Sodium 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:

Cadmium	(Cd)	13 atoms
Zinc	(Zn)	5 atoms

The binding sites of Sodium 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 Sodium atom.
In total 7 binding sites of Sodium where determined in the Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp., PDB code: 6sc4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na903 b:52.1 occ:1.00 O A:HOH1004 2.3 38.5 1.0 OE2 A:GLU168 2.7 72.4 1.0 OE1 A:GLU171 2.7 66.3 1.0 OE1 A:GLU168 3.4 74.9 1.0 CD A:GLU168 3.4 70.4 1.0 CD A:GLU171 3.7 63.6 1.0 NH2 A:ARG175 3.9 60.4 1.0 OE2 A:GLU171 4.1 66.8 1.0 CG A:GLU168 4.9 64.6 1.0 CZ A:ARG175 5.0 59.4 1.0

Sodium binding site 2 out of 7 in the Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na903 b:50.5 occ:1.00 O B:HOH1004 2.3 47.0 1.0 OE2 B:GLU171 2.7 75.4 1.0 OE2 B:GLU168 3.0 65.3 1.0 OE1 B:GLU168 3.0 68.1 1.0 CD B:GLU168 3.4 64.7 1.0 CD B:GLU171 3.8 71.7 1.0 NH2 B:ARG175 3.8 69.8 1.0 OE1 B:GLU171 4.2 77.8 1.0 CG B:GLU168 4.9 59.7 1.0 CZ B:ARG175 5.0 68.3 1.0

Sodium binding site 3 out of 7 in the Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp. within 5.0Å range: probe atom residue distance (Å) B Occ C:Na203 b:45.9 occ:1.00 O C:HOH1004 2.3 42.3 1.0 OE2 C:GLU168 2.8 67.1 1.0 OE1 C:GLU171 2.9 75.5 1.0 OE1 C:GLU168 3.0 68.0 1.0 CD C:GLU168 3.3 64.4 1.0 NH2 C:ARG175 3.7 70.3 1.0 CD C:GLU171 3.9 70.8 1.0 OE2 C:GLU171 4.5 75.0 1.0 CG C:GLU168 4.8 59.1 1.0 CZ C:ARG175 4.8 68.7 1.0 CG C:GLU171 5.0 64.6 1.0

Sodium binding site 4 out of 7 in the Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp. within 5.0Å range: probe atom residue distance (Å) B Occ D:Na205 b:37.9 occ:1.00 O D:HOH1004 2.3 42.4 1.0 OE1 D:GLU168 2.6 56.1 1.0 OE1 D:GLU171 2.9 68.1 1.0 CD D:GLU168 3.4 53.8 1.0 OE2 D:GLU168 3.4 55.8 1.0 CD D:GLU171 3.7 64.8 1.0 NH2 D:ARG175 3.8 60.7 1.0 OE2 D:GLU171 4.0 71.3 1.0 CG D:GLU168 4.9 49.3 1.0 CG D:GLU171 4.9 57.6 1.0 CZ D:ARG175 4.9 59.3 1.0

Sodium binding site 5 out of 7 in the Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp. within 5.0Å range: probe atom residue distance (Å) B Occ E:Na903 b:46.1 occ:1.00 O E:HOH1078 2.3 69.5 1.0 OE2 E:GLU152 2.8 66.0 1.0 OE1 E:GLU152 2.8 64.5 1.0 CD E:GLU152 3.2 65.2 1.0 CG E:GLU152 4.7 62.9 1.0

Sodium binding site 6 out of 7 in the Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp. within 5.0Å range: probe atom residue distance (Å) B Occ E:Na904 b:35.9 occ:1.00 O E:HOH1003 2.1 45.1 1.0 O E:HOH1002 2.2 39.7 1.0 OD2 E:ASP100 2.7 41.0 1.0 OD1 E:ASP100 3.2 38.5 1.0 CG E:ASP100 3.3 39.1 1.0 CB E:ASP100 4.8 38.4 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Gamma-Carbonic Anhydrase From the Haloarchaeon Halobacterium Sp. within 5.0Å range: probe atom residue distance (Å) B Occ E:Na905 b:57.0 occ:1.00 O E:HOH1030 2.3 58.4 1.0 O E:HOH1007 2.4 49.9 1.0 OE1 E:GLU168 2.9 66.7 1.0 OE2 E:GLU171 3.0 66.6 1.0 CD E:GLU171 3.7 64.1 1.0 CD E:GLU168 3.7 62.7 1.0 OE2 E:GLU168 3.7 65.9 1.0 OE1 E:GLU171 3.8 71.4 1.0 NH2 E:ARG175 4.0 58.1 1.0 CG E:GLU171 4.9 57.4 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