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Nickel in PDB 1g3v: Crystal Structure of Nickel-D[Cgtgtacacg]2

Protein crystallography data

The structure of Crystal Structure of Nickel-D[Cgtgtacacg]2, PDB code: 1g3v was solved by J.A.Subirana, N.G.A.Abrescia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 3.10
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 53.031, 53.031, 97.787, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 27

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Nickel-D[Cgtgtacacg]2 (pdb code 1g3v). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 8 binding sites of Nickel where determined in the Crystal Structure of Nickel-D[Cgtgtacacg]2, PDB code: 1g3v:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Nickel binding site 1 out of 8 in 1g3v

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Nickel binding site 1 out of 8 in the Crystal Structure of Nickel-D[Cgtgtacacg]2


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 Nickel-D[Cgtgtacacg]2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni100

b:18.9
occ:1.00
O A:HOH103 2.0 8.9 1.0
N7 A:DG10 2.0 14.4 1.0
O A:HOH101 2.0 8.9 1.0
O A:HOH102 2.1 8.9 1.0
O A:HOH104 2.1 8.9 1.0
C8 A:DG10 2.7 14.4 1.0
C5 A:DG10 3.2 14.4 1.0
O6 A:DG10 3.9 14.4 1.0
C6 A:DG10 3.9 14.4 1.0
N9 A:DG10 3.9 14.4 1.0
OP2 A:DG10 4.1 17.6 1.0
C4 A:DG10 4.2 14.4 1.0
O A:HOH706 4.6 50.1 1.0
O5' A:DG10 4.9 17.6 1.0
P A:DG10 4.9 17.6 1.0

Nickel binding site 2 out of 8 in 1g3v

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Nickel binding site 2 out of 8 in the Crystal Structure of Nickel-D[Cgtgtacacg]2


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 Nickel-D[Cgtgtacacg]2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni300

b:38.3
occ:1.00
O A:HOH304 2.0 40.3 1.0
N7 A:DG2 2.0 13.6 1.0
O A:HOH302 2.0 40.3 1.0
O A:HOH301 2.1 40.3 1.0
O A:HOH303 2.1 40.3 1.0
O A:HOH305 2.1 40.3 1.0
C8 A:DG2 2.9 13.6 1.0
C5 A:DG2 3.2 13.6 1.0
O6 A:DG2 3.6 13.6 1.0
C6 A:DG2 3.7 13.6 1.0
OP1 A:DG2 3.9 55.8 1.0
O4 A:DT3 3.9 13.6 1.0
N9 A:DG2 4.2 13.6 1.0
C7 A:DT3 4.3 13.6 1.0
C4 A:DG2 4.3 13.6 1.0
C4 A:DT3 4.6 13.6 1.0
C5 A:DT3 4.8 13.6 1.0
P A:DG2 5.0 55.8 1.0

Nickel binding site 3 out of 8 in 1g3v

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Nickel binding site 3 out of 8 in the Crystal Structure of Nickel-D[Cgtgtacacg]2


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 Nickel-D[Cgtgtacacg]2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni700

b:36.1
occ:1.00
O A:HOH706 2.0 50.1 1.0
O A:HOH703 2.0 50.1 1.0
O A:HOH701 2.1 50.1 1.0
O A:HOH702 2.1 50.1 1.0
O A:HOH704 2.1 50.1 1.0
O A:HOH705 2.2 50.1 1.0
OP1 A:DC9 3.9 13.6 1.0
O A:HOH101 4.1 8.9 1.0
OP2 A:DG10 4.6 17.6 1.0
O6 A:DG10 4.9 14.4 1.0

Nickel binding site 4 out of 8 in 1g3v

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Nickel binding site 4 out of 8 in the Crystal Structure of Nickel-D[Cgtgtacacg]2


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 Nickel-D[Cgtgtacacg]2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni200

b:32.5
occ:1.00
N7 B:DG20 2.0 20.7 1.0
O B:HOH202 2.1 27.9 1.0
O B:HOH203 2.1 27.9 1.0
O B:HOH201 2.1 27.9 1.0
O B:HOH204 2.1 27.9 1.0
O B:HOH205 2.1 27.9 1.0
C8 B:DG20 2.6 20.7 1.0
C5 B:DG20 3.2 20.7 1.0
N9 B:DG20 3.9 20.7 1.0
C6 B:DG20 4.0 20.7 1.0
O6 B:DG20 4.0 20.7 1.0
C4 B:DG20 4.2 20.7 1.0
OP2 B:DG20 4.3 16.0 1.0
C5' D:DG34 4.5 13.9 1.0
C4' D:DG34 4.9 13.9 1.0
O5' B:DG20 4.9 16.0 1.0

Nickel binding site 5 out of 8 in 1g3v

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Nickel binding site 5 out of 8 in the Crystal Structure of Nickel-D[Cgtgtacacg]2


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 Nickel-D[Cgtgtacacg]2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni600

b:39.3
occ:1.00
O B:HOH601 2.0 29.3 1.0
O B:HOH604 2.0 29.3 1.0
N7 B:DG12 2.1 16.9 1.0
O B:HOH603 2.1 29.3 1.0
O B:HOH602 2.1 29.3 1.0
O B:HOH605 2.1 29.3 1.0
C8 B:DG12 2.9 16.9 1.0
C5 B:DG12 3.2 16.9 1.0
O6 B:DG12 3.7 16.9 1.0
C6 B:DG12 3.8 16.9 1.0
OP1 B:DG12 4.0 58.6 1.0
N9 B:DG12 4.2 16.9 1.0
C7 B:DT13 4.2 14.4 1.0
C4 B:DG12 4.3 16.9 1.0
O4 B:DT13 4.4 14.4 1.0
O5' B:DG12 4.6 58.6 1.0
P B:DG12 4.8 58.6 1.0
C5 B:DT13 5.0 14.4 1.0

Nickel binding site 6 out of 8 in 1g3v

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Nickel binding site 6 out of 8 in the Crystal Structure of Nickel-D[Cgtgtacacg]2


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 Nickel-D[Cgtgtacacg]2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni800

b:47.0
occ:1.00
O C:HOH801 2.0 34.5 1.0
N7 C:DG22 2.0 13.6 1.0
O C:HOH805 2.1 34.5 1.0
O C:HOH803 2.1 34.5 1.0
O C:HOH804 2.1 34.5 1.0
O C:HOH802 2.1 34.5 1.0
C8 C:DG22 2.8 13.6 1.0
C5 C:DG22 3.3 13.6 1.0
O6 C:DG22 3.9 13.6 1.0
C6 C:DG22 4.0 13.6 1.0
OP2 C:DG22 4.0 49.7 1.0
N9 C:DG22 4.1 13.6 1.0
C4 C:DG22 4.3 13.6 1.0
C7 C:DT23 4.3 14.3 1.0
O4 C:DT23 4.4 14.3 1.0
O5' C:DG22 4.9 49.7 1.0
C4 C:DT23 5.0 14.3 1.0

Nickel binding site 7 out of 8 in 1g3v

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Nickel binding site 7 out of 8 in the Crystal Structure of Nickel-D[Cgtgtacacg]2


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 Nickel-D[Cgtgtacacg]2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni400

b:40.9
occ:1.00
O D:HOH401 2.0 39.1 1.0
O D:HOH403 2.0 39.1 1.0
N7 D:DG40 2.0 19.2 1.0
O D:HOH404 2.1 39.1 1.0
O D:HOH402 2.1 39.1 1.0
O D:HOH405 2.1 39.1 1.0
C8 D:DG40 2.6 19.2 1.0
C5 D:DG40 3.3 19.2 1.0
OP2 D:DG40 3.9 13.6 1.0
N9 D:DG40 4.0 19.2 1.0
O6 D:DG40 4.1 19.2 1.0
C6 D:DG40 4.1 19.2 1.0
C4 D:DG40 4.3 19.2 1.0
P D:DG40 4.7 13.6 1.0
O5' D:DG40 4.7 13.6 1.0
OP1 D:DG40 5.0 13.6 1.0

Nickel binding site 8 out of 8 in 1g3v

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Nickel binding site 8 out of 8 in the Crystal Structure of Nickel-D[Cgtgtacacg]2


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 Nickel-D[Cgtgtacacg]2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni500

b:50.1
occ:1.00
O D:HOH505 2.0 49.3 1.0
O D:HOH501 2.0 49.3 1.0
O D:HOH503 2.1 49.3 1.0
O D:HOH504 2.1 49.3 1.0
O D:HOH502 2.1 49.3 1.0
N7 D:DG32 2.3 13.6 1.0
C8 D:DG32 3.1 13.6 1.0
C5 D:DG32 3.4 13.6 1.0
O6 D:DG32 3.7 13.6 1.0
C6 D:DG32 3.9 13.6 1.0
N9 D:DG32 4.4 13.6 1.0
OP1 D:DG32 4.5 14.8 1.0
C4 D:DG32 4.5 13.6 1.0
O4 D:DT33 4.9 13.6 1.0
N4 B:DC19 4.9 13.6 1.0

Reference:

N.A.Abrescia, T.Huynh-Dinh, J.A.Subirana. Nickel-Guanine Interactions in Dna: Crystal Structure of Nickel-D[Cgtgtacacg]2. J.Biol.Inorg.Chem. V. 7 195 2002.
ISSN: ISSN 0949-8257
PubMed: 11862555
DOI: 10.1007/S007750100286
Page generated: Fri Sep 25 07:53:35 2020
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