Calcium in PDB 6dhb: Crystal Structure of the Human Tim-3 with Bound Calcium

Protein crystallography data

The structure of Crystal Structure of the Human Tim-3 with Bound Calcium, PDB code: 6dhb was solved by A.K.Gandhi, W.M.Kim, Y.H.Huang, D.Bonsor, E.Sundberg, Z.-Y.Sun, G.A.Petsko, V.Kuchroo, R.S.Blumberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.09 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.310, 43.060, 51.720, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 18.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Human Tim-3 with Bound Calcium (pdb code 6dhb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of the Human Tim-3 with Bound Calcium, PDB code: 6dhb:

Calcium binding site 1 out of 1 in 6dhb

Go back to Calcium Binding Sites List in 6dhb
Calcium binding site 1 out of 1 in the Crystal Structure of the Human Tim-3 with Bound Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Human Tim-3 with Bound Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:10.7
occ:1.00
O A:ILE92 2.3 11.6 1.0
OD1 A:ASN97 2.3 11.2 1.0
OD1 A:ASP98 2.3 8.2 1.0
O2 A:BEZ202 2.3 10.9 1.0
O A:GLY94 2.3 18.9 1.0
O A:HOH387 2.3 24.5 1.0
CG A:ASP98 3.4 7.8 1.0
C A:GLY94 3.4 16.1 1.0
C A:ILE92 3.5 13.9 1.0
C A:BEZ202 3.5 10.0 1.0
CG A:ASN97 3.5 11.4 1.0
N A:GLY94 3.9 18.0 1.0
N A:ASP98 4.0 7.3 1.0
OD2 A:ASP98 4.0 7.0 1.0
C A:PRO93 4.1 14.8 1.0
CA A:GLY94 4.2 17.1 1.0
O1 A:BEZ202 4.2 9.1 1.0
ND2 A:ASN97 4.2 14.2 1.0
N A:ILE92 4.2 11.1 1.0
N A:ASN97 4.2 9.6 1.0
CA A:ILE92 4.3 13.6 1.0
C A:ASN97 4.3 9.1 1.0
N A:ILE95 4.4 13.6 1.0
CA A:ASP98 4.4 7.6 1.0
N A:PRO93 4.5 16.8 1.0
CA A:PRO93 4.5 16.7 1.0
CB A:ASP98 4.5 7.4 1.0
C6 A:BEZ202 4.5 10.8 1.0
C A:GLN91 4.5 10.7 1.0
C1 A:BEZ202 4.5 10.1 1.0
O A:PRO93 4.5 14.6 1.0
CA A:ASN97 4.6 9.6 1.0
CB A:ILE92 4.6 15.2 1.0
CB A:ASN97 4.6 10.5 1.0
CA A:ILE95 4.6 14.9 1.0
N A:MET96 4.8 12.9 1.0
C A:ILE95 4.8 14.2 1.0
O A:GLN91 4.9 12.1 1.0
CA A:GLN91 4.9 10.5 1.0
O A:ASN97 5.0 9.7 1.0

Reference:

A.K.Gandhi, W.M.Kim, Z.J.Sun, Y.H.Huang, D.A.Bonsor, E.J.Sundberg, Y.Kondo, G.Wagner, V.K.Kuchroo, G.Petsko, R.S.Blumberg. High Resolution X-Ray and uc(Nmr) Structural Study of Human T-Cell Immunoglobulin and Mucin Domain Containing Protein-3. Sci Rep V. 8 17512 2018.
ISSN: ESSN 2045-2322
PubMed: 30504845
DOI: 10.1038/S41598-018-35754-0
Page generated: Sat Dec 12 06:03:23 2020

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