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Nickel in PDB 473d: NI2+/Guanine Interactions and Netropsin/Guanine Stacking in D(Cgtatatacg)2

Protein crystallography data

The structure of NI2+/Guanine Interactions and Netropsin/Guanine Stacking in D(Cgtatatacg)2, PDB code: 473d was solved by N.G.A.Abrescia, L.Malinina, J.A.Subirana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.58
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 25.180, 39.110, 53.470, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Nickel Binding Sites:

The binding sites of Nickel atom in the NI2+/Guanine Interactions and Netropsin/Guanine Stacking in D(Cgtatatacg)2 (pdb code 473d). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the NI2+/Guanine Interactions and Netropsin/Guanine Stacking in D(Cgtatatacg)2, PDB code: 473d:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 473d

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Nickel binding site 1 out of 4 in the NI2+/Guanine Interactions and Netropsin/Guanine Stacking in D(Cgtatatacg)2


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of NI2+/Guanine Interactions and Netropsin/Guanine Stacking in D(Cgtatatacg)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni350

b:17.8
occ:1.00
O A:HOH1004 2.0 16.7 1.0
O A:HOH1003 2.0 18.2 1.0
N7 A:DG10 2.1 12.8 1.0
O A:HOH1002 2.1 20.4 1.0
O A:HOH1000 2.1 18.6 1.0
O A:HOH1001 2.2 13.5 1.0
C8 A:DG10 2.9 15.8 1.0
C5 A:DG10 3.2 14.2 1.0
O6 A:DG10 3.6 13.2 1.0
C6 A:DG10 3.8 11.2 1.0
O A:HOH1022 4.2 19.3 1.0
N9 A:DG10 4.2 13.0 1.0
O A:HOH1061 4.3 49.2 1.0
C4 A:DG10 4.3 10.4 1.0
O A:HOH1035 4.6 26.9 1.0

Nickel binding site 2 out of 4 in 473d

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Nickel binding site 2 out of 4 in the NI2+/Guanine Interactions and Netropsin/Guanine Stacking in D(Cgtatatacg)2


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of NI2+/Guanine Interactions and Netropsin/Guanine Stacking in D(Cgtatatacg)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni352

b:26.9
occ:1.00
O A:HOH1014 1.9 20.1 1.0
N7 A:DG2 2.1 18.0 1.0
O A:HOH1012 2.2 25.2 1.0
O A:HOH1011 2.2 28.4 1.0
O A:HOH1013 2.3 41.9 0.8
O A:HOH1010 2.3 23.2 1.0
C8 A:DG2 3.0 21.5 1.0
C5 A:DG2 3.2 14.9 1.0
O6 A:DG2 3.7 16.8 1.0
C6 A:DG2 3.8 14.7 1.0
N9 A:DG2 4.3 18.2 1.0
C4 A:DG2 4.4 15.7 1.0
OP2 A:DG2 4.5 30.4 1.0
OP1 A:DG2 4.5 42.6 1.0
O4 A:DT3 4.8 14.5 1.0
O B:HOH1062 4.8 30.1 1.0
P A:DG2 4.9 32.8 1.0

Nickel binding site 3 out of 4 in 473d

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Nickel binding site 3 out of 4 in the NI2+/Guanine Interactions and Netropsin/Guanine Stacking in D(Cgtatatacg)2


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of NI2+/Guanine Interactions and Netropsin/Guanine Stacking in D(Cgtatatacg)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni351

b:18.6
occ:1.00
O B:HOH1007 1.9 16.9 1.0
O B:HOH1008 2.0 16.5 1.0
O B:HOH1006 2.0 17.0 1.0
O B:HOH1005 2.0 18.7 1.0
O B:HOH1009 2.1 21.7 1.0
N7 B:DG12 2.1 15.6 1.0
C8 B:DG12 3.0 11.9 1.0
C5 B:DG12 3.2 15.4 1.0
O6 B:DG12 3.7 13.2 1.0
C6 B:DG12 3.8 13.5 1.0
O B:HOH1042 4.0 19.6 1.0
O B:HOH1040 4.0 37.1 1.0
OP1 B:DG12 4.1 36.5 1.0
O B:HOH1073 4.1 50.2 1.0
O B:HOH1044 4.2 39.4 1.0
O4 B:DT13 4.2 15.7 1.0
N9 B:DG12 4.2 13.8 1.0
O B:HOH1056 4.2 30.9 1.0
O A:HOH1065 4.3 32.5 1.0
C4 B:DG12 4.3 13.1 1.0
C7 B:DT13 4.5 22.6 1.0
OP2 B:DG12 4.8 30.0 1.0
P B:DG12 4.8 28.8 1.0
C4 B:DT13 4.9 11.7 1.0

Nickel binding site 4 out of 4 in 473d

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Nickel binding site 4 out of 4 in the NI2+/Guanine Interactions and Netropsin/Guanine Stacking in D(Cgtatatacg)2


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of NI2+/Guanine Interactions and Netropsin/Guanine Stacking in D(Cgtatatacg)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni353

b:13.4
occ:1.00
O B:HOH1018 2.0 16.9 1.0
O B:HOH1015 2.0 12.2 1.0
O B:HOH1016 2.1 13.9 1.0
N7 B:DG20 2.1 10.2 1.0
O B:HOH1017 2.1 12.2 1.0
C8 B:DG20 3.0 15.6 1.0
C5 B:DG20 3.2 13.6 1.0
O6 B:DG20 3.6 15.9 1.0
C6 B:DG20 3.8 15.4 1.0
OP2 B:DG20 4.0 15.5 1.0
O B:HOH1074 4.2 48.1 1.0
N9 B:DG20 4.2 14.4 1.0
O B:HOH1045 4.3 25.6 1.0
C4 B:DG20 4.3 12.0 1.0

Reference:

N.G.Abrescia, L.Malinina, J.A.Subirana. Stacking Interaction of Guanine with Netropsin in the Minor Groove of D(Cgtatatacg)2. J.Mol.Biol. V. 294 657 1999.
ISSN: ISSN 0022-2836
PubMed: 10610787
DOI: 10.1006/JMBI.1999.3280
Page generated: Fri Sep 25 08:38:24 2020
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