Sodium in PDB 6gz8: First Germn Domain of the Sporulation Protein Germ From Bacillus Subtilis

The structure of First Germn Domain of the Sporulation Protein Germ From Bacillus Subtilis, PDB code: 6gz8 was solved by J.Trouve, A.Mohamed, F.Leisico, C.Contreras-Martel, B.Liu, C.Mas, D.Z.Rudner, C.D.A.Rodrigues, C.Morlot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.32 / 1.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.360, 53.601, 64.861, 90.00, 90.00, 90.00
R / Rfree (%)	13.5 / 15.4

Pages:

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

Binding sites:

The binding sites of Sodium atom in the First Germn Domain of the Sporulation Protein Germ From Bacillus Subtilis (pdb code 6gz8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 11 binding sites of Sodium where determined in the First Germn Domain of the Sporulation Protein Germ From Bacillus Subtilis, PDB code: 6gz8:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 11 in the First Germn Domain of the Sporulation Protein Germ From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of First Germn Domain of the Sporulation Protein Germ From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:8.6 occ:1.00 O A:ILE178 2.3 9.0 1.0 O A:PHE175 2.4 9.0 1.0 O A:THR173 2.4 8.4 1.0 O A:HOH520 2.4 11.0 1.0 H A:ILE178 3.4 8.3 1.0 C A:ILE178 3.4 8.0 1.0 C A:THR173 3.4 7.8 1.0 C A:PHE175 3.5 8.4 1.0 HA A:ASP179 3.6 9.4 1.0 HA A:THR173 3.6 8.1 1.0 HB A:THR173 3.9 8.1 1.0 HA A:SER176 3.9 12.2 1.0 N A:PHE175 4.0 8.3 1.0 C A:GLN174 4.0 8.1 1.0 CA A:THR173 4.0 7.9 1.0 N A:ILE178 4.2 8.2 1.0 O A:HOH513 4.2 26.9 1.0 H A:PHE175 4.2 7.7 1.0 HB A:ILE178 4.2 8.2 1.0 O A:GLN174 4.2 9.0 1.0 HB3 A:ASP179 4.2 9.4 1.0 N A:ASP179 4.3 8.0 1.0 CA A:PHE175 4.3 8.2 1.0 CA A:ILE178 4.3 7.9 1.0 N A:SER176 4.3 9.2 1.0 CA A:ASP179 4.4 8.9 1.0 CA A:SER176 4.4 11.3 1.0 N A:GLN174 4.4 8.0 1.0 C A:SER176 4.4 8.8 1.0 HA A:GLN174 4.5 8.1 1.0 CB A:THR173 4.5 8.2 1.0 O A:SER176 4.5 9.3 1.0 CA A:GLN174 4.6 8.0 1.0 CB A:ASP179 4.8 9.8 1.0 CB A:ILE178 4.8 8.1 1.0 HG21 A:THR173 4.9 8.8 1.0 N A:SER177 5.0 8.4 1.0 HA A:PHE175 5.0 8.5 1.0 HG21 A:ILE178 5.0 8.5 1.0

Sodium binding site 2 out of 11 in the First Germn Domain of the Sporulation Protein Germ From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of First Germn Domain of the Sporulation Protein Germ From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:28.9 occ:1.00 O A:ASN87 2.7 11.2 1.0 O A:HOH460 2.8 25.3 1.0 HA3 A:GLY88 3.2 8.9 1.0 HZ2 A:LYS163 3.6 12.4 1.0 C A:ASN87 3.8 10.2 1.0 CA A:GLY88 4.0 9.5 1.0 HZ3 A:LYS163 4.1 12.2 1.0 C A:GLY88 4.1 9.8 1.0 O A:GLY88 4.3 10.4 1.0 HH A:TYR89 4.3 62.0 0.0 NZ A:LYS163 4.3 12.2 1.0 N A:GLY88 4.4 9.5 1.0 CZ A:TYR89 4.4 39.6 1.0 CE1 A:TYR89 4.4 49.2 1.0 HB3 A:ASN87 4.6 13.7 1.0 CE2 A:TYR89 4.6 38.8 1.0 HE1 A:TYR89 4.7 44.0 1.0 OH A:TYR89 4.7 66.7 1.0 N A:TYR89 4.7 9.8 1.0 HA2 A:GLY88 4.8 9.8 1.0 CD1 A:TYR89 4.8 31.6 1.0 HZ1 A:LYS163 4.8 11.9 1.0 CD2 A:TYR89 4.9 26.2 1.0 HE2 A:TYR89 4.9 39.2 1.0

Sodium binding site 3 out of 11 in the First Germn Domain of the Sporulation Protein Germ From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of First Germn Domain of the Sporulation Protein Germ From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:19.7 occ:1.00 O A:LYS99 2.8 11.2 1.0 NA A:NA304 3.1 17.8 1.0 HA A:SER100 3.1 10.5 1.0 O A:HOH508 3.7 18.4 1.0 C A:LYS99 3.8 10.0 1.0 CA A:SER100 4.0 10.1 1.0 N A:SER100 4.3 10.5 1.0 H A:GLU101 4.4 12.9 1.0 HB3 A:LYS99 4.6 13.0 0.4 HB2 A:SER100 4.7 10.3 1.0 HB2 A:LYS99 4.7 13.3 0.6 HG2 A:LYS99 4.8 19.9 0.4 CB A:SER100 4.9 10.4 1.0 C A:SER100 4.9 12.1 1.0 N A:GLU101 4.9 12.8 1.0 CA A:LYS99 5.0 10.6 0.4 CA A:LYS99 5.0 10.9 0.6

Sodium binding site 4 out of 11 in the First Germn Domain of the Sporulation Protein Germ From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of First Germn Domain of the Sporulation Protein Germ From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:17.8 occ:1.00 O A:LYS99 2.8 11.2 1.0 HB2 A:PRO98 2.9 9.5 1.0 NA A:NA303 3.1 19.7 1.0 HB2 A:SER100 3.4 10.3 1.0 HE22 A:GLN106 3.4 8.7 0.0 HE21 A:GLN106 3.6 8.7 0.0 HA A:SER100 3.7 10.5 1.0 O A:HOH415 3.7 11.8 1.0 NE2 A:GLN106 3.7 8.7 1.0 C A:LYS99 3.8 10.0 1.0 CB A:PRO98 3.9 10.0 1.0 HB3 A:PRO98 4.1 9.8 1.0 CB A:SER100 4.1 10.4 1.0 CA A:SER100 4.2 10.1 1.0 O A:PRO98 4.3 10.5 1.0 C A:PRO98 4.4 9.3 1.0 HG2 A:PRO98 4.5 10.8 1.0 N A:SER100 4.5 10.5 1.0 OG A:SER100 4.7 11.0 1.0 CD A:GLN106 4.7 8.4 1.0 N A:LYS99 4.7 9.8 1.0 CG A:PRO98 4.7 10.4 1.0 CA A:PRO98 4.8 9.0 1.0 HG3 A:GLN106 4.8 8.6 1.0 HD2 A:PRO98 4.8 9.7 1.0 HB3 A:SER100 4.9 10.5 1.0 HG A:SER100 4.9 10.9 0.0 O A:HOH508 4.9 18.4 1.0 CA A:LYS99 4.9 10.9 0.6 CA A:LYS99 4.9 10.6 0.4

Sodium binding site 5 out of 11 in the First Germn Domain of the Sporulation Protein Germ From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of First Germn Domain of the Sporulation Protein Germ From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:24.5 occ:1.00 H A:THR103 2.1 8.5 1.0 HG23 A:THR103 2.8 11.3 1.0 N A:THR103 2.9 9.1 1.0 OG1 A:THR103 3.0 10.2 1.0 HA A:SER102 3.1 9.7 1.0 O A:HOH496 3.1 44.8 1.0 O A:GLU101 3.1 14.7 1.0 O A:HOH523 3.2 21.9 1.0 HG1 A:THR103 3.3 10.2 0.0 C A:GLU101 3.4 12.6 1.0 CG2 A:THR103 3.6 11.2 1.0 N A:SER102 3.6 10.0 1.0 CA A:SER102 3.6 9.5 1.0 CB A:THR103 3.7 9.2 1.0 C A:SER102 3.8 8.3 1.0 CA A:THR103 3.9 7.8 1.0 HG22 A:THR103 3.9 10.6 1.0 HA A:GLU101 4.0 15.0 1.0 O A:HOH438 4.0 36.3 1.0 H A:ALA104 4.1 8.1 1.0 H A:SER102 4.2 10.1 1.0 CA A:GLU101 4.3 14.6 1.0 O A:HOH519 4.3 16.1 1.0 O A:HOH458 4.3 20.0 1.0 HG21 A:THR103 4.4 11.2 1.0 O A:SER100 4.4 13.6 1.0 HA A:THR103 4.5 8.4 1.0 HB A:THR103 4.6 9.5 1.0 N A:ALA104 4.8 8.2 1.0 C A:THR103 4.9 8.1 1.0 O A:SER102 5.0 8.7 1.0 C A:SER100 5.0 12.1 1.0

Sodium binding site 6 out of 11 in the First Germn Domain of the Sporulation Protein Germ From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of First Germn Domain of the Sporulation Protein Germ From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:23.3 occ:1.00 H A:ALA131 1.9 8.5 1.0 HE22 A:GLN113 2.3 12.4 0.0 HA A:PRO130 2.8 7.9 1.0 N A:ALA131 2.9 8.3 1.0 NE2 A:GLN113 2.9 12.5 1.0 HE21 A:GLN113 2.9 12.4 0.0 O A:HOH536 3.0 21.8 1.0 O A:HOH556 3.0 34.7 1.0 HB1 A:ALA131 3.1 11.0 1.0 HB3 A:ALA131 3.3 11.4 1.0 HB2 A:GLN113 3.4 9.2 1.0 CB A:ALA131 3.5 11.1 1.0 CA A:PRO130 3.6 7.9 1.0 HB3 A:PRO130 3.7 8.3 1.0 C A:PRO130 3.7 7.7 1.0 CA A:ALA131 3.8 8.8 1.0 O A:HOH568 4.0 56.3 1.0 O A:HOH444 4.0 20.2 1.0 HB3 A:GLN113 4.0 8.0 1.0 CD A:GLN113 4.1 12.1 1.0 CB A:GLN113 4.1 8.7 1.0 CB A:PRO130 4.2 8.2 1.0 HA A:ALA131 4.3 9.1 1.0 HB2 A:ALA131 4.5 10.8 1.0 CG A:GLN113 4.6 11.2 1.0 O A:HOH549 4.6 24.4 1.0 O A:HOH436 4.6 13.4 1.0 O A:LEU129 4.7 8.1 1.0 HB2 A:PRO130 4.8 8.2 1.0 N A:PRO130 4.8 7.6 1.0 O A:PRO130 4.9 7.8 1.0 HG3 A:GLN113 4.9 10.7 1.0 C A:ALA131 4.9 8.8 1.0 HG3 A:PRO130 5.0 9.0 1.0

Sodium binding site 7 out of 11 in the First Germn Domain of the Sporulation Protein Germ From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of First Germn Domain of the Sporulation Protein Germ From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:21.9 occ:1.00 H A:LYS86 2.0 10.1 1.0 HB2 A:ASP85 2.7 10.6 1.0 HB3 A:LYS86 2.8 14.4 1.0 O A:HOH559 2.9 34.1 1.0 N A:LYS86 2.9 11.1 1.0 HG2 A:LYS86 3.0 18.5 1.0 HA3 A:GLY124 3.0 13.5 1.0 HA A:ASP85 3.3 9.4 1.0 HD3 A:LYS86 3.4 28.0 1.0 O A:ASN123 3.4 16.4 1.0 CB A:LYS86 3.5 14.5 1.0 HE1 A:PHE125 3.5 18.8 1.0 CE1 A:PHE125 3.5 18.2 1.0 CG A:LYS86 3.5 18.2 1.0 CB A:ASP85 3.5 10.3 1.0 C A:GLY124 3.6 11.1 1.0 O A:GLY124 3.6 11.9 1.0 CD1 A:PHE125 3.6 14.2 1.0 HD1 A:PHE125 3.6 16.3 1.0 CA A:GLY124 3.7 12.9 1.0 CA A:ASP85 3.8 9.1 1.0 CA A:LYS86 3.8 11.1 1.0 C A:ASP85 3.8 10.1 1.0 CD A:LYS86 4.0 27.1 1.0 N A:PHE125 4.1 10.2 1.0 CZ A:PHE125 4.1 17.1 1.0 HB3 A:ASP85 4.1 10.5 1.0 HA A:PHE125 4.2 9.1 1.0 HA A:LYS86 4.2 11.4 1.0 CG A:PHE125 4.3 11.8 1.0 HB2 A:LYS86 4.3 13.9 1.0 C A:ASN123 4.4 12.9 1.0 HA2 A:GLY124 4.4 12.8 1.0 HE2 A:LYS86 4.4 45.2 1.0 HG3 A:LYS86 4.4 19.3 1.0 CG A:ASP85 4.5 10.4 1.0 H A:PHE125 4.5 10.1 1.0 HZ A:PHE125 4.5 16.7 1.0 O A:HOH476 4.5 36.4 1.0 N A:GLY124 4.5 14.1 1.0 CA A:PHE125 4.6 8.8 1.0 H A:ASN87 4.7 10.5 1.0 HD2 A:LYS86 4.7 28.3 1.0 NA A:NA308 4.7 29.0 1.0 CE2 A:PHE125 4.7 19.0 1.0 CE A:LYS86 4.8 43.4 1.0 CD2 A:PHE125 4.8 14.7 1.0 OD2 A:ASP85 4.9 12.8 1.0 O A:ASP85 5.0 9.5 1.0

Sodium binding site 8 out of 11 in the First Germn Domain of the Sporulation Protein Germ From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of First Germn Domain of the Sporulation Protein Germ From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na308 b:29.0 occ:1.00 OD2 A:ASP85 2.7 12.8 1.0 O A:HOH559 2.9 34.1 1.0 HG22 A:VAL91 2.9 20.3 1.0 HG12 A:VAL91 3.1 19.2 1.0 HZ A:PHE125 3.1 16.7 1.0 HB2 A:ASP85 3.2 10.6 1.0 HB3 A:ASP85 3.3 10.5 1.0 CB A:ASP85 3.5 10.3 1.0 CG A:ASP85 3.5 10.4 1.0 CZ A:PHE125 3.8 17.1 1.0 CG2 A:VAL91 3.9 19.0 1.0 O A:HOH408 3.9 47.1 1.0 CG1 A:VAL91 4.0 18.4 1.0 HB A:VAL91 4.2 17.0 1.0 CB A:VAL91 4.3 16.3 1.0 HG21 A:VAL91 4.4 19.9 1.0 HE1 A:PHE125 4.4 18.8 1.0 HG23 A:VAL91 4.4 15.5 1.0 HG13 A:VAL91 4.4 18.8 1.0 CE1 A:PHE125 4.5 18.2 1.0 HE2 A:PHE125 4.5 19.6 1.0 HG11 A:VAL91 4.6 17.6 1.0 CE2 A:PHE125 4.6 19.0 1.0 OD1 A:ASP85 4.7 10.5 1.0 NA A:NA307 4.7 21.9 1.0 H A:LYS86 5.0 10.1 1.0

Sodium binding site 9 out of 11 in the First Germn Domain of the Sporulation Protein Germ From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of First Germn Domain of the Sporulation Protein Germ From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na309 b:19.6 occ:1.00 O A:SER177 2.7 8.6 1.0 O A:LYS140 2.7 13.2 1.0 H A:GLY143 2.8 13.0 1.0 HB2 A:SER177 2.9 10.3 1.0 HA2 A:GLY143 3.0 11.4 1.0 HG21 A:ILE139 3.0 10.8 1.0 HA A:LYS141 3.4 14.3 1.0 N A:GLY143 3.5 12.2 1.0 HG22 A:ILE139 3.6 11.0 1.0 CG2 A:ILE139 3.6 11.7 1.0 HG23 A:ILE139 3.7 12.5 1.0 CA A:GLY143 3.7 11.2 1.0 C A:SER177 3.7 7.8 1.0 C A:LYS140 3.8 10.9 1.0 CB A:SER177 3.8 10.1 1.0 HA A:SER177 3.8 7.8 1.0 C A:LYS141 4.0 13.7 1.0 CA A:SER177 4.1 8.2 1.0 CA A:LYS141 4.1 14.3 1.0 O A:LYS141 4.1 19.1 1.0 HA3 A:GLY143 4.4 11.9 1.0 HB3 A:SER177 4.4 9.7 1.0 N A:LYS141 4.4 12.1 1.0 C A:GLY143 4.6 9.8 1.0 OG A:SER177 4.6 14.7 1.0 N A:ASP142 4.7 14.2 1.0 C A:ASP142 4.7 13.6 1.0 HA A:ILE178 4.8 8.1 1.0 HG A:SER177 4.8 14.6 0.0 N A:LYS140 4.9 10.2 1.0 N A:ILE178 4.9 8.2 1.0 CA A:LYS140 5.0 10.4 1.0

Sodium binding site 10 out of 11 in the First Germn Domain of the Sporulation Protein Germ From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of First Germn Domain of the Sporulation Protein Germ From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na310 b:18.3 occ:1.00 HH21 A:ARG79 2.3 14.6 1.0 HE A:ARG79 2.4 14.0 1.0 HG12 A:VAL77 2.7 13.1 0.5 OE1 A:GLN106 2.7 9.6 1.0 HG13 A:VAL77 2.8 11.1 0.5 O A:PRO98 2.9 10.5 1.0 CG1 A:VAL77 3.0 12.8 0.5 NH2 A:ARG79 3.1 15.2 1.0 HG21 A:THR103 3.1 11.2 1.0 HG11 A:VAL77 3.1 13.5 0.5 NE A:ARG79 3.2 16.0 1.0 HB A:VAL77 3.2 11.6 0.5 HB2 A:LEU97 3.4 10.4 1.0 HB3 A:SER100 3.4 10.5 1.0 HA A:LYS99 3.4 10.9 0.6 HA A:LYS99 3.4 10.7 0.4 O A:HOH525 3.5 16.5 1.0 HE21 A:GLN106 3.5 8.7 0.0 O A:HOH469 3.6 9.6 1.0 CZ A:ARG79 3.6 12.8 1.0 HG22 A:VAL77 3.6 11.8 0.5 CD A:GLN106 3.7 8.4 1.0 HH22 A:ARG79 3.7 14.5 1.0 H A:SER100 3.7 10.5 1.0 HG3 A:ARG79 3.8 11.2 1.0 C A:PRO98 3.9 9.3 1.0 CG2 A:THR103 3.9 11.2 1.0 HG22 A:THR103 4.0 10.6 1.0 NE2 A:GLN106 4.0 8.7 1.0 CB A:VAL77 4.0 11.6 0.5 N A:SER100 4.0 10.5 1.0 HB3 A:LEU97 4.0 10.0 1.0 HG23 A:VAL77 4.1 11.8 0.5 HB2 A:SER100 4.1 10.3 1.0 CG2 A:VAL77 4.1 11.8 0.5 CB A:SER100 4.2 10.4 1.0 CA A:LYS99 4.2 10.9 0.6 CB A:LEU97 4.2 10.2 1.0 CA A:LYS99 4.2 10.6 0.4 HG2 A:ARG79 4.2 10.9 1.0 HG12 A:VAL77 4.2 11.7 0.5 O A:LEU97 4.3 11.4 1.0 HB A:THR103 4.3 9.5 1.0 CG A:ARG79 4.3 11.1 1.0 C A:LYS99 4.3 10.0 1.0 CD A:ARG79 4.4 13.2 1.0 HD11 A:LEU97 4.4 11.6 1.0 HA A:THR103 4.5 8.4 1.0 N A:LYS99 4.5 9.8 1.0 CB A:VAL77 4.5 13.3 0.5 C A:LEU97 4.5 9.8 1.0 HG23 A:THR103 4.6 11.3 1.0 CG1 A:VAL77 4.6 12.1 0.5 CB A:THR103 4.6 9.2 1.0 CA A:SER100 4.8 10.1 1.0 HG22 A:VAL77 4.8 13.7 0.5 HE22 A:GLN106 4.9 8.7 0.0 HD2 A:ARG79 4.9 13.1 1.0 NH1 A:ARG79 4.9 12.4 1.0 HG11 A:VAL77 4.9 11.4 0.5 HB3 A:GLN106 4.9 7.6 1.0 HB A:VAL77 4.9 12.5 0.5 HG21 A:VAL77 4.9 13.8 0.5 N A:PRO98 5.0 9.4 1.0 H A:VAL77 5.0 9.7 1.0 HD3 A:ARG79 5.0 13.3 1.0 CA A:LEU97 5.0 9.9 1.0

J.Trouve, A.Mohamed, F.Leisico, C.Contreras-Martel, B.Liu, C.Mas, D.Z.Rudner, C.D.A.Rodrigues, C.Morlot. Structural Characterization of the Sporulation Protein Germ From Bacillus Subtilis. J. Struct. Biol. V. 204 481 2018.
ISSN: ESSN 1095-8657
PubMed: 30266596
DOI: 10.1016/J.JSB.2018.09.010