Nickel in PDB 2it0: Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form II

The structure of Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form II, PDB code: 2it0 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 / 2.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	54.009, 70.363, 79.569, 108.95, 103.08, 94.84
R / Rfree (%)	22.6 / 27.3

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 II (pdb code 2it0). 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 II, PDB code: 2it0:
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 II


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 II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1001 b:20.1 occ:1.00 OE2 A:GLU83 2.0 18.2 1.0 ND1 A:HIS98 2.0 18.0 1.0 NE2 A:HIS79 2.0 16.3 1.0 O A:ACT2001 2.1 26.3 1.0 OXT A:ACT2001 2.3 25.2 1.0 C A:ACT2001 2.4 27.2 1.0 CE1 A:HIS98 2.8 17.6 1.0 CE1 A:HIS79 3.0 15.9 1.0 CD A:GLU83 3.0 16.8 1.0 CD2 A:HIS79 3.1 15.8 1.0 CG A:HIS98 3.1 16.7 1.0 OE1 A:GLU83 3.5 15.4 1.0 CH3 A:ACT2001 3.6 25.0 1.0 CB A:HIS98 3.6 16.5 1.0 NE2 A:HIS98 4.0 16.8 1.0 ND1 A:HIS79 4.1 15.2 1.0 CA A:HIS98 4.1 16.8 1.0 CD2 A:HIS98 4.2 16.0 1.0 CG A:HIS79 4.2 15.5 1.0 CG A:GLU83 4.3 17.3 1.0 CE1 A:PHE128 4.8 29.5 1.0 O A:HIS98 4.9 16.4 1.0 C A:HIS98 5.0 16.4 1.0 CD1 A:PHE128 5.0 29.3 1.0

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


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 II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1002 b:15.4 occ:1.00 OE2 A:GLU105 1.9 16.5 1.0 O A:CYS102 2.0 16.7 1.0 NE2 A:HIS106 2.0 9.7 1.0 SD A:MET10 2.3 18.1 1.0 SG A:CYS102 2.7 12.5 1.0 CE1 A:HIS106 3.0 9.1 1.0 C A:CYS102 3.0 15.1 1.0 CD2 A:HIS106 3.0 9.3 1.0 CD A:GLU105 3.1 16.1 1.0 CE A:MET10 3.1 16.5 1.0 CG A:MET10 3.4 15.2 1.0 CA A:CYS102 3.5 15.3 1.0 CG A:GLU105 3.6 15.8 1.0 CB A:CYS102 3.7 15.1 1.0 NH2 A:ARG13 3.9 21.7 1.0 ND1 A:HIS106 4.1 8.6 1.0 CG A:HIS106 4.1 8.7 1.0 OE1 A:GLU105 4.1 16.1 1.0 N A:ARG103 4.2 14.3 1.0 O A:LEU4 4.2 18.5 1.0 CA A:ARG103 4.6 14.7 1.0 CB A:MET10 4.8 15.1 1.0 N A:CYS102 4.9 14.6 1.0 CZ A:ARG13 4.9 20.9 1.0

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


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 II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1003 b:29.6 occ:1.00 ND1 A:HIS61 2.0 25.9 1.0 O A:ACT2003 2.1 20.2 1.0 O A:ACT2002 2.2 41.3 1.0 C A:ACT2003 2.5 21.4 1.0 OXT A:ACT2003 2.7 20.1 1.0 C A:ACT2002 2.8 41.4 1.0 OXT A:ACT2002 2.9 40.8 1.0 CE1 A:HIS61 2.9 24.8 1.0 CG A:HIS61 3.1 24.4 1.0 CB A:HIS61 3.5 24.4 1.0 CH3 A:ACT2003 3.5 19.6 1.0 OE1 A:GLU63 3.7 20.4 1.0 OD2 A:ASP59 3.8 25.4 1.0 NE2 A:HIS61 4.0 23.0 1.0 OD1 A:ASP59 4.1 24.2 1.0 CH3 A:ACT2002 4.1 40.2 1.0 CD2 A:HIS61 4.1 23.4 1.0 CG A:ASP59 4.4 24.7 1.0 CD A:GLU63 4.8 19.6 1.0

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


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 II within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1001 b:16.6 occ:1.00 OE2 B:GLU83 1.9 14.8 1.0 NE2 B:HIS79 2.0 17.1 1.0 ND1 B:HIS98 2.0 16.8 1.0 OXT B:ACT2001 2.5 16.2 1.0 O B:ACT2001 2.5 18.2 1.0 C B:ACT2001 2.6 18.1 1.0 CE1 B:HIS79 2.6 16.6 1.0 CE1 B:HIS98 2.7 16.5 1.0 CD B:GLU83 3.0 14.8 1.0 CG B:HIS98 3.2 16.6 1.0 CD2 B:HIS79 3.3 16.5 1.0 OE1 B:GLU83 3.4 15.7 1.0 CH3 B:ACT2001 3.7 16.4 1.0 CB B:HIS98 3.8 17.0 1.0 ND1 B:HIS79 3.9 16.7 1.0 NE2 B:HIS98 3.9 15.9 1.0 CD2 B:HIS98 4.2 16.6 1.0 CG B:HIS79 4.2 15.7 1.0 CA B:HIS98 4.3 17.9 1.0 CG B:GLU83 4.3 13.9 1.0 CE1 B:PHE128 4.9 22.2 1.0 CD1 B:PHE128 4.9 22.6 1.0 O B:HIS98 4.9 17.7 1.0

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


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 II within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1002 b:16.9 occ:1.00 OE2 B:GLU105 1.9 20.3 1.0 O B:CYS102 1.9 15.3 1.0 NE2 B:HIS106 2.0 15.8 1.0 SD B:MET10 2.3 17.6 1.0 SG B:CYS102 2.7 18.1 1.0 CD2 B:HIS106 3.0 15.6 1.0 C B:CYS102 3.0 15.7 1.0 CE1 B:HIS106 3.0 14.7 1.0 CD B:GLU105 3.0 19.8 1.0 CG B:MET10 3.5 17.0 1.0 CA B:CYS102 3.5 16.6 1.0 CG B:GLU105 3.5 18.7 1.0 CE B:MET10 3.6 16.6 1.0 CB B:CYS102 3.7 17.0 1.0 NH2 B:ARG13 4.0 30.0 1.0 CG B:HIS106 4.1 14.7 1.0 ND1 B:HIS106 4.1 14.7 1.0 OE1 B:GLU105 4.1 18.7 1.0 N B:ARG103 4.2 13.8 1.0 O B:LEU4 4.2 25.1 1.0 CA B:ARG103 4.7 13.9 1.0 CB B:MET10 4.9 16.0 1.0 N B:CYS102 4.9 17.6 1.0

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


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 II within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1003 b:42.0 occ:1.00 O B:ACT2002 1.9 8.3 1.0 ND1 B:HIS61 2.0 39.3 1.0 OXT B:ACT2002 2.1 11.2 1.0 C B:ACT2002 2.4 11.2 1.0 CE1 B:HIS61 3.0 38.4 1.0 CG B:HIS61 3.0 38.4 1.0 OE2 B:GLU63 3.3 31.3 1.0 CB B:HIS61 3.4 37.1 1.0 OD1 B:ASP59 3.4 38.0 1.0 OD2 B:ASP59 3.4 38.9 1.0 CG B:ASP59 3.9 38.2 1.0 CH3 B:ACT2002 3.9 12.8 1.0 NE2 B:HIS61 4.1 37.5 1.0 CD2 B:HIS61 4.1 38.2 1.0 CD B:GLU63 4.5 29.9 1.0 CA B:HIS61 4.9 36.3 1.0 CB B:ALA57 4.9 35.3 1.0

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


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 II within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni1001 b:27.0 occ:1.00 OE2 C:GLU83 1.9 26.0 1.0 NE2 C:HIS79 2.0 21.4 1.0 ND1 C:HIS98 2.0 21.4 1.0 O C:ACT2001 2.2 39.8 1.0 OXT C:ACT2001 2.3 40.0 1.0 C C:ACT2001 2.6 40.3 1.0 CE1 C:HIS98 2.7 19.6 1.0 CE1 C:HIS79 2.9 21.0 1.0 CD C:GLU83 3.0 25.4 1.0 CD2 C:HIS79 3.1 20.8 1.0 CG C:HIS98 3.2 20.5 1.0 OE1 C:GLU83 3.5 24.6 1.0 CB C:HIS98 3.9 21.1 1.0 NE2 C:HIS98 3.9 19.1 1.0 ND1 C:HIS79 4.1 20.8 1.0 CH3 C:ACT2001 4.1 38.9 1.0 CG C:HIS79 4.2 20.9 1.0 CD2 C:HIS98 4.2 19.0 1.0 CG C:GLU83 4.3 25.4 1.0 CA C:HIS98 4.4 23.1 1.0

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


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 II within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni1002 b:19.8 occ:1.00 OE2 C:GLU105 1.9 22.0 1.0 O C:CYS102 1.9 20.9 1.0 NE2 C:HIS106 2.0 16.3 1.0 O C:HOH2007 2.3 20.1 1.0 SD C:MET10 2.4 20.0 1.0 SG C:CYS102 2.8 19.9 1.0 CE1 C:HIS106 2.8 16.0 1.0 C C:CYS102 3.0 20.1 1.0 CD C:GLU105 3.1 21.9 1.0 CD2 C:HIS106 3.1 16.1 1.0 CE C:MET10 3.4 17.1 1.0 CA C:CYS102 3.4 20.1 1.0 CG C:MET10 3.6 17.1 1.0 CG C:GLU105 3.6 21.6 1.0 CB C:CYS102 3.7 20.0 1.0 ND1 C:HIS106 4.0 15.9 1.0 NH2 C:ARG13 4.1 28.6 1.0 OE1 C:GLU105 4.1 23.4 1.0 N C:ARG103 4.1 19.1 1.0 CG C:HIS106 4.2 15.6 1.0 O C:LEU4 4.4 20.7 1.0 CA C:ARG103 4.6 19.0 1.0 N C:CYS102 4.8 20.1 1.0 CZ C:ARG13 4.9 27.8 1.0 CB C:MET10 4.9 16.7 1.0 O C:ALA101 5.0 20.8 1.0

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


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 II within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni1003 b:23.5 occ:1.00 ND1 C:HIS61 2.0 25.2 1.0 O C:ACT2002 2.4 22.2 1.0 OXT C:ACT2002 2.5 22.8 1.0 OXT C:ACT2003 2.5 21.2 1.0 O C:ACT2003 2.7 19.4 1.0 C C:ACT2002 2.7 23.6 1.0 C C:ACT2003 2.8 20.8 1.0 CE1 C:HIS61 2.9 25.1 1.0 CG C:HIS61 3.1 24.6 1.0 OD2 C:ASP59 3.2 30.9 1.0 OE1 C:GLU63 3.3 23.9 1.0 CB C:HIS61 3.5 24.5 1.0 CH3 C:ACT2003 3.9 19.2 1.0 NE2 C:HIS61 4.0 23.8 1.0 OD1 C:ASP59 4.0 30.7 1.0 CG C:ASP59 4.0 29.8 1.0 CD2 C:HIS61 4.1 24.0 1.0 CH3 C:ACT2002 4.1 21.4 1.0 CD C:GLU63 4.4 22.8 1.0

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


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 II within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni1001 b:25.4 occ:1.00 OXT D:ACT2001 1.9 28.5 1.0 OE2 D:GLU83 1.9 25.8 1.0 ND1 D:HIS98 2.0 22.3 1.0 NE2 D:HIS79 2.0 23.0 1.0 C D:ACT2001 2.3 29.9 1.0 O D:ACT2001 2.5 30.0 1.0 CE1 D:HIS79 2.6 22.1 1.0 CE1 D:HIS98 2.7 22.0 1.0 CD D:GLU83 3.0 25.3 1.0 CG D:HIS98 3.2 22.2 1.0 CD2 D:HIS79 3.3 22.0 1.0 OE1 D:GLU83 3.3 27.6 1.0 CH3 D:ACT2001 3.4 28.8 1.0 CB D:HIS98 3.7 21.5 1.0 ND1 D:HIS79 3.9 20.9 1.0 NE2 D:HIS98 3.9 22.0 1.0 CD2 D:HIS98 4.2 21.6 1.0 CG D:HIS79 4.2 21.1 1.0 CA D:HIS98 4.2 22.3 1.0 CG D:GLU83 4.3 24.6 1.0 CE1 D:PHE128 4.5 29.4 1.0 CD1 D:PHE128 4.7 29.1 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