Magnesium in PDB 4fk9: High Resolution Structure of the Catalytic Domain of Mannanase SACTE_2347 From Streptomyces Sp. Sirexaa-E

The structure of High Resolution Structure of the Catalytic Domain of Mannanase SACTE_2347 From Streptomyces Sp. Sirexaa-E, PDB code: 4fk9 was solved by J.F.Acheson, T.E.Takasuka, B.G.Fox, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.77 / 1.06
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.805, 102.360, 45.346, 90.00, 90.00, 90.00
R / Rfree (%)	11.9 / 13.2

The structure of High Resolution Structure of the Catalytic Domain of Mannanase SACTE_2347 From Streptomyces Sp. Sirexaa-E also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the High Resolution Structure of the Catalytic Domain of Mannanase SACTE_2347 From Streptomyces Sp. Sirexaa-E (pdb code 4fk9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the High Resolution Structure of the Catalytic Domain of Mannanase SACTE_2347 From Streptomyces Sp. Sirexaa-E, PDB code: 4fk9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the High Resolution Structure of the Catalytic Domain of Mannanase SACTE_2347 From Streptomyces Sp. Sirexaa-E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of High Resolution Structure of the Catalytic Domain of Mannanase SACTE_2347 From Streptomyces Sp. Sirexaa-E within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:12.4 occ:1.00 OD1 A:ASP283 2.0 15.3 1.0 O A:GLY276 2.1 13.0 1.0 O A:HOH619 2.1 16.0 1.0 O A:PRO284 2.1 11.8 1.0 O A:HOH579 2.1 14.4 1.0 OE1 A:GLU286 2.1 12.9 1.0 C A:GLY276 3.1 12.5 1.0 CG A:ASP283 3.2 16.1 1.0 CD A:GLU286 3.2 13.4 1.0 HA2 A:GLY276 3.2 14.7 1.0 C A:PRO284 3.3 11.6 1.0 H A:GLU286 3.4 13.2 1.0 OE2 A:GLU286 3.5 15.9 1.0 HD2 A:PRO284 3.6 15.7 1.0 CA A:GLY276 3.7 12.2 1.0 OD2 A:ASP283 3.7 17.9 1.0 HA A:ASP285 3.7 13.9 1.0 O A:HOH913 3.9 36.1 1.0 N A:PRO284 3.9 13.3 1.0 C A:ASP283 4.0 14.6 1.0 O A:HOH865 4.0 28.5 1.0 HA3 A:GLY276 4.1 14.7 1.0 O A:HOH593 4.1 20.9 1.0 HB2 A:PRO284 4.1 14.4 1.0 HA A:PRO277 4.1 17.4 1.0 CA A:PRO284 4.1 12.2 1.0 N A:PRO277 4.2 13.2 1.0 N A:GLU286 4.2 11.0 1.0 O A:HOH582 4.2 13.8 1.0 N A:ASP285 4.3 11.5 1.0 CD A:PRO284 4.3 13.1 1.0 O A:ASP283 4.3 15.0 1.0 CB A:ASP283 4.4 16.1 1.0 HA A:ASP283 4.4 19.3 1.0 HB3 A:GLU286 4.4 13.8 1.0 CA A:ASP285 4.4 11.6 1.0 CA A:PRO277 4.5 14.5 1.0 CA A:ASP283 4.5 16.1 1.0 CG A:GLU286 4.5 12.5 1.0 CB A:PRO284 4.6 12.0 1.0 C A:PRO277 4.6 14.9 1.0 HB3 A:ASP283 4.7 19.3 1.0 H A:ALA278 4.8 19.8 1.0 N A:ALA278 4.8 16.5 1.0 C A:ASP285 4.9 11.0 1.0 CB A:GLU286 4.9 11.5 1.0 N A:GLY276 4.9 11.7 1.0 HG2 A:GLU286 5.0 14.9 1.0

Magnesium binding site 2 out of 5 in the High Resolution Structure of the Catalytic Domain of Mannanase SACTE_2347 From Streptomyces Sp. Sirexaa-E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of High Resolution Structure of the Catalytic Domain of Mannanase SACTE_2347 From Streptomyces Sp. Sirexaa-E within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:11.2 occ:0.79 O A:HOH707 2.0 20.6 1.0 O A:HOH606 2.0 20.0 1.0 O A:HOH657 2.0 24.7 1.0 O A:HOH996 2.1 23.2 1.0 O A:HOH986 2.1 18.7 1.0 O A:HOH572 2.1 13.8 1.0 O A:HOH852 2.2 29.4 1.0 O A:HOH821 2.3 23.0 1.0 O A:HOH987 2.4 27.2 1.0 OD2 A:ASP169 4.1 9.8 1.0 O A:HOH655 4.1 20.8 1.0 O A:SER50 4.2 11.9 1.0 OD1 A:ASP169 4.2 8.0 1.0 O A:HOH701 4.2 20.0 1.0 O A:HOH584 4.3 17.8 1.0 HA2 A:GLY53 4.3 7.6 1.0 O A:HOH1003 4.3 38.0 1.0 O A:ALA52 4.4 8.8 1.0 O A:HOH717 4.4 31.3 1.0 HB3 A:GLN49 4.5 21.0 1.0 HB2 A:SER50 4.6 19.9 1.0 O A:HOH704 4.6 23.7 1.0 CG A:ASP169 4.6 7.7 1.0 HA3 A:GLY64 4.7 12.2 1.0 H A:SER50 4.7 16.6 1.0 OE1 A:GLN49 5.0 25.4 1.0

Magnesium binding site 3 out of 5 in the High Resolution Structure of the Catalytic Domain of Mannanase SACTE_2347 From Streptomyces Sp. Sirexaa-E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of High Resolution Structure of the Catalytic Domain of Mannanase SACTE_2347 From Streptomyces Sp. Sirexaa-E within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:10.8 occ:0.34 O A:HOH700 2.0 20.5 1.0 O A:HOH706 2.1 23.3 1.0 O A:HOH848 2.1 24.1 1.0 O A:HOH847 2.1 31.0 1.0 O A:HOH841 2.1 23.1 1.0 O A:HOH849 2.2 29.6 1.0 O A:HOH936 3.2 27.7 1.0 O A:HOH711 3.8 22.5 1.0 HG22 A:VAL222 4.1 10.8 1.0 OD1 A:ASP226 4.2 11.6 1.0 OD2 A:ASP226 4.4 10.7 1.0 O A:HOH691 4.4 24.4 1.0 HB1 A:ALA186 4.5 13.7 1.0 HB2 A:ALA186 4.5 13.7 1.0 HG13 A:VAL222 4.5 10.2 1.0 HA A:VAL222 4.6 8.8 1.0 HB3 A:ALA225 4.7 10.0 1.0 CG A:ASP226 4.7 9.4 1.0 HA A:ALA186 4.9 12.0 1.0 CB A:ALA186 4.9 11.4 1.0 HB1 A:ALA225 5.0 10.0 1.0

Magnesium binding site 4 out of 5 in the High Resolution Structure of the Catalytic Domain of Mannanase SACTE_2347 From Streptomyces Sp. Sirexaa-E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of High Resolution Structure of the Catalytic Domain of Mannanase SACTE_2347 From Streptomyces Sp. Sirexaa-E within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:26.1 occ:1.00 HD1 A:HIS36 1.9 22.8 0.5 HD1 A:HIS38 2.4 20.1 1.0 ND1 A:HIS36 2.5 19.0 0.5 HA A:HIS38 2.7 21.6 1.0 HB3 A:HIS36 3.0 24.1 0.5 O A:HOH597 3.0 15.6 1.0 ND1 A:HIS38 3.2 16.8 1.0 CE1 A:HIS36 3.3 18.8 0.5 CG A:HIS36 3.3 19.5 0.5 HE1 A:HIS36 3.5 22.5 0.5 HB2 A:HIS38 3.6 20.5 1.0 H A:HIS38 3.6 22.6 0.5 CA A:HIS38 3.6 18.0 1.0 CB A:HIS36 3.6 20.1 0.5 CB A:HIS38 3.9 17.1 1.0 CG A:HIS38 4.0 16.4 1.0 N A:HIS38 4.0 18.8 1.0 HB2 A:HIS36 4.1 24.1 0.5 CE1 A:HIS38 4.3 14.9 1.0 NE2 A:HIS36 4.3 18.9 0.5 CD2 A:HIS36 4.3 19.6 0.5 HE1 A:HIS38 4.4 17.9 1.0 C A:HIS38 4.7 17.9 1.0 HB3 A:HIS38 4.8 20.5 1.0 CA A:HIS36 4.9 20.9 0.5 C A:HIS36 4.9 20.0 0.5 O A:HIS36 4.9 19.9 0.5

Magnesium binding site 5 out of 5 in the High Resolution Structure of the Catalytic Domain of Mannanase SACTE_2347 From Streptomyces Sp. Sirexaa-E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of High Resolution Structure of the Catalytic Domain of Mannanase SACTE_2347 From Streptomyces Sp. Sirexaa-E within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:13.4 occ:1.00 HE A:ARG123 2.4 8.9 1.0 O A:HOH786 3.0 22.3 1.0 HG2 A:ARG123 3.1 8.2 1.0 NE A:ARG123 3.3 7.4 1.0 HG1 A:THR85 3.3 16.0 1.0 O A:HOH528 3.4 9.7 1.0 O A:HOH997 3.5 31.1 1.0 HB A:THR85 3.5 11.0 1.0 HH11 A:ARG123 3.6 9.9 1.0 OG1 A:THR85 3.6 13.3 1.0 HB2 A:ARG123 3.7 7.6 1.0 CG A:ARG123 3.8 6.8 1.0 CD A:ARG123 4.0 7.0 1.0 HD2 A:ARG123 4.1 8.4 1.0 CB A:THR85 4.1 9.2 1.0 CZ A:ARG123 4.2 7.3 1.0 NH1 A:ARG123 4.2 8.2 1.0 CB A:ARG123 4.3 6.3 1.0 O A:HOH568 4.6 10.2 1.0 O A:HOH907 4.6 39.7 0.5 HB3 A:ARG123 4.6 7.6 1.0 HD12 A:LEU88 4.6 10.7 1.0 HG3 A:ARG123 4.7 8.2 1.0 O A:THR85 4.8 8.0 1.0 HG22 A:THR85 4.8 12.6 1.0 HD3 A:ARG123 4.9 8.4 1.0 HG A:SER119 4.9 7.6 1.0 O A:HOH656 4.9 18.4 1.0 C A:THR85 5.0 7.4 1.0 HH12 A:ARG123 5.0 9.9 1.0

T.E.Takasuka, J.F.Acheson, C.M.Bianchetti, B.M.Prom, L.F.Bergeman, A.J.Book, C.R.Currie, B.G.Fox. Biochemical Properties and Atomic Resolution Structure of A Proteolytically Processed Beta-Mannanase From Cellulolytic Streptomyces Sp. Sirexaa-E. Plos One V. 9 94166 2014.
ISSN: ESSN 1932-6203
PubMed: 24710170
DOI: 10.1371/JOURNAL.PONE.0094166