Zinc in PDB 3mdw: The Structure of N-Formimino-L-Glutamate Iminohydrolase From Pseudomonas Aeruginosa Complexed with N-Formimino-L-Aspartate

The structure of The Structure of N-Formimino-L-Glutamate Iminohydrolase From Pseudomonas Aeruginosa Complexed with N-Formimino-L-Aspartate, PDB code: 3mdw was solved by A.A.Fedorov, E.V.Fedorov, R.Marti-Arbona, F.M.Raushel, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.43 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	304.046, 67.247, 98.229, 90.00, 91.50, 90.00
R / Rfree (%)	17 / 20.3

The binding sites of Zinc atom in the The Structure of N-Formimino-L-Glutamate Iminohydrolase From Pseudomonas Aeruginosa Complexed with N-Formimino-L-Aspartate (pdb code 3mdw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Structure of N-Formimino-L-Glutamate Iminohydrolase From Pseudomonas Aeruginosa Complexed with N-Formimino-L-Aspartate, PDB code: 3mdw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the The Structure of N-Formimino-L-Glutamate Iminohydrolase From Pseudomonas Aeruginosa Complexed with N-Formimino-L-Aspartate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of N-Formimino-L-Glutamate Iminohydrolase From Pseudomonas Aeruginosa Complexed with N-Formimino-L-Aspartate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn455 b:29.0 occ:0.94 O A:HOH1026 2.1 20.6 1.0 NE2 A:HIS58 2.1 14.7 1.0 NE2 A:HIS56 2.1 16.8 1.0 NE2 A:HIS232 2.2 16.2 1.0 OD1 A:ASP320 2.8 18.8 1.0 CE1 A:HIS58 3.0 17.2 1.0 CE1 A:HIS56 3.0 16.1 1.0 CD2 A:HIS58 3.0 16.9 1.0 CD2 A:HIS56 3.1 15.6 1.0 CD2 A:HIS232 3.1 17.2 1.0 CE1 A:HIS232 3.1 18.2 1.0 CG A:ASP320 3.5 18.3 1.0 OD2 A:ASP320 3.6 23.1 1.0 NE2 A:HIS269 4.0 20.3 1.0 ND1 A:HIS58 4.1 17.1 1.0 ND1 A:HIS56 4.1 15.8 1.0 CG A:HIS58 4.1 13.9 1.0 O A:HOH508 4.2 18.4 1.0 N A:NFQ454 4.2 19.0 1.0 CG A:HIS56 4.2 13.3 1.0 ND1 A:HIS232 4.2 19.8 1.0 CG A:HIS232 4.3 18.8 1.0 CF A:NFQ454 4.4 18.1 1.0 O1 A:NFQ454 4.5 20.5 1.0 CA A:NFQ454 4.5 17.8 1.0 NF A:NFQ454 4.6 19.0 1.0 C A:NFQ454 4.6 19.3 1.0 CG1 A:VAL268 4.7 14.8 1.0 CB A:ASP320 4.7 17.0 1.0 CE1 A:HIS269 4.7 18.2 1.0 CD2 A:HIS269 4.9 19.4 1.0

Zinc binding site 2 out of 4 in the The Structure of N-Formimino-L-Glutamate Iminohydrolase From Pseudomonas Aeruginosa Complexed with N-Formimino-L-Aspartate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of N-Formimino-L-Glutamate Iminohydrolase From Pseudomonas Aeruginosa Complexed with N-Formimino-L-Aspartate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn455 b:26.1 occ:0.96 O B:HOH1021 2.0 18.7 1.0 NE2 B:HIS58 2.1 18.8 1.0 NE2 B:HIS56 2.1 16.0 1.0 NE2 B:HIS232 2.2 21.4 1.0 OD1 B:ASP320 2.6 18.9 1.0 CE1 B:HIS58 3.0 21.6 1.0 CE1 B:HIS56 3.0 13.9 1.0 CD2 B:HIS58 3.1 18.4 1.0 CD2 B:HIS232 3.1 16.0 1.0 CD2 B:HIS56 3.1 13.0 1.0 CE1 B:HIS232 3.2 20.0 1.0 CG B:ASP320 3.4 19.8 1.0 OD2 B:ASP320 3.6 20.8 1.0 O B:HOH495 4.0 23.9 1.0 N B:NFQ454 4.0 28.8 1.0 NE2 B:HIS269 4.1 18.1 1.0 ND1 B:HIS58 4.1 21.6 1.0 ND1 B:HIS56 4.2 14.1 1.0 CG B:HIS58 4.2 17.2 1.0 CG B:HIS56 4.3 14.1 1.0 CG B:HIS232 4.3 18.9 1.0 ND1 B:HIS232 4.3 17.9 1.0 CA B:NFQ454 4.4 26.7 1.0 C B:NFQ454 4.4 27.0 1.0 CF B:NFQ454 4.5 26.4 1.0 NF B:NFQ454 4.5 28.1 1.0 O2 B:NFQ454 4.5 25.1 1.0 CB B:ASP320 4.7 16.7 1.0 CE1 B:HIS269 4.8 18.9 1.0 CG1 B:VAL268 4.9 13.6 1.0

Zinc binding site 3 out of 4 in the The Structure of N-Formimino-L-Glutamate Iminohydrolase From Pseudomonas Aeruginosa Complexed with N-Formimino-L-Aspartate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure of N-Formimino-L-Glutamate Iminohydrolase From Pseudomonas Aeruginosa Complexed with N-Formimino-L-Aspartate within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn455 b:26.0 occ:0.95 NE2 C:HIS56 2.0 12.9 1.0 NE2 C:HIS58 2.1 16.2 1.0 O C:HOH1024 2.1 17.1 1.0 NE2 C:HIS232 2.2 15.1 1.0 OD1 C:ASP320 2.7 17.5 1.0 CE1 C:HIS56 3.0 15.2 1.0 CE1 C:HIS58 3.0 19.5 1.0 CD2 C:HIS58 3.0 17.5 1.0 CD2 C:HIS56 3.1 13.2 1.0 CD2 C:HIS232 3.1 16.1 1.0 CE1 C:HIS232 3.1 19.6 1.0 CG C:ASP320 3.4 20.1 1.0 OD2 C:ASP320 3.7 20.5 1.0 NE2 C:HIS269 4.0 18.2 1.0 ND1 C:HIS58 4.1 16.7 1.0 ND1 C:HIS56 4.1 13.8 1.0 O C:HOH489 4.1 20.1 1.0 CG C:HIS58 4.1 17.2 1.0 CG C:HIS56 4.2 14.5 1.0 N C:NFQ454 4.2 21.4 1.0 ND1 C:HIS232 4.2 16.0 1.0 CG C:HIS232 4.3 14.8 1.0 O1 C:NFQ454 4.4 21.7 1.0 CF C:NFQ454 4.5 26.0 1.0 CA C:NFQ454 4.5 24.8 1.0 NF C:NFQ454 4.6 22.8 1.0 C C:NFQ454 4.6 23.6 1.0 CB C:ASP320 4.7 16.4 1.0 CE1 C:HIS269 4.8 18.6 1.0 CG1 C:VAL268 4.8 14.2 1.0 CD2 C:HIS269 5.0 16.8 1.0

Zinc binding site 4 out of 4 in the The Structure of N-Formimino-L-Glutamate Iminohydrolase From Pseudomonas Aeruginosa Complexed with N-Formimino-L-Aspartate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structure of N-Formimino-L-Glutamate Iminohydrolase From Pseudomonas Aeruginosa Complexed with N-Formimino-L-Aspartate within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn455 b:26.4 occ:0.98 O D:HOH1023 2.0 20.5 1.0 NE2 D:HIS58 2.1 19.2 1.0 NE2 D:HIS56 2.1 16.6 1.0 NE2 D:HIS232 2.3 18.5 1.0 OD1 D:ASP320 2.6 16.4 1.0 CE1 D:HIS58 3.0 18.7 1.0 CD2 D:HIS58 3.0 18.7 1.0 CE1 D:HIS56 3.1 16.0 1.0 CD2 D:HIS56 3.1 15.8 1.0 CE1 D:HIS232 3.2 19.9 1.0 CD2 D:HIS232 3.2 16.9 1.0 CG D:ASP320 3.4 19.1 1.0 OD2 D:ASP320 3.6 22.6 1.0 O D:HOH511 3.9 22.8 1.0 NE2 D:HIS269 4.1 19.6 1.0 ND1 D:HIS58 4.1 18.7 1.0 CG D:HIS58 4.1 20.6 1.0 N D:NFQ454 4.2 27.4 1.0 ND1 D:HIS56 4.2 14.0 1.0 CG D:HIS56 4.3 14.4 1.0 ND1 D:HIS232 4.3 18.1 1.0 CG D:HIS232 4.4 16.5 1.0 O1 D:NFQ454 4.4 24.7 1.0 CF D:NFQ454 4.5 25.2 1.0 NF D:NFQ454 4.5 22.4 1.0 CA D:NFQ454 4.5 26.7 1.0 C D:NFQ454 4.5 25.1 1.0 CB D:ASP320 4.6 14.9 1.0 CE1 D:HIS269 4.8 19.6 1.0 CG1 D:VAL268 4.9 14.1 1.0 CD2 D:HIS269 5.0 17.0 1.0 CA D:ASP320 5.0 18.1 1.0

A.A.Fedorov, R.Marti-Arbona, V.V.Nemmara, D.Hitchcock, E.V.Fedorov, S.C.Almo, F.M.Raushel. Structure of N-Formimino-L-Glutamate Iminohydrolase From Pseudomonas Aeruginosa. Biochemistry V. 54 890 2015.
ISSN: ISSN 0006-2960
PubMed: 25559274
DOI: 10.1021/BI501299Y