Zinc in PDB 4ixm: Crystal Structure of Zn(II)-Bound Yjia Gtpase From E. Coli

The structure of Crystal Structure of Zn(II)-Bound Yjia Gtpase From E. Coli, PDB code: 4ixm was solved by M.Jost, K.S.Ryan, K.E.Turo, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.13 / 2.57
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.295, 68.869, 77.829, 90.00, 104.09, 90.00
R / Rfree (%)	22 / 26.2

The binding sites of Zinc atom in the Crystal Structure of Zn(II)-Bound Yjia Gtpase From E. Coli (pdb code 4ixm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Zn(II)-Bound Yjia Gtpase From E. Coli, PDB code: 4ixm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Zn(II)-Bound Yjia Gtpase From E. Coli


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 Zn(II)-Bound Yjia Gtpase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:89.7 occ:1.00 OE2 A:GLU42 2.1 0.1 1.0 OE1 A:GLU37 2.1 99.2 1.0 SG A:CYS66 2.3 97.3 1.0 CD A:GLU37 3.1 92.2 1.0 CD A:GLU42 3.2 0.9 1.0 CG A:GLU37 3.4 83.6 1.0 CG A:GLU42 3.6 0.5 1.0 O A:GLU39 3.7 0.6 1.0 CA A:PHE40 3.8 0.7 1.0 CB A:CYS66 4.0 76.1 1.0 N A:GLY41 4.1 0.5 1.0 OE2 A:GLU37 4.2 92.3 1.0 OE1 A:GLU42 4.3 0.4 1.0 C A:GLU39 4.4 1.0 1.0 N A:PHE40 4.4 0.6 1.0 C A:PHE40 4.5 0.3 1.0 CD1 A:LEU25 4.5 64.4 1.0 CD1 A:PHE40 4.5 0.6 1.0 CB A:PHE40 4.7 0.2 1.0 N A:GLU42 4.8 0.5 1.0 CB A:GLU37 4.9 77.0 1.0 CG A:PHE40 4.9 0.3 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Zn(II)-Bound Yjia Gtpase From E. Coli


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 Zn(II)-Bound Yjia Gtpase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:70.2 occ:1.00 NE2 B:HIS114 2.1 66.8 1.0 OE1 A:GLU74 2.1 70.4 1.0 NE2 A:HIS114 2.2 71.9 1.0 OE1 B:GLU74 2.2 75.7 1.0 CE1 B:HIS114 2.6 67.3 1.0 OE2 B:GLU74 2.6 71.9 1.0 OE2 A:GLU74 2.6 70.9 1.0 CD A:GLU74 2.7 68.9 1.0 CD B:GLU74 2.7 71.2 1.0 CD2 A:HIS114 3.1 69.0 1.0 CE1 A:HIS114 3.2 76.6 1.0 CD2 B:HIS114 3.3 66.9 1.0 ND1 B:HIS114 3.8 67.7 1.0 CG A:GLU74 4.2 68.6 1.0 CG B:HIS114 4.2 67.8 1.0 CG B:GLU74 4.2 67.7 1.0 CG A:HIS114 4.2 74.2 1.0 ND1 A:HIS114 4.3 77.1 1.0 OG A:SER113 4.5 66.0 1.0 CB A:SER113 4.5 68.5 1.0 OG B:SER113 4.7 75.4 1.0 CB B:SER113 4.8 72.3 1.0 OE1 B:GLU72 4.8 89.0 1.0 OE1 A:GLU72 4.9 79.0 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Zn(II)-Bound Yjia Gtpase From E. Coli


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 Zn(II)-Bound Yjia Gtpase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:89.3 occ:1.00 ND1 A:HIS170 2.2 89.1 1.0 OE1 A:GLU167 2.8 97.7 1.0 OE2 A:GLU167 2.8 98.3 1.0 CG A:HIS170 3.0 84.9 1.0 CD A:GLU167 3.1 98.1 1.0 CB A:HIS170 3.1 77.8 1.0 CE1 A:HIS170 3.3 90.6 1.0 CD2 A:HIS170 4.2 87.0 1.0 NE2 A:HIS170 4.3 90.0 1.0 CG A:GLU167 4.6 97.2 1.0 CA A:HIS170 4.7 71.7 1.0 O A:GLU167 4.9 89.0 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Zn(II)-Bound Yjia Gtpase From E. Coli


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 Zn(II)-Bound Yjia Gtpase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:89.7 occ:1.00 NE2 A:HIS187 2.1 0.5 1.0 CD2 A:HIS187 2.6 0.7 1.0 CE1 A:HIS187 3.4 0.7 1.0 CG A:HIS187 3.9 0.2 1.0 ND1 A:HIS187 4.2 0.4 1.0 CB A:THR186 4.9 0.8 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Zn(II)-Bound Yjia Gtpase From E. Coli


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 Zn(II)-Bound Yjia Gtpase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:94.4 occ:1.00 OE1 B:GLU37 2.1 85.9 1.0 OE2 B:GLU42 2.1 0.2 1.0 SG B:CYS66 2.3 0.7 1.0 CD B:GLU37 3.0 84.5 1.0 CD B:GLU42 3.2 0.5 1.0 CG B:GLU37 3.3 76.3 1.0 O B:GLU39 3.7 90.9 1.0 CG B:GLU42 3.7 0.0 1.0 CB B:CYS66 4.0 53.3 1.0 CA B:PHE40 4.0 0.4 1.0 OE2 B:GLU37 4.2 89.6 1.0 N B:GLY41 4.2 0.7 1.0 OE1 B:GLU42 4.3 0.8 1.0 C B:GLU39 4.4 95.1 1.0 CD1 B:LEU25 4.4 68.3 1.0 N B:PHE40 4.5 0.0 1.0 C B:PHE40 4.7 0.5 1.0 CB B:GLU37 4.9 69.9 1.0 CD1 B:PHE40 4.9 0.9 1.0 N B:GLU42 5.0 0.3 1.0 CB B:PHE40 5.0 0.1 1.0

A.M.Sydor, M.Jost, K.S.Ryan, K.E.Turo, C.D.Douglas, C.L.Drennan, D.B.Zamble. Metal Binding Properties of Escherichia Coli Yjia, A Member of the Metal Homeostasis-Associated COG0523 Family of Gtpases. Biochemistry V. 52 1788 2013.
ISSN: ISSN 0006-2960
PubMed: 24449932
DOI: 10.1021/BI301600Z