Zinc in PDB 4ege: Crystal Structure of Dipeptidase Pepe From Mycobacterium Ulcerans

The structure of Crystal Structure of Dipeptidase Pepe From Mycobacterium Ulcerans, PDB code: 4ege was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.20
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	120.420, 120.420, 58.240, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 24.6

The binding sites of Zinc atom in the Crystal Structure of Dipeptidase Pepe From Mycobacterium Ulcerans (pdb code 4ege). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of Dipeptidase Pepe From Mycobacterium Ulcerans, PDB code: 4ege:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Crystal Structure of Dipeptidase Pepe From Mycobacterium Ulcerans


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 Dipeptidase Pepe From Mycobacterium Ulcerans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn409 b:24.8 occ:1.00 OE1 A:GLU368 1.9 14.8 1.0 CD A:GLU368 2.7 15.1 1.0 OE2 A:GLU368 2.8 15.4 1.0 UNK A:UNX422 3.0 2.0 1.0 ZN A:ZN410 3.3 23.7 1.0 NE2 A:GLN264 3.9 12.2 1.0 CG A:GLU368 4.2 15.2 1.0 N A:HIS367 4.3 14.2 1.0 UNK A:UNX423 4.4 19.4 1.0 CB A:HIS367 4.7 14.1 1.0 N A:GLU368 4.7 15.5 1.0 O A:HOH567 4.7 17.4 1.0 CA A:HIS367 4.9 14.3 1.0 ND1 A:HIS367 5.0 14.5 1.0

Zinc binding site 2 out of 9 in the Crystal Structure of Dipeptidase Pepe From Mycobacterium Ulcerans


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 Dipeptidase Pepe From Mycobacterium Ulcerans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn410 b:23.7 occ:1.00 ND1 A:HIS367 2.1 14.5 1.0 UNK A:UNX423 2.2 19.4 1.0 UNK A:UNX422 3.1 2.0 1.0 CE1 A:HIS367 3.1 14.6 1.0 CG A:HIS367 3.1 14.0 1.0 ZN A:ZN409 3.3 24.8 1.0 CB A:HIS367 3.5 14.1 1.0 NH2 A:ARG268 3.7 24.3 1.0 N A:HIS367 3.8 14.2 1.0 O A:HOH567 3.8 17.4 1.0 O A:HOH640 4.0 31.5 1.0 NE2 A:HIS367 4.2 14.7 1.0 CA A:HIS367 4.3 14.3 1.0 CD2 A:HIS367 4.3 13.6 1.0 O A:ARG365 4.7 15.7 1.0 CZ A:ARG268 4.7 24.3 1.0 C A:PRO366 4.7 15.1 1.0 OE1 A:GLU368 4.8 14.8 1.0 CA A:PRO366 4.8 14.3 1.0 OE2 A:GLU368 4.9 15.4 1.0 NE2 A:GLN264 4.9 12.2 1.0

Zinc binding site 3 out of 9 in the Crystal Structure of Dipeptidase Pepe From Mycobacterium Ulcerans


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 Dipeptidase Pepe From Mycobacterium Ulcerans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn411 b:19.0 occ:1.00 OD2 A:ASP242 2.0 13.3 1.0 NE2 A:HIS306 2.1 15.3 1.0 OE2 A:GLU349 2.1 13.3 1.0 OE2 A:GLU335 2.2 16.6 1.0 UNK A:UNX418 2.3 19.6 1.0 CG A:ASP242 3.0 14.9 1.0 CD A:GLU349 3.1 14.1 1.0 ZN A:ZN412 3.1 23.1 1.0 CD2 A:HIS306 3.1 15.2 1.0 CE1 A:HIS306 3.1 15.7 1.0 UNK A:UNX420 3.1 10.3 1.0 CD A:GLU335 3.2 17.5 1.0 OE1 A:GLU349 3.3 14.3 1.0 OD1 A:ASP242 3.4 15.3 1.0 OE1 A:GLU335 3.6 18.4 1.0 OG A:SER333 4.0 13.9 1.0 CB A:SER333 4.0 13.3 1.0 ND1 A:HIS306 4.2 15.1 1.0 CG A:HIS306 4.2 15.4 1.0 CB A:ASP242 4.3 14.8 1.0 UNK A:UNX421 4.3 33.2 1.0 CG A:GLU349 4.4 14.1 1.0 CG A:GLU335 4.4 16.7 1.0 NE2 A:HIS313 4.5 21.5 1.0 UNK A:UNX419 4.7 31.0 1.0 CD2 A:HIS313 4.9 19.3 1.0

Zinc binding site 4 out of 9 in the Crystal Structure of Dipeptidase Pepe From Mycobacterium Ulcerans


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 Dipeptidase Pepe From Mycobacterium Ulcerans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn412 b:23.1 occ:1.00 OD1 A:ASP242 2.0 15.3 1.0 OE1 A:GLU349 2.1 14.3 1.0 OD1 A:ASP230 2.1 14.6 1.0 UNK A:UNX418 2.2 19.6 1.0 OD2 A:ASP230 2.6 14.0 1.0 CG A:ASP230 2.7 14.4 1.0 CG A:ASP242 2.9 14.9 1.0 CD A:GLU349 3.0 14.1 1.0 ZN A:ZN411 3.1 19.0 1.0 OD2 A:ASP242 3.1 13.3 1.0 OE2 A:GLU349 3.3 13.3 1.0 OG1 A:THR244 3.7 12.8 1.0 UNK A:UNX420 3.7 10.3 1.0 UNK A:UNX419 4.0 31.0 1.0 CE1 A:PHE200 4.0 18.4 1.0 CZ A:PHE200 4.1 19.9 1.0 CB A:ASP230 4.2 14.0 1.0 CB A:ASP242 4.3 14.8 1.0 OE1 A:GLU335 4.3 18.4 1.0 CG A:GLU349 4.4 14.1 1.0 OE2 A:GLU335 4.5 16.6 1.0 C A:ASP242 4.5 14.7 1.0 N A:SER243 4.6 14.2 1.0 CA A:ASP242 4.7 14.4 1.0 CD A:GLU335 4.7 17.5 1.0 O A:ASP242 4.8 15.0 1.0 CA A:ASP230 4.8 14.1 1.0 CB A:GLU349 4.9 13.5 1.0 C A:SER243 4.9 13.9 1.0

Zinc binding site 5 out of 9 in the Crystal Structure of Dipeptidase Pepe From Mycobacterium Ulcerans


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 Dipeptidase Pepe From Mycobacterium Ulcerans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn413 b:88.6 occ:1.00 OD2 A:ASP37 2.5 18.8 1.0 O A:HOH604 2.8 27.4 1.0 OD1 A:ASP37 3.0 19.6 1.0 OD1 A:ASP115 3.0 23.6 1.0 CG A:ASP37 3.1 18.6 1.0 O A:HOH663 3.1 43.4 1.0 CG A:ASP115 3.2 21.3 1.0 OD2 A:ASP115 3.3 24.1 1.0 O2 A:EDO405 3.5 35.7 1.0 NH1 A:ARG144 3.7 17.4 1.0 O A:HOH662 3.9 36.6 1.0 OG1 A:THR114 4.0 12.9 1.0 N A:ASP115 4.1 15.4 1.0 CB A:ASP115 4.4 19.4 1.0 CB A:ASP37 4.5 16.7 1.0 CA A:ASP115 4.8 16.4 1.0 C2 A:EDO405 4.8 31.9 1.0 CZ A:ARG144 4.9 18.1 1.0 OG1 A:THR137 4.9 19.4 1.0

Zinc binding site 6 out of 9 in the Crystal Structure of Dipeptidase Pepe From Mycobacterium Ulcerans


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 Dipeptidase Pepe From Mycobacterium Ulcerans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn414 b:32.8 occ:1.00 O A:HOH628 2.0 17.8 1.0 OE1 A:GLU50 2.0 12.8 1.0 CD A:GLU50 2.8 13.0 1.0 O A:HOH598 2.8 26.8 1.0 OE2 A:GLU50 2.9 12.8 1.0 CB A:PHE49 3.9 16.6 1.0 N A:GLU50 4.1 13.2 1.0 CG A:GLU50 4.2 12.9 1.0 N A:PHE49 4.4 18.7 1.0 CA A:PHE49 4.6 16.6 1.0 CB A:GLU50 4.8 12.6 1.0 C A:PHE49 4.9 14.8 1.0

Zinc binding site 7 out of 9 in the Crystal Structure of Dipeptidase Pepe From Mycobacterium Ulcerans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Dipeptidase Pepe From Mycobacterium Ulcerans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn415 b:42.0 occ:1.00 O A:HOH629 2.1 18.3 1.0 SG A:CYS86 2.4 25.2 1.0 CB A:CYS86 3.2 20.6 1.0 CA A:CYS86 3.6 18.9 1.0 NH1 A:ARG88 4.0 16.2 1.0 NH2 A:ARG88 4.0 15.8 1.0 CZ A:ARG88 4.4 16.2 1.0 N A:CYS86 4.6 18.3 1.0 N A:VAL87 4.7 17.4 1.0 C A:CYS86 4.7 17.2 1.0

Zinc binding site 8 out of 9 in the Crystal Structure of Dipeptidase Pepe From Mycobacterium Ulcerans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Dipeptidase Pepe From Mycobacterium Ulcerans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn416 b:47.9 occ:1.00 NE2 A:HIS208 2.1 20.7 1.0 O A:HOH638 2.2 32.1 1.0 O A:HOH648 2.4 50.6 1.0 O A:HOH637 2.7 38.4 1.0 CE1 A:HIS208 3.0 19.4 1.0 CD2 A:HIS208 3.1 19.3 1.0 ND1 A:HIS208 4.1 19.3 1.0 CG A:HIS208 4.2 19.6 1.0

Zinc binding site 9 out of 9 in the Crystal Structure of Dipeptidase Pepe From Mycobacterium Ulcerans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Dipeptidase Pepe From Mycobacterium Ulcerans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn417 b:54.6 occ:1.00 OE1 A:GLU71 2.3 26.7 1.0 O A:HOH606 2.7 43.1 1.0 O A:HOH607 2.8 30.7 1.0 OE2 A:GLU71 2.9 29.4 1.0 CD A:GLU71 2.9 26.9 1.0 CG A:GLU71 4.4 23.8 1.0 CG2 A:THR48 5.0 20.6 1.0

L.Baugh, I.Phan, D.W.Begley, M.C.Clifton, B.Armour, D.M.Dranow, B.M.Taylor, M.M.Muruthi, J.Abendroth, J.W.Fairman, D.Fox, S.H.Dieterich, B.L.Staker, A.S.Gardberg, R.Choi, S.N.Hewitt, A.J.Napuli, J.Myers, L.K.Barrett, Y.Zhang, M.Ferrell, E.Mundt, K.Thompkins, N.Tran, S.Lyons-Abbott, A.Abramov, A.Sekar, D.Serbzhinskiy, D.Lorimer, G.W.Buchko, R.Stacy, L.J.Stewart, T.E.Edwards, W.C.Van Voorhis, P.J.Myler. Increasing the Structural Coverage of Tuberculosis Drug Targets. Tuberculosis (Edinb) V. 95 142 2015.
ISSN: ISSN 1472-9792
PubMed: 25613812
DOI: 10.1016/J.TUBE.2014.12.003