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

The structure of Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp-Glc and Manganese Ion, PDB code: 2vkd 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)	90.17 / 2.53
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.287, 190.322, 204.419, 90.00, 90.00, 90.00
R / Rfree (%)	24.4 / 28.8

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

Manganese binding site 1 out of 5 in the Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp-Glc and Manganese Ion


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp-Glc and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1543 b:35.4 occ:1.00 O1A A:UPG1544 1.8 32.5 1.0 OE1 A:GLU515 1.9 37.7 1.0 O A:HOH2047 2.0 29.5 1.0 O A:HOH2046 2.0 32.3 1.0 O1B A:UPG1544 2.1 37.9 1.0 OD2 A:ASP288 2.5 21.3 1.0 CD A:GLU515 2.9 38.5 1.0 PA A:UPG1544 3.2 35.0 1.0 CG A:ASP288 3.3 22.1 1.0 OE2 A:GLU515 3.3 39.1 1.0 OD1 A:ASP288 3.3 22.9 1.0 PB A:UPG1544 3.4 38.3 1.0 O2' A:UPG1544 3.7 36.6 1.0 O3A A:UPG1544 3.8 37.2 1.0 O2A A:UPG1544 4.0 37.4 1.0 OD2 A:ASP286 4.0 16.8 1.0 CG A:GLU515 4.3 37.5 1.0 OE1 A:GLN385 4.3 17.5 1.0 O2B A:UPG1544 4.3 39.0 1.0 CA A:GLU515 4.4 37.7 1.0 O5C A:UPG1544 4.4 33.9 1.0 O A:GLU515 4.5 38.8 1.0 O3B A:UPG1544 4.5 37.7 1.0 O A:THR517 4.6 40.7 1.0 C5C A:UPG1544 4.6 33.2 1.0 CB A:GLU515 4.6 37.8 1.0 CB A:ASP288 4.8 21.9 1.0 C2' A:UPG1544 4.9 36.1 1.0 CE A:MET289 4.9 20.1 1.0 CG A:ASP286 4.9 18.7 1.0 C A:GLU515 4.9 38.3 1.0 CB A:ASP286 5.0 18.2 1.0

Manganese binding site 2 out of 5 in the Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp-Glc and Manganese Ion


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp-Glc and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1551 b:56.4 occ:1.00 OD1 A:ASP280 2.4 24.4 1.0 OE2 B:GLU219 2.5 46.0 1.0 CD B:GLU219 3.0 45.0 1.0 OE1 B:GLU219 3.2 45.7 1.0 CG A:ASP280 3.6 22.4 1.0 NZ A:LYS128 4.1 18.2 1.0 O A:ASP280 4.3 20.2 1.0 CG B:GLU219 4.3 43.5 1.0 OD2 A:ASP280 4.4 23.8 1.0 ND2 A:ASN97 4.4 18.0 1.0 CA A:ASP280 4.4 20.7 1.0 CB A:ASP280 4.6 21.2 1.0 C A:ASP280 4.9 20.1 1.0 OD1 A:ASN97 4.9 21.3 1.0

Manganese binding site 3 out of 5 in the Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp-Glc and Manganese Ion


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp-Glc and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1552 b:63.7 occ:1.00 OE1 A:GLU219 2.7 33.3 1.0 OE2 A:GLU219 2.8 34.1 1.0 CD A:GLU219 3.1 33.6 1.0 CG A:GLU219 4.6 32.7 1.0

Manganese binding site 4 out of 5 in the Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp-Glc and Manganese Ion


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp-Glc and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1541 b:35.3 occ:1.00 O1B B:UPG1544 2.0 41.3 1.0 O1A B:UPG1544 2.1 40.8 1.0 OE1 B:GLU515 2.2 39.6 1.0 OD2 B:ASP288 2.3 23.3 1.0 PB B:UPG1544 3.3 43.8 1.0 CG B:ASP288 3.3 23.9 1.0 CD B:GLU515 3.3 39.5 1.0 PA B:UPG1544 3.3 40.3 1.0 OD1 B:ASP288 3.6 25.0 1.0 O3A B:UPG1544 3.7 42.4 1.0 OE2 B:GLU515 3.8 38.8 1.0 O2' B:UPG1544 3.9 41.7 1.0 O2A B:UPG1544 4.1 41.6 1.0 O B:HOH2057 4.1 17.3 1.0 O2B B:UPG1544 4.1 42.4 1.0 O B:GLU515 4.3 41.5 1.0 OD2 B:ASP286 4.4 21.1 1.0 O3B B:UPG1544 4.4 42.2 1.0 CA B:GLU515 4.5 40.0 1.0 O5C B:UPG1544 4.5 38.9 1.0 CG B:GLU515 4.6 39.5 1.0 OE1 B:GLN385 4.6 16.6 1.0 C5C B:UPG1544 4.7 36.6 1.0 CB B:ASP288 4.7 23.0 1.0 O B:THR517 4.8 47.6 1.0 CB B:GLU515 4.8 39.7 1.0 C B:GLU515 4.9 41.2 1.0 C2' B:UPG1544 4.9 40.8 1.0

Manganese binding site 5 out of 5 in the Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp-Glc and Manganese Ion


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of the Catalytic Domain of Lethal Toxin From Clostridium Sordellii in Complex with Udp-Glc and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1542 b:31.3 occ:1.00 O C:HOH2044 2.1 28.9 1.0 OE1 C:GLU515 2.1 35.3 1.0 O1A C:UPG1544 2.2 30.9 1.0 OD2 C:ASP288 2.3 19.3 1.0 O1B C:UPG1544 2.3 35.6 1.0 CG C:ASP288 3.1 19.9 1.0 OD1 C:ASP288 3.2 21.1 1.0 CD C:GLU515 3.3 34.5 1.0 PB C:UPG1544 3.6 36.9 1.0 PA C:UPG1544 3.6 34.2 1.0 OE2 C:GLU515 3.9 34.0 1.0 O2' C:UPG1544 4.0 35.3 1.0 O3A C:UPG1544 4.1 35.6 1.0 OD2 C:ASP286 4.1 20.1 1.0 OE1 C:GLN385 4.3 13.4 1.0 CA C:GLU515 4.3 36.1 1.0 O2B C:UPG1544 4.4 38.8 1.0 O2A C:UPG1544 4.5 34.0 1.0 O C:GLU515 4.5 37.3 1.0 CG C:GLU515 4.5 35.2 1.0 CB C:ASP288 4.5 18.8 1.0 CB C:GLU515 4.6 35.8 1.0 O5C C:UPG1544 4.7 32.8 1.0 CE C:MET289 4.7 18.1 1.0 C5C C:UPG1544 4.8 31.3 1.0 O3B C:UPG1544 4.8 36.0 1.0 CG C:ASP286 4.8 17.9 1.0 CB C:ASP286 4.9 16.4 1.0 C C:GLU515 4.9 37.0 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