Atomistry » Zinc » PDB 5amj-5b2p » 5awr
Atomistry »
  Zinc »
    PDB 5amj-5b2p »
      5awr »

Zinc in PDB 5awr: Crystal Structure of the SGIP1 Mu Homology Domain in the P4212 Space Group

Protein crystallography data

The structure of Crystal Structure of the SGIP1 Mu Homology Domain in the P4212 Space Group, PDB code: 5awr 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) 38.83 / 2.50
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 109.826, 109.826, 79.492, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 24.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the SGIP1 Mu Homology Domain in the P4212 Space Group (pdb code 5awr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the SGIP1 Mu Homology Domain in the P4212 Space Group, PDB code: 5awr:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5awr

Go back to Zinc Binding Sites List in 5awr
Zinc binding site 1 out of 4 in the Crystal Structure of the SGIP1 Mu Homology Domain in the P4212 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 P4212 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:0.5
occ:1.00
O A:HOH1033 2.5 70.0 1.0
OE2 A:GLU589 2.6 76.5 1.0
OE1 A:GLU589 2.7 82.7 1.0
OD2 A:ASP672 2.8 75.2 1.0
CD A:GLU589 3.0 76.8 1.0
OD1 A:ASP672 3.1 71.2 1.0
CG A:ASP672 3.3 68.9 1.0
NZ A:LYS675 4.3 55.9 1.0
CG A:GLU589 4.5 67.1 1.0
CG2 A:VAL591 4.8 43.2 1.0
CB A:ASP672 4.8 58.5 1.0

Zinc binding site 2 out of 4 in 5awr

Go back to Zinc Binding Sites List in 5awr
Zinc binding site 2 out of 4 in the Crystal Structure of the SGIP1 Mu Homology Domain in the P4212 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 P4212 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:92.5
occ:1.00
ND1 A:HIS601 1.9 88.1 1.0
CE1 A:HIS601 2.3 87.3 1.0
OD2 A:ASP558 2.3 0.1 1.0
CG A:HIS601 3.1 83.4 1.0
CG A:ASP558 3.2 0.5 1.0
OD1 A:ASP558 3.3 0.0 1.0
NE2 A:HIS601 3.4 82.7 1.0
CD2 A:HIS601 3.8 78.3 1.0
CB A:HIS601 3.9 83.0 1.0
CA A:HIS601 4.5 85.4 1.0
CB A:ASP558 4.6 0.7 1.0
O A:ASP558 4.6 0.9 1.0
ND2 A:ASN605 4.8 0.7 1.0
CA A:ASP558 5.0 0.5 1.0

Zinc binding site 3 out of 4 in 5awr

Go back to Zinc Binding Sites List in 5awr
Zinc binding site 3 out of 4 in the Crystal Structure of the SGIP1 Mu Homology Domain in the P4212 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 P4212 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn903

b:72.4
occ:1.00
ND1 A:HIS655 1.9 56.1 1.0
O A:HOH1031 2.3 51.2 1.0
O A:HOH1016 2.3 36.7 1.0
O A:HOH1030 2.5 44.3 1.0
CE1 A:HIS655 2.7 53.6 1.0
CG A:HIS655 3.1 56.2 1.0
NZ A:LYS658 3.3 86.6 1.0
CB A:HIS655 3.6 53.5 1.0
NE2 A:HIS655 3.9 52.8 1.0
O A:HOH1015 4.0 53.2 1.0
CD2 A:HIS655 4.1 54.7 1.0
CA A:HIS655 4.2 60.0 1.0
CE A:LYS658 4.4 87.8 1.0

Zinc binding site 4 out of 4 in 5awr

Go back to Zinc Binding Sites List in 5awr
Zinc binding site 4 out of 4 in the Crystal Structure of the SGIP1 Mu Homology Domain in the P4212 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 P4212 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn904

b:0.4
occ:1.00
O A:HOH1027 2.6 54.5 1.0
O A:THR642 3.8 81.5 1.0
OE2 A:GLU644 4.0 1.0 1.0
CG A:GLU644 4.3 85.2 1.0
CB A:ASP639 4.3 0.4 1.0
CD A:GLU644 4.4 97.6 1.0
N A:GLU644 4.4 65.9 1.0
CG2 A:THR642 4.6 84.6 1.0
C A:THR642 4.7 75.2 1.0
CA A:LYS643 4.7 64.3 1.0
CB A:GLU644 4.9 71.6 1.0
C A:LYS643 5.0 62.9 1.0

Reference:

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
Page generated: Sun Oct 27 13:12:43 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy