Calcium in PDB 6i5c: Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex

The structure of Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex, PDB code: 6i5c was solved by S.Basu, V.Olieric, N.Matsugaki, Y.Kawano, T.Takashi, C.Y.Huang, F.Leonarski, Y.Yamada, L.Vera, N.Olieric, J.Basquin, J.A.Wojdyla, K.Diederichs, M.Yamamoto, O.Bunk, M.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.46 / 2.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.240, 156.830, 179.540, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20.8

The structure of Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex also contains other interesting chemical elements:

Magnesium	(Mg)	3 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Calcium atom in the Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex (pdb code 6i5c). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex, PDB code: 6i5c:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:85.3 occ:1.00 O A:GLY44 2.4 77.6 1.0 OD1 A:ASP39 2.4 77.8 1.0 OD2 A:ASP39 2.4 92.6 1.0 OE2 A:GLU55 2.5 94.9 1.0 O A:HOH601 2.5 0.3 1.0 OE1 A:GLU55 2.6 90.0 1.0 O A:THR41 2.7 0.8 1.0 OG1 A:THR41 2.7 0.7 1.0 CG A:ASP39 2.8 76.6 1.0 CD A:GLU55 2.9 91.6 1.0 C A:GLY44 3.6 82.5 1.0 C A:THR41 3.7 0.8 1.0 CB A:THR41 3.7 81.8 1.0 O A:HOH606 4.0 91.1 1.0 CA A:THR41 4.1 85.3 1.0 CZ A:PHE49 4.2 84.4 1.0 CB A:ASP39 4.3 82.0 1.0 OD2 A:ASP47 4.3 92.0 1.0 CA A:GLY45 4.3 99.8 1.0 N A:THR41 4.3 85.3 1.0 OD1 A:ASN50 4.3 97.0 1.0 CG A:GLU55 4.4 93.0 1.0 N A:GLY45 4.4 89.4 1.0 N A:GLY44 4.6 89.6 1.0 CE1 A:PHE49 4.6 83.8 1.0 NE2 A:HIS61 4.6 95.4 1.0 CA A:GLY44 4.6 90.0 1.0 ND2 A:ASN50 4.7 73.3 1.0 N A:ILE42 4.9 0.6 1.0 CG A:ASN50 5.0 78.5 1.0

Calcium binding site 2 out of 5 in the Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:0.4 occ:1.00 O B:HOH625 2.5 63.5 1.0 OE2 B:GLU113 3.1 92.2 1.0 OE1 B:GLU113 3.4 96.3 1.0 CD B:GLU113 3.7 82.2 1.0 OE1 B:GLU110 4.8 64.5 1.0

Calcium binding site 3 out of 5 in the Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:94.4 occ:1.00 OE1 B:GLN11 2.4 70.7 1.0 O1A B:GDP501 2.4 53.4 1.0 O C:HOH792 2.4 80.5 1.0 O B:HOH613 2.4 75.0 1.0 O B:HOH689 2.5 50.6 1.0 O B:HOH614 2.9 80.9 1.0 CD B:GLN11 3.5 70.3 1.0 PA B:GDP501 3.7 55.3 1.0 O3A B:GDP501 3.9 53.0 1.0 OD2 B:ASP179 4.1 62.9 1.0 CB B:GLN11 4.1 67.8 1.0 OD1 B:ASN101 4.2 56.4 1.0 CG B:GLN11 4.3 67.7 1.0 O1B B:GDP501 4.5 43.0 1.0 NE2 B:GLN11 4.5 80.9 1.0 C5' B:GDP501 4.5 59.6 1.0 O5' B:GDP501 4.6 46.5 1.0 O2A B:GDP501 4.7 44.2 1.0 OE1 C:GLU254 4.7 76.4 1.0 O C:HOH772 4.8 69.2 1.0 PB B:GDP501 4.8 56.7 1.0 ND2 B:ASN101 4.9 60.4 1.0 CG B:ASN101 5.0 53.4 1.0

Calcium binding site 4 out of 5 in the Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:97.1 occ:1.00 O C:THR41 2.4 88.5 1.0 O C:GLY44 2.4 67.3 1.0 O C:HOH701 2.4 73.3 1.0 OD2 C:ASP39 2.5 67.7 1.0 OE2 C:GLU55 2.5 66.3 1.0 OE1 C:GLU55 2.5 66.6 1.0 OG1 C:THR41 2.5 89.7 1.0 OD1 C:ASP39 2.6 67.9 1.0 CD C:GLU55 2.8 70.6 1.0 CG C:ASP39 2.9 63.8 1.0 C C:THR41 3.4 81.7 1.0 CB C:THR41 3.5 85.9 1.0 C C:GLY44 3.6 65.5 1.0 CA C:THR41 3.9 81.9 1.0 N C:THR41 4.1 71.7 1.0 OD2 C:ASP47 4.2 92.0 1.0 O C:HOH706 4.2 62.4 1.0 CG C:GLU55 4.3 58.7 1.0 CA C:GLY45 4.4 73.6 1.0 CB C:ASP39 4.4 67.5 1.0 N C:GLY45 4.4 66.8 1.0 OD1 C:ASN50 4.4 78.0 1.0 N C:GLY44 4.4 74.2 1.0 CA C:GLY44 4.6 68.9 1.0 N C:ILE42 4.6 79.2 1.0 CZ C:PHE49 4.6 56.9 1.0 NE2 C:HIS61 4.7 70.0 1.0 O C:HOH824 4.8 73.0 1.0 CG2 C:THR41 4.9 66.5 1.0 ND2 C:ASN50 4.9 58.0 1.0 CE1 C:PHE49 4.9 63.5 1.0

Calcium binding site 5 out of 5 in the Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Long Wavelength Native-Sad Phasing of Tubulin-Stathmin-Ttl Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca502 b:0.7 occ:1.00 O D:HOH624 2.8 69.0 1.0 O1A D:GDP501 2.9 79.7 1.0 O D:HOH639 3.1 77.2 1.0 OE1 D:GLN11 3.1 76.3 1.0 OD1 D:ASN101 3.6 93.1 1.0 O D:HOH636 3.8 56.9 1.0 O3A D:GDP501 3.9 82.5 1.0 PA D:GDP501 4.0 75.0 1.0 ND2 D:ASN101 4.2 0.4 1.0 C5' D:GDP501 4.3 69.1 1.0 CG D:ASN101 4.3 91.1 1.0 CD D:GLN11 4.4 94.2 1.0 O5' D:GDP501 4.7 73.7 1.0

S.Basu, V.Olieric, F.Leonarski, N.Matsugaki, Y.Kawano, T.Takashi, C.Y.Huang, Y.Yamada, L.Vera, N.Olieric, J.Basquin, J.A.Wojdyla, O.Bunk, K.Diederichs, M.Yamamoto, M.Wang. Long-Wavelength Native-Sad Phasing: Opportunities and Challenges. Iucrj V. 6 373 2019.
ISSN: ESSN 2052-2525
PubMed: 31098019
DOI: 10.1107/S2052252519002756