Zinc in PDB 1u10: Mepa, Active Form with Zn in P1

The structure of Mepa, Active Form with Zn in P1, PDB code: 1u10 was solved by M.Marcyjaniak, S.G.Odintsov, I.Sabala, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	35.613, 77.988, 127.663, 93.15, 95.93, 90.75
R / Rfree (%)	23.4 / 26.6

The binding sites of Zinc atom in the Mepa, Active Form with Zn in P1 (pdb code 1u10). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Mepa, Active Form with Zn in P1, PDB code: 1u10:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Mepa, Active Form with Zn in P1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mepa, Active Form with Zn in P1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:25.9 occ:1.00 ND1 A:HIS110 2.0 29.9 1.0 ND1 A:HIS211 2.0 17.4 1.0 NE2 A:HIS113 2.0 29.0 1.0 OD1 A:ASP120 2.1 18.5 1.0 CE1 A:HIS211 2.6 18.7 1.0 CG A:ASP120 2.8 19.6 1.0 OD2 A:ASP120 2.8 21.7 1.0 CE1 A:HIS110 2.8 29.3 1.0 CE1 A:HIS113 2.9 28.8 1.0 CD2 A:HIS113 3.1 26.9 1.0 CG A:HIS110 3.1 31.5 1.0 CG A:HIS211 3.3 20.2 1.0 CB A:HIS110 3.6 32.4 1.0 NE2 A:HIS211 3.8 20.0 1.0 CB A:HIS211 4.0 20.4 1.0 NE2 A:HIS110 4.0 30.5 1.0 ND1 A:HIS113 4.1 26.5 1.0 CD2 A:HIS110 4.2 30.1 1.0 CD2 A:HIS211 4.2 18.5 1.0 CG A:HIS113 4.2 25.8 1.0 CB A:ASP120 4.2 18.5 1.0 CA A:HIS211 4.6 22.2 1.0 CA A:ASP120 4.8 18.7 1.0 N A:ASP120 4.8 17.4 1.0 NE2 A:HIS206 4.8 28.8 1.0

Zinc binding site 2 out of 9 in the Mepa, Active Form with Zn in P1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mepa, Active Form with Zn in P1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:49.4 occ:1.00 OD2 A:ASP147 1.9 42.5 1.0 NE2 A:HIS150 2.0 32.4 1.0 NE2 B:HIS150 2.0 35.4 1.0 OD2 B:ASP147 2.3 42.1 1.0 CD2 A:HIS150 2.6 30.9 1.0 CD2 B:HIS150 2.8 35.7 1.0 CG A:ASP147 2.9 41.0 1.0 CE1 B:HIS150 3.1 35.1 1.0 OD1 A:ASP147 3.2 39.6 1.0 CE1 A:HIS150 3.3 31.6 1.0 CG B:ASP147 3.4 43.0 1.0 OD1 B:ASP147 3.9 40.9 1.0 CG A:HIS150 3.9 32.6 1.0 CG B:HIS150 4.0 36.7 1.0 CB A:LYS149 4.1 38.4 1.0 ND1 B:HIS150 4.1 36.6 1.0 ND1 A:HIS150 4.2 32.2 1.0 CB A:ASP147 4.2 39.5 1.0 CG A:LYS149 4.3 41.8 1.0 CG B:LYS149 4.4 40.0 1.0 CB B:LYS149 4.4 37.6 1.0 CB B:ASP147 4.6 42.7 1.0 OG A:SER145 4.7 39.4 1.0 CA A:LYS149 4.9 36.7 1.0 N A:LYS149 4.9 35.3 1.0

Zinc binding site 3 out of 9 in the Mepa, Active Form with Zn in P1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mepa, Active Form with Zn in P1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn400 b:15.9 occ:1.00 ND1 B:HIS110 2.0 28.1 1.0 NE2 B:HIS113 2.0 11.7 1.0 ND1 B:HIS211 2.0 15.4 1.0 OD1 B:ASP120 2.1 13.1 1.0 CE1 B:HIS211 2.7 19.4 1.0 CG B:ASP120 2.8 12.5 1.0 OD2 B:ASP120 2.8 12.4 1.0 CE1 B:HIS110 2.9 29.1 1.0 CE1 B:HIS113 3.0 11.3 1.0 CD2 B:HIS113 3.1 11.1 1.0 CG B:HIS110 3.1 27.2 1.0 CG B:HIS211 3.3 17.0 1.0 CB B:HIS110 3.5 26.0 1.0 CB B:HIS211 3.9 14.4 1.0 NE2 B:HIS211 3.9 18.2 1.0 NE2 B:HIS110 4.1 29.5 1.0 ND1 B:HIS113 4.1 11.8 1.0 CD2 B:HIS110 4.2 27.9 1.0 CG B:HIS113 4.2 12.2 1.0 CB B:ASP120 4.2 10.2 1.0 CD2 B:HIS211 4.2 17.0 1.0 CA B:HIS211 4.6 15.3 1.0 CA B:ASP120 4.7 10.0 1.0 N B:ASP120 4.8 10.3 1.0 NE2 B:HIS206 4.8 25.8 1.0 CA B:HIS110 5.0 25.4 1.0

Zinc binding site 4 out of 9 in the Mepa, Active Form with Zn in P1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mepa, Active Form with Zn in P1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn400 b:15.0 occ:1.00 ND1 C:HIS110 2.0 24.7 1.0 OD1 C:ASP120 2.0 7.0 1.0 NE2 C:HIS113 2.0 8.9 1.0 ND1 C:HIS211 2.1 15.1 1.0 CE1 C:HIS211 2.7 16.7 1.0 CG C:ASP120 2.8 11.2 1.0 CE1 C:HIS110 2.8 26.6 1.0 OD2 C:ASP120 2.9 8.6 1.0 CE1 C:HIS113 3.0 13.0 1.0 CD2 C:HIS113 3.0 11.0 1.0 CG C:HIS110 3.1 25.6 1.0 CG C:HIS211 3.4 14.9 1.0 CB C:HIS110 3.5 25.2 1.0 NE2 C:HIS211 3.9 18.2 1.0 NE2 C:HIS110 4.0 26.1 1.0 CB C:HIS211 4.0 14.1 1.0 ND1 C:HIS113 4.1 10.1 1.0 CG C:HIS113 4.2 11.8 1.0 CD2 C:HIS110 4.2 25.1 1.0 CB C:ASP120 4.2 10.3 1.0 CD2 C:HIS211 4.3 15.4 1.0 NE2 C:HIS209 4.7 33.5 1.0 CA C:ASP120 4.7 9.9 1.0 N C:ASP120 4.7 7.8 1.0 CA C:HIS211 4.8 15.2 1.0 NE2 C:HIS206 4.9 27.1 1.0 OG C:SER112 4.9 20.6 1.0

Zinc binding site 5 out of 9 in the Mepa, Active Form with Zn in P1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Mepa, Active Form with Zn in P1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn400 b:11.8 occ:1.00 OD1 D:ASP120 1.9 8.9 1.0 ND1 D:HIS110 2.0 16.5 1.0 NE2 D:HIS113 2.0 10.9 1.0 ND1 D:HIS211 2.0 15.2 1.0 CG D:ASP120 2.7 9.3 1.0 CE1 D:HIS211 2.8 14.2 1.0 OD2 D:ASP120 2.8 10.1 1.0 CE1 D:HIS110 2.9 17.6 1.0 CE1 D:HIS113 2.9 10.7 1.0 CG D:HIS110 3.0 19.6 1.0 CD2 D:HIS113 3.1 8.6 1.0 CG D:HIS211 3.2 14.2 1.0 CB D:HIS110 3.5 20.6 1.0 CB D:HIS211 3.8 11.8 1.0 NE2 D:HIS211 4.0 13.1 1.0 NE2 D:HIS110 4.0 20.3 1.0 ND1 D:HIS113 4.1 8.5 1.0 CB D:ASP120 4.1 8.5 1.0 CD2 D:HIS110 4.1 19.5 1.0 O D:HOH607 4.2 28.4 1.0 CG D:HIS113 4.2 8.2 1.0 CD2 D:HIS211 4.2 12.5 1.0 NE2 D:HIS206 4.5 24.8 1.0 CA D:HIS211 4.6 13.0 1.0 CA D:ASP120 4.6 9.8 1.0 N D:ASP120 4.7 10.7 1.0 CA D:HIS110 4.9 21.9 1.0

Zinc binding site 6 out of 9 in the Mepa, Active Form with Zn in P1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Mepa, Active Form with Zn in P1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:27.9 occ:1.00 NE2 D:HIS150 2.0 31.4 1.0 NE2 C:HIS150 2.0 31.4 1.0 OD2 D:ASP147 2.1 39.9 1.0 OD2 C:ASP147 2.1 44.0 1.0 CD2 C:HIS150 2.8 31.2 1.0 CD2 D:HIS150 2.9 30.6 1.0 CG D:ASP147 3.1 39.7 1.0 CE1 D:HIS150 3.1 32.4 1.0 CE1 C:HIS150 3.2 32.5 1.0 CG C:ASP147 3.3 44.2 1.0 OD1 D:ASP147 3.5 37.8 1.0 OD1 C:ASP147 3.7 44.5 1.0 CG C:HIS150 4.0 32.8 1.0 CG D:HIS150 4.1 31.8 1.0 ND1 D:HIS150 4.2 31.8 1.0 ND1 C:HIS150 4.2 32.4 1.0 CB C:LYS149 4.2 40.6 1.0 CB D:ASP147 4.4 38.9 1.0 CB C:ASP147 4.5 43.7 1.0 CG C:LYS149 4.6 43.6 1.0 CB D:LYS149 4.6 33.8 1.0 CG D:LYS149 5.0 37.0 1.0

Zinc binding site 7 out of 9 in the Mepa, Active Form with Zn in P1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Mepa, Active Form with Zn in P1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn400 b:16.4 occ:1.00 ND1 E:HIS110 2.0 19.7 1.0 OD1 E:ASP120 2.0 9.9 1.0 NE2 E:HIS113 2.0 12.6 1.0 ND1 E:HIS211 2.0 15.3 1.0 CG E:ASP120 2.7 10.7 1.0 CE1 E:HIS211 2.8 14.4 1.0 CE1 E:HIS110 2.8 21.3 1.0 OD2 E:ASP120 2.9 7.2 1.0 CE1 E:HIS113 3.0 12.1 1.0 CD2 E:HIS113 3.0 12.5 1.0 CG E:HIS110 3.1 19.2 1.0 CG E:HIS211 3.2 13.6 1.0 CB E:HIS110 3.6 17.4 1.0 CB E:HIS211 3.8 12.7 1.0 NE2 E:HIS211 4.0 15.0 1.0 NE2 E:HIS110 4.0 20.4 1.0 ND1 E:HIS113 4.1 12.6 1.0 CG E:HIS113 4.2 12.4 1.0 CD2 E:HIS110 4.2 18.7 1.0 CB E:ASP120 4.2 10.5 1.0 CD2 E:HIS211 4.2 13.1 1.0 CA E:HIS211 4.5 14.2 1.0 CA E:ASP120 4.7 10.8 1.0 NE2 E:HIS206 4.7 23.0 1.0 N E:ASP120 4.7 9.7 1.0

Zinc binding site 8 out of 9 in the Mepa, Active Form with Zn in P1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Mepa, Active Form with Zn in P1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn603 b:33.1 occ:1.00 NE2 E:HIS150 2.0 32.4 1.0 NE2 F:HIS150 2.0 29.9 1.0 OD2 E:ASP147 2.0 35.0 1.0 OD2 F:ASP147 2.1 39.1 1.0 CE1 E:HIS150 2.5 31.6 1.0 CD2 F:HIS150 2.9 30.3 1.0 CG E:ASP147 2.9 38.5 1.0 CE1 F:HIS150 3.1 29.1 1.0 CG F:ASP147 3.2 40.5 1.0 OD1 E:ASP147 3.2 40.6 1.0 CD2 E:HIS150 3.3 30.9 1.0 OD1 F:ASP147 3.6 42.1 1.0 ND1 E:HIS150 3.8 32.2 1.0 CG F:HIS150 4.1 31.3 1.0 ND1 F:HIS150 4.2 31.2 1.0 OG E:SER145 4.2 39.1 1.0 CG E:HIS150 4.2 32.6 1.0 OG F:SER145 4.3 42.7 1.0 CB E:ASP147 4.3 39.2 1.0 CB F:ASP147 4.5 41.0 1.0 CB E:SER145 4.6 39.0 1.0 CB E:LYS149 4.9 41.3 1.0 CB F:SER145 5.0 42.0 1.0

Zinc binding site 9 out of 9 in the Mepa, Active Form with Zn in P1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Mepa, Active Form with Zn in P1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn400 b:18.9 occ:1.00 ND1 F:HIS110 2.0 24.5 1.0 NE2 F:HIS113 2.0 8.2 1.0 OD1 F:ASP120 2.0 5.7 1.0 ND1 F:HIS211 2.1 14.6 1.0 CG F:ASP120 2.7 6.8 1.0 OD2 F:ASP120 2.8 8.3 1.0 CE1 F:HIS211 2.8 14.7 1.0 CE1 F:HIS110 2.8 27.7 1.0 CE1 F:HIS113 2.9 6.9 1.0 CD2 F:HIS113 3.1 8.2 1.0 CG F:HIS110 3.1 25.8 1.0 CG F:HIS211 3.3 14.5 1.0 CB F:HIS110 3.6 24.8 1.0 CB F:HIS211 3.8 12.7 1.0 NE2 F:HIS110 4.0 27.4 1.0 NE2 F:HIS211 4.0 15.4 1.0 ND1 F:HIS113 4.0 5.9 1.0 CB F:ASP120 4.2 5.4 1.0 CD2 F:HIS110 4.2 26.3 1.0 CG F:HIS113 4.2 7.4 1.0 CD2 F:HIS211 4.3 14.6 1.0 CA F:HIS211 4.6 12.7 1.0 NE2 F:HIS206 4.6 24.4 1.0 CA F:ASP120 4.7 9.0 1.0 N F:ASP120 4.7 9.7 1.0 OG F:SER112 5.0 14.2 1.0

M.Marcyjaniak, S.G.Odintsov, I.Sabala, M.Bochtler. Peptidoglycan Amidase Mepa Is A Las Metallopeptidase J.Biol.Chem. V. 279 43982 2004.
ISSN: ISSN 0021-9258
PubMed: 15292190
DOI: 10.1074/JBC.M406735200