Calcium in PDB 7cek: Crystal Structure of T2R-Ttl-Bml-284 Complex

Protein crystallography data

The structure of Crystal Structure of T2R-Ttl-Bml-284 Complex, PDB code: 7cek was solved by L.J.Chen, Q.Chen, Y.Yu, J.H.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.26 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.571, 158.078, 181.292, 90, 90, 90
R / Rfree (%) 22.8 / 27.1

Other elements in 7cek:

The structure of Crystal Structure of T2R-Ttl-Bml-284 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-Bml-284 Complex (pdb code 7cek). 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-Bml-284 Complex, PDB code: 7cek:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7cek

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Calcium binding site 1 out of 6 in the Crystal Structure of T2R-Ttl-Bml-284 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-Bml-284 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:79.4
occ:1.00
HG1 A:THR41 1.8 99.2 1.0
OE2 A:GLU55 2.2 77.2 1.0
OD2 A:ASP39 2.3 77.0 1.0
OG1 A:THR41 2.4 82.2 1.0
OD1 A:ASP39 2.4 72.8 1.0
OE1 A:GLU55 2.6 77.6 1.0
O A:THR41 2.6 77.1 1.0
CG A:ASP39 2.7 76.1 1.0
CD A:GLU55 2.7 77.2 1.0
O A:GLY44 2.8 76.1 1.0
HZ A:PHE49 3.0 89.3 1.0
CB A:THR41 3.6 79.1 1.0
C A:THR41 3.6 78.2 1.0
HA3 A:GLY45 3.7 91.4 1.0
HB A:THR41 3.7 95.6 1.0
HD21 A:ASN50 3.8 89.1 1.0
CZ A:PHE49 3.9 73.9 1.0
H A:THR41 3.9 93.2 1.0
C A:GLY44 3.9 76.5 1.0
H A:GLY44 3.9 92.1 1.0
CA A:THR41 4.0 77.5 1.0
CB A:ASP39 4.1 76.0 1.0
NE2 A:HIS61 4.1 75.8 1.0
CG A:GLU55 4.2 75.2 1.0
OD1 A:ASN50 4.2 76.9 1.0
N A:THR41 4.2 77.1 1.0
HB2 A:ASP39 4.2 91.8 1.0
HG2 A:GLU55 4.5 90.9 1.0
HE2 A:PHE49 4.5 90.0 1.0
CA A:GLY45 4.5 75.6 1.0
ND2 A:ASN50 4.6 73.8 1.0
HG3 A:GLU55 4.6 90.9 1.0
HE1 A:PHE49 4.6 86.6 1.0
HB3 A:ASP39 4.6 91.8 1.0
CE2 A:PHE49 4.6 74.5 1.0
N A:GLY45 4.6 72.6 1.0
N A:GLY44 4.6 76.2 1.0
OD2 A:ASP47 4.7 78.5 1.0
CE1 A:PHE49 4.7 71.7 1.0
CG2 A:THR41 4.8 79.3 1.0
HA A:ILE42 4.8 91.9 1.0
N A:ILE42 4.8 77.6 1.0
HD2 A:HIS61 4.8 89.9 1.0
CG A:ASN50 4.8 73.1 1.0
HA A:ASP39 4.9 90.0 1.0
CA A:GLY44 4.9 76.6 1.0
CD2 A:HIS61 4.9 74.4 1.0
HG21 A:THR41 4.9 95.8 1.0
HA A:THR41 4.9 93.7 1.0
HG23 A:THR41 5.0 95.8 1.0
CA A:ASP39 5.0 74.5 1.0
HB3 A:GLU55 5.0 87.9 1.0

Calcium binding site 2 out of 6 in 7cek

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Calcium binding site 2 out of 6 in the Crystal Structure of T2R-Ttl-Bml-284 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-Bml-284 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:97.1
occ:1.00
O B:HOH619 2.5 64.3 1.0
HB3 B:ASP114 3.4 79.2 1.0
OD2 B:ASP114 3.5 79.2 1.0
CG B:ASP114 4.1 71.8 1.0
CB B:ASP114 4.2 65.5 1.0
OD1 B:ASP118 4.4 62.7 1.0
OD2 B:ASP118 4.4 67.2 1.0
HB2 B:ASP114 4.8 79.2 1.0
CG B:ASP118 4.9 64.6 1.0
HH22 B:ARG121 4.9 86.8 1.0

Calcium binding site 3 out of 6 in 7cek

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Calcium binding site 3 out of 6 in the Crystal Structure of T2R-Ttl-Bml-284 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-Bml-284 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca505

b:88.9
occ:1.00
OE1 B:GLU111 2.4 80.4 1.0
OE2 B:GLU111 3.0 76.0 1.0
CD B:GLU111 3.0 77.1 1.0
OE1 B:GLU108 4.4 65.3 1.0
CG B:GLU111 4.5 70.0 1.0
HB2 B:GLU111 4.8 79.1 1.0
HG3 B:GLU111 4.8 84.6 1.0

Calcium binding site 4 out of 6 in 7cek

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Calcium binding site 4 out of 6 in the Crystal Structure of T2R-Ttl-Bml-284 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-Bml-284 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:66.1
occ:1.00
O C:THR41 2.2 64.2 1.0
OE2 C:GLU55 2.3 61.9 1.0
OG1 C:THR41 2.4 64.5 1.0
OD2 C:ASP39 2.4 61.0 1.0
O C:GLY44 2.5 62.7 1.0
OD1 C:ASP39 2.6 62.1 1.0
O C:HOH602 2.6 60.2 1.0
CG C:ASP39 2.8 61.5 1.0
OE1 C:GLU55 2.9 57.7 1.0
CD C:GLU55 2.9 59.8 1.0
C C:THR41 3.2 63.6 1.0
HA3 C:GLY45 3.3 76.3 1.0
CB C:THR41 3.3 62.2 1.0
HB C:THR41 3.3 75.3 1.0
C C:GLY44 3.5 62.8 1.0
H C:THR41 3.7 76.2 1.0
HZ C:PHE49 3.7 68.4 1.0
CA C:THR41 3.7 63.6 1.0
H C:GLY44 3.9 76.2 1.0
CA C:GLY45 4.1 63.0 1.0
HD21 C:ASN50 4.1 70.1 1.0
N C:THR41 4.1 63.0 1.0
HE1 C:HIS61 4.1 71.9 1.0
N C:GLY45 4.2 62.5 1.0
OD2 C:ASP47 4.2 65.4 1.0
HE2 C:PHE49 4.3 69.5 1.0
CB C:ASP39 4.3 62.6 1.0
OD1 C:ASN50 4.3 60.4 1.0
CG C:GLU55 4.4 60.2 1.0
N C:ILE42 4.4 62.7 1.0
CZ C:PHE49 4.4 56.5 1.0
N C:GLY44 4.5 63.0 1.0
HA2 C:GLY45 4.5 76.3 1.0
CA C:GLY44 4.5 63.8 1.0
HA C:ILE42 4.5 75.2 1.0
O C:HOH603 4.6 61.3 1.0
HA C:THR41 4.6 77.0 1.0
CG2 C:THR41 4.6 56.4 1.0
HG3 C:GLU55 4.7 72.8 1.0
HB3 C:ASP39 4.7 75.8 1.0
HA2 C:GLY44 4.7 77.1 1.0
HB2 C:ASP39 4.7 75.8 1.0
CE2 C:PHE49 4.8 57.4 1.0
HG21 C:THR41 4.8 68.3 1.0
ND2 C:ASN50 4.8 57.9 1.0
HG2 C:GLU55 4.9 72.8 1.0
CE1 C:HIS61 4.9 59.4 1.0
CA C:ILE42 4.9 62.1 1.0
H C:GLY45 4.9 75.7 1.0
HG23 C:THR41 5.0 68.3 1.0

Calcium binding site 5 out of 6 in 7cek

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Calcium binding site 5 out of 6 in the Crystal Structure of T2R-Ttl-Bml-284 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-Bml-284 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:98.2
occ:1.00
HG13 D:VAL175 3.2 96.9 1.0
O D:VAL175 3.7 79.9 1.0
HA D:THR221 4.1 95.4 1.0
CZ D:TYR222 4.1 72.2 1.0
O D:PRO220 4.1 80.7 1.0
CG1 D:VAL175 4.1 80.2 1.0
CE2 D:TYR222 4.2 73.0 1.0
HG12 D:VAL175 4.2 96.9 1.0
CE1 D:TYR222 4.3 72.5 1.0
HA D:VAL175 4.3 94.9 1.0
H D:TYR222 4.4 92.3 1.0
HE2 D:TYR222 4.4 88.2 1.0
CD2 D:TYR222 4.5 73.5 1.0
OH D:TYR222 4.5 74.2 1.0
HG11 D:VAL175 4.6 96.9 1.0
CD1 D:TYR222 4.6 71.6 1.0
HH D:TYR222 4.6 89.6 1.0
HE1 D:TYR222 4.7 87.7 1.0
CG D:TYR222 4.7 73.5 1.0
C D:VAL175 4.7 78.9 1.0
N D:TYR222 4.8 76.4 1.0
HD2 D:TYR222 4.9 88.9 1.0
CA D:VAL175 4.9 78.5 1.0
CA D:THR221 5.0 79.0 1.0

Calcium binding site 6 out of 6 in 7cek

Go back to Calcium Binding Sites List in 7cek
Calcium binding site 6 out of 6 in the Crystal Structure of T2R-Ttl-Bml-284 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-Bml-284 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca201

b:95.9
occ:1.00
OD2 E:ASP44 3.4 86.3 1.0
HZ1 A:LYS166 3.4 77.5 1.0
HG A:SER158 3.6 80.2 1.0
HZ3 A:LYS166 3.6 77.5 1.0
OG A:SER158 3.8 66.3 1.0
NZ A:LYS166 3.9 64.0 1.0
HA A:HIS197 4.0 74.8 1.0
HB3 A:SER158 4.1 80.1 1.0
HZ2 A:LYS166 4.2 77.5 1.0
O A:GLY162 4.4 73.6 1.0
CB A:SER158 4.5 66.2 1.0
HA A:SER158 4.5 78.5 1.0
CG E:ASP44 4.5 87.5 1.0
O A:GLU196 4.5 70.0 1.0
OD1 A:ASP199 4.7 62.0 1.0
CA A:HIS197 4.9 61.8 1.0
O A:HIS197 5.0 61.7 1.0

Reference:

L.J.Chen, Q.Chen, J.H.Yang, Y.Yu. Small Molecular Promote Selective Destabilization and Degradation of Tubular Heterodimers By Specific Charging of GLU198 of Beta-Tubulin Through A Low Barrier Hydrogen Bond To Be Published.
Page generated: Sat Jul 10 11:18:24 2021

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