Zinc in PDB 2iyb: Structure of Complex Between the 3RD Lim Domain of Tes and the EVH1 Domain of Mena

The structure of Structure of Complex Between the 3RD Lim Domain of Tes and the EVH1 Domain of Mena, PDB code: 2iyb was solved by D.C.Briggs, N.Q.Mcdonald, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.96 / 2.35
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	66.548, 292.927, 37.126, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 25.9

The binding sites of Zinc atom in the Structure of Complex Between the 3RD Lim Domain of Tes and the EVH1 Domain of Mena (pdb code 2iyb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Structure of Complex Between the 3RD Lim Domain of Tes and the EVH1 Domain of Mena, PDB code: 2iyb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Structure of Complex Between the 3RD Lim Domain of Tes and the EVH1 Domain of Mena


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Complex Between the 3RD Lim Domain of Tes and the EVH1 Domain of Mena within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1422 b:26.2 occ:1.00 SG E:CYS388 2.2 25.9 1.0 ND1 E:HIS383 2.2 24.9 1.0 SG E:CYS364 2.3 23.5 1.0 SG E:CYS361 2.4 24.6 1.0 CB E:CYS361 3.0 24.2 1.0 CB E:CYS388 3.1 27.1 1.0 CG E:HIS383 3.2 25.7 1.0 CE1 E:HIS383 3.2 25.6 1.0 CB E:CYS364 3.3 22.9 1.0 CB E:HIS383 3.5 26.6 1.0 N E:CYS364 3.7 23.0 1.0 N E:HIS383 4.0 26.3 1.0 CA E:CYS364 4.1 22.9 1.0 NE2 E:HIS383 4.3 25.2 1.0 CD2 E:HIS383 4.3 25.3 1.0 OG1 E:THR386 4.4 33.7 1.0 CA E:HIS383 4.4 26.8 1.0 CA E:CYS388 4.5 26.9 1.0 CA E:CYS361 4.5 24.5 1.0 C E:GLY363 4.7 23.2 1.0 CA E:GLY363 4.9 23.1 1.0 C E:CYS364 4.9 22.7 1.0

Zinc binding site 2 out of 9 in the Structure of Complex Between the 3RD Lim Domain of Tes and the EVH1 Domain of Mena


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Complex Between the 3RD Lim Domain of Tes and the EVH1 Domain of Mena within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1423 b:22.7 occ:1.00 SG E:CYS412 2.2 25.8 1.0 SG E:CYS394 2.3 20.8 1.0 SG E:CYS391 2.3 20.4 1.0 SG E:CYS416 2.4 27.1 1.0 CB E:CYS412 2.7 26.9 1.0 CB E:CYS391 3.1 21.6 1.0 CB E:CYS416 3.2 28.3 1.0 CB E:CYS394 3.4 22.5 1.0 N E:CYS394 3.8 23.1 1.0 CA E:CYS412 4.2 26.3 1.0 CA E:CYS394 4.2 22.5 1.0 OG E:SER413 4.5 27.7 1.0 CA E:CYS391 4.6 21.6 1.0 CB E:CYS393 4.6 23.1 1.0 CA E:CYS416 4.7 28.4 1.0 N E:SER413 4.7 26.9 1.0 CB E:LYS396 4.8 23.2 1.0 C E:CYS412 4.8 26.5 1.0 C E:CYS394 4.8 22.7 1.0 C E:CYS393 4.9 23.2 1.0

Zinc binding site 3 out of 9 in the Structure of Complex Between the 3RD Lim Domain of Tes and the EVH1 Domain of Mena


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Complex Between the 3RD Lim Domain of Tes and the EVH1 Domain of Mena within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1424 b:45.9 occ:1.00 OE1 E:GLU387 2.2 36.6 1.0 SG E:CYS397 2.5 23.6 1.0 O E:HOH2040 2.6 24.6 1.0 O E:HOH2042 2.8 27.3 1.0 O E:HOH2041 2.9 46.3 1.0 CD E:GLU387 3.0 36.4 1.0 OE2 E:GLU387 3.0 36.9 1.0 CB E:CYS397 3.4 22.6 1.0 O E:HOH2029 4.2 27.1 1.0 CG E:GLU387 4.4 33.7 1.0 CD1 E:ILE399 4.5 24.1 1.0 CA E:CYS397 4.8 22.4 1.0

Zinc binding site 4 out of 9 in the Structure of Complex Between the 3RD Lim Domain of Tes and the EVH1 Domain of Mena


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Complex Between the 3RD Lim Domain of Tes and the EVH1 Domain of Mena within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1421 b:21.5 occ:1.00 ND1 F:HIS383 2.2 21.4 1.0 SG F:CYS388 2.2 23.0 1.0 SG F:CYS364 2.4 20.4 1.0 SG F:CYS361 2.4 23.8 1.0 CB F:CYS361 3.1 24.1 1.0 CE1 F:HIS383 3.1 21.6 1.0 CG F:HIS383 3.1 23.2 1.0 CB F:CYS388 3.2 25.9 1.0 CB F:CYS364 3.2 21.4 1.0 CB F:HIS383 3.4 24.2 1.0 N F:CYS364 3.7 22.2 1.0 N F:HIS383 4.1 24.0 1.0 CA F:CYS364 4.1 21.4 1.0 O F:HOH2019 4.2 35.8 1.0 NE2 F:HIS383 4.2 21.5 1.0 CD2 F:HIS383 4.3 22.6 1.0 CA F:HIS383 4.4 24.4 1.0 CA F:CYS388 4.5 26.1 1.0 CA F:CYS361 4.6 24.6 1.0 C F:GLY363 4.8 22.8 1.0 CA F:GLY363 5.0 23.3 1.0 C F:CYS364 5.0 21.3 1.0

Zinc binding site 5 out of 9 in the Structure of Complex Between the 3RD Lim Domain of Tes and the EVH1 Domain of Mena


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Complex Between the 3RD Lim Domain of Tes and the EVH1 Domain of Mena within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1422 b:22.8 occ:1.00 SG F:CYS412 2.2 29.8 1.0 SG F:CYS394 2.3 17.7 1.0 SG F:CYS416 2.3 25.8 1.0 SG F:CYS391 2.3 19.6 1.0 CB F:CYS412 2.6 30.5 1.0 CB F:CYS391 3.1 20.7 1.0 CB F:CYS416 3.2 27.8 1.0 CB F:CYS394 3.5 20.2 1.0 N F:CYS394 3.8 20.8 1.0 CA F:CYS412 4.1 29.7 1.0 CA F:CYS394 4.2 20.3 1.0 CB F:CYS393 4.5 21.4 1.0 OG F:SER413 4.5 29.8 1.0 CA F:CYS391 4.6 20.7 1.0 CA F:CYS416 4.7 27.7 1.0 CB F:LYS396 4.7 22.5 1.0 N F:SER413 4.8 29.9 1.0 C F:CYS412 4.8 29.9 1.0 C F:CYS393 4.9 21.3 1.0 C F:CYS394 4.9 20.5 1.0

Zinc binding site 6 out of 9 in the Structure of Complex Between the 3RD Lim Domain of Tes and the EVH1 Domain of Mena


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Complex Between the 3RD Lim Domain of Tes and the EVH1 Domain of Mena within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1421 b:27.9 occ:1.00 ND1 G:HIS383 2.1 27.8 1.0 SG G:CYS361 2.3 29.2 1.0 SG G:CYS388 2.3 32.7 1.0 SG G:CYS364 2.3 25.0 1.0 CB G:CYS361 3.0 28.9 1.0 CE1 G:HIS383 3.0 28.0 1.0 CG G:HIS383 3.2 28.5 1.0 CB G:CYS364 3.3 25.2 1.0 CB G:CYS388 3.3 35.3 1.0 CB G:HIS383 3.5 29.1 1.0 N G:CYS364 3.7 25.9 1.0 CA G:CYS364 4.1 25.4 1.0 N G:HIS383 4.1 29.0 1.0 NE2 G:HIS383 4.1 27.3 1.0 CD2 G:HIS383 4.2 28.1 1.0 CA G:HIS383 4.5 29.5 1.0 CA G:CYS361 4.5 29.2 1.0 CA G:CYS388 4.5 35.5 1.0 C G:GLY363 4.7 26.6 1.0 O G:ASN366 4.9 23.7 1.0 C G:CYS364 4.9 25.0 1.0 CA G:GLY363 4.9 27.1 1.0

Zinc binding site 7 out of 9 in the Structure of Complex Between the 3RD Lim Domain of Tes and the EVH1 Domain of Mena


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Complex Between the 3RD Lim Domain of Tes and the EVH1 Domain of Mena within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1422 b:39.5 occ:1.00 SG G:CYS394 2.2 36.8 1.0 SG G:CYS416 2.3 47.1 1.0 SG G:CYS391 2.3 36.8 1.0 SG G:CYS412 2.4 37.9 1.0 CB G:CYS391 3.2 36.2 1.0 CB G:CYS416 3.3 46.7 1.0 CB G:CYS394 3.4 36.5 1.0 CB G:CYS412 3.7 38.8 1.0 N G:CYS394 3.7 36.7 1.0 N G:CYS412 4.1 38.1 1.0 CA G:CYS394 4.1 36.6 1.0 CB G:CYS393 4.4 36.5 1.0 CA G:CYS412 4.5 39.0 1.0 CA G:CYS391 4.6 36.4 1.0 OG G:SER413 4.6 41.7 1.0 CA G:CYS416 4.7 46.8 1.0 C G:CYS393 4.8 36.7 1.0 C G:CYS394 4.8 36.6 1.0 CB G:LYS396 4.9 36.2 1.0 N G:SER395 5.0 36.5 1.0

Zinc binding site 8 out of 9 in the Structure of Complex Between the 3RD Lim Domain of Tes and the EVH1 Domain of Mena


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Complex Between the 3RD Lim Domain of Tes and the EVH1 Domain of Mena within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn1421 b:25.6 occ:1.00 ND1 H:HIS383 2.1 26.1 1.0 SG H:CYS364 2.2 25.3 1.0 SG H:CYS388 2.2 29.8 1.0 SG H:CYS361 2.4 24.7 1.0 CB H:CYS361 3.0 24.9 1.0 CE1 H:HIS383 3.0 26.7 1.0 CG H:HIS383 3.1 27.3 1.0 CB H:CYS364 3.2 23.5 1.0 CB H:CYS388 3.2 32.6 1.0 CB H:HIS383 3.5 27.8 1.0 N H:CYS364 3.7 23.4 1.0 CA H:CYS364 4.0 23.6 1.0 N H:HIS383 4.1 27.4 1.0 NE2 H:HIS383 4.2 26.9 1.0 CD2 H:HIS383 4.2 27.4 1.0 CA H:HIS383 4.4 27.8 1.0 CA H:CYS361 4.5 25.2 1.0 CA H:CYS388 4.5 32.8 1.0 C H:GLY363 4.7 23.4 1.0 C H:CYS364 4.9 23.2 1.0 O H:ASN366 5.0 22.9 1.0

Zinc binding site 9 out of 9 in the Structure of Complex Between the 3RD Lim Domain of Tes and the EVH1 Domain of Mena


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Complex Between the 3RD Lim Domain of Tes and the EVH1 Domain of Mena within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn1422 b:36.6 occ:1.00 SG H:CYS391 2.1 31.8 1.0 SG H:CYS394 2.2 31.1 1.0 SG H:CYS412 2.4 35.1 1.0 SG H:CYS416 2.4 36.0 1.0 CB H:CYS391 3.2 31.7 1.0 CB H:CYS416 3.2 37.1 1.0 CB H:CYS394 3.4 31.1 1.0 CB H:CYS412 3.5 34.2 1.0 N H:CYS394 3.7 31.3 1.0 N H:CYS412 4.0 33.6 1.0 O H:HOH2024 4.1 45.5 1.0 CA H:CYS394 4.1 31.1 1.0 CA H:CYS412 4.3 34.3 1.0 OG H:SER413 4.4 34.8 1.0 CB H:CYS393 4.5 31.1 1.0 CA H:CYS391 4.6 31.6 1.0 CB H:LYS396 4.7 31.1 1.0 CA H:CYS416 4.7 37.3 1.0 C H:CYS394 4.8 31.1 1.0 C H:CYS393 4.8 31.4 1.0 N H:SER413 4.9 35.1 1.0 C H:CYS412 5.0 34.5 1.0 N H:SER395 5.0 30.7 1.0

B.Boeda, D.C.Briggs, T.Higgins, B.K.Garvalov, A.J.Fadden, N.Q.Mcdonald, M.Way. Tes, A Specific Mena Interacting Partner, Breaks the Rules For EVH1 Binding. Mol. Cell V. 28 1071 2007.
ISSN: ISSN 1097-2765
PubMed: 18158903
DOI: 10.1016/J.MOLCEL.2007.10.033