HOH2022 2.9 41.1 1.0 CE1 C:HIS61 2.9 50.6 1.0 CG C:HIS61 3.1 47.9 1.0 CB C:HIS61 3.5 45.3 1.0 OD2 C:ASP59 3.9 42.1 1.0 NE2 C:HIS61 4.1 50.1 1.0 OD1 C:ASP59 4.2 41.7 1.0 CD2 C:HIS61 4.2 49.4 1.0 CG C:ASP59 4.5 41.5 1.0

Nickel binding site 10 out of 12 in the Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni1001 b:56.5 occ:1.00 OE2 D:GLU83 2.0 45.5 1.0 NE2 D:HIS79 2.0 46.3 1.0 ND1 D:HIS98 2.0 51.9 1.0 O D:HOH2017 2.6 33.9 1.0 CE1 D:HIS98 2.7 50.9 1.0 CD2 D:HIS79 3.0 42.9 1.0 CE1 D:HIS79 3.0 43.4 1.0 CD D:GLU83 3.1 40.3 1.0 CG D:HIS98 3.2 50.4 1.0 O D:HOH2016 3.5 46.9 1.0 OE1 D:GLU83 3.7 41.8 1.0 CB D:HIS98 3.8 48.7 1.0 NE2 D:HIS98 4.0 51.2 1.0 O D:HOH2011 4.0 44.1 1.0 ND1 D:HIS79 4.1 43.0 1.0 CG D:HIS79 4.2 41.4 1.0 CD2 D:HIS98 4.2 50.7 1.0 CA D:HIS98 4.2 47.2 1.0 CG D:GLU83 4.3 38.7 1.0 O D:HIS98 4.9 44.8 1.0

G.Wisedchaisri, C.J.Chou, M.Wu, C.Roach, A.E.Rice, R.K.Holmes, C.Beeson, W.G.Hol. Crystal Structures, Metal Activation, and Dna-Binding Properties of Two-Domain Ider From Mycobacterium Tuberculosis Biochemistry V. 46 436 2007.
ISSN: ISSN 0006-2960
PubMed: 17209554
DOI: 10.1021/BI0609826