Calcium in PDB 2vl8: Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp, Castanospermine and Calcium Ion

The structure of Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp, Castanospermine and Calcium Ion, PDB code: 2vl8 was solved by T.Jank, M.O.P.Ziegler, G.E.Schulz, K.Aktories, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	95.78 / 2.31
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.689, 191.332, 205.384, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 25.5

The binding sites of Calcium atom in the Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp, Castanospermine and Calcium Ion (pdb code 2vl8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp, Castanospermine and Calcium Ion, PDB code: 2vl8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp, Castanospermine 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, Castanospermine and Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1545 b:33.9 occ:1.00 OE1 A:GLU515 2.2 41.8 1.0 OD2 A:ASP288 2.3 35.3 1.0 O A:HOH2077 2.5 28.1 1.0 O2B A:UDP1543 2.5 48.3 1.0 O2A A:UDP1543 2.5 38.0 1.0 OG A:SER518 2.8 64.5 1.0 CG A:ASP288 3.3 33.7 1.0 CD A:GLU515 3.4 42.4 1.0 OD1 A:ASP288 3.6 36.2 1.0 PB A:UDP1543 3.6 50.1 1.0 PA A:UDP1543 3.7 41.8 1.0 CB A:SER518 3.9 65.2 1.0 O3B A:UDP1543 3.9 48.6 1.0 OE2 A:GLU515 3.9 42.7 1.0 O3A A:UDP1543 4.1 45.0 1.0 O A:HOH2135 4.2 40.5 1.0 O A:HOH2138 4.2 31.0 1.0 OD2 A:ASP286 4.4 33.3 1.0 O1A A:UDP1543 4.4 42.0 1.0 O2 A:CTS1544 4.4 41.5 1.0 CG A:GLU515 4.6 41.5 1.0 CA A:GLU515 4.6 42.3 1.0 CB A:ASP288 4.7 33.2 1.0 OE1 A:GLN385 4.7 27.4 1.0 CB A:GLU515 4.7 42.0 1.0 O1B A:UDP1543 4.9 48.4 1.0 O A:GLU515 4.9 44.6 1.0 O5' A:UDP1543 4.9 40.2 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp, Castanospermine 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, Castanospermine and Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1546 b:42.2 occ:1.00 OD1 A:ASP280 2.4 36.3 1.0 O A:HOH2074 2.4 31.5 1.0 OE2 B:GLU219 2.8 37.0 1.0 OE1 B:GLU219 3.0 38.4 1.0 CD B:GLU219 3.3 37.5 1.0 CG A:ASP280 3.5 35.5 1.0 OD2 A:ASP280 4.3 34.7 1.0 CA A:ASP280 4.3 32.3 1.0 O A:ASP280 4.3 32.0 1.0 NZ A:LYS128 4.4 31.6 1.0 CB A:ASP280 4.4 33.1 1.0 ND2 A:ASN97 4.7 29.6 1.0 CG B:GLU219 4.8 36.0 1.0 C A:ASP280 4.8 31.7 1.0 O A:GLU279 4.9 30.8 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp, Castanospermine 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, Castanospermine and Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1547 b:48.6 occ:1.00 OE2 A:GLU219 2.5 42.2 1.0 OE1 A:GLU219 2.8 42.5 1.0 CD A:GLU219 3.0 40.4 1.0 CG A:GLU219 4.5 38.6 1.0 NZ A:LYS223 4.9 50.0 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp, Castanospermine and Calcium Ion


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 the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp, Castanospermine and Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1545 b:40.0 occ:1.00 OE1 B:GLU515 2.3 36.7 1.0 O2B B:UDP1543 2.4 46.8 1.0 O B:HOH2081 2.4 34.8 1.0 O2A B:UDP1543 2.5 41.4 1.0 OD2 B:ASP288 2.5 34.9 1.0 OG B:SER518 2.6 49.8 1.0 CD B:GLU515 3.4 37.0 1.0 CG B:ASP288 3.5 34.4 1.0 PB B:UDP1543 3.7 50.1 1.0 PA B:UDP1543 3.7 43.5 1.0 CB B:SER518 3.8 52.7 1.0 OD1 B:ASP288 3.8 33.0 1.0 OE2 B:GLU515 3.9 36.9 1.0 O3A B:UDP1543 4.0 47.7 1.0 O B:HOH2129 4.1 30.5 1.0 O3B B:UDP1543 4.2 50.3 1.0 OD2 B:ASP286 4.3 28.1 1.0 O1A B:UDP1543 4.4 45.0 1.0 OE1 B:GLN385 4.5 27.7 1.0 CG B:GLU515 4.6 37.1 1.0 O2 B:CTS1544 4.6 49.5 1.0 CA B:GLU515 4.6 38.7 1.0 CB B:GLU515 4.8 38.5 1.0 CB B:ASP288 4.8 33.0 1.0 O1B B:UDP1543 4.8 48.6 1.0 O5' B:UDP1543 4.9 42.2 1.0 O B:SER518 4.9 54.5 1.0 O B:GLU515 4.9 39.4 1.0 C5' B:UDP1543 5.0 38.5 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp, Castanospermine and Calcium Ion


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 the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp, Castanospermine and Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1545 b:34.8 occ:1.00 OE1 C:GLU515 2.2 37.2 1.0 OD2 C:ASP288 2.2 24.8 1.0 O3B C:UDP1543 2.3 51.5 1.0 O C:HOH2076 2.4 23.5 1.0 O2A C:UDP1543 2.6 43.1 1.0 OG C:SER518 2.7 57.0 1.0 CG C:ASP288 3.3 30.7 1.0 CD C:GLU515 3.4 36.2 1.0 PB C:UDP1543 3.5 53.0 1.0 OD1 C:ASP288 3.6 28.9 1.0 O1B C:UDP1543 3.7 52.2 1.0 PA C:UDP1543 3.8 46.5 1.0 CB C:SER518 3.8 59.3 1.0 O C:HOH2075 3.9 39.3 1.0 OE2 C:GLU515 3.9 35.8 1.0 O3A C:UDP1543 4.1 49.5 1.0 O C:HOH2132 4.2 47.7 1.0 OD2 C:ASP286 4.3 28.8 1.0 O2 C:CTS1544 4.3 46.0 1.0 OE1 C:GLN385 4.4 27.8 1.0 O1A C:UDP1543 4.5 45.6 1.0 CB C:ASP288 4.6 30.7 1.0 CG C:GLU515 4.6 34.2 1.0 CA C:GLU515 4.6 35.0 1.0 O2B C:UDP1543 4.7 52.1 1.0 CB C:GLU515 4.7 34.5 1.0 O C:GLU515 5.0 36.4 1.0

T.Jank, M.O.P.Ziegler, G.E.Schulz, K.Aktories. Inhibition of the Glucosyltransferase Activity of Clostridial Rho/Ras-Glucosylating Toxins By Castanospermine. Febs Lett. V. 582 2277 2008.
ISSN: ISSN 0014-5793
PubMed: 18505687
DOI: 10.1016/J.FEBSLET.2008.05.025