Zinc in PDB 5awt: Crystal Structure of the SGIP1 Mu Homology Domain in Complex with An EPS15 Fragment Containing Two Dpf Motifs (Ydpfggdpfkg)

The structure of Crystal Structure of the SGIP1 Mu Homology Domain in Complex with An EPS15 Fragment Containing Two Dpf Motifs (Ydpfggdpfkg), PDB code: 5awt 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)	41.27 / 2.70
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	107.716, 107.716, 79.978, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 23.4

The binding sites of Zinc atom in the Crystal Structure of the SGIP1 Mu Homology Domain in Complex with An EPS15 Fragment Containing Two Dpf Motifs (Ydpfggdpfkg) (pdb code 5awt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the SGIP1 Mu Homology Domain in Complex with An EPS15 Fragment Containing Two Dpf Motifs (Ydpfggdpfkg), PDB code: 5awt:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of the SGIP1 Mu Homology Domain in Complex with An EPS15 Fragment Containing Two Dpf Motifs (Ydpfggdpfkg)


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 Complex with An EPS15 Fragment Containing Two Dpf Motifs (Ydpfggdpfkg) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:95.6 occ:1.00 OD2 A:ASP558 1.9 0.3 1.0 OD1 A:ASP558 2.1 0.4 1.0 CD2 A:HIS601 2.2 97.5 1.0 CG A:ASP558 2.3 0.6 1.0 NE2 A:HIS601 2.7 98.0 1.0 CG A:HIS601 3.0 87.0 1.0 CE1 A:HIS601 3.6 92.6 1.0 ND1 A:HIS601 3.8 86.7 1.0 CB A:HIS601 3.8 79.4 1.0 CB A:ASP558 3.8 0.8 1.0 CA A:HIS601 4.4 72.3 1.0 CA A:ASP558 4.8 0.3 1.0 O A:ASP558 4.9 0.7 1.0 N A:ASP558 4.9 0.9 1.0 C A:ASP558 5.0 0.3 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of the SGIP1 Mu Homology Domain in Complex with An EPS15 Fragment Containing Two Dpf Motifs (Ydpfggdpfkg)


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 Complex with An EPS15 Fragment Containing Two Dpf Motifs (Ydpfggdpfkg) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:85.6 occ:1.00 OE1 A:GLU589 2.3 0.7 1.0 OE2 A:GLU589 2.5 94.3 1.0 O A:HOH1032 2.6 52.4 1.0 CD A:GLU589 2.7 90.7 1.0 OD2 A:ASP672 2.8 62.2 1.0 OD1 A:ASP672 2.8 57.4 1.0 CG A:ASP672 3.2 57.8 1.0 CG A:GLU589 4.2 68.0 1.0 NZ A:LYS675 4.3 54.7 1.0 CB A:ASP672 4.6 47.3 1.0 CG2 A:VAL591 5.0 42.6 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of the SGIP1 Mu Homology Domain in Complex with An EPS15 Fragment Containing Two Dpf Motifs (Ydpfggdpfkg)


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 Complex with An EPS15 Fragment Containing Two Dpf Motifs (Ydpfggdpfkg) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:97.2 occ:1.00 ND1 A:HIS655 2.1 67.4 1.0 O A:HOH1031 2.4 45.6 1.0 CE1 A:HIS655 2.9 65.3 1.0 CG A:HIS655 3.2 62.6 1.0 CB A:HIS655 3.7 50.6 1.0 CA A:HIS655 3.9 55.3 1.0 NE2 A:HIS655 4.1 58.9 1.0 CD2 A:HIS655 4.3 56.0 1.0 O A:HIS655 4.8 60.4 1.0 C A:HIS655 4.8 61.0 1.0 N A:HIS655 4.9 56.0 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the SGIP1 Mu Homology Domain in Complex with An EPS15 Fragment Containing Two Dpf Motifs (Ydpfggdpfkg)


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 Complex with An EPS15 Fragment Containing Two Dpf Motifs (Ydpfggdpfkg) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn904 b:0.1 occ:1.00 OD2 A:ASP639 2.0 0.8 1.0 CG A:ASP639 2.5 0.8 1.0 O A:HOH1004 3.0 56.6 1.0 CB A:ASP639 3.1 0.6 1.0 OD1 A:ASP639 3.3 0.3 1.0 O A:THR642 3.8 59.0 1.0 OE2 A:GLU644 4.0 0.9 1.0 CG A:GLU644 4.2 73.8 1.0 N A:GLU644 4.2 49.9 1.0 CD A:GLU644 4.4 95.6 1.0 CA A:LYS643 4.4 49.4 1.0 C A:THR642 4.5 58.2 1.0 CG2 A:THR642 4.5 76.9 1.0 CA A:ASP639 4.6 0.1 1.0 CB A:GLU644 4.6 62.3 1.0 C A:LYS643 4.7 50.2 1.0 N A:LYS643 4.9 51.5 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the SGIP1 Mu Homology Domain in Complex with An EPS15 Fragment Containing Two Dpf Motifs (Ydpfggdpfkg)


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 Complex with An EPS15 Fragment Containing Two Dpf Motifs (Ydpfggdpfkg) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn905 b:0.1 occ:1.00 NE2 A:GLN677 2.8 81.6 1.0 CG A:GLN677 2.8 61.3 1.0 CD A:GLN677 3.1 72.3 1.0 CD2 A:HIS623 3.4 89.2 1.0 CB A:HIS623 3.7 67.9 1.0 CG A:HIS623 3.7 81.8 1.0 CB A:GLN677 3.8 45.4 1.0 NZ A:LYS585 4.2 71.3 1.0 OE1 A:GLN677 4.2 72.6 1.0 NE2 A:HIS623 4.4 97.1 1.0 CE A:LYS585 4.5 61.0 1.0 O A:HOH1029 4.6 53.7 1.0 CA A:GLN677 4.9 42.3 1.0 ND1 A:HIS623 4.9 87.9 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of the SGIP1 Mu Homology Domain in Complex with An EPS15 Fragment Containing Two Dpf Motifs (Ydpfggdpfkg)


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 Complex with An EPS15 Fragment Containing Two Dpf Motifs (Ydpfggdpfkg) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn906 b:0.6 occ:1.00 OD1 A:ASP758 3.4 0.8 1.0 OD2 A:ASP758 3.8 1.0 1.0 CG A:ASP758 4.0 0.7 1.0 O A:PRO757 4.6 81.5 1.0 ND2 A:ASN721 4.6 53.8 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