Cobalt in PDB 3alq: Crystal Structure of Tnf-TNFR2 Complex

The structure of Crystal Structure of Tnf-TNFR2 Complex, PDB code: 3alq was solved by Y.Mukai, T.Nakamura, Y.Yamagata, Y.Tsutsumi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.96 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.470, 117.356, 246.835, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 28.1

The binding sites of Cobalt atom in the Crystal Structure of Tnf-TNFR2 Complex (pdb code 3alq). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 6 binding sites of Cobalt where determined in the Crystal Structure of Tnf-TNFR2 Complex, PDB code: 3alq:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6;

Cobalt binding site 1 out of 6 in the Crystal Structure of Tnf-TNFR2 Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Tnf-TNFR2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ R:Co2 b:45.1 occ:1.00 OD1 R:ASP54 2.1 53.0 1.0 NE2 R:HIS40 2.3 45.2 1.0 OE2 R:GLU57 3.0 76.3 1.0 CE1 R:HIS40 3.2 41.9 1.0 CD2 R:HIS40 3.4 43.0 1.0 CG R:ASP54 3.4 53.6 1.0 OE1 R:GLU57 3.4 71.1 1.0 CD R:GLU57 3.6 79.3 1.0 O R:SER55 3.9 50.9 1.0 OE1 R:GLU70 4.1 43.1 1.0 OD2 R:ASP54 4.2 56.1 1.0 CB R:ASP54 4.3 45.7 1.0 ND1 R:HIS40 4.3 40.8 1.0 CG R:HIS40 4.5 41.3 1.0

Cobalt binding site 2 out of 6 in the Crystal Structure of Tnf-TNFR2 Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Tnf-TNFR2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ S:Co1 b:57.2 occ:1.00 NE2 S:HIS40 2.2 48.2 1.0 OD1 S:ASP54 2.3 61.9 1.0 CE1 S:HIS40 3.0 49.3 1.0 CD2 S:HIS40 3.3 46.2 1.0 CG S:ASP54 3.3 53.4 1.0 OE1 S:GLU57 3.4 98.2 1.0 OE2 S:GLU57 3.6 85.3 1.0 CD S:GLU57 3.7 96.9 1.0 CB S:ASP54 3.8 47.4 1.0 O S:SER55 4.1 57.7 1.0 ND1 S:HIS40 4.2 44.4 1.0 OE1 S:GLU70 4.2 53.5 1.0 CG S:HIS40 4.3 43.4 1.0 OD2 S:ASP54 4.4 53.6 1.0 OE2 S:GLU70 4.7 56.2 1.0 CD S:GLU70 4.9 52.6 1.0 O S:ASP54 4.9 56.9 1.0 C S:ASP54 5.0 54.9 1.0

Cobalt binding site 3 out of 6 in the Crystal Structure of Tnf-TNFR2 Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Tnf-TNFR2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ T:Co3 b:52.4 occ:1.00 OD1 T:ASP54 2.3 61.3 1.0 NE2 T:HIS40 2.4 53.7 1.0 OE2 T:GLU57 2.8 74.6 1.0 OE1 T:GLU57 2.9 80.5 1.0 CE1 T:HIS40 3.0 48.2 1.0 CD T:GLU57 3.2 90.3 1.0 CG T:ASP54 3.4 61.8 1.0 CD2 T:HIS40 3.6 50.6 1.0 OE1 T:GLU70 3.9 48.6 1.0 CB T:ASP54 3.9 51.1 1.0 ND1 T:HIS40 4.3 44.2 1.0 O T:SER55 4.4 57.6 1.0 OD2 T:ASP54 4.5 64.7 1.0 CG T:HIS40 4.6 47.4 1.0 CD T:GLU70 4.7 45.6 1.0 OE2 T:GLU70 4.7 47.4 1.0 CG T:GLU57 4.8 87.0 1.0

Cobalt binding site 4 out of 6 in the Crystal Structure of Tnf-TNFR2 Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of Tnf-TNFR2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ U:Co4 b:48.6 occ:1.00 NE2 U:HIS40 2.2 47.7 1.0 OD1 U:ASP54 2.5 62.1 1.0 CE1 U:HIS40 3.0 47.2 1.0 CD2 U:HIS40 3.3 49.2 1.0 CG U:ASP54 3.4 58.8 1.0 CB U:ASP54 3.7 49.3 1.0 O U:SER55 4.2 55.4 1.0 OE1 U:GLU70 4.2 48.5 1.0 ND1 U:HIS40 4.2 44.5 1.0 CG U:HIS40 4.4 47.2 1.0 OD2 U:ASP54 4.6 55.9 1.0 OE2 U:GLU70 4.8 58.0 1.0 CD U:GLU70 4.9 53.1 1.0 O U:ASP54 4.9 48.4 1.0 C U:ASP54 5.0 53.3 1.0 CA U:ASP54 5.0 54.8 1.0

Cobalt binding site 5 out of 6 in the Crystal Structure of Tnf-TNFR2 Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of Tnf-TNFR2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ V:Co5 b:71.0 occ:1.00 NE2 V:HIS40 2.3 73.7 1.0 OD1 V:ASP54 2.8 88.9 1.0 CE1 V:HIS40 3.2 68.4 1.0 CD2 V:HIS40 3.4 74.4 1.0 CG V:ASP54 3.7 87.7 1.0 OE1 V:GLU57 3.7 0.6 1.0 CB V:ASP54 3.8 81.1 1.0 OE2 V:GLU57 4.0 0.6 1.0 O V:SER55 4.1 87.7 1.0 OE1 V:GLU70 4.2 60.7 1.0 CD V:GLU57 4.3 0.9 1.0 ND1 V:HIS40 4.3 69.9 1.0 CG V:HIS40 4.5 72.3 1.0 O V:ASP54 4.8 75.1 1.0 OD2 V:ASP54 4.8 81.1 1.0 C V:ASP54 4.9 77.3 1.0 CA V:ASP54 5.0 77.2 1.0

Cobalt binding site 6 out of 6 in the Crystal Structure of Tnf-TNFR2 Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure of Tnf-TNFR2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ W:Co6 b:63.5 occ:1.00 OD1 W:ASP54 2.4 72.1 1.0 NE2 W:HIS40 2.4 61.8 1.0 OE2 W:GLU57 3.2 97.2 1.0 CD2 W:HIS40 3.4 61.4 1.0 CE1 W:HIS40 3.4 62.9 1.0 CG W:ASP54 3.5 72.3 1.0 CD W:GLU57 3.9 98.8 1.0 O W:SER55 4.1 54.5 1.0 OE1 W:GLU57 4.1 95.9 1.0 CB W:ASP54 4.1 68.6 1.0 OE1 W:GLU70 4.3 58.3 1.0 OD2 W:ASP54 4.4 66.7 1.0 ND1 W:HIS40 4.5 60.9 1.0 CG W:HIS40 4.5 60.6 1.0 CG W:GLU57 5.0 80.8 1.0

Y.Mukai, T.Nakamura, M.Yoshikawa, Y.Yoshioka, S.I.Tsunoda, S.Nakagawa, Y.Yamagata, Y.Tsutsumi. Solution of the Structure of the Tnf-TNFR2 Complex Sci.Signal. V. 3 RA83 2010.
ISSN: ESSN 1937-9145
PubMed: 21081755
DOI: 10.1126/SCISIGNAL.2000954