Calcium in PDB 7dp8: Crystal Structure of T2R-Ttl-Cevipabulin-Eribulin Complex

Protein crystallography data

The structure of Crystal Structure of T2R-Ttl-Cevipabulin-Eribulin Complex, PDB code: 7dp8 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) 59.46 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 103.937, 159.071, 176.236, 90, 90, 90
R / Rfree (%) 22.7 / 26.4

Other elements in 7dp8:

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

Chlorine (Cl) 2 atoms
Fluorine (F) 10 atoms
Magnesium (Mg) 5 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of T2R-Ttl-Cevipabulin-Eribulin Complex (pdb code 7dp8). 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-Cevipabulin-Eribulin Complex, PDB code: 7dp8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7dp8

Go back to Calcium Binding Sites List in 7dp8
Calcium binding site 1 out of 6 in the Crystal Structure of T2R-Ttl-Cevipabulin-Eribulin 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-Cevipabulin-Eribulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:82.0
occ:1.00
OG1 A:THR41 2.2 86.8 1.0
OE2 A:GLU55 2.4 78.3 1.0
OD2 A:ASP39 2.5 75.5 1.0
O A:THR41 2.5 76.6 1.0
O A:GLY44 2.5 73.2 1.0
OE1 A:GLU55 2.6 72.1 1.0
OD1 A:ASP39 2.6 75.1 1.0
CD A:GLU55 2.8 74.7 1.0
CG A:ASP39 2.9 73.5 1.0
CB A:THR41 3.2 78.9 1.0
HB A:THR41 3.2 94.9 1.0
HA3 A:GLY45 3.2 91.0 1.0
C A:THR41 3.5 75.1 1.0
C A:GLY44 3.6 71.7 1.0
HZ A:PHE49 3.6 79.0 1.0
H A:THR41 3.7 98.7 1.0
HD21 A:ASN50 3.7 80.4 1.0
CA A:THR41 3.8 80.8 1.0
H A:GLY44 3.9 93.9 1.0
CA A:GLY45 4.0 75.7 1.0
OD2 A:ASP47 4.0 70.0 1.0
HE1 A:PHE49 4.1 85.2 1.0
OD1 A:ASN50 4.1 72.1 1.0
N A:THR41 4.1 82.1 1.0
N A:GLY45 4.2 75.0 1.0
CG A:GLU55 4.3 72.9 1.0
CZ A:PHE49 4.3 65.6 1.0
CB A:ASP39 4.4 82.2 1.0
NE2 A:HIS61 4.4 71.4 1.0
ND2 A:ASN50 4.4 66.9 1.0
HA2 A:GLY45 4.4 91.0 1.0
CG2 A:THR41 4.5 75.9 1.0
CE1 A:PHE49 4.6 70.8 1.0
HG2 A:GLU55 4.6 87.7 1.0
HG21 A:THR41 4.6 91.2 1.0
HG3 A:GLU55 4.6 87.7 1.0
N A:GLY44 4.6 78.1 1.0
HA A:THR41 4.7 97.2 1.0
N A:ILE42 4.7 79.3 1.0
HB2 A:ASP39 4.7 98.8 1.0
CG A:ASN50 4.7 72.4 1.0
CA A:GLY44 4.7 71.0 1.0
HG23 A:THR41 4.8 91.2 1.0
HB3 A:ASP39 4.8 98.8 1.0
HA A:ILE42 4.8 97.2 1.0
HD2 A:HIS61 4.9 85.5 1.0

Calcium binding site 2 out of 6 in 7dp8

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Calcium binding site 2 out of 6 in the Crystal Structure of T2R-Ttl-Cevipabulin-Eribulin 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-Cevipabulin-Eribulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:96.5
occ:1.00
O A:HOH617 2.5 76.1 1.0
HG A:SER158 3.5 74.8 1.0
O A:HOH618 3.6 72.7 1.0
OD2 E:ASP44 3.7 76.3 1.0
OG A:SER158 3.7 62.2 1.0
O A:GLY162 3.9 77.7 1.0
HZ1 A:LYS166 4.1 72.0 1.0
HZ3 A:LYS166 4.2 72.0 1.0
HA A:HIS197 4.2 71.7 1.0
HB3 A:SER158 4.3 71.4 1.0
HA A:SER158 4.5 78.0 1.0
CB A:SER158 4.5 59.4 1.0
NZ A:LYS166 4.6 59.9 1.0
O A:GLU196 4.8 64.3 1.0
CG E:ASP44 4.9 86.4 1.0
HZ2 A:LYS166 4.9 72.0 1.0
HA2 A:GLY162 4.9 83.0 1.0
C A:GLY162 5.0 72.7 1.0

Calcium binding site 3 out of 6 in 7dp8

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Calcium binding site 3 out of 6 in the Crystal Structure of T2R-Ttl-Cevipabulin-Eribulin 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-Cevipabulin-Eribulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:101.8
occ:1.00
HB3 B:ASP114 3.9 72.4 1.0
OD2 B:ASP118 4.2 61.6 1.0
OD1 B:ASP118 4.4 62.3 1.0
CG B:ASP118 4.8 71.2 1.0
CB B:ASP114 4.8 60.2 1.0

Calcium binding site 4 out of 6 in 7dp8

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Calcium binding site 4 out of 6 in the Crystal Structure of T2R-Ttl-Cevipabulin-Eribulin 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-Cevipabulin-Eribulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca505

b:94.7
occ:1.00
OE1 B:GLU111 2.7 83.8 1.0
CD B:GLU111 3.8 79.1 1.0
OE1 B:GLU108 4.3 55.6 1.0
OE2 B:GLU111 4.4 80.0 1.0
HB2 B:GLU111 4.8 83.0 1.0
CG B:GLU111 4.9 68.0 1.0
HG3 B:GLU111 5.0 81.8 1.0

Calcium binding site 5 out of 6 in 7dp8

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Calcium binding site 5 out of 6 in the Crystal Structure of T2R-Ttl-Cevipabulin-Eribulin 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-Cevipabulin-Eribulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca604

b:75.1
occ:1.00
H C:GLY43 2.4 71.3 1.0
OE1 C:GLU55 2.5 56.1 1.0
HA C:ILE42 2.5 69.2 1.0
HA2 C:GLY59 2.7 58.1 1.0
HB3 C:GLU55 2.9 60.2 1.0
N C:GLY43 3.2 59.3 1.0
HG23 C:ILE42 3.3 72.6 1.0
CA C:ILE42 3.4 57.5 1.0
NE2 C:HIS61 3.5 50.8 1.0
CD C:GLU55 3.5 55.8 1.0
O C:THR41 3.6 62.4 1.0
CA C:GLY59 3.6 48.3 1.0
CB C:GLU55 3.8 50.0 1.0
C C:ILE42 3.8 57.6 1.0
HG2 C:GLU55 3.8 65.6 1.0
HG22 C:ILE42 3.9 72.6 1.0
O C:THR56 3.9 47.2 1.0
CG2 C:ILE42 3.9 60.4 1.0
CG C:GLU55 3.9 54.5 1.0
C C:GLY59 3.9 54.0 1.0
O C:GLY59 4.0 50.0 1.0
H C:GLY59 4.1 64.3 1.0
H C:GLY44 4.1 70.5 1.0
OD2 C:ASP39 4.1 54.5 1.0
HB2 C:GLU55 4.2 60.2 1.0
CD2 C:HIS61 4.2 51.1 1.0
HA3 C:GLY59 4.2 58.1 1.0
CE1 C:HIS61 4.2 56.6 1.0
CB C:ILE42 4.2 63.0 1.0
HA2 C:GLY43 4.3 74.7 1.0
CA C:GLY43 4.3 62.1 1.0
HG12 C:ILE42 4.3 77.0 1.0
HD2 C:HIS61 4.3 61.5 1.0
HE1 C:HIS61 4.3 68.2 1.0
N C:GLY59 4.3 53.4 1.0
N C:ILE42 4.4 61.6 1.0
C C:THR41 4.4 58.7 1.0
CA C:CA606 4.4 47.7 1.0
N C:GLY44 4.6 58.6 1.0
OE2 C:GLU55 4.6 61.6 1.0
N C:LYS60 4.7 48.1 1.0
O C:HOH724 4.7 53.1 1.0
HG21 C:ILE42 4.8 72.6 1.0
C C:GLY43 4.8 58.7 1.0
CG1 C:ILE42 4.8 64.0 1.0
H C:THR56 4.8 65.3 1.0
HA C:GLU55 4.9 64.9 1.0
HG3 C:GLU55 4.9 65.6 1.0
CA C:GLU55 4.9 54.0 1.0
H C:LYS60 4.9 58.0 1.0
CG C:ASP39 5.0 56.5 1.0
O C:LYS60 5.0 51.1 1.0

Calcium binding site 6 out of 6 in 7dp8

Go back to Calcium Binding Sites List in 7dp8
Calcium binding site 6 out of 6 in the Crystal Structure of T2R-Ttl-Cevipabulin-Eribulin 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-Cevipabulin-Eribulin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca606

b:47.7
occ:1.00
O C:THR41 2.2 62.4 1.0
OD2 C:ASP39 2.3 54.5 1.0
O C:GLY44 2.5 54.5 1.0
OE1 C:GLU55 2.5 56.1 1.0
OE2 C:GLU55 2.6 61.6 1.0
OG1 C:THR41 2.6 63.5 1.0
OD1 C:ASP39 2.8 58.6 1.0
CG C:ASP39 2.9 56.5 1.0
CD C:GLU55 2.9 55.8 1.0
C C:THR41 3.1 58.7 1.0
HB C:THR41 3.2 75.2 1.0
CB C:THR41 3.3 62.5 1.0
HA3 C:GLY45 3.5 65.5 1.0
C C:GLY44 3.6 54.7 1.0
CA C:THR41 3.7 62.3 1.0
H C:GLY44 3.7 70.5 1.0
HZ C:PHE49 3.8 60.6 1.0
H C:THR41 3.8 73.5 1.0
HE1 C:HIS61 4.1 68.2 1.0
N C:THR41 4.1 61.1 1.0
HD21 C:ASN50 4.1 64.7 1.0
N C:ILE42 4.2 61.6 1.0
HA C:ILE42 4.3 69.2 1.0
CA C:GLY45 4.3 54.4 1.0
N C:GLY45 4.3 58.6 1.0
OD1 C:ASP47 4.4 59.6 1.0
CB C:ASP39 4.4 55.1 1.0
N C:GLY44 4.4 58.6 1.0
CA C:CA604 4.4 75.1 1.0
CG C:GLU55 4.4 54.5 1.0
HE1 C:PHE49 4.5 60.5 1.0
CA C:GLY44 4.5 59.9 1.0
CZ C:PHE49 4.6 50.4 1.0
HA C:THR41 4.6 74.9 1.0
OD1 C:ASN50 4.6 50.2 1.0
HB3 C:ASP39 4.7 66.4 1.0
HA2 C:GLY44 4.7 72.1 1.0
CA C:ILE42 4.7 57.5 1.0
CE1 C:HIS61 4.7 56.6 1.0
HA2 C:GLY45 4.8 65.5 1.0
CG2 C:THR41 4.8 54.5 1.0
HB2 C:ASP39 4.8 66.4 1.0
HG3 C:GLU55 4.8 65.6 1.0
HG2 C:GLU55 4.8 65.6 1.0
H C:ILE42 4.9 74.1 1.0
ND2 C:ASN50 4.9 53.8 1.0
CE1 C:PHE49 4.9 50.2 1.0
HG21 C:THR41 4.9 65.7 1.0
H C:GLY43 5.0 71.3 1.0
HB2 C:GLU55 5.0 60.2 1.0

Reference:

J.Yang, Y.Yu, Y.Li, W.Yan, H.Ye, L.Niu, M.Tang, Z.Wang, Z.Yang, H.Pei, H.Wei, M.Zhao, J.Wen, L.Yang, L.Ouyang, Y.Wei, Q.Chen, W.Li, L.Chen. Cevipabulin-Tubulin Complex Reveals A Novel Agent Binding Site on Alpha-Tubulin with Tubulin Degradation Effect. Sci Adv V. 7 2021.
ISSN: ESSN 2375-2548
PubMed: 34138737
DOI: 10.1126/SCIADV.ABG4168
Page generated: Sat Jul 10 11:24:19 2021

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