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Nickel in PDB 1keg: Antibody 64M-2 Fab Complexed with Dtt(6-4)Tt

Protein crystallography data

The structure of Antibody 64M-2 Fab Complexed with Dtt(6-4)Tt, PDB code: 1keg was solved by H.Yokoyama, R.Mizutani, Y.Satow, K.Sato, Y.Komatsu, E.Ohtsuka, O.Nikaido, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.567, 137.274, 49.615, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 26.8

Nickel Binding Sites:

The binding sites of Nickel atom in the Antibody 64M-2 Fab Complexed with Dtt(6-4)Tt (pdb code 1keg). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Antibody 64M-2 Fab Complexed with Dtt(6-4)Tt, PDB code: 1keg:

Nickel binding site 1 out of 1 in 1keg

Go back to Nickel Binding Sites List in 1keg
Nickel binding site 1 out of 1 in the Antibody 64M-2 Fab Complexed with Dtt(6-4)Tt


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Antibody 64M-2 Fab Complexed with Dtt(6-4)Tt within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni213

b:30.6
occ:1.00
N L:ASP1 1.9 19.1 1.0
O L:ASP1 2.2 29.8 1.0
OD1 L:ASP1 2.2 35.7 1.0
CA L:ASP1 2.8 24.6 1.0
C L:ASP1 2.8 24.7 1.0
CG L:ASP1 3.2 32.4 1.0
O L:HOH242 3.2 23.7 1.0
CB L:ASP1 3.5 27.3 1.0
N L:VAL2 4.1 25.9 1.0
OD2 L:ASP1 4.4 31.9 1.0
NE2 L:GLN27 4.7 47.0 1.0
CG L:LEU3 4.8 19.3 1.0
CA L:VAL2 4.9 23.2 1.0

Reference:

H.Yokoyama, R.Mizutani, Y.Satow, K.Sato, Y.Komatsu, E.Ohtsuka, O.Nikaido. Structure of the Dna (6-4) Photoproduct Dtt(6-4)Tt in Complex with the 64M-2 Antibody Fab Fragment Implies Increased Antibody-Binding Affinity By the Flanking Nucleotides. Acta Crystallogr.,Sect.D V. 68 232 2012.
ISSN: ISSN 0907-4449
PubMed: 22349224
DOI: 10.1107/S0907444912000327
Page generated: Fri Sep 25 07:56:27 2020
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