Calcium in PDB 2vkh: Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp-Glc and Calcium Ion

The structure of Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp-Glc and Calcium Ion, PDB code: 2vkh was solved by M.O.P.Ziegler, T.Jank, K.Aktories, G.E.Schulz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.17 / 2.3
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.170, 188.590, 203.100, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 27.3

The binding sites of Calcium atom in the Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp-Glc and Calcium Ion (pdb code 2vkh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp-Glc and Calcium Ion, PDB code: 2vkh:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp-Glc and Calcium Ion


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 Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp-Glc and Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1543 b:27.8 occ:1.00 O A:HOH2064 2.3 25.4 1.0 OD2 A:ASP288 2.4 37.2 1.0 O1A A:UPG1544 2.4 33.7 1.0 OG A:SER518 2.4 39.7 1.0 O1B A:UPG1544 2.5 38.2 1.0 OE1 A:GLU515 2.7 36.5 1.0 CB A:SER518 3.4 41.8 1.0 CG A:ASP288 3.5 31.5 1.0 PA A:UPG1544 3.6 32.7 1.0 O2' A:UPG1544 3.6 41.7 1.0 PB A:UPG1544 3.6 40.7 1.0 O3B A:UPG1544 3.8 39.7 1.0 CD A:GLU515 3.8 36.7 1.0 OD1 A:ASP288 3.9 33.3 1.0 O3A A:UPG1544 4.0 35.1 1.0 O2A A:UPG1544 4.2 31.8 1.0 OE2 A:GLU515 4.4 36.4 1.0 C1' A:UPG1544 4.4 41.0 1.0 O A:GLU515 4.5 35.7 1.0 C2' A:UPG1544 4.6 41.1 1.0 CA A:GLU515 4.6 35.5 1.0 CA A:SER518 4.7 42.3 1.0 OD2 A:ASP286 4.7 31.6 1.0 OE1 A:GLN385 4.7 21.2 1.0 CB A:ASP288 4.7 28.2 1.0 C A:SER518 4.8 44.0 1.0 O5C A:UPG1544 4.8 32.1 1.0 O A:SER518 4.8 44.7 1.0 O2B A:UPG1544 4.9 40.1 1.0 OE1 A:GLN514 5.0 42.3 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp-Glc and Calcium Ion


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 the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp-Glc and Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1543 b:28.3 occ:1.00 O1A B:UPG1544 2.5 33.5 1.0 OE1 B:GLU515 2.6 39.0 1.0 OG B:SER518 2.6 33.1 1.0 O1B B:UPG1544 2.6 38.5 1.0 OD2 B:ASP288 2.7 30.7 1.0 CD B:GLU515 3.5 35.8 1.0 O2' B:UPG1544 3.6 41.9 1.0 CB B:SER518 3.7 36.4 1.0 PB B:UPG1544 3.7 40.8 1.0 OE2 B:GLU515 3.7 38.7 1.0 CG B:ASP288 3.7 28.7 1.0 O3B B:UPG1544 3.7 40.0 1.0 PA B:UPG1544 3.7 33.0 1.0 OD1 B:ASP288 4.0 32.2 1.0 O3A B:UPG1544 4.2 35.3 1.0 O B:HOH2060 4.2 30.6 1.0 O2A B:UPG1544 4.4 32.2 1.0 OE1 B:GLN385 4.5 22.0 1.0 O B:SER518 4.5 39.2 1.0 OD2 B:ASP286 4.6 25.9 1.0 C1' B:UPG1544 4.7 41.2 1.0 C2' B:UPG1544 4.7 41.6 1.0 O B:GLU515 4.7 32.6 1.0 CA B:GLU515 4.8 32.5 1.0 CG B:GLU515 4.8 33.3 1.0 O5C B:UPG1544 4.8 32.6 1.0 O2B B:UPG1544 4.9 40.4 1.0 CA B:SER518 4.9 37.0 1.0 C5C B:UPG1544 4.9 29.2 1.0 C B:SER518 5.0 38.2 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp-Glc and Calcium Ion


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 the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp-Glc and Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1543 b:29.9 occ:1.00 OG C:SER518 2.4 33.6 1.0 O C:HOH2044 2.5 17.2 1.0 O1A C:UPG1544 2.5 29.5 1.0 O1B C:UPG1544 2.5 32.2 1.0 OE1 C:GLU515 2.5 36.1 1.0 OD2 C:ASP288 2.5 22.5 1.0 O2' C:UPG1544 3.4 39.6 1.0 CB C:SER518 3.5 36.0 1.0 CD C:GLU515 3.6 30.2 1.0 CG C:ASP288 3.6 23.4 1.0 PB C:UPG1544 3.6 33.8 1.0 PA C:UPG1544 3.8 29.2 1.0 O3B C:UPG1544 3.9 35.3 1.0 OD1 C:ASP288 3.9 21.4 1.0 OE2 C:GLU515 3.9 31.0 1.0 O C:HOH2045 4.0 39.8 1.0 O3A C:UPG1544 4.1 27.2 1.0 O C:HOH2075 4.4 25.4 1.0 C1' C:UPG1544 4.4 37.4 1.0 O2A C:UPG1544 4.4 29.1 1.0 C2' C:UPG1544 4.5 37.5 1.0 OE1 C:GLN385 4.5 21.1 1.0 OD2 C:ASP286 4.6 24.3 1.0 CA C:GLU515 4.7 28.2 1.0 O C:GLU515 4.8 28.3 1.0 CA C:SER518 4.8 36.2 1.0 CG C:GLU515 4.9 28.3 1.0 CB C:ASP288 4.9 22.4 1.0 C C:SER518 4.9 38.0 1.0 O5C C:UPG1544 4.9 30.3 1.0 O2B C:UPG1544 4.9 33.0 1.0

M.O.P.Ziegler, T.Jank, K.Aktories, G.E.Schulz. Conformational Changes and Reaction of Clostridial Glycosylating Toxins. J.Mol.Biol. V. 377 1346 2008.
ISSN: ISSN 0022-2836
PubMed: 18325534
DOI: 10.1016/J.JMB.2007.12.065