Zinc in PDB 3wxa: X-Ray Crystal Structural Analysis of the Complex Between Alg-2 and SEC31A Peptide

The structure of X-Ray Crystal Structural Analysis of the Complex Between Alg-2 and SEC31A Peptide, PDB code: 3wxa was solved by T.Takahashi, H.Suzuki, M.Kawasaki, H.Shibata, S.Wakatsuki, M.Maki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.09 / 2.36
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	81.973, 81.973, 103.232, 90.00, 90.00, 120.00
R / Rfree (%)	22.5 / 26.3

The binding sites of Zinc atom in the X-Ray Crystal Structural Analysis of the Complex Between Alg-2 and SEC31A Peptide (pdb code 3wxa). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the X-Ray Crystal Structural Analysis of the Complex Between Alg-2 and SEC31A Peptide, PDB code: 3wxa:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in the X-Ray Crystal Structural Analysis of the Complex Between Alg-2 and SEC31A Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Crystal Structural Analysis of the Complex Between Alg-2 and SEC31A Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:55.9 occ:1.00 OE2 A:GLU47 2.1 49.2 1.0 OD1 A:ASP36 2.1 44.0 1.0 O A:VAL42 2.1 38.4 1.0 OD1 A:ASP38 2.3 58.4 1.0 OE1 A:GLU47 2.3 54.8 1.0 CD A:GLU47 2.5 42.1 1.0 C A:VAL42 3.3 38.0 1.0 CG A:ASP38 3.3 42.7 1.0 OG A:SER40 3.3 44.3 1.0 CG A:ASP36 3.4 56.8 1.0 OD2 A:ASP38 3.6 43.0 1.0 N A:SER44 3.9 35.8 1.0 CG A:GLU47 4.0 41.2 1.0 CA A:ILE43 4.1 34.4 1.0 N A:ILE43 4.1 34.5 1.0 OD2 A:ASP36 4.1 71.1 1.0 N A:VAL42 4.2 51.2 1.0 CA A:VAL42 4.3 41.2 1.0 CA A:ASP36 4.3 48.2 1.0 CB A:ASP36 4.4 49.9 1.0 N A:SER40 4.4 33.0 1.0 N A:ASP38 4.4 43.4 1.0 C A:ILE43 4.4 32.1 1.0 CB A:SER40 4.5 33.4 1.0 N A:LYS37 4.5 51.2 1.0 CB A:ASP38 4.6 40.5 1.0 CB A:SER44 4.6 37.1 1.0 N A:ARG39 4.7 49.4 1.0 C A:ASP36 4.7 55.0 1.0 CB A:GLU47 4.8 39.8 1.0 CA A:SER44 4.9 35.5 1.0 CB A:VAL42 4.9 40.5 1.0 N A:GLY41 4.9 36.6 1.0 CA A:ASP38 4.9 41.6 1.0 CA A:SER40 5.0 33.5 1.0

Zinc binding site 2 out of 10 in the X-Ray Crystal Structural Analysis of the Complex Between Alg-2 and SEC31A Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Crystal Structural Analysis of the Complex Between Alg-2 and SEC31A Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:58.3 occ:1.00 OD1 A:ASP105 2.1 53.7 1.0 OE1 A:GLU114 2.2 32.9 1.0 O A:MET109 2.3 43.0 1.0 OD2 A:ASP105 2.5 44.8 1.0 CG A:ASP105 2.7 54.3 1.0 OD1 A:ASP103 2.7 34.7 1.0 OG A:SER107 3.1 41.7 1.0 CD A:GLU114 3.1 34.0 1.0 ZN A:ZN203 3.3 53.9 1.0 OE2 A:GLU114 3.5 47.4 1.0 OD2 A:ASP111 3.5 29.7 1.0 C A:MET109 3.5 27.5 1.0 CG A:ASP103 3.9 36.1 1.0 N A:ASP111 4.0 24.3 1.0 CA A:ILE110 4.1 25.4 1.0 CB A:ASP105 4.2 51.7 1.0 CB A:SER107 4.2 40.0 1.0 CG A:ASP111 4.2 29.6 1.0 N A:ILE110 4.3 23.1 1.0 N A:SER107 4.4 42.5 1.0 CG A:GLU114 4.4 31.7 1.0 C A:ILE110 4.5 25.6 1.0 CA A:MET109 4.6 31.6 1.0 N A:MET109 4.6 35.5 1.0 CA A:ASP103 4.6 36.9 1.0 N A:ASN106 4.7 45.1 1.0 CB A:ASP111 4.7 28.6 1.0 N A:ASP105 4.8 40.4 1.0 OD2 A:ASP103 4.8 41.8 1.0 CB A:ASP103 4.8 32.7 1.0 CA A:SER107 4.9 41.3 1.0 CA A:ASP105 4.9 46.7 1.0 OE1 A:GLN145 4.9 38.8 1.0 CB A:GLU114 4.9 27.4 1.0 C A:ASP105 5.0 47.6 1.0 CA A:ASP111 5.0 23.9 1.0

Zinc binding site 3 out of 10 in the X-Ray Crystal Structural Analysis of the Complex Between Alg-2 and SEC31A Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Crystal Structural Analysis of the Complex Between Alg-2 and SEC31A Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:53.9 occ:1.00 OD2 A:ASP111 2.2 29.7 1.0 OD2 A:ASP105 2.3 44.8 1.0 CG A:ASP111 3.3 29.6 1.0 ZN A:ZN202 3.3 58.3 1.0 OE1 A:GLN145 3.4 38.8 1.0 CG A:ASP105 3.5 54.3 1.0 CB A:ASP111 3.6 28.6 1.0 OD1 A:ASP105 4.2 53.7 1.0 OG A:SER107 4.3 41.7 1.0 OD1 A:ASP111 4.4 28.8 1.0 OE1 A:GLU114 4.4 32.9 1.0 CB A:ASP105 4.5 51.7 1.0 CD A:GLN145 4.5 26.7 1.0 N A:ASP111 4.8 24.3 1.0 CA A:ASP111 4.8 23.9 1.0 CD A:GLU114 4.8 34.0 1.0 O A:MET109 4.9 43.0 1.0

Zinc binding site 4 out of 10 in the X-Ray Crystal Structural Analysis of the Complex Between Alg-2 and SEC31A Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Crystal Structural Analysis of the Complex Between Alg-2 and SEC31A Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:54.3 occ:1.00 OD2 A:ASP171 1.8 60.5 1.0 OD2 A:ASP173 2.6 49.0 1.0 CG A:ASP171 2.6 46.1 1.0 CG A:ASP173 3.2 44.9 1.0 OD1 A:ASP171 3.3 50.0 1.0 OD1 A:ASP173 3.4 62.6 1.0 CB A:ASP171 3.6 46.4 1.0 O A:HOH313 4.3 43.8 1.0 CB A:ASP173 4.4 42.8 1.0 O A:TRP175 4.8 36.2 1.0 CB A:TRP175 4.9 38.5 1.0

Zinc binding site 5 out of 10 in the X-Ray Crystal Structural Analysis of the Complex Between Alg-2 and SEC31A Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of X-Ray Crystal Structural Analysis of the Complex Between Alg-2 and SEC31A Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:53.3 occ:1.00 OD1 B:ASP38 2.0 44.5 1.0 OD1 B:ASP36 2.1 45.3 1.0 O B:VAL42 2.1 57.0 1.0 O B:HOH311 2.2 40.0 1.0 OE1 B:GLU47 2.6 33.7 1.0 CG B:ASP38 2.9 43.6 1.0 OG B:SER40 3.0 51.4 1.0 OD2 B:ASP38 3.1 37.3 1.0 OE2 B:GLU47 3.2 36.8 1.0 C B:VAL42 3.2 37.6 1.0 CG B:ASP36 3.2 51.8 1.0 CD B:GLU47 3.2 34.6 1.0 OD2 B:ASP36 3.8 68.7 1.0 N B:SER40 3.9 38.4 1.0 CA B:ILE43 3.9 33.2 1.0 N B:ILE43 3.9 34.3 1.0 CB B:SER40 4.1 45.4 1.0 N B:VAL42 4.1 43.6 1.0 N B:SER44 4.1 31.0 1.0 CA B:VAL42 4.2 41.7 1.0 N B:ARG39 4.3 49.9 1.0 CB B:ASP38 4.3 37.2 1.0 CB B:ASP36 4.4 41.6 1.0 C B:ILE43 4.5 37.9 1.0 CA B:ASP36 4.5 40.9 1.0 N B:ASP38 4.5 35.3 1.0 CA B:SER40 4.5 33.9 1.0 CG B:GLU47 4.7 33.6 1.0 N B:GLY41 4.7 36.9 1.0 C B:ASP38 4.8 37.4 1.0 C B:ASP36 4.8 41.3 1.0 CA B:ASP38 4.8 35.3 1.0 N B:LYS37 4.9 39.1 1.0 CA B:ARG39 4.9 40.9 1.0 C B:ARG39 4.9 38.0 1.0 CB B:VAL42 4.9 41.5 1.0

Zinc binding site 6 out of 10 in the X-Ray Crystal Structural Analysis of the Complex Between Alg-2 and SEC31A Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of X-Ray Crystal Structural Analysis of the Complex Between Alg-2 and SEC31A Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:63.7 occ:1.00 O B:MET109 2.0 33.4 1.0 OD1 B:ASP103 2.1 44.8 1.0 OE1 B:GLU114 2.2 45.1 1.0 OD1 B:ASP105 2.4 54.4 1.0 CG B:ASP103 2.7 41.9 1.0 OE2 B:GLU114 2.7 53.0 1.0 CD B:GLU114 2.8 38.8 1.0 OD2 B:ASP103 3.2 50.1 1.0 OG B:SER107 3.2 42.1 1.0 C B:MET109 3.2 29.6 1.0 CG B:ASP105 3.4 44.8 1.0 ZN B:ZN203 3.6 71.1 1.0 CA B:ASP103 3.6 45.3 1.0 OD2 B:ASP105 3.7 43.0 1.0 CB B:ASP103 3.7 41.1 1.0 C B:ASP103 4.1 56.9 1.0 CA B:ILE110 4.1 27.2 1.0 N B:ILE110 4.1 26.7 1.0 N B:MET109 4.1 47.4 1.0 N B:SER107 4.2 47.1 1.0 OD2 B:ASP111 4.2 33.8 1.0 CB B:SER107 4.2 49.1 1.0 CA B:MET109 4.2 35.1 1.0 CG B:GLU114 4.3 31.0 1.0 N B:ASP111 4.3 24.8 1.0 N B:ARG104 4.3 59.7 1.0 N B:ASP105 4.4 68.0 1.0 N B:ASN106 4.6 50.1 1.0 O B:ASP103 4.6 57.9 1.0 CA B:SER107 4.7 46.6 1.0 CB B:ASP105 4.7 47.3 1.0 C B:ILE110 4.7 25.8 1.0 CG B:ASP111 4.8 28.8 1.0 N B:GLY108 4.8 47.1 1.0 CD1 B:ILE110 4.8 33.1 1.0 CB B:GLU114 4.9 29.6 1.0 OE1 B:GLN145 4.9 27.1 1.0 N B:ASP103 4.9 48.7 1.0 CA B:ASP105 5.0 47.9 1.0 CB B:MET109 5.0 31.7 1.0

Zinc binding site 7 out of 10 in the X-Ray Crystal Structural Analysis of the Complex Between Alg-2 and SEC31A Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of X-Ray Crystal Structural Analysis of the Complex Between Alg-2 and SEC31A Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:71.1 occ:1.00 OD2 B:ASP111 2.0 33.8 1.0 OD2 B:ASP105 2.1 43.0 1.0 CG B:ASP111 3.0 28.8 1.0 CG B:ASP105 3.1 44.8 1.0 OD1 B:ASP105 3.4 54.4 1.0 CB B:ASP111 3.4 26.6 1.0 NE2 B:GLN145 3.5 31.2 1.0 OE1 B:GLN145 3.5 27.1 1.0 OG B:SER107 3.6 42.1 1.0 ZN B:ZN202 3.6 63.7 1.0 CD B:GLN145 3.8 27.1 1.0 OE1 B:GLU114 4.0 45.1 1.0 OE2 B:GLU114 4.0 53.0 1.0 OD1 B:ASP111 4.2 34.6 1.0 CD B:GLU114 4.2 38.8 1.0 CB B:SER107 4.2 49.1 1.0 N B:ASP111 4.4 24.8 1.0 O B:MET109 4.4 33.4 1.0 CB B:ASP105 4.4 47.3 1.0 CA B:ASP111 4.5 25.4 1.0

Zinc binding site 8 out of 10 in the X-Ray Crystal Structural Analysis of the Complex Between Alg-2 and SEC31A Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of X-Ray Crystal Structural Analysis of the Complex Between Alg-2 and SEC31A Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:53.2 occ:1.00 OD2 B:ASP173 2.1 34.7 1.0 O B:HOH306 2.3 33.0 1.0 OD2 B:ASP171 2.4 50.1 1.0 O B:HOH310 2.5 38.4 1.0 CG B:ASP173 2.7 37.3 1.0 CG B:ASP171 3.0 48.1 1.0 OD1 B:ASP173 3.0 48.6 1.0 CB B:ASP171 3.1 40.0 1.0 CB B:ASP173 3.8 38.1 1.0 OD1 B:ASP171 4.0 77.4 1.0 CA B:ASP171 4.5 43.5 1.0 O B:TRP175 4.7 42.1 1.0 N B:ASP171 4.9 50.0 1.0

Zinc binding site 9 out of 10 in the X-Ray Crystal Structural Analysis of the Complex Between Alg-2 and SEC31A Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of X-Ray Crystal Structural Analysis of the Complex Between Alg-2 and SEC31A Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:61.4 occ:1.00 OD1 C:ASN1 2.1 48.2 1.0 ND2 C:ASN12 2.4 49.2 1.0 CG C:ASN1 3.3 53.7 1.0 CG C:ASN12 3.4 55.5 1.0 CB C:ASN12 3.7 56.5 1.0 O C:ASN1 3.9 73.8 1.0 ND2 C:ASN1 4.2 51.2 1.0 CB C:ASN1 4.2 67.9 1.0 OD1 C:ASN12 4.5 74.1 1.0 C C:ASN1 4.9 66.5 1.0

Zinc binding site 10 out of 10 in the X-Ray Crystal Structural Analysis of the Complex Between Alg-2 and SEC31A Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of X-Ray Crystal Structural Analysis of the Complex Between Alg-2 and SEC31A Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn101 b:51.6 occ:1.00 OD1 D:ASN1 3.1 63.2 1.0 CA D:GLY11 3.4 78.7 1.0 O D:HIS10 3.5 61.8 1.0 CG D:ASN1 4.0 63.9 1.0 ND2 D:ASN1 4.2 66.2 1.0 N D:GLY11 4.3 81.1 1.0 C D:HIS10 4.3 63.1 1.0 N D:ASN12 4.4 79.7 1.0 C D:GLY11 4.4 79.0 1.0 OD1 D:ASN12 4.5 78.8 1.0 O D:ASN1 4.6 75.0 1.0

T.Takahashi, K.Kojima, W.Zhang, K.Sasaki, M.Ito, H.Suzuki, M.Kawasaki, S.Wakatsuki, T.Takahara, H.Shibata, M.Maki. Structural Analysis of the Complex Between Penta-Ef-Hand Alg-2 Protein and SEC31A Peptide Reveals A Novel Target Recognition Mechanism of Alg-2 Int J Mol Sci V. 16 3677 2015.
ISSN: ESSN 1422-0067
PubMed: 25667979
DOI: 10.3390/IJMS16023677