Cadmium in PDB 2w5e: Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 Angstrom Resolution

The structure of Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 Angstrom Resolution, PDB code: 2w5e was solved by S.Speroni, J.Rohayem, S.Nenci, D.Bonivento, I.Robel, J.Barthel, B.Coutard, B.Canard, A.Mattevi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.047, 135.047, 189.955, 90.00, 90.00, 120.00
R / Rfree (%)	23.4 / 25.8

The structure of Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 Angstrom Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

28 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Cadmium atom in the Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 Angstrom Resolution (pdb code 2w5e). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 18 binding sites of Cadmium where determined in the Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 Angstrom Resolution, PDB code: 2w5e:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 18 in the Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1587 b:27.9 occ:1.00 SG A:CYS515 2.2 31.2 1.0 ND1 A:HIS-5 2.4 30.4 1.0 NE2 A:HIS-3 2.4 23.9 1.0 CL A:CL1588 2.5 32.9 1.0 CB A:CYS515 3.2 29.4 1.0 CE1 A:HIS-5 3.2 30.7 1.0 CD2 A:HIS-3 3.3 23.6 1.0 CG A:HIS-5 3.4 29.5 1.0 CE1 A:HIS-3 3.4 24.4 1.0 CB A:HIS-5 3.7 28.8 1.0 CL A:CL1590 3.8 26.1 1.0 CA A:HIS-5 4.0 28.7 1.0 NE2 A:HIS-5 4.4 30.7 1.0 CG A:HIS-3 4.5 23.8 1.0 CD2 A:HIS-5 4.5 30.3 1.0 ND1 A:HIS-3 4.5 23.4 1.0 CA A:CYS515 4.6 29.4 1.0 C A:HIS-5 4.8 28.0 1.0 CB A:LYS558 4.8 27.4 1.0 N A:HIS-4 5.0 26.9 1.0

Cadmium binding site 2 out of 18 in the Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1589 b:23.2 occ:1.00 OE2 B:GLU474 1.9 23.1 1.0 ND1 F:HIS500 2.0 20.6 1.0 NE2 A:HIS-2 2.2 23.0 1.0 ND1 A:HIS-4 2.3 26.8 1.0 O A:HIS-4 2.4 24.0 1.0 CD B:GLU474 2.5 24.1 1.0 OE1 B:GLU474 2.5 21.5 1.0 CE1 F:HIS500 2.8 22.9 1.0 CG F:HIS500 3.1 22.9 1.0 CE1 A:HIS-2 3.2 23.8 1.0 CD2 A:HIS-2 3.2 22.6 1.0 CE1 A:HIS-4 3.3 26.8 1.0 CG A:HIS-4 3.3 26.2 1.0 C A:HIS-4 3.5 25.4 1.0 CB A:HIS-4 3.6 26.0 1.0 CB F:HIS500 3.6 24.3 1.0 CG B:GLU474 4.0 25.8 1.0 NE2 F:HIS500 4.0 21.7 1.0 CA A:HIS-4 4.1 25.8 1.0 CD2 F:HIS500 4.2 22.2 1.0 ND1 A:HIS-2 4.3 23.0 1.0 CG A:HIS-2 4.3 23.8 1.0 NE2 A:HIS-4 4.4 26.2 1.0 CD2 A:HIS-4 4.4 26.1 1.0 O B:HOH2019 4.5 23.2 1.0 N A:HIS-3 4.6 24.2 1.0 O B:HOH2017 4.9 23.3 1.0 CB B:GLU474 4.9 26.8 1.0 N A:HIS-4 4.9 26.9 1.0 O A:HOH2003 4.9 28.4 1.0 CA A:HIS-3 5.0 23.7 1.0

Cadmium binding site 3 out of 18 in the Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1591 b:58.9 occ:1.00 CL B:CL1587 2.7 39.3 1.0 SG B:CYS472 2.7 28.6 1.0 SD B:MET477 3.3 42.8 1.0 CB B:CYS472 3.4 27.9 1.0 CL A:CL1592 3.8 19.9 1.0 N A:LYS-7 4.0 35.2 1.0 CG B:MET477 4.0 36.6 1.0 CE B:MET477 4.4 42.7 1.0 CE1 A:HIS-6 4.4 31.2 1.0 ND1 A:HIS-6 4.5 30.4 1.0 CA B:CYS472 4.8 27.9 1.0 O B:HOH2012 5.0 54.9 1.0

Cadmium binding site 4 out of 18 in the Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1593 b:58.5 occ:1.00 CL B:CL1591 2.2 36.1 1.0 CL A:CL1594 2.2 29.3 1.0 ND1 B:HIS-6 2.6 31.5 1.0 SG A:CYS472 2.7 29.4 1.0 O A:HOH2021 3.0 26.1 1.0 CE1 B:HIS-6 3.1 31.6 1.0 N B:LYS-7 3.2 35.6 1.0 CB A:CYS472 3.5 27.8 1.0 CG B:HIS-6 3.9 32.4 1.0 CA B:LYS-7 4.0 35.4 1.0 N B:HIS-6 4.1 33.5 1.0 C B:LYS-7 4.3 34.6 1.0 NE2 B:HIS-6 4.4 32.5 1.0 CB B:HIS-6 4.5 32.2 1.0 O A:HOH2031 4.7 31.7 1.0 CD2 B:HIS-6 4.8 31.9 1.0 CA B:HIS-6 5.0 32.2 1.0 CA A:CYS472 5.0 27.8 1.0

Cadmium binding site 5 out of 18 in the Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd1588 b:26.1 occ:1.00 SG B:CYS515 2.3 30.9 1.0 ND1 B:HIS-5 2.3 30.9 1.0 NE2 B:HIS-3 2.4 24.5 1.0 CL B:CL1589 2.5 28.9 1.0 CB B:CYS515 3.2 28.8 1.0 CE1 B:HIS-5 3.2 31.3 1.0 CD2 B:HIS-3 3.2 23.3 1.0 CG B:HIS-5 3.4 29.4 1.0 CE1 B:HIS-3 3.5 24.7 1.0 CB B:HIS-5 3.8 28.9 1.0 CL B:CL1592 3.8 17.5 1.0 CA B:HIS-5 4.0 28.9 1.0 NE2 B:HIS-5 4.3 30.7 1.0 CG B:HIS-3 4.4 23.7 1.0 CD2 B:HIS-5 4.5 30.9 1.0 ND1 B:HIS-3 4.5 22.7 1.0 CA B:CYS515 4.6 28.7 1.0 CB B:LYS558 4.8 26.8 1.0 C B:HIS-5 4.8 28.1 1.0 N B:HIS-4 4.9 26.7 1.0

Cadmium binding site 6 out of 18 in the Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd1590 b:20.9 occ:1.00 OE2 A:GLU474 1.8 19.8 1.0 ND1 C:HIS500 2.0 20.2 1.0 NE2 B:HIS-2 2.3 22.4 1.0 ND1 B:HIS-4 2.4 24.5 1.0 O B:HIS-4 2.4 23.7 1.0 OE1 A:GLU474 2.5 23.2 1.0 CD A:GLU474 2.5 22.6 1.0 CE1 C:HIS500 2.9 23.0 1.0 CG C:HIS500 3.2 23.4 1.0 CD2 B:HIS-2 3.2 22.5 1.0 CE1 B:HIS-2 3.3 23.4 1.0 CG B:HIS-4 3.3 25.6 1.0 CE1 B:HIS-4 3.3 26.7 1.0 C B:HIS-4 3.5 24.6 1.0 CB B:HIS-4 3.5 25.1 1.0 CB C:HIS500 3.6 23.8 1.0 CG A:GLU474 3.9 24.9 1.0 NE2 C:HIS500 4.1 21.6 1.0 CA B:HIS-4 4.1 25.3 1.0 CD2 C:HIS500 4.2 22.2 1.0 CG B:HIS-2 4.3 23.5 1.0 ND1 B:HIS-2 4.3 22.9 1.0 O A:HOH2033 4.4 24.7 1.0 NE2 B:HIS-4 4.5 24.9 1.0 CD2 B:HIS-4 4.5 25.6 1.0 N B:HIS-3 4.6 23.7 1.0 O A:HOH2034 4.7 20.5 1.0 CB A:GLU474 4.8 26.4 1.0 N B:HIS-4 4.9 26.7 1.0 O B:HOH2004 4.9 26.5 1.0 CA B:HIS-3 4.9 23.6 1.0

Cadmium binding site 7 out of 18 in the Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd1587 b:26.6 occ:1.00 OE2 D:GLU474 1.8 22.1 1.0 ND1 E:HIS500 2.1 22.8 1.0 NE2 C:HIS-2 2.3 24.8 1.0 ND1 C:HIS-4 2.4 26.9 1.0 O C:HIS-4 2.5 26.0 1.0 CD D:GLU474 2.5 24.6 1.0 OE1 D:GLU474 2.5 24.0 1.0 CE1 E:HIS500 2.9 24.5 1.0 CD2 C:HIS-2 3.2 23.8 1.0 CG E:HIS500 3.2 24.4 1.0 CE1 C:HIS-2 3.3 25.0 1.0 CE1 C:HIS-4 3.3 27.0 1.0 CG C:HIS-4 3.4 26.9 1.0 C C:HIS-4 3.5 26.3 1.0 CB C:HIS-4 3.6 26.6 1.0 CB E:HIS500 3.7 25.1 1.0 CG D:GLU474 4.0 26.6 1.0 NE2 E:HIS500 4.1 23.2 1.0 CA C:HIS-4 4.2 26.7 1.0 CD2 E:HIS500 4.3 23.6 1.0 ND1 C:HIS-2 4.4 24.4 1.0 CG C:HIS-2 4.4 24.9 1.0 NE2 C:HIS-4 4.5 26.9 1.0 O D:HOH2018 4.5 25.2 1.0 CD2 C:HIS-4 4.5 27.2 1.0 N C:HIS-3 4.6 25.5 1.0 O D:HOH2019 4.7 25.1 1.0 CB D:GLU474 4.8 28.2 1.0 O C:HOH2003 4.8 35.3 1.0 N C:HIS-4 5.0 27.5 1.0 CA C:HIS-3 5.0 25.0 1.0

Cadmium binding site 8 out of 18 in the Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd1589 b:29.4 occ:1.00 SG C:CYS515 2.2 30.2 1.0 ND1 C:HIS-5 2.3 30.4 1.0 CL C:CL1588 2.4 34.1 1.0 NE2 C:HIS-3 2.5 24.7 1.0 CE1 C:HIS-5 3.2 31.4 1.0 CB C:CYS515 3.2 29.7 1.0 CD2 C:HIS-3 3.3 24.5 1.0 CG C:HIS-5 3.4 29.7 1.0 CE1 C:HIS-3 3.6 24.9 1.0 CB C:HIS-5 3.7 29.2 1.0 CL C:CL1590 3.8 28.4 1.0 CA C:HIS-5 4.0 29.2 1.0 NE2 C:HIS-5 4.3 31.1 1.0 CD2 C:HIS-5 4.5 30.1 1.0 CG C:HIS-3 4.5 24.7 1.0 ND1 C:HIS-3 4.6 24.5 1.0 CA C:CYS515 4.7 29.5 1.0 C C:HIS-5 4.8 28.8 1.0 CB C:LYS558 4.9 27.4 1.0 N C:HIS-4 5.0 27.5 1.0

Cadmium binding site 9 out of 18 in the Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd1592 b:68.3 occ:1.00 CL D:CL1587 2.5 52.5 1.0 SG D:CYS472 2.7 31.8 1.0 CL C:CL1591 3.0 33.2 1.0 CE1 C:HIS-6 3.3 32.1 1.0 CB D:CYS472 3.3 29.6 1.0 ND1 C:HIS-6 3.4 32.0 1.0 N C:LYS-7 3.9 36.0 1.0 SD D:MET477 3.9 43.8 1.0 NE2 C:HIS-6 4.6 32.5 1.0 O C:HOH2005 4.7 33.0 1.0 CG C:HIS-6 4.7 32.5 1.0 CA C:LYS-7 4.8 36.2 1.0 CA D:CYS472 4.8 29.8 1.0

Cadmium binding site 10 out of 18 in the Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd1594 b:55.4 occ:1.00 CL C:CL1593 2.3 41.8 1.0 SG C:CYS472 2.7 30.9 1.0 CL D:CL1593 2.8 38.1 1.0 CE1 D:HIS-6 3.0 30.6 1.0 ND1 D:HIS-6 3.2 31.2 1.0 CB C:CYS472 3.3 29.4 1.0 N D:LYS-7 3.8 35.1 1.0 NE2 D:HIS-6 4.3 32.5 1.0 SD C:MET477 4.4 44.1 1.0 CG D:HIS-6 4.5 31.5 1.0 CA C:CYS472 4.8 29.2 1.0 CB C:VAL439 4.8 27.3 1.0 O D:HOH2006 4.9 28.8 1.0 CA D:LYS-7 4.9 35.5 1.0 CG1 C:VAL439 4.9 27.4 1.0

S.Speroni, J.Rohayem, S.Nenci, D.Bonivento, I.Robel, J.Barthel, V.B.Luzhkov, B.Coutard, B.Canard, A.Mattevi. Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 A Resolution. J.Mol.Biol. V. 387 1137 2009.
ISSN: ISSN 0022-2836
PubMed: 19249313
DOI: 10.1016/J.JMB.2009.02.044