Nickel in PDB 5xew: Crystal Structure of the [NI2+-(Chromomycin A3)2]-Ccg Repeats Complex

The structure of Crystal Structure of the [NI2+-(Chromomycin A3)2]-Ccg Repeats Complex, PDB code: 5xew was solved by W.H.Tseng, P.C.Wu, M.H.Hou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.19 / 1.75
Space group	P 32 1 2
Cell size a, b, c (Å), α, β, γ (°)	48.291, 48.291, 83.356, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 23.8

The binding sites of Nickel atom in the Crystal Structure of the [NI2+-(Chromomycin A3)2]-Ccg Repeats Complex (pdb code 5xew). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of the [NI2+-(Chromomycin A3)2]-Ccg Repeats Complex, PDB code: 5xew:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Crystal Structure of the [NI2+-(Chromomycin A3)2]-Ccg Repeats Complex


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 the [NI2+-(Chromomycin A3)2]-Ccg Repeats Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni107 b:28.2 occ:1.00 O9 B:CPH103 1.9 27.0 1.0 O9 A:CPH106 1.9 26.8 1.0 O1 A:CPH106 2.0 27.4 1.0 O1 B:CPH103 2.0 28.1 1.0 O A:HOH205 2.1 26.4 1.0 O B:HOH207 2.1 26.6 1.0 C1 A:CPH106 3.0 27.2 1.0 C1 B:CPH103 3.0 27.9 1.0 C9 B:CPH103 3.0 25.9 1.0 C9 A:CPH106 3.0 25.5 1.0 C9A B:CPH103 3.4 26.8 1.0 C9A A:CPH106 3.5 26.7 1.0 O8 B:CPH103 4.0 23.9 1.0 O8 A:CPH106 4.0 24.4 1.0 C8A B:CPH103 4.2 20.7 1.0 C8A A:CPH106 4.3 20.9 1.0 O2 A:DC9 4.3 27.5 1.0 O2 B:DC22 4.3 27.3 1.0 C2 A:CPH106 4.3 32.0 1.0 C2 B:CPH103 4.3 32.2 1.0 O4' B:DC23 4.4 28.3 1.0 O4' A:DC10 4.4 28.6 1.0 C1 B:CDR104 4.5 30.9 1.0 OGL B:CDR104 4.5 30.9 1.0 C1 A:CDR101 4.5 29.8 1.0 OGL A:CDR101 4.6 31.6 1.0 C8 B:CPH103 4.6 24.5 1.0 C8 A:CPH106 4.6 23.6 1.0 C2 B:CDR104 4.7 30.0 1.0 C2' B:DC22 4.7 25.3 1.0 C2' A:DC9 4.7 25.4 1.0 C2 A:CDR101 4.8 30.8 1.0 C4A B:CPH103 4.8 27.1 1.0 C1' B:DC22 4.9 28.5 1.0 C4A A:CPH106 4.9 25.9 1.0 C4' A:DC10 4.9 25.2 1.0 C4' B:DC23 4.9 24.9 1.0 C1' A:DC9 4.9 27.7 1.0

Nickel binding site 2 out of 3 in the Crystal Structure of the [NI2+-(Chromomycin A3)2]-Ccg Repeats Complex


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 the [NI2+-(Chromomycin A3)2]-Ccg Repeats Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni108 b:40.9 occ:1.00 O A:HOH209 1.8 40.0 1.0 O A:HOH218 1.9 42.8 1.0 O A:HOH211 2.0 44.4 1.0 O A:HOH206 2.0 35.4 1.0 N7 A:DG8 2.1 34.0 1.0 O A:HOH238 2.3 44.7 1.0 C8 A:DG8 3.0 29.1 1.0 C5 A:DG8 3.3 32.3 1.0 O6 A:DG8 3.7 34.0 1.0 C6 A:DG8 3.8 34.9 1.0 N7 A:DG5 4.1 37.8 1.0 O A:HOH212 4.1 47.8 1.0 O6 A:DG5 4.2 36.1 1.0 N9 A:DG8 4.3 30.6 1.0 OP1 A:DG8 4.3 44.2 1.0 C4 A:DG8 4.4 26.1 1.0 O A:HOH229 4.4 49.0 1.0 OP2 A:DG8 4.5 39.1 1.0 C5 A:DG5 4.7 35.8 1.0 C6 A:DG5 4.8 33.3 1.0 P A:DG8 4.8 38.3 1.0 C8 A:DG5 5.0 43.6 1.0

Nickel binding site 3 out of 3 in the Crystal Structure of the [NI2+-(Chromomycin A3)2]-Ccg Repeats Complex


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 the [NI2+-(Chromomycin A3)2]-Ccg Repeats Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni107 b:40.3 occ:1.00 O B:HOH213 1.8 37.7 1.0 O B:HOH223 1.9 45.3 1.0 O B:HOH212 2.0 42.7 1.0 O B:HOH208 2.0 35.4 1.0 N7 B:DG21 2.1 33.8 1.0 O A:HOH236 2.3 49.5 1.0 C8 B:DG21 3.0 30.1 1.0 C5 B:DG21 3.3 32.9 1.0 O6 B:DG21 3.7 34.8 1.0 C6 B:DG21 3.8 35.0 1.0 O B:HOH232 4.0 48.5 1.0 N7 B:DG18 4.1 38.6 1.0 O A:HOH227 4.1 53.0 1.0 O6 B:DG18 4.2 36.7 1.0 N9 B:DG21 4.3 29.6 1.0 OP1 B:DG21 4.4 45.1 1.0 C4 B:DG21 4.4 26.7 1.0 OP2 B:DG21 4.5 38.6 1.0 C5 B:DG18 4.7 35.8 1.0 C6 B:DG18 4.8 34.0 1.0 P B:DG21 4.8 39.0 1.0

W.H.Tseng, C.K.Chang, P.C.Wu, N.J.Hu, G.H.Lee, C.C.Tzeng, S.Neidle, M.H.Hou. Induced-Fit Recognition of Ccg Trinucleotide Repeats By A Nickel-Chromomycin Complex Resulting in Large-Scale Dna Deformation Angew. Chem. Int. Ed. Engl. V. 56 8761 2017.
ISSN: ESSN 1521-3773
PubMed: 28544401
DOI: 10.1002/ANIE.201703989