Zinc in PDB 6ifg: Crystal Structure of M1 Zinc Metallopeptidase E323A Mutant Bound to Tyr-Ser-Ala Substrate From Deinococcus Radiodurans

The structure of Crystal Structure of M1 Zinc Metallopeptidase E323A Mutant Bound to Tyr-Ser-Ala Substrate From Deinococcus Radiodurans, PDB code: 6ifg was solved by R.Agrawal, A.Kumar, A.Kumar, R.D.Makde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.14 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	51.598, 57.594, 69.321, 89.77, 82.14, 67.80
R / Rfree (%)	18.1 / 21.4

The binding sites of Zinc atom in the Crystal Structure of M1 Zinc Metallopeptidase E323A Mutant Bound to Tyr-Ser-Ala Substrate From Deinococcus Radiodurans (pdb code 6ifg). 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 M1 Zinc Metallopeptidase E323A Mutant Bound to Tyr-Ser-Ala Substrate From Deinococcus Radiodurans, PDB code: 6ifg:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of M1 Zinc Metallopeptidase E323A Mutant Bound to Tyr-Ser-Ala Substrate From Deinococcus Radiodurans


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 M1 Zinc Metallopeptidase E323A Mutant Bound to Tyr-Ser-Ala Substrate From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:17.7 occ:1.00 OE1 A:GLU345 1.9 16.2 1.0 NE2 A:HIS322 2.0 18.2 1.0 NE2 A:HIS326 2.2 15.7 1.0 O E:TYR1 2.5 20.1 1.0 N E:TYR1 2.5 22.7 1.0 CD A:GLU345 2.8 15.6 1.0 CE1 A:HIS322 3.0 18.5 1.0 CD2 A:HIS326 3.0 15.5 1.0 OE2 A:GLU345 3.0 15.6 1.0 CD2 A:HIS322 3.0 18.5 1.0 C E:TYR1 3.1 21.6 1.0 CE1 A:HIS326 3.3 15.4 1.0 CA E:TYR1 3.3 21.9 1.0 O A:HOH659 3.7 19.7 1.0 CE2 A:TYR396 4.0 16.3 1.0 OE1 A:GLU303 4.1 19.5 1.0 ND1 A:HIS322 4.1 18.7 1.0 OH A:TYR396 4.1 16.2 1.0 CG A:HIS322 4.1 18.2 1.0 CG A:HIS326 4.2 15.2 1.0 CG A:GLU345 4.2 15.1 1.0 N E:SER2 4.2 25.6 1.0 ND1 A:HIS326 4.3 15.4 1.0 CB E:TYR1 4.4 20.9 1.0 CZ A:TYR396 4.4 16.6 1.0 CA A:GLU345 4.5 14.3 1.0 O A:HOH608 4.5 25.8 1.0 OE2 A:GLU303 4.6 19.4 1.0 CB A:GLU345 4.6 14.8 1.0 CD A:GLU303 4.7 18.8 1.0 CB A:ALA348 4.8 15.6 1.0 CB E:SER2 4.8 29.3 1.0 CD2 A:TYR396 4.9 16.4 1.0 CA E:SER2 4.9 29.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of M1 Zinc Metallopeptidase E323A Mutant Bound to Tyr-Ser-Ala Substrate From Deinococcus Radiodurans


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 M1 Zinc Metallopeptidase E323A Mutant Bound to Tyr-Ser-Ala Substrate From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:26.2 occ:1.00 HO2 A:FMT503 1.8 26.6 1.0 OD1 A:ASP52 2.3 19.0 1.0 O A:VAL53 2.3 18.0 1.0 OD1 A:ASP181 2.3 16.0 1.0 O A:HOH719 2.4 16.0 1.0 O A:PRO182 2.4 14.4 1.0 O2 A:FMT503 2.6 22.1 1.0 C A:VAL53 3.4 17.5 1.0 CG A:ASP181 3.5 15.7 1.0 CG A:ASP52 3.6 18.7 1.0 C A:PRO182 3.6 14.3 1.0 C A:FMT503 3.6 22.1 1.0 N A:VAL53 3.9 15.8 1.0 C A:ASP181 4.0 15.6 1.0 O1 A:FMT503 4.0 22.1 1.0 C A:ASP52 4.1 15.9 1.0 N A:PRO182 4.1 16.3 1.0 CA A:ASP181 4.2 15.3 1.0 O A:HOH654 4.2 23.0 1.0 CA A:VAL53 4.2 16.2 1.0 O A:ASP181 4.2 15.6 1.0 CA A:ASP52 4.3 16.7 1.0 OD2 A:ASP181 4.3 15.9 1.0 N A:GLN54 4.3 18.7 1.0 OD2 A:ASP52 4.4 19.3 1.0 CA A:GLN54 4.4 19.9 1.0 H A:FMT503 4.5 26.6 1.0 CA A:PRO182 4.5 15.9 1.0 CB A:ASP181 4.5 15.7 1.0 CB A:ASP52 4.5 17.9 1.0 N A:ALA183 4.5 14.0 1.0 CA A:ALA183 4.6 13.8 1.0 CD A:PRO182 4.6 16.7 1.0 O A:HOH705 4.6 18.4 1.0 O A:HOH725 4.7 33.4 1.0 CB A:ALA183 4.7 12.5 1.0 O A:ASP52 4.7 15.5 1.0 CB A:VAL53 4.9 14.9 1.0 CG A:PRO182 4.9 16.9 1.0 H A:FMT505 4.9 37.3 1.0 CG A:GLN54 5.0 26.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of M1 Zinc Metallopeptidase E323A Mutant Bound to Tyr-Ser-Ala Substrate From Deinococcus Radiodurans


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 M1 Zinc Metallopeptidase E323A Mutant Bound to Tyr-Ser-Ala Substrate From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:19.7 occ:1.00 H2 F:TYR1 1.7 36.6 1.0 OE2 B:GLU345 1.9 18.7 1.0 NE2 B:HIS322 2.0 20.0 1.0 NE2 B:HIS326 2.1 18.9 1.0 O F:TYR1 2.5 27.7 1.0 N F:TYR1 2.6 30.5 1.0 CD B:GLU345 2.7 18.4 1.0 H1 F:TYR1 2.8 36.6 1.0 OE1 B:GLU345 2.9 18.4 1.0 CD2 B:HIS326 3.0 18.9 1.0 CE1 B:HIS322 3.0 20.2 1.0 CD2 B:HIS322 3.1 20.2 1.0 H3 F:TYR1 3.1 36.6 1.0 C F:TYR1 3.1 29.2 1.0 CE1 B:HIS326 3.2 18.9 1.0 HE2 B:TYR396 3.2 25.6 1.0 CA F:TYR1 3.4 29.3 1.0 HH B:TYR396 3.6 26.5 1.0 O B:HOH675 3.9 21.4 1.0 HB2 F:SER2 3.9 41.1 1.0 CE2 B:TYR396 3.9 21.3 1.0 HA F:TYR1 4.1 35.2 1.0 ND1 B:HIS322 4.1 20.3 1.0 OE1 B:GLU303 4.2 20.2 1.0 CG B:GLU345 4.2 17.9 1.0 CG B:HIS326 4.2 18.1 1.0 CG B:HIS322 4.2 19.9 1.0 OH B:TYR396 4.2 22.1 1.0 N F:SER2 4.2 32.6 1.0 HB2 F:TYR1 4.2 32.8 1.0 ND1 B:HIS326 4.3 18.6 1.0 CB F:TYR1 4.5 27.3 1.0 CZ B:TYR396 4.5 21.9 1.0 CA B:GLU345 4.5 16.9 1.0 O B:HOH606 4.6 21.0 1.0 CB B:GLU345 4.6 17.6 1.0 CB B:ALA348 4.7 18.0 1.0 OE2 B:GLU303 4.7 20.4 1.0 CD B:GLU303 4.7 19.8 1.0 CB F:SER2 4.8 34.3 1.0 H F:SER2 4.8 39.1 1.0 CD2 B:TYR396 4.9 21.0 1.0 HD2 B:TYR396 4.9 25.2 1.0 HB3 F:TYR1 4.9 32.8 1.0 CA F:SER2 4.9 36.4 1.0 HA F:SER2 5.0 43.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of M1 Zinc Metallopeptidase E323A Mutant Bound to Tyr-Ser-Ala Substrate From Deinococcus Radiodurans


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 M1 Zinc Metallopeptidase E323A Mutant Bound to Tyr-Ser-Ala Substrate From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:28.9 occ:1.00 HO2 B:FMT504 2.1 25.1 1.0 OD1 B:ASP181 2.3 15.8 1.0 O B:PRO182 2.3 13.8 1.0 O B:VAL53 2.4 17.2 1.0 OD1 B:ASP52 2.4 19.5 1.0 O B:HOH701 2.4 15.7 1.0 O2 B:FMT504 2.5 20.9 1.0 C B:VAL53 3.4 17.7 1.0 CG B:ASP181 3.5 15.8 1.0 C B:FMT504 3.5 20.8 1.0 C B:PRO182 3.5 14.6 1.0 CG B:ASP52 3.6 18.8 1.0 C B:ASP181 3.9 15.4 1.0 N B:VAL53 3.9 16.6 1.0 N B:PRO182 4.0 15.5 1.0 O1 B:FMT504 4.0 20.4 1.0 C B:ASP52 4.1 16.7 1.0 CA B:ASP181 4.1 15.7 1.0 H B:FMT504 4.2 25.0 1.0 OD2 B:ASP181 4.2 16.0 1.0 O B:ASP181 4.2 15.3 1.0 CA B:VAL53 4.3 16.8 1.0 O B:HOH661 4.3 20.6 1.0 N B:GLN54 4.3 19.8 1.0 CA B:ASP52 4.4 16.9 1.0 CA B:GLN54 4.4 21.9 1.0 CA B:PRO182 4.4 15.4 1.0 CB B:ASP181 4.4 15.9 1.0 OD2 B:ASP52 4.4 19.4 1.0 N B:ALA183 4.5 14.8 1.0 CA B:ALA183 4.5 15.0 1.0 CD B:PRO182 4.6 15.5 1.0 O B:HOH658 4.6 15.7 1.0 CB B:ASP52 4.6 17.8 1.0 CB B:ALA183 4.6 15.1 1.0 O B:ASP52 4.7 16.8 1.0 CG B:PRO182 4.9 15.7 1.0 CB B:VAL53 4.9 16.0 1.0

R.Agrawal, V.D.Goyal, A.Kumar, N.K.Gaur, S.N.Jamdar, A.Kumar, R.D.Makde. Two-Domain Aminopeptidase of M1 Family: Structural Features For Substrate Binding and Gating in Absence of C-Terminal Domain. J.Struct.Biol. V. 208 51 2019.
ISSN: ESSN 1095-8657
PubMed: 31351924
DOI: 10.1016/J.JSB.2019.07.010