Cadmium in PDB 6sc4: Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp.

The structure of Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp., PDB code: 6sc4 was solved by M.Vogler, R.Karan, D.Renn, A.Vancea, V.-T.Vielberg, S.W.Groetzinger, P.Dassarma, S.Das Sarma, J.Eppinger, M.Groll, M.Rueping, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.60
Space group	F 4 3 2 4
Cell size a, b, c (Å), α, β, γ (°)	362.640, 362.640, 362.640, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 20.4

The structure of Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp. also contains other interesting chemical elements:

Zinc	(Zn)	5 atoms
Sodium	(Na)	7 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Cadmium atom in the Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp. (pdb code 6sc4). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 13 binding sites of Cadmium where determined in the Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp., PDB code: 6sc4:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 13 in the Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd905 b:41.6 occ:1.00 O E:HOH1014 2.1 37.6 1.0 ND1 E:HIS172 2.3 44.8 1.0 OE2 A:GLU14 2.4 48.2 1.0 OE1 A:GLU14 2.5 49.7 1.0 CD A:GLU14 2.8 48.6 1.0 CE1 E:HIS172 3.2 45.7 1.0 CG E:HIS172 3.3 43.7 1.0 CB E:HIS172 3.6 42.4 1.0 O A:HOH1036 4.0 41.3 1.0 CA E:HIS172 4.3 41.8 1.0 CG A:GLU14 4.3 48.1 1.0 NE2 E:HIS172 4.3 45.6 1.0 CD2 E:HIS172 4.4 44.8 1.0 O E:HIS172 4.5 39.3 1.0 OE2 E:GLU176 4.6 66.9 1.0 C E:HIS172 4.8 40.4 1.0 NH1 E:ARG175 4.9 57.8 1.0

Cadmium binding site 2 out of 13 in the Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd906 b:43.5 occ:1.00 OE1 C:GLU6 2.1 48.0 1.0 O A:HOH1017 2.1 38.0 1.0 ND1 A:HIS172 2.2 47.2 1.0 OE2 E:GLU14 2.5 50.2 1.0 OE1 E:GLU14 2.6 47.0 1.0 CD C:GLU6 2.8 49.9 1.0 CD E:GLU14 2.9 47.1 1.0 OE2 C:GLU6 2.9 48.5 1.0 CE1 A:HIS172 3.1 47.5 1.0 CG A:HIS172 3.3 47.2 1.0 CB A:HIS172 3.7 45.9 1.0 CG C:GLU6 4.2 50.0 1.0 O A:HOH1067 4.2 58.7 1.0 NE2 A:HIS172 4.3 48.2 1.0 OE2 A:GLU176 4.4 62.4 1.0 CG E:GLU14 4.4 46.2 1.0 CD2 A:HIS172 4.4 47.1 1.0 CA A:HIS172 4.4 45.9 1.0 O A:HIS172 4.6 46.1 1.0 O C:HOH1061 4.6 44.0 1.0 O C:HOH1041 4.6 49.1 1.0 NH1 A:ARG175 4.6 59.6 1.0 C A:HIS172 4.9 46.1 1.0

Cadmium binding site 3 out of 13 in the Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd905 b:71.9 occ:1.00 OE1 D:GLU73 2.3 62.1 1.0 O B:HOH1058 2.4 40.9 1.0 O D:HOH1090 2.4 45.4 1.0 OD2 B:ASP100 2.6 49.9 1.0 OD1 B:ASP100 2.6 53.8 1.0 O B:HOH1075 2.8 58.5 1.0 CG B:ASP100 3.0 49.4 1.0 CD D:GLU73 3.2 61.8 1.0 OE2 D:GLU73 3.4 65.5 1.0 CB B:ASP100 4.5 47.8 1.0 CA B:GLY82 4.5 41.1 1.0 CG D:GLU73 4.6 59.2 1.0 O B:HOH1054 4.6 43.0 1.0 OD2 B:ASP83 4.7 44.5 1.0 N B:ASP83 4.7 40.9 1.0 CB D:GLU73 4.9 56.4 1.0 N B:ASP100 4.9 45.2 1.0 CG B:ASP83 4.9 42.5 1.0 C B:ASN99 5.0 44.3 1.0

Cadmium binding site 4 out of 13 in the Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd906 b:44.5 occ:1.00 ND1 C:HIS172 2.2 47.1 1.0 OE2 B:GLU6 2.5 49.3 1.0 O C:HOH1063 2.7 47.9 1.0 OE1 B:GLU6 2.8 50.5 1.0 CD B:GLU6 3.0 50.5 1.0 CE1 C:HIS172 3.1 48.1 1.0 CG C:HIS172 3.3 48.2 1.0 CB C:HIS172 3.6 48.2 1.0 O B:HOH1036 4.1 55.6 1.0 NE2 C:HIS172 4.3 48.3 1.0 CA C:HIS172 4.3 49.4 1.0 CD2 C:HIS172 4.4 47.8 1.0 O C:HIS172 4.4 51.6 1.0 CG B:GLU6 4.5 50.4 1.0 OE2 C:GLU176 4.7 73.7 1.0 C C:HIS172 4.8 50.0 1.0 NH1 C:ARG175 5.0 69.7 1.0

Cadmium binding site 5 out of 13 in the Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd907 b:69.5 occ:1.00 O D:HOH1103 2.4 37.7 1.0 OE1 B:GLU73 2.5 68.6 1.0 O B:HOH1021 2.6 56.8 1.0 OD2 D:ASP100 2.7 44.4 1.0 OD1 D:ASP100 2.7 41.4 1.0 CG D:ASP100 3.0 42.0 1.0 CD B:GLU73 3.2 67.9 1.0 OE2 B:GLU73 3.3 69.3 1.0 CA D:GLY82 4.4 33.1 1.0 CB D:ASP100 4.5 41.0 1.0 OD2 D:ASP83 4.5 36.0 1.0 O D:HOH1073 4.6 42.8 1.0 N D:ASP83 4.6 32.4 1.0 CG B:GLU73 4.6 65.8 1.0 N D:ASP100 4.9 39.0 1.0 C D:ASN99 4.9 37.9 1.0 CG D:ASP83 4.9 34.1 1.0

Cadmium binding site 6 out of 13 in the Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd908 b:94.4 occ:1.00 O D:HOH1038 2.3 39.0 1.0 ND1 B:HIS70 2.5 55.7 1.0 OE2 D:GLU133 2.7 50.0 1.0 OE1 D:GLU133 2.9 50.5 1.0 CD D:GLU133 3.1 48.1 1.0 CE1 B:HIS70 3.3 54.8 1.0 O B:HOH1072 3.5 55.3 1.0 CG B:HIS70 3.5 55.1 1.0 CB B:HIS70 3.8 55.3 1.0 NZ B:LYS131 4.0 64.3 1.0 NZ D:LYS117 4.4 45.0 1.0 NE2 B:HIS70 4.4 55.0 1.0 CD2 B:HIS70 4.5 55.6 1.0 CG D:GLU133 4.6 46.8 1.0 CE B:LYS131 4.8 63.0 1.0 O D:HOH1008 4.8 46.8 1.0 CE D:LYS117 4.9 43.6 1.0

Cadmium binding site 7 out of 13 in the Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd909 b:71.6 occ:1.00 OE2 B:GLU75 2.2 65.1 1.0 OE2 D:GLU115 2.3 44.3 1.0 NE2 B:HIS70 2.4 55.0 1.0 O B:HOH1017 2.7 55.0 1.0 OE1 D:GLU115 2.7 44.1 1.0 CD D:GLU115 2.8 42.5 1.0 CE1 B:HIS70 3.1 54.8 1.0 CD B:GLU75 3.1 61.0 1.0 O B:HOH1024 3.3 48.6 1.0 OE1 B:GLU75 3.5 60.6 1.0 CD2 B:HIS70 3.6 55.6 1.0 NZ D:LYS97 4.0 42.9 1.0 ND1 B:HIS70 4.3 55.7 1.0 CG D:GLU115 4.3 41.2 1.0 CG B:GLU75 4.3 58.9 1.0 O B:HOH1027 4.4 49.1 1.0 O B:HOH1072 4.5 55.3 1.0 CG B:HIS70 4.6 55.1 1.0 ND2 D:ASN99 4.6 36.8 1.0 NZ B:LYS113 4.6 58.1 1.0 CB B:GLU75 4.8 54.5 1.0

Cadmium binding site 8 out of 13 in the Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd910 b:77.7 occ:1.00 OE2 D:GLU75 2.1 55.7 1.0 OE2 B:GLU115 2.3 46.7 1.0 NE2 D:HIS70 2.4 49.6 1.0 OE1 B:GLU115 2.7 46.7 1.0 CD B:GLU115 2.9 45.6 1.0 CE1 D:HIS70 3.0 49.6 1.0 CD D:GLU75 3.2 55.7 1.0 O D:HOH1094 3.4 33.5 1.0 CD2 D:HIS70 3.5 48.2 1.0 OE1 D:GLU75 3.7 57.2 1.0 NZ D:LYS113 3.8 50.6 1.0 NZ B:LYS97 3.8 45.4 1.0 ND1 D:HIS70 4.2 49.9 1.0 CG B:GLU115 4.4 44.8 1.0 CG D:GLU75 4.4 53.0 1.0 O D:HOH1053 4.4 49.4 1.0 CG D:HIS70 4.5 47.6 1.0 CE D:LYS113 4.6 49.6 1.0 CB D:GLU75 4.7 48.5 1.0 ND2 B:ASN99 4.7 41.4 1.0 CG1 D:VAL68 4.8 37.5 1.0

Cadmium binding site 9 out of 13 in the Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp. within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd204 b:44.8 occ:1.00 OE2 C:GLU14 2.3 43.9 1.0 O C:HOH1052 2.4 30.6 1.0 OE1 C:GLU14 2.4 44.9 1.0 CD C:GLU14 2.7 44.2 1.0 CG C:GLU14 4.2 44.2 1.0

Cadmium binding site 10 out of 13 in the Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp. within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd201 b:98.5 occ:1.00 O B:HOH1012 2.2 36.3 1.0 ND1 D:HIS70 2.5 49.9 1.0 OE2 B:GLU133 2.8 61.3 1.0 OE1 B:GLU133 2.9 59.5 1.0 CD B:GLU133 3.2 58.8 1.0 O D:HOH1053 3.3 49.4 1.0 CE1 D:HIS70 3.4 49.6 1.0 CG D:HIS70 3.5 47.6 1.0 O D:HOH1092 3.7 46.1 1.0 NZ D:LYS131 3.8 60.5 1.0 CB D:HIS70 3.9 45.8 1.0 NE2 D:HIS70 4.5 49.6 1.0 CE D:LYS131 4.5 59.0 1.0 NZ B:LYS117 4.6 48.6 1.0 CD2 D:HIS70 4.6 48.2 1.0 CG B:GLU133 4.7 57.8 1.0

M.Vogler, R.Karan, D.Renn, A.Vancea, V.-T.Vielberg, S.W.Groetzinger, P.Dassarma, S.Das Sarma, J.Eppinger, M.Groll, M.Rueping. Crystal Structure and Active Site Engineering of A Halophilic Gamma-Carbonic Anhydrase Front Microbiol 2020.
ISSN: ESSN 1664-302X
DOI: 10.3389/FMICB.2020.00742