Manganese in PDB 5jju: Crystal Structure of RV2837C Complexed with 5'-Papa and 5'-Amp

The structure of Crystal Structure of RV2837C Complexed with 5'-Papa and 5'-Amp, PDB code: 5jju was solved by F.Wang, Q.He, S.Liu, L.Gu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.67 / 2.31
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.374, 99.267, 108.677, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 28.9

The binding sites of Manganese atom in the Crystal Structure of RV2837C Complexed with 5'-Papa and 5'-Amp (pdb code 5jju). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of RV2837C Complexed with 5'-Papa and 5'-Amp, PDB code: 5jju:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of RV2837C Complexed with 5'-Papa and 5'-Amp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of RV2837C Complexed with 5'-Papa and 5'-Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1001 b:26.9 occ:1.00 OD2 A:ASP181 2.2 24.6 1.0 NE2 A:HIS131 2.3 25.9 1.0 OD2 A:ASP47 2.3 23.1 1.0 O A:HOH1129 2.5 36.4 1.0 OD2 A:ASP106 2.5 22.3 1.0 CE1 A:HIS131 3.0 24.5 1.0 CG A:ASP106 3.1 25.9 1.0 CG A:ASP181 3.1 24.8 1.0 OD1 A:ASP106 3.1 26.1 1.0 CG A:ASP47 3.2 23.7 1.0 OD1 A:ASP181 3.3 23.1 1.0 OP2 C:A1004 3.4 41.7 1.0 CD2 A:HIS131 3.5 22.4 1.0 CB A:ASP47 3.6 20.9 1.0 MN A:MN1002 4.1 27.8 1.0 OG1 A:THR151 4.1 18.3 1.0 ND1 A:HIS131 4.2 25.7 1.0 CE1 A:HIS132 4.3 29.8 1.0 P C:A1004 4.3 48.2 1.0 OD1 A:ASP47 4.3 20.6 1.0 N A:THR151 4.3 21.5 1.0 CB A:ASP106 4.4 23.8 1.0 O5' C:A1004 4.5 49.2 1.0 CG A:HIS131 4.5 24.0 1.0 CB A:ASP181 4.5 28.6 1.0 NE2 A:HIS312 4.5 34.1 1.0 OP1 C:A1004 4.5 42.8 1.0 C5' C:A1004 4.6 47.6 1.0 CA A:SER150 4.6 23.1 1.0 CB A:SER150 4.9 24.3 1.0 CB A:THR151 4.9 22.7 1.0 ND1 A:HIS132 5.0 32.5 1.0 C A:SER150 5.0 24.4 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of RV2837C Complexed with 5'-Papa and 5'-Amp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of RV2837C Complexed with 5'-Papa and 5'-Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1002 b:27.8 occ:1.00 OD1 A:ASP106 2.1 26.1 1.0 OP1 C:A1004 2.2 42.8 1.0 O A:HOH1129 2.3 36.4 1.0 OD1 A:ASP45 2.3 30.4 1.0 NE2 A:HIS41 2.4 25.9 1.0 OD2 A:ASP45 2.6 27.5 1.0 CG A:ASP45 2.8 26.5 1.0 CG A:ASP106 3.2 25.9 1.0 P C:A1004 3.3 48.2 1.0 CE1 A:HIS41 3.3 26.6 1.0 CD2 A:HIS41 3.3 24.0 1.0 O5' C:A1004 3.6 49.2 1.0 OD2 A:ASP106 3.8 22.3 1.0 OP2 C:A1004 3.9 41.7 1.0 MN A:MN1001 4.1 26.9 1.0 CB A:ASP45 4.3 20.4 1.0 CB A:ASP106 4.4 23.8 1.0 N A:THR48 4.4 21.1 1.0 ND1 A:HIS41 4.4 26.6 1.0 CB A:THR48 4.4 24.2 1.0 CG A:HIS41 4.4 25.1 1.0 CB A:ASP47 4.5 20.9 1.0 O A:ASP106 4.5 20.6 1.0 O2' C:A1003 4.5 58.7 1.0 O3' C:A1003 4.6 45.5 1.0 C5' C:A1004 4.8 47.6 1.0 CG2 A:THR48 4.8 23.0 1.0 OD2 A:ASP47 4.9 23.1 1.0 N A:ASP45 4.9 23.6 1.0 OD1 A:ASP181 4.9 23.1 1.0 CA A:THR48 5.0 22.5 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of RV2837C Complexed with 5'-Papa and 5'-Amp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of RV2837C Complexed with 5'-Papa and 5'-Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1001 b:26.0 occ:1.00 OD2 B:ASP181 2.2 28.0 1.0 NE2 B:HIS131 2.3 29.4 1.0 OD2 B:ASP47 2.3 24.3 1.0 OD1 B:ASP106 2.3 27.5 1.0 O1P B:AMP1004 2.5 38.6 1.0 O2P B:AMP1004 2.6 31.5 1.0 CE1 B:HIS131 2.9 29.4 1.0 CG B:ASP106 3.0 27.2 1.0 P B:AMP1004 3.0 32.2 1.0 CG B:ASP47 3.1 26.4 1.0 OD2 B:ASP106 3.1 28.4 1.0 CG B:ASP181 3.2 26.5 1.0 CB B:ASP47 3.5 24.5 1.0 CD2 B:HIS131 3.5 29.6 1.0 OD1 B:ASP181 3.5 27.5 1.0 OG1 B:THR151 3.9 25.4 1.0 MN B:MN1002 4.0 27.3 1.0 O3P B:AMP1004 4.0 30.6 1.0 ND1 B:HIS131 4.1 30.0 1.0 OD1 B:ASP47 4.2 26.7 1.0 O5' B:AMP1004 4.3 30.8 1.0 N B:THR151 4.3 23.5 1.0 CB B:ASP106 4.3 22.8 1.0 CE1 B:HIS132 4.3 28.9 1.0 CG B:HIS131 4.4 28.2 1.0 CB B:ASP181 4.5 27.6 1.0 CA B:SER150 4.7 24.3 1.0 NE2 B:HIS312 4.7 37.4 1.0 C2 B:AMP1004 4.7 34.5 1.0 NE2 B:HIS132 4.9 33.4 1.0 CB B:THR151 4.9 28.0 1.0 CB B:SER150 4.9 24.9 1.0 CA B:ASP47 5.0 24.7 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of RV2837C Complexed with 5'-Papa and 5'-Amp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of RV2837C Complexed with 5'-Papa and 5'-Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1002 b:27.3 occ:1.00 OD2 B:ASP106 2.1 28.4 1.0 O2P B:AMP1004 2.1 31.5 1.0 OD2 B:ASP45 2.1 25.6 1.0 NE2 B:HIS41 2.6 26.0 1.0 OD1 B:ASP45 2.6 27.5 1.0 CG B:ASP45 2.7 25.2 1.0 CG B:ASP106 3.2 27.2 1.0 O3P B:AMP1004 3.2 30.6 1.0 P B:AMP1004 3.2 32.2 1.0 CD2 B:HIS41 3.4 25.4 1.0 CE1 B:HIS41 3.6 28.8 1.0 OD1 B:ASP106 3.8 27.5 1.0 MN B:MN1001 4.0 26.0 1.0 C5' B:AMP1004 4.1 40.4 1.0 O5' B:AMP1004 4.2 30.8 1.0 CB B:ASP45 4.2 27.3 1.0 CB B:ASP106 4.3 22.8 1.0 O1P B:AMP1004 4.4 38.6 1.0 CB B:ASP47 4.5 24.5 1.0 N B:THR48 4.5 22.5 1.0 CB B:THR48 4.5 25.1 1.0 CG B:HIS41 4.6 31.1 1.0 CG2 B:THR48 4.6 23.8 1.0 O B:ASP106 4.6 22.2 1.0 ND1 B:HIS41 4.7 32.3 1.0 N B:ASP45 4.9 28.4 1.0 OD2 B:ASP47 4.9 24.3 1.0 O B:HOH1134 5.0 30.2 1.0 OD1 B:ASP181 5.0 27.5 1.0

Q.He, F.Wang, S.Liu, D.Zhu, H.Cong, F.Gao, B.Li, H.Wang, Z.Lin, J.Liao, L.Gu. Structural and Biochemical Insight Into the Mechanism of RV2837C From Mycobacterium Tuberculosis As A C-Di-Nmp Phosphodiesterase J.Biol.Chem. V. 291 14386 2016.
ISSN: ESSN 1083-351X
PubMed: 27371563
DOI: 10.1074/JBC.A115.699801