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Calcium in PDB 8jjb: Crystal Structure of T2R-Ttl-Y61 Complex

Protein crystallography data

The structure of Crystal Structure of T2R-Ttl-Y61 Complex, PDB code: 8jjb was solved by J.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.06 / 2.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.287, 157.915, 181.748, 90, 90, 90
R / Rfree (%) 22.7 / 26

Other elements in 8jjb:

The structure of Crystal Structure of T2R-Ttl-Y61 Complex also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Magnesium (Mg) 5 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of T2R-Ttl-Y61 Complex (pdb code 8jjb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of T2R-Ttl-Y61 Complex, PDB code: 8jjb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8jjb

Go back to Calcium Binding Sites List in 8jjb
Calcium binding site 1 out of 6 in the Crystal Structure of T2R-Ttl-Y61 Complex


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 T2R-Ttl-Y61 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:84.2
occ:0.00
 HZ A:PHE49 2.0 91.2 1.0
HG1 A:THR41 2.0 121.2 1.0
OG1 A:THR41 2.3 100.9 1.0
OE2 A:GLU55 2.5 90.8 1.0
OD1 A:ASP39 2.6 75.0 1.0
CZ A:PHE49 2.7 75.9 1.0
OD2 A:ASP39 2.8 90.1 1.0
OD2 A:ASP47 2.9 68.8 1.0
CG A:ASP39 2.9 82.4 1.0
OD1 A:ASN50 3.4 85.1 1.0
HE2 A:PHE49 3.5 97.9 1.0
CE2 A:PHE49 3.5 81.5 1.0
HD21 A:ASN50 3.5 90.6 1.0
CD A:GLU55 3.6 94.5 1.0
CE1 A:PHE49 3.6 76.4 1.0
HE1 A:PHE49 3.6 91.7 1.0
HA3 A:GLY45 3.7 97.4 1.0
CB A:THR41 3.7 107.0 1.0
HB2 A:ASP47 3.8 82.7 1.0
O A:GLY44 3.8 73.2 1.0
HG23 A:THR41 3.9 105.2 1.0
CG A:ASP47 4.0 71.6 1.0
OE1 A:GLU55 4.1 98.6 1.0
O A:THR41 4.1 102.8 1.0
HG21 A:THR41 4.1 105.2 1.0
H A:THR41 4.1 108.8 1.0
CG2 A:THR41 4.1 87.6 1.0
HB A:THR41 4.2 128.5 1.0
ND2 A:ASN50 4.2 75.5 1.0
CG A:ASN50 4.2 73.4 1.0
CB A:ASP39 4.2 75.2 1.0
HB2 A:ASP39 4.3 90.3 1.0
CB A:ASP47 4.4 68.8 1.0
H A:ASP47 4.5 97.6 1.0
NE2 A:HIS61 4.6 90.2 1.0
CA A:GLY45 4.6 81.1 1.0
CA A:THR41 4.6 92.1 1.0
HA A:ASP39 4.7 95.0 1.0
C A:GLY44 4.7 82.6 1.0
N A:THR41 4.8 90.6 1.0
CD2 A:PHE49 4.8 72.7 1.0
CG A:GLU55 4.8 88.0 1.0
C A:THR41 4.8 99.5 1.0
CD1 A:PHE49 4.8 75.8 1.0
HD2 A:HIS61 4.9 106.2 1.0
HG3 A:GLU55 4.9 105.7 1.0
HB3 A:ASP39 4.9 90.3 1.0
HD22 A:ASN50 5.0 90.6 1.0
HG2 A:GLU55 5.0 105.7 1.0

Calcium binding site 2 out of 6 in 8jjb

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Calcium binding site 2 out of 6 in the Crystal Structure of T2R-Ttl-Y61 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of T2R-Ttl-Y61 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:70.7
occ:0.00
 HB3 B:ASP114 3.2 57.7 1.0
CB B:ASP114 4.1 48.0 1.0
OD2 B:ASP114 4.1 78.7 1.0
CG B:ASP114 4.3 64.6 1.0
OD1 B:ASP118 4.3 58.8 1.0
OD2 B:ASP118 4.5 67.1 1.0
HH22 B:ARG121 4.5 99.7 1.0
HB2 B:ASP114 4.6 57.7 1.0
CG B:ASP118 4.9 64.1 1.0
HH21 B:ARG121 4.9 99.7 1.0

Calcium binding site 3 out of 6 in 8jjb

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Calcium binding site 3 out of 6 in the Crystal Structure of T2R-Ttl-Y61 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of T2R-Ttl-Y61 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:76.6
occ:0.00
 OE1 B:GLU111 2.7 85.6 1.0
OE2 B:GLU111 3.2 100.1 1.0
CD B:GLU111 3.3 92.0 1.0
OE1 B:GLU108 4.6 64.0 1.0
CG B:GLU111 4.7 56.9 1.0
HB2 B:GLU111 4.9 81.0 1.0
HG3 B:GLU111 4.9 68.4 1.0
OE2 B:GLU108 5.0 63.8 1.0

Calcium binding site 4 out of 6 in 8jjb

Go back to Calcium Binding Sites List in 8jjb
Calcium binding site 4 out of 6 in the Crystal Structure of T2R-Ttl-Y61 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of T2R-Ttl-Y61 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:66.1
occ:0.00
 OG1 C:THR41 2.3 84.0 1.0
OE2 C:GLU55 2.4 72.7 1.0
HA3 C:GLY45 2.6 88.5 1.0
O C:GLY44 2.7 66.4 1.0
OD2 C:ASP47 2.9 78.9 1.0
OD1 C:ASP39 3.0 61.4 1.0
OD2 C:ASP39 3.0 63.3 1.0
HZ C:PHE49 3.1 64.4 1.0
OD1 C:ASN50 3.2 65.7 1.0
CG C:ASP39 3.3 63.5 1.0
CD C:GLU55 3.4 65.2 1.0
CA C:GLY45 3.5 73.7 1.0
O C:THR41 3.6 76.3 1.0
HD21 C:ASN50 3.6 66.8 1.0
C C:GLY44 3.7 69.1 1.0
CB C:THR41 3.7 67.5 1.0
CZ C:PHE49 3.8 53.6 1.0
OE1 C:GLU55 3.8 73.5 1.0
HE2 C:PHE49 3.9 65.1 1.0
CG C:ASP47 4.0 59.6 1.0
N C:GLY45 4.0 68.5 1.0
HB C:THR41 4.0 81.0 1.0
HA2 C:GLY45 4.0 88.5 1.0
HB2 C:ASP47 4.0 75.6 1.0
CG C:ASN50 4.1 57.2 1.0
H C:ASP47 4.1 66.0 1.0
CE2 C:PHE49 4.2 54.2 1.0
ND2 C:ASN50 4.2 55.6 1.0
H C:THR41 4.4 64.9 1.0
C C:GLY45 4.4 65.6 1.0
HG21 C:THR41 4.4 61.6 1.0
C C:THR41 4.5 65.6 1.0
CG2 C:THR41 4.6 51.3 1.0
CB C:ASP47 4.6 63.0 1.0
CA C:THR41 4.6 62.8 1.0
H C:GLY44 4.6 81.3 1.0
HG3 C:GLU55 4.7 68.2 1.0
HG23 C:THR41 4.7 61.6 1.0
CG C:GLU55 4.7 56.8 1.0
CB C:ASP39 4.7 64.6 1.0
H C:ASP46 4.7 91.9 1.0
CE1 C:PHE49 4.8 57.5 1.0
H C:GLY45 4.8 82.3 1.0
N C:ASP46 4.8 76.5 1.0
HB2 C:ASP39 4.9 77.6 1.0
HE1 C:PHE49 4.9 69.1 1.0
N C:THR41 4.9 54.0 1.0
OD1 C:ASP47 4.9 60.0 1.0
CA C:GLY44 4.9 68.1 1.0
N C:ASP47 5.0 54.9 1.0

Calcium binding site 5 out of 6 in 8jjb

Go back to Calcium Binding Sites List in 8jjb
Calcium binding site 5 out of 6 in the Crystal Structure of T2R-Ttl-Y61 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of T2R-Ttl-Y61 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:74.5
occ:0.00
 HG13 D:VAL175 3.1 109.7 1.0
CZ D:TYR222 3.9 63.4 1.0
O D:VAL175 3.9 84.5 1.0
CE1 D:TYR222 3.9 72.8 1.0
CG1 D:VAL175 4.0 91.4 1.0
HG12 D:VAL175 4.0 109.7 1.0
O D:PRO220 4.1 81.3 1.0
HA D:THR221 4.1 103.8 1.0
CE2 D:TYR222 4.1 69.8 1.0
HE1 D:TYR222 4.2 87.5 1.0
CD1 D:TYR222 4.2 66.0 1.0
OH D:TYR222 4.3 69.4 1.0
H D:TYR222 4.4 92.6 1.0
HG11 D:VAL175 4.4 109.7 1.0
HA D:VAL175 4.4 98.8 1.0
CD2 D:TYR222 4.4 77.8 1.0
CG D:TYR222 4.5 73.9 1.0
HE2 D:TYR222 4.5 83.9 1.0
HH D:TYR222 4.5 83.4 1.0
HD1 D:TYR222 4.6 79.3 1.0
N D:TYR222 4.7 77.1 1.0
C D:VAL175 4.9 89.2 1.0
HD2 D:TYR222 4.9 93.4 1.0
CA D:THR221 5.0 86.4 1.0

Calcium binding site 6 out of 6 in 8jjb

Go back to Calcium Binding Sites List in 8jjb
Calcium binding site 6 out of 6 in the Crystal Structure of T2R-Ttl-Y61 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of T2R-Ttl-Y61 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca201

b:75.2
occ:0.00
 OD2 E:ASP44 3.4 104.1 1.0
HZ1 A:LYS166 3.4 96.1 1.0
HG A:SER158 3.6 84.4 1.0
HZ3 A:LYS166 3.8 96.1 1.0
HA A:HIS197 3.9 68.8 1.0
OG A:SER158 3.9 70.2 1.0
HB3 A:SER158 4.0 70.5 1.0
NZ A:LYS166 4.0 80.0 1.0
O A:GLY162 4.2 94.4 1.0
O A:GLU196 4.4 65.2 1.0
CB A:SER158 4.4 58.7 1.0
CG E:ASP44 4.5 99.5 1.0
HZ2 A:LYS166 4.5 96.1 1.0
HA A:SER158 4.6 78.6 1.0
CA A:HIS197 4.8 57.3 1.0
HA2 A:GLY162 4.8 91.9 1.0
O A:HIS197 4.9 55.4 1.0
OD1 A:ASP199 4.9 55.2 1.0
HE2 A:LYS166 4.9 75.8 1.0
OD1 E:ASP44 4.9 82.9 1.0

Reference:

C.Zhang, W.Yan, Y.Liu, M.Tang, Y.Teng, F.Wang, X.Hu, M.Zhao, J.Yang, Y.Li. Structure-Based Design and Synthesis of BML284 Derivatives: A Novel Class of Colchicine-Site Noncovalent Tubulin Degradation Agents. Eur.J.Med.Chem. V. 268 16265 2024.
ISSN: ISSN 0223-5234
PubMed: 38430854
DOI: 10.1016/J.EJMECH.2024.116265
Page generated: Fri Jul 19 09:57:38 2024

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