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Nickel in PDB 4xid: Antphd with 15BP Dna Duplex

Protein crystallography data

The structure of Antphd with 15BP Dna Duplex, PDB code: 4xid was solved by M.A.White, L.Zandarashvili, J.Iwahara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.60 / 2.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.443, 96.443, 90.142, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 27.4

Nickel Binding Sites:

The binding sites of Nickel atom in the Antphd with 15BP Dna Duplex (pdb code 4xid). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Antphd with 15BP Dna Duplex, PDB code: 4xid:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 4xid

Go back to Nickel Binding Sites List in 4xid
Nickel binding site 1 out of 3 in the Antphd with 15BP Dna Duplex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Antphd with 15BP Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni101

b:85.3
occ:1.00
N7 B:DG1 2.2 65.4 1.0
O C:HOH202 2.2 61.9 1.0
C8 B:DG1 3.2 69.0 1.0
C5 B:DG1 3.2 55.3 1.0
O6 B:DG1 3.4 66.7 1.0
C6 B:DG1 3.7 55.9 1.0
N9 B:DG1 4.4 52.4 1.0
C4 B:DG1 4.4 53.2 1.0
O5' B:DA0 4.6 63.7 1.0
N6 B:DA2 4.7 58.3 1.0
O4 C:DT37 4.7 74.3 1.0
C2' B:DA0 4.8 48.4 1.0
N3 B:DA0 4.9 55.3 1.0

Nickel binding site 2 out of 3 in 4xid

Go back to Nickel Binding Sites List in 4xid
Nickel binding site 2 out of 3 in the Antphd with 15BP Dna Duplex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Antphd with 15BP Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni101

b:90.4
occ:1.00
NE2 D:HIS21 2.3 78.2 1.0
O D:HOH201 2.3 55.4 1.0
CE1 D:HIS21 2.8 80.5 1.0
CD2 D:HIS21 3.5 69.3 1.0
ND1 D:HIS21 4.0 78.4 1.0
CG D:HIS21 4.3 69.5 1.0

Nickel binding site 3 out of 3 in 4xid

Go back to Nickel Binding Sites List in 4xid
Nickel binding site 3 out of 3 in the Antphd with 15BP Dna Duplex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Antphd with 15BP Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni102

b:0.9
occ:1.00
O6 E:DG1 2.7 0.7 1.0
N7 E:DG1 3.1 0.1 1.0
C6 E:DG1 3.5 0.5 1.0
C5 E:DG1 3.6 0.3 1.0
C8 E:DG1 4.3 0.5 1.0
C2 E:DA0 4.6 0.7 1.0
N1 E:DG1 4.8 0.5 1.0
C4 E:DG1 5.0 1.0 1.0
N3 E:DA0 5.0 0.6 1.0

Reference:

L.Zandarashvili, D.Nguyen, K.M.Anderson, M.A.White, D.G.Gorenstein, J.Iwahara. Entropic Enhancement of Protein-Dna Affinity By Oxygen-to-Sulfur Substitution in Dna Phosphate. Biophys.J. V. 109 1026 2015.
ISSN: ESSN 1542-0086
PubMed: 26331260
DOI: 10.1016/J.BPJ.2015.07.032
Page generated: Wed Dec 16 01:38:13 2020

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