Manganese in PDB 4ucg: NMEDAH7PS R126S Variant

All present enzymatic activity of NMEDAH7PS R126S Variant:
2.5.1.54;

The structure of NMEDAH7PS R126S Variant, PDB code: 4ucg was solved by P.J.Cross, L.C.Heyes, S.Zhang, A.R.Nazmi, E.J.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	98.70 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	78.949, 132.660, 147.722, 90.00, 90.00, 90.00
R / Rfree (%)	18.007 / 22

The binding sites of Manganese atom in the NMEDAH7PS R126S Variant (pdb code 4ucg). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the NMEDAH7PS R126S Variant, PDB code: 4ucg:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the NMEDAH7PS R126S Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of NMEDAH7PS R126S Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1351 b:27.0 occ:1.00 OD2 A:ASP324 2.0 25.9 1.0 OE2 A:GLU304 2.1 27.0 1.0 O A:HOH2039 2.1 24.7 1.0 NE2 A:HIS270 2.4 24.3 1.0 SG A:CYS63 2.6 23.2 1.0 O1 A:PEP1352 2.8 26.8 0.8 CD A:GLU304 3.0 25.7 1.0 CG A:ASP324 3.1 27.8 1.0 OE1 A:GLU304 3.2 26.8 1.0 CD2 A:HIS270 3.3 23.7 1.0 CE1 A:HIS270 3.4 23.5 1.0 CB A:ASP324 3.5 27.1 1.0 CB A:CYS63 3.6 24.6 1.0 C1 A:PEP1352 3.6 28.7 0.8 NZ A:LYS99 4.0 25.5 1.0 OD1 A:ASP324 4.1 27.9 1.0 C2 A:PEP1352 4.2 27.5 0.8 CA A:CYS63 4.2 24.0 1.0 NH2 A:ARG94 4.3 24.7 1.0 O A:HOH2243 4.4 34.4 1.0 CG A:GLU304 4.4 24.9 1.0 O A:HOH2211 4.4 25.0 1.0 CG A:HIS270 4.5 23.1 1.0 ND1 A:HIS270 4.5 23.5 1.0 C3 A:PEP1352 4.5 26.6 0.8 O2' A:PEP1352 4.5 28.7 0.8 O A:HOH2138 4.7 48.6 1.0 CA A:ASP324 4.8 27.0 1.0 N A:ASP324 4.8 27.1 1.0 O A:CYS63 4.8 22.1 1.0 CE A:LYS99 4.9 25.1 1.0 C A:CYS63 4.9 24.1 1.0 O2 A:PEP1352 4.9 27.5 0.8

Manganese binding site 2 out of 4 in the NMEDAH7PS R126S Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of NMEDAH7PS R126S Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1350 b:25.2 occ:1.00 OD2 B:ASP324 2.0 23.1 1.0 OE2 B:GLU304 2.0 25.2 1.0 O B:HOH2022 2.2 25.2 1.0 NE2 B:HIS270 2.4 23.8 1.0 O1 B:PEP1351 2.6 30.2 0.8 SG B:CYS63 2.6 23.2 1.0 CD B:GLU304 3.0 24.9 1.0 CG B:ASP324 3.0 25.4 1.0 OE1 B:GLU304 3.2 25.6 1.0 CE1 B:HIS270 3.3 25.4 1.0 CD2 B:HIS270 3.3 25.4 1.0 C1 B:PEP1351 3.5 28.2 0.8 CB B:ASP324 3.6 25.3 1.0 CB B:CYS63 3.6 23.9 1.0 NZ B:LYS99 4.0 25.7 1.0 OD1 B:ASP324 4.1 24.3 1.0 C2 B:PEP1351 4.1 28.7 0.8 CA B:CYS63 4.2 24.4 1.0 O2' B:PEP1351 4.3 25.9 0.8 NH2 B:ARG94 4.3 26.4 1.0 CG B:GLU304 4.4 25.6 1.0 O B:HOH2145 4.4 25.9 1.0 ND1 B:HIS270 4.4 25.2 1.0 O B:HOH2008 4.4 36.7 1.0 CG B:HIS270 4.5 24.1 1.0 O B:HOH2174 4.5 39.6 1.0 C3 B:PEP1351 4.6 27.8 0.8 O B:CYS63 4.8 24.4 1.0 CA B:ASP324 4.8 25.4 1.0 CE B:LYS99 4.8 25.5 1.0 N B:ASP324 4.9 24.7 1.0 O2 B:PEP1351 4.9 26.3 0.8 C B:CYS63 4.9 24.1 1.0

Manganese binding site 3 out of 4 in the NMEDAH7PS R126S Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of NMEDAH7PS R126S Variant within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1350 b:46.6 occ:1.00 OE2 C:GLU304 2.1 39.9 1.0 OD2 C:ASP324 2.2 43.8 1.0 NE2 C:HIS270 2.5 46.6 1.0 SG C:CYS63 2.5 35.8 1.0 CD C:GLU304 2.9 36.0 1.0 OE1 C:GLU304 3.1 33.6 1.0 CG C:ASP324 3.1 44.1 1.0 CB C:ASP324 3.3 43.9 1.0 CD2 C:HIS270 3.3 46.4 1.0 O2' C:PEP1351 3.4 20.5 0.5 CE1 C:HIS270 3.5 44.7 1.0 CB C:CYS63 3.5 36.6 1.0 O C:HOH2156 4.0 45.4 1.0 CA C:CYS63 4.1 33.1 1.0 C1 C:PEP1351 4.2 23.1 0.5 NH2 C:ARG94 4.2 35.6 1.0 OD1 C:ASP324 4.2 46.8 1.0 NZ C:LYS99 4.3 39.5 1.0 CG C:GLU304 4.4 34.3 1.0 CG C:HIS270 4.5 45.8 1.0 ND1 C:HIS270 4.5 44.8 1.0 CA C:ASP324 4.6 43.4 1.0 N C:ASP324 4.6 42.1 1.0 O C:HOH2037 4.6 46.7 1.0 O C:CYS63 4.8 33.4 1.0 C2 C:PEP1351 4.8 24.9 0.5 C C:CYS63 4.8 31.7 1.0 O1 C:PEP1351 4.9 22.8 0.5

Manganese binding site 4 out of 4 in the NMEDAH7PS R126S Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of NMEDAH7PS R126S Variant within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1350 b:37.9 occ:1.00 O D:HOH2019 2.2 42.1 1.0 OE2 D:GLU304 2.2 35.6 1.0 OD2 D:ASP324 2.2 40.2 1.0 NE2 D:HIS270 2.4 38.9 1.0 SG D:CYS63 2.5 33.8 1.0 CD D:GLU304 3.0 34.6 1.0 OE1 D:GLU304 3.1 34.7 1.0 O2' D:PEP1351 3.1 37.5 0.8 CG D:ASP324 3.2 40.6 1.0 CE1 D:HIS270 3.3 39.8 1.0 CD2 D:HIS270 3.3 41.2 1.0 CB D:ASP324 3.6 40.8 1.0 CB D:CYS63 3.6 33.7 1.0 C1 D:PEP1351 3.9 39.1 0.8 NZ D:LYS99 4.1 35.1 1.0 NH2 D:ARG94 4.2 32.6 1.0 O D:HOH2102 4.2 49.8 1.0 CA D:CYS63 4.2 31.0 1.0 OD1 D:ASP324 4.3 41.8 1.0 ND1 D:HIS270 4.4 40.9 1.0 CG D:GLU304 4.4 32.0 1.0 C2 D:PEP1351 4.4 43.4 0.8 CG D:HIS270 4.4 40.4 1.0 O1 D:PEP1351 4.7 33.5 0.8 C3 D:PEP1351 4.8 43.8 0.8 O D:CYS63 4.8 27.4 1.0 N D:ASP324 4.8 38.0 1.0 CA D:ASP324 4.8 40.2 1.0 C D:CYS63 4.9 29.5 1.0 CZ D:ARG94 4.9 31.5 1.0 CE D:LYS99 5.0 37.9 1.0

P.J.Cross, L.C.Heyes, S.Zhang, A.R.Nazmi. The Functional Unit of Neisseria Meningitidis 3-Deoxy-D- Arabino-Heptulosonate 7-Phosphate Synthase Is Dimeric. Plos One V. 11 45187 2016.
ISSN: ESSN 1932-6203
PubMed: 26828675
DOI: 10.1371/JOURNAL.PONE.0145187