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Nickel in PDB 1s9b: Crystal Structure Analysis of the B-Dna Gaattcg

Protein crystallography data

The structure of Crystal Structure Analysis of the B-Dna Gaattcg, PDB code: 1s9b was solved by N.Valls, I.Uson, C.Gouyette, J.A.Subirana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.40 / 2.81
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 70.867, 70.867, 70.867, 90.00, 90.00, 90.00
R / Rfree (%) 28.1 / 26.4

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure Analysis of the B-Dna Gaattcg (pdb code 1s9b). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure Analysis of the B-Dna Gaattcg, PDB code: 1s9b:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 1s9b

Go back to Nickel Binding Sites List in 1s9b
Nickel binding site 1 out of 4 in the Crystal Structure Analysis of the B-Dna Gaattcg


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure Analysis of the B-Dna Gaattcg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni101

b:38.1
occ:0.70
O A:HOH110 2.0 37.6 0.7
O A:HOH111 2.0 38.1 0.7
O A:HOH112 2.0 37.6 0.7
O A:HOH113 2.0 37.9 0.7
O A:HOH102 2.0 37.9 0.7
N7 A:DG1 2.0 32.0 1.0
C5 A:DG1 3.1 27.9 1.0
C8 A:DG1 3.1 31.9 1.0
O6 A:DG1 3.2 29.9 1.0
C6 A:DG1 3.5 28.1 1.0
C4 A:DG1 4.2 28.4 1.0
N9 A:DG1 4.3 33.1 1.0
N6 A:DA2 4.8 26.9 1.0
N1 A:DG1 4.9 24.4 1.0

Nickel binding site 2 out of 4 in 1s9b

Go back to Nickel Binding Sites List in 1s9b
Nickel binding site 2 out of 4 in the Crystal Structure Analysis of the B-Dna Gaattcg


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure Analysis of the B-Dna Gaattcg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni103

b:48.9
occ:0.70
O A:HOH119 2.0 48.6 0.7
O A:HOH121 2.0 48.5 0.7
O A:HOH122 2.0 48.4 0.7
O A:HOH109 2.0 48.1 0.7
O A:HOH120 2.0 48.3 0.7
N7 A:DG7 2.0 45.7 1.0
C8 A:DG7 2.5 44.3 1.0
C5 A:DG7 3.4 45.7 1.0
N9 A:DG7 3.9 42.5 1.0
O6 A:DG7 4.2 51.6 1.0
OP2 A:DG7 4.2 39.0 1.0
C6 A:DG7 4.3 47.5 1.0
C4 A:DG7 4.3 43.8 1.0
O5' A:DG7 4.8 42.0 1.0
C2' A:DG7 4.9 42.0 1.0
C1' A:DG7 5.0 40.9 1.0
P A:DG7 5.0 40.0 1.0

Nickel binding site 3 out of 4 in 1s9b

Go back to Nickel Binding Sites List in 1s9b
Nickel binding site 3 out of 4 in the Crystal Structure Analysis of the B-Dna Gaattcg


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure Analysis of the B-Dna Gaattcg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni102

b:43.8
occ:0.70
O B:HOH116 2.0 44.1 0.7
O B:HOH115 2.0 44.0 0.7
N7 B:DG1 2.0 32.7 1.0
O B:HOH114 2.0 43.1 0.7
O B:HOH118 2.0 43.5 0.7
O B:HOH117 2.0 43.6 0.7
O6 B:DG1 2.8 29.6 1.0
C5 B:DG1 2.9 28.1 1.0
C8 B:DG1 3.1 32.3 1.0
C6 B:DG1 3.2 28.1 1.0
C4 B:DG1 4.2 28.5 1.0
N9 B:DG1 4.2 33.0 1.0
N6 B:DA2 4.5 27.5 1.0
N1 B:DG1 4.6 24.4 1.0
O4 A:DT5 5.0 18.5 1.0

Nickel binding site 4 out of 4 in 1s9b

Go back to Nickel Binding Sites List in 1s9b
Nickel binding site 4 out of 4 in the Crystal Structure Analysis of the B-Dna Gaattcg


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure Analysis of the B-Dna Gaattcg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni104

b:44.1
occ:0.70
N7 B:DG7 2.0 45.6 1.0
O B:HOH125 2.0 42.5 0.7
O B:HOH124 2.0 43.5 0.7
O B:HOH123 2.0 42.7 0.7
O B:HOH101 2.0 43.4 0.7
O B:HOH103 2.0 43.3 0.7
C8 B:DG7 2.6 44.3 1.0
C5 B:DG7 3.3 45.7 1.0
N9 B:DG7 3.9 42.5 1.0
OP2 B:DG7 3.9 39.0 1.0
O6 B:DG7 4.0 51.9 1.0
C6 B:DG7 4.1 47.6 1.0
C4 B:DG7 4.2 43.7 1.0
O5' B:DG7 4.8 41.5 1.0
P B:DG7 4.9 39.1 1.0

Reference:

N.Valls, I.Uson, C.Gouyette, J.A.Subirana. A Cubic Arrangement of Dna Double Helices Based on Nickel-Guanine Interactions J.Am.Chem.Soc. V. 126 7812 2004.
ISSN: ISSN 0002-7863
PubMed: 15212528
DOI: 10.1021/JA049393I
Page generated: Fri Sep 25 08:01:21 2020
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