Cadmium in PDB 5bza: Crystal Structure of Cbsa From Thermotoga Neapolitana

All present enzymatic activity of Crystal Structure of Cbsa From Thermotoga Neapolitana:
3.2.1.52;

The structure of Crystal Structure of Cbsa From Thermotoga Neapolitana, PDB code: 5bza was solved by N.C.Ha, J.S.Kim, B.Y.Yoon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.74 / 2.00
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	158.965, 158.965, 517.242, 90.00, 90.00, 120.00
R / Rfree (%)	23.8 / 27.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 33;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of Cbsa From Thermotoga Neapolitana (pdb code 5bza). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 33 binding sites of Cadmium where determined in the Crystal Structure of Cbsa From Thermotoga Neapolitana, PDB code: 5bza:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 33 in the Crystal Structure of Cbsa From Thermotoga Neapolitana


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Cbsa From Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd501 b:64.3 occ:1.00 OD2 A:ASP245 2.9 19.1 1.0 NE2 A:HIS161 3.0 23.7 1.0 CD2 A:HIS161 3.5 17.2 1.0 OD1 A:ASP245 3.5 21.1 1.0 CG A:ASP245 3.6 16.2 1.0 CE1 A:HIS161 4.1 16.4 1.0 NH2 A:ARG130 4.4 12.8 1.0 CG A:HIS161 4.7 16.6 1.0 O A:HOH683 4.8 20.2 1.0 ND1 A:HIS161 5.0 18.6 1.0

Cadmium binding site 2 out of 33 in the Crystal Structure of Cbsa From Thermotoga Neapolitana


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Cbsa From Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd502 b:69.5 occ:1.00 OD2 A:ASP171 2.5 35.0 1.0 ND1 A:HIS173 2.6 38.5 1.0 OD1 A:ASP171 2.7 30.7 1.0 CG A:ASP171 2.9 33.4 1.0 CG A:HIS173 3.2 33.3 1.0 CB A:HIS173 3.4 38.5 1.0 CE1 A:HIS173 3.4 36.3 1.0 CD2 A:HIS173 4.1 32.2 1.0 NE2 A:HIS173 4.2 37.6 1.0 CB A:ASP171 4.3 34.1 1.0 N A:HIS173 4.3 33.9 1.0 CA A:HIS173 4.5 35.5 1.0

Cadmium binding site 3 out of 33 in the Crystal Structure of Cbsa From Thermotoga Neapolitana


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Cbsa From Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd503 b:0.8 occ:1.00 OE2 A:GLU189 2.8 40.5 1.0 OE1 A:GLU189 2.8 37.0 1.0 CD A:GLU189 3.1 33.2 1.0 OE2 A:GLU185 3.2 30.6 1.0 CD A:GLU185 3.7 28.2 1.0 CG A:GLU185 3.9 22.0 1.0 NH2 A:ARG188 4.1 39.5 1.0 NZ A:LYS167 4.4 19.1 1.0 CE A:LYS167 4.4 20.8 1.0 CG A:GLU189 4.6 25.6 1.0 OE1 A:GLU185 4.7 30.1 1.0

Cadmium binding site 4 out of 33 in the Crystal Structure of Cbsa From Thermotoga Neapolitana


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Cbsa From Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd504 b:98.2 occ:1.00 OE2 A:GLU234 2.8 50.0 1.0 OE1 A:GLU234 2.9 39.0 1.0 CD A:GLU234 3.2 39.9 1.0 CG A:GLU230 4.0 31.4 1.0 CG2 A:THR229 4.5 23.0 1.0 CD A:GLU230 4.6 48.3 1.0 OE2 A:GLU230 4.6 58.3 1.0 CG A:GLU234 4.7 30.4 1.0

Cadmium binding site 5 out of 33 in the Crystal Structure of Cbsa From Thermotoga Neapolitana


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Cbsa From Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd505 b:60.7 occ:1.00 OE1 A:GLU327 2.7 25.9 1.0 O A:HOH618 2.8 19.7 1.0 OE2 A:GLU327 2.8 31.4 1.0 NH1 A:ARG54 2.9 44.7 1.0 CD A:GLU327 3.1 23.3 1.0 NH2 A:ARG54 3.1 38.1 1.0 CZ A:ARG54 3.1 45.3 1.0 OE2 A:GLU330 3.2 34.8 1.0 OE1 A:GLU330 3.2 37.4 1.0 CD A:GLU330 3.3 29.6 1.0 NE A:ARG54 4.0 47.2 1.0 CG A:GLU330 4.4 15.8 1.0 O A:HOH688 4.6 24.4 1.0 CG A:GLU327 4.6 18.6 1.0 ND2 A:ASN50 4.6 18.9 1.0 CD A:ARG54 4.8 37.1 1.0 CB A:GLU330 4.9 15.4 1.0

Cadmium binding site 6 out of 33 in the Crystal Structure of Cbsa From Thermotoga Neapolitana


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Cbsa From Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd506 b:21.4 occ:1.00 OE2 A:GLU346 2.1 9.3 1.0 O A:HOH737 2.3 12.8 1.0 OE2 A:GLU398 2.6 19.9 1.0 OE1 A:GLU398 2.7 17.2 1.0 CD A:GLU398 3.0 17.6 1.0 CD A:GLU346 3.1 14.1 1.0 CG A:GLU346 3.4 13.4 1.0 NH2 A:ARG381 4.0 15.8 1.0 OE1 A:GLU346 4.3 15.9 1.0 CG A:GLU398 4.5 18.8 1.0 N A:GLU346 4.5 16.4 1.0 CB A:GLU346 4.5 15.4 1.0 NZ A:LYS379 4.8 16.5 1.0

Cadmium binding site 7 out of 33 in the Crystal Structure of Cbsa From Thermotoga Neapolitana


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Cbsa From Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd507 b:78.8 occ:1.00 NE2 A:HIS448 2.7 18.9 1.0 NZ B:LYS86 2.8 34.8 1.0 OE2 A:GLU334 3.2 32.6 1.0 CD2 A:HIS448 3.6 16.6 1.0 CE1 A:HIS448 3.7 16.4 1.0 CE B:LYS86 4.0 27.5 1.0 CD B:LYS86 4.2 18.1 1.0 CB A:PRO433 4.4 27.3 1.0 CD A:GLU334 4.4 33.5 1.0 CG A:PRO433 4.8 33.0 1.0 CG A:HIS448 4.8 14.9 1.0 ND1 A:HIS448 4.8 16.3 1.0 CG B:LYS86 4.8 16.3 1.0 CG2 A:ILE446 4.8 14.2 1.0 CD1 A:ILE446 4.9 18.9 1.0

Cadmium binding site 8 out of 33 in the Crystal Structure of Cbsa From Thermotoga Neapolitana


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Cbsa From Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd508 b:95.3 occ:1.00 NE2 A:HIS461 2.3 38.3 1.0 O A:HOH754 3.0 28.5 1.0 NH1 A:ARG465 3.1 58.8 1.0 CE1 A:HIS461 3.1 33.4 1.0 CZ A:ARG465 3.1 56.6 1.0 NE A:ARG465 3.2 50.7 1.0 CD A:ARG465 3.2 54.8 1.0 CD2 A:HIS461 3.3 35.8 1.0 O A:HOH603 3.5 25.2 1.0 O A:ILE333 3.8 18.4 1.0 NH2 A:ARG465 3.9 51.6 1.0 ND1 A:HIS461 4.2 33.0 1.0 O A:GLU330 4.3 16.3 1.0 CG A:HIS461 4.3 27.4 1.0 O A:HOH739 4.5 35.7 1.0 CG A:ARG465 4.7 46.0 1.0 C A:ILE333 4.9 17.5 1.0

Cadmium binding site 9 out of 33 in the Crystal Structure of Cbsa From Thermotoga Neapolitana


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Cbsa From Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd501 b:74.3 occ:1.00 NE2 B:HIS448 2.7 18.8 1.0 O B:HOH699 3.1 36.1 1.0 OE2 B:GLU334 3.4 31.6 1.0 CE A:LYS86 3.4 25.0 1.0 NZ A:LYS86 3.5 25.2 1.0 CE1 B:HIS448 3.6 18.4 1.0 CD2 B:HIS448 3.7 18.9 1.0 CD B:GLU334 4.1 32.1 1.0 CD A:LYS86 4.1 18.3 1.0 O A:HOH756 4.2 24.6 1.0 CB B:PRO433 4.3 27.3 1.0 OE1 B:GLU334 4.4 30.1 1.0 CG B:PRO433 4.7 25.8 1.0 ND1 B:HIS448 4.8 19.5 1.0 CG B:HIS448 4.8 18.6 1.0 CG A:LYS86 4.9 20.9 1.0 CD1 B:ILE446 5.0 23.1 1.0 CG2 B:ILE446 5.0 18.2 1.0

Cadmium binding site 10 out of 33 in the Crystal Structure of Cbsa From Thermotoga Neapolitana


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of Cbsa From Thermotoga Neapolitana within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd502 b:48.2 occ:1.00 NE2 B:HIS161 2.7 12.9 1.0 OD2 B:ASP245 2.9 15.8 1.0 CD2 B:HIS161 3.3 13.2 1.0 CG B:ASP245 3.8 15.8 1.0 CE1 B:HIS161 3.8 13.5 1.0 OD1 B:ASP245 3.9 20.1 1.0 NH2 B:ARG130 4.4 13.8 1.0 CG B:HIS161 4.6 16.6 1.0 ND1 B:HIS161 4.7 14.7 1.0 O B:HOH689 4.9 12.8 1.0

J.S.Kim, B.Y.Yoon, J.Ahn, J.Cha, N.C.Ha. Crystal Structure of Beta-N-Acetylglucosaminidase Cbsa From Thermotoga Neapolitana Biochem.Biophys.Res.Commun. V. 464 869 2015.
ISSN: ESSN 1090-2104
PubMed: 26187666
DOI: 10.1016/J.BBRC.2015.07.053