Zinc in PDB 5aws: Crystal Structure of the SGIP1 Mu Homology Domain in the P1 Space Group

The structure of Crystal Structure of the SGIP1 Mu Homology Domain in the P1 Space Group, PDB code: 5aws was solved by A.Shimada, A.Yamaguchi, D.Kohda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.05 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	37.552, 53.634, 75.199, 101.87, 86.91, 95.61
R / Rfree (%)	19.9 / 24.1

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the SGIP1 Mu Homology Domain in the P1 Space Group (pdb code 5aws). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of the SGIP1 Mu Homology Domain in the P1 Space Group, PDB code: 5aws:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Crystal Structure of the SGIP1 Mu Homology Domain in the P1 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the SGIP1 Mu Homology Domain in the P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:97.6 occ:1.00 O A:HOH1008 2.1 42.0 1.0 O A:HOH1020 2.2 69.4 1.0 OE2 A:GLU589 2.7 64.9 1.0 OD2 A:ASP672 2.8 61.5 1.0 OE1 A:GLU589 2.9 76.8 1.0 CD A:GLU589 3.1 65.7 1.0 OD1 A:ASP672 3.3 41.2 1.0 CG A:ASP672 3.3 48.6 1.0 O A:HOH1005 3.6 65.5 1.0 NZ A:LYS675 4.0 67.7 1.0 CB A:ASP672 4.5 30.1 1.0 CG A:GLU589 4.6 49.5 1.0

Zinc binding site 2 out of 12 in the Crystal Structure of the SGIP1 Mu Homology Domain in the P1 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the SGIP1 Mu Homology Domain in the P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:91.3 occ:1.00 ND1 A:HIS655 1.9 59.5 1.0 O A:HOH1088 2.1 60.2 1.0 O A:HOH1015 2.1 68.0 1.0 O A:HOH1012 2.3 61.5 1.0 CE1 A:HIS655 2.3 62.2 1.0 CG A:HIS655 3.2 57.8 1.0 OE1 A:GLN629 3.4 87.9 1.0 O A:HOH1013 3.6 79.5 1.0 NE2 A:HIS655 3.6 54.8 1.0 CB A:HIS655 4.0 61.6 1.0 CD2 A:HIS655 4.0 53.9 1.0 CA A:HIS655 4.5 68.1 1.0 CD A:GLN629 4.5 83.3 1.0 NE2 A:GLN629 5.0 86.6 1.0

Zinc binding site 3 out of 12 in the Crystal Structure of the SGIP1 Mu Homology Domain in the P1 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the SGIP1 Mu Homology Domain in the P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:42.9 occ:1.00 SG A:CYS632 2.3 44.4 1.0 CB A:CYS632 3.1 41.0 1.0 N A:CYS632 3.6 44.5 1.0 O B:HOH1080 3.8 38.3 1.0 CA A:CYS632 3.9 42.8 1.0 O A:TRP646 3.9 43.6 1.0 C A:LEU631 4.1 46.0 1.0 ND2 A:ASN648 4.5 63.5 1.0 CB A:ASN648 4.5 47.6 1.0 O A:LEU631 4.5 45.8 1.0 O A:HOH1087 4.6 63.4 1.0 N A:ASN648 4.7 44.5 1.0 CA A:ASN648 4.8 45.1 1.0 CB A:TRP646 4.8 44.2 1.0 C A:TRP646 4.8 44.4 1.0 CA A:LEU631 4.8 41.2 1.0 C A:CYS632 4.9 43.4 1.0

Zinc binding site 4 out of 12 in the Crystal Structure of the SGIP1 Mu Homology Domain in the P1 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the SGIP1 Mu Homology Domain in the P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn904 b:41.8 occ:1.00 O B:HOH1076 2.0 18.5 1.0 NE2 A:HIS623 2.1 42.3 1.0 SG B:CYS633 2.1 46.3 1.0 OE2 A:GLU622 2.1 62.0 1.0 CE1 A:HIS623 3.0 37.8 1.0 CD2 A:HIS623 3.1 38.6 1.0 CB B:CYS633 3.2 48.1 1.0 CD A:GLU622 3.3 58.5 1.0 O B:HOH1028 3.4 53.7 1.0 N B:CYS633 3.7 49.4 1.0 CA B:CYS633 4.0 50.2 1.0 CG A:GLU622 4.0 45.1 1.0 ND1 A:HIS623 4.1 36.8 1.0 CG A:HIS623 4.2 34.6 1.0 OE1 A:GLU622 4.3 58.1 1.0 CG B:PRO626 4.3 41.7 1.0 C B:CYS632 4.4 44.0 1.0 O A:HOH1048 4.4 46.3 1.0 CE2 B:PHE645 4.5 40.7 1.0 C B:CYS633 4.6 50.7 1.0 CA B:CYS632 4.7 37.5 1.0 O B:CYS633 4.9 52.0 1.0 OE1 A:GLN677 4.9 46.1 1.0

Zinc binding site 5 out of 12 in the Crystal Structure of the SGIP1 Mu Homology Domain in the P1 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the SGIP1 Mu Homology Domain in the P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn905 b:63.0 occ:1.00 OD2 A:ASP558 2.1 82.7 1.0 ND1 A:HIS601 2.2 94.8 1.0 CE1 A:HIS601 2.2 97.1 1.0 CG A:ASP558 3.1 86.1 1.0 OD1 A:ASP558 3.4 88.0 1.0 NE2 A:HIS601 3.4 96.2 1.0 CG A:HIS601 3.4 88.4 1.0 O A:HIS601 3.7 85.5 1.0 CD2 A:HIS601 4.0 89.8 1.0 CB A:HIS601 4.4 83.2 1.0 CB A:ASP558 4.4 78.5 1.0 C A:HIS601 4.5 84.1 1.0 CA A:HIS601 4.7 78.4 1.0

Zinc binding site 6 out of 12 in the Crystal Structure of the SGIP1 Mu Homology Domain in the P1 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the SGIP1 Mu Homology Domain in the P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn906 b:0.6 occ:1.00 OE2 A:GLU804 2.4 91.5 1.0 OE1 A:GLU804 2.6 94.9 1.0 CD A:GLU804 2.8 88.0 1.0 CG A:GLU804 4.2 74.4 1.0 NH1 A:ARG614 4.4 76.7 1.0 CB A:GLU804 5.0 63.5 1.0

Zinc binding site 7 out of 12 in the Crystal Structure of the SGIP1 Mu Homology Domain in the P1 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the SGIP1 Mu Homology Domain in the P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn907 b:40.3 occ:1.00 OE1 B:GLU622 1.8 59.5 1.0 O B:HOH1075 2.0 14.8 1.0 NE2 B:HIS623 2.2 44.7 1.0 SG A:CYS633 2.3 44.8 1.0 CD B:GLU622 3.0 56.8 1.0 CB A:CYS633 3.1 42.3 1.0 CD2 B:HIS623 3.1 40.8 1.0 CE1 B:HIS623 3.2 40.8 1.0 N A:CYS633 3.7 43.1 1.0 OE2 B:GLU622 3.8 51.1 1.0 CG B:GLU622 3.9 54.5 1.0 CA A:CYS633 4.0 37.1 1.0 CG B:HIS623 4.3 41.7 1.0 ND1 B:HIS623 4.3 37.6 1.0 CG A:PRO626 4.4 36.0 1.0 C A:CYS632 4.4 43.4 1.0 CE2 A:PHE645 4.5 35.2 1.0 O B:HOH1041 4.5 49.6 1.0 C A:CYS633 4.7 43.7 1.0 CA A:CYS632 4.7 42.8 1.0 O B:HOH1045 4.9 43.0 1.0 OD1 A:ASN635 4.9 73.3 1.0 O A:CYS633 4.9 41.8 1.0 CD2 A:PHE645 5.0 35.5 1.0

Zinc binding site 8 out of 12 in the Crystal Structure of the SGIP1 Mu Homology Domain in the P1 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the SGIP1 Mu Homology Domain in the P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:72.5 occ:1.00 ND1 B:HIS655 1.9 68.0 1.0 O B:HOH1074 2.0 66.0 1.0 O B:HOH1016 2.2 58.8 1.0 O B:HOH1003 2.3 46.0 1.0 O B:HOH1073 2.4 68.2 1.0 CE1 B:HIS655 2.7 66.4 1.0 CG B:HIS655 3.0 67.0 1.0 CB B:HIS655 3.5 62.0 1.0 OE1 B:GLN629 3.8 79.8 1.0 NE2 B:HIS655 3.9 62.5 1.0 CD2 B:HIS655 4.0 63.2 1.0 CA B:HIS655 4.2 65.2 1.0 CD B:GLN629 4.9 74.5 1.0

Zinc binding site 9 out of 12 in the Crystal Structure of the SGIP1 Mu Homology Domain in the P1 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the SGIP1 Mu Homology Domain in the P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:0.4 occ:1.00 OE2 B:GLU589 3.0 68.7 1.0 OE1 B:GLU589 3.1 64.3 1.0 OD1 B:ASP672 3.2 49.8 1.0 CD B:GLU589 3.3 63.1 1.0 OD2 B:ASP672 3.4 54.8 1.0 CG B:ASP672 3.6 48.0 1.0 CG B:GLU589 4.7 52.2 1.0 CG2 B:VAL591 4.8 38.5 1.0 CB B:ASP672 5.0 34.1 1.0

Zinc binding site 10 out of 12 in the Crystal Structure of the SGIP1 Mu Homology Domain in the P1 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the SGIP1 Mu Homology Domain in the P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn903 b:0.5 occ:1.00 O B:HOH1072 2.2 74.2 1.0 O B:HOH1084 2.3 48.6 1.0 SG B:CYS632 3.0 0.2 1.0 CB B:CYS632 3.5 42.2 1.0 O B:HOH1085 3.5 65.1 1.0 ND2 B:ASN648 4.0 69.1 1.0 CG2 A:ILE583 4.6 43.8 1.0 N B:CYS632 4.6 34.0 1.0 CA B:CYS632 4.6 37.5 1.0 CB B:ASN648 4.7 51.4 1.0 CG B:ASN648 4.8 60.4 1.0

A.Shimada, A.Yamaguchi, D.Kohda. Structural Basis For the Recognition of Two Consecutive Mutually Interacting Dpf Motifs By the SGIP1 Mu Homology Domain. Sci Rep V. 6 19565 2016.
ISSN: ESSN 2045-2322
PubMed: 26822536
DOI: 10.1038/SREP19565