Potassium in PDB 4h5j: Crystal Structure of the Guanine Nucleotide Exchange Factor SEC12 (P64 Form)

The structure of Crystal Structure of the Guanine Nucleotide Exchange Factor SEC12 (P64 Form), PDB code: 4h5j was solved by C.Mcmahon, P.D.Jeffrey, F.M.Hughson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.37 / 2.60
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	189.473, 189.473, 53.424, 90.00, 90.00, 120.00
R / Rfree (%)	17.9 / 21.6

The binding sites of Potassium atom in the Crystal Structure of the Guanine Nucleotide Exchange Factor SEC12 (P64 Form) (pdb code 4h5j). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Crystal Structure of the Guanine Nucleotide Exchange Factor SEC12 (P64 Form), PDB code: 4h5j:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in the Crystal Structure of the Guanine Nucleotide Exchange Factor SEC12 (P64 Form)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of the Guanine Nucleotide Exchange Factor SEC12 (P64 Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:K401 b:30.1 occ:1.00 O A:GLY34 2.5 24.8 1.0 OD1 A:ASN36 2.7 28.1 1.0 O A:ASP68 2.8 38.4 1.0 O A:GLY32 2.8 32.1 1.0 O A:ILE38 3.0 31.7 1.0 CG A:ASN36 3.5 23.9 1.0 C A:GLY34 3.7 25.4 1.0 ND2 A:ASN36 3.8 16.7 1.0 C A:ASP68 3.8 32.4 1.0 C A:GLY32 4.0 23.4 1.0 N A:GLY34 4.0 21.5 1.0 C A:GLU33 4.1 25.2 1.0 CA A:ASP68 4.2 28.9 1.0 C A:ILE38 4.2 29.2 1.0 N A:ASN36 4.2 21.0 1.0 ND2 A:ASN40 4.2 31.2 1.0 CA A:GLY34 4.4 17.9 1.0 O A:GLU33 4.4 28.9 1.0 CB A:ASP68 4.4 32.0 1.0 CA A:GLU33 4.6 27.5 1.0 N A:ILE38 4.7 28.0 1.0 CB A:ASN36 4.7 25.2 1.0 N A:GLU33 4.7 25.1 1.0 N A:ASN35 4.7 22.6 1.0 N A:GLY32 4.9 25.2 1.0 CA A:ASN35 4.9 24.1 1.0 CA A:ILE38 4.9 26.8 1.0 CA A:ASN36 4.9 20.7 1.0 CG A:ASN40 4.9 29.4 1.0 N A:GLY37 5.0 23.0 1.0 OD1 A:ASP68 5.0 50.8 1.0 C A:GLY31 5.0 24.2 1.0

Potassium binding site 2 out of 6 in the Crystal Structure of the Guanine Nucleotide Exchange Factor SEC12 (P64 Form)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of the Guanine Nucleotide Exchange Factor SEC12 (P64 Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:K402 b:41.3 occ:1.00 OG A:SER72 2.8 24.8 1.0 OD2 A:ASP71 2.9 27.4 1.0 O A:SER72 3.0 35.9 1.0 OD1 A:ASP71 3.0 31.2 1.0 CG A:ASP71 3.2 28.0 1.0 CG2 A:THR74 3.6 9.6 1.0 C A:SER72 3.8 30.0 1.0 N A:SER72 3.8 28.4 1.0 CB A:SER72 4.0 22.3 1.0 CA A:SER72 4.1 26.3 1.0 CB A:ASP71 4.5 22.4 1.0 O A:PRO73 4.7 24.8 1.0 C A:ASP71 4.8 24.3 1.0 C A:PRO73 4.9 24.4 1.0 O A:HOH505 4.9 28.3 1.0 N A:PRO73 5.0 27.3 1.0 CB A:THR74 5.0 23.1 1.0

Potassium binding site 3 out of 6 in the Crystal Structure of the Guanine Nucleotide Exchange Factor SEC12 (P64 Form)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of the Guanine Nucleotide Exchange Factor SEC12 (P64 Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:K403 b:41.9 occ:1.00 O A:ILE222 2.8 38.8 1.0 OH A:TYR137 2.8 23.7 1.0 O A:LEU179 2.8 39.7 1.0 OD1 A:ASP178 2.9 38.3 1.0 OD2 A:ASP178 3.2 34.1 1.0 CZ A:TYR137 3.3 22.9 1.0 CG A:ASP178 3.4 32.3 1.0 CE1 A:TYR137 3.6 25.1 1.0 OD1 A:ASN223 3.6 41.8 1.0 CD2 A:HIS180 3.7 35.1 1.0 ND2 A:ASN223 3.8 41.2 1.0 C A:LEU179 3.8 34.1 1.0 CG A:ASN223 3.9 42.5 1.0 C A:ILE222 3.9 34.2 1.0 CG A:HIS180 4.0 37.1 1.0 CB A:HIS180 4.0 34.8 1.0 CE2 A:TYR137 4.2 17.8 1.0 N A:LEU179 4.3 30.6 1.0 N A:ILE222 4.5 31.1 1.0 CA A:HIS180 4.6 34.7 1.0 CD1 A:TYR137 4.6 26.1 1.0 N A:HIS180 4.6 33.5 1.0 NE2 A:HIS180 4.7 32.9 1.0 CA A:LEU179 4.7 32.2 1.0 CB A:ASP178 4.7 28.5 1.0 CG2 A:ILE222 4.8 32.4 1.0 CA A:ILE222 4.8 32.8 1.0 N A:ASN223 4.8 32.0 1.0 O A:MSE272 4.9 35.2 1.0 CA A:ASN223 4.9 39.2 1.0

Potassium binding site 4 out of 6 in the Crystal Structure of the Guanine Nucleotide Exchange Factor SEC12 (P64 Form)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of the Guanine Nucleotide Exchange Factor SEC12 (P64 Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:K401 b:22.0 occ:1.00 O B:GLY34 2.7 26.8 1.0 O B:GLY32 2.7 16.5 1.0 O B:ILE38 2.7 17.1 1.0 OD1 B:ASN36 2.8 23.1 1.0 O B:ASP68 2.9 24.1 1.0 CG B:ASN36 3.8 17.5 1.0 C B:ILE38 3.9 18.0 1.0 C B:GLY34 3.9 23.7 1.0 C B:GLY32 3.9 18.5 1.0 C B:ASP68 4.0 14.8 1.0 ND2 B:ASN40 4.1 21.2 1.0 N B:ASN36 4.3 28.2 1.0 N B:GLY34 4.3 22.0 1.0 C B:GLU33 4.3 20.6 1.0 N B:ILE38 4.3 16.3 1.0 CA B:ASP68 4.4 13.3 1.0 ND2 B:ASN36 4.4 13.6 1.0 C B:GLY31 4.4 14.7 1.0 N B:GLY32 4.5 14.5 1.0 O B:GLU33 4.5 22.9 1.0 CB B:ASP68 4.6 17.5 1.0 CA B:ILE38 4.6 17.8 1.0 CA B:GLY34 4.6 15.9 1.0 CA B:GLU33 4.7 17.7 1.0 O B:GLY31 4.7 22.7 1.0 N B:GLU33 4.7 17.7 1.0 N B:GLY37 4.8 14.8 1.0 CA B:GLY31 4.8 17.8 1.0 N B:PRO39 4.8 17.6 1.0 CA B:GLY32 4.8 7.3 1.0 N B:ASN35 4.9 27.8 1.0 CB B:ASN36 4.9 9.5 1.0 CA B:PRO39 5.0 14.9 1.0 CA B:ASN35 5.0 27.0 1.0 CG B:ASN40 5.0 21.3 1.0 CA B:ASN36 5.0 11.0 1.0

Potassium binding site 5 out of 6 in the Crystal Structure of the Guanine Nucleotide Exchange Factor SEC12 (P64 Form)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of the Guanine Nucleotide Exchange Factor SEC12 (P64 Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:K402 b:25.0 occ:1.00 O B:ILE222 2.6 19.0 1.0 O B:LEU179 2.9 25.4 1.0 OD1 B:ASP178 2.9 16.5 1.0 OH B:TYR137 3.0 31.8 1.0 O B:HOH545 3.1 22.8 1.0 CZ B:TYR137 3.3 23.6 1.0 OD2 B:ASP178 3.4 21.8 1.0 CG B:ASP178 3.4 18.3 1.0 CE1 B:TYR137 3.5 22.2 1.0 CD2 B:HIS180 3.6 21.1 1.0 OD1 B:ASN223 3.6 32.8 1.0 O B:HOH555 3.6 35.5 1.0 ND2 B:ASN223 3.7 32.6 1.0 CG B:ASN223 3.8 32.5 1.0 C B:ILE222 3.8 17.3 1.0 C B:LEU179 3.8 22.6 1.0 CB B:HIS180 3.8 18.9 1.0 CG B:HIS180 3.9 20.4 1.0 CE2 B:TYR137 4.2 16.6 1.0 O B:HOH505 4.3 19.1 1.0 N B:LEU179 4.3 21.8 1.0 CA B:HIS180 4.4 22.7 1.0 CD1 B:TYR137 4.4 13.4 1.0 N B:HIS180 4.5 21.0 1.0 N B:ILE222 4.5 14.4 1.0 NE2 B:HIS180 4.6 9.2 1.0 N B:ASN223 4.6 15.9 1.0 CA B:ASN223 4.7 15.2 1.0 CG2 B:ILE222 4.7 21.2 1.0 CA B:LEU179 4.7 23.2 1.0 CA B:ILE222 4.7 16.2 1.0 CB B:ASP178 4.8 9.2 1.0 CB B:ASN223 4.8 21.8 1.0 ND1 B:HIS180 4.9 20.9 1.0 CD2 B:TYR137 5.0 18.7 1.0

Potassium binding site 6 out of 6 in the Crystal Structure of the Guanine Nucleotide Exchange Factor SEC12 (P64 Form)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of the Guanine Nucleotide Exchange Factor SEC12 (P64 Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:K403 b:38.9 occ:1.00 O B:ILE76 2.7 13.1 1.0 O B:VAL136 2.7 24.2 1.0 O B:HOH553 2.7 30.3 1.0 O B:HOH538 2.9 21.3 1.0 O B:HOH510 3.3 15.1 1.0 O B:HOH554 3.3 37.4 1.0 CE1 B:TYR137 3.8 22.2 1.0 C B:ILE76 3.8 17.3 1.0 CZ B:TYR137 3.9 23.6 1.0 C B:VAL136 3.9 24.4 1.0 CD1 B:TYR137 4.1 13.4 1.0 CE2 B:TYR137 4.2 16.6 1.0 CB B:ASP77 4.3 18.8 1.0 OH B:TYR137 4.3 31.8 1.0 OE1 B:GLU314 4.3 37.1 1.0 CG B:ASP77 4.4 22.7 1.0 CG B:TYR137 4.4 15.6 1.0 N B:ILE76 4.5 11.8 1.0 N B:VAL136 4.5 20.5 1.0 CD2 B:TYR137 4.5 18.7 1.0 N B:ASP77 4.6 17.0 1.0 OE2 B:GLU314 4.6 35.1 1.0 CA B:VAL136 4.6 21.3 1.0 CA B:ASP77 4.7 14.5 1.0 OD1 B:ASP77 4.7 16.9 1.0 CA B:ILE76 4.8 13.8 1.0 OD2 B:ASP77 4.8 23.9 1.0 N B:TYR137 4.9 26.3 1.0 CB B:VAL136 4.9 18.8 1.0 CD B:GLU314 4.9 32.5 1.0 CA B:TYR137 5.0 21.0 1.0

C.Mcmahon, S.M.Studer, C.Clendinen, G.P.Dann, P.D.Jeffrey, F.M.Hughson. The Structure of SEC12 Implicates Potassium Ion Coordination in SAR1 Activation. J.Biol.Chem. V. 287 43599 2012.
ISSN: ISSN 0021-9258
PubMed: 23109340
DOI: 10.1074/JBC.M112.420141