Manganese in PDB 2yb1: Structure of An Amidohydrolase From Chromobacterium Violaceum (Efi Target Efi-500202) with Bound Mn, Amp and Phosphate.

The structure of Structure of An Amidohydrolase From Chromobacterium Violaceum (Efi Target Efi-500202) with Bound Mn, Amp and Phosphate., PDB code: 2yb1 was solved by M.W.Vetting, B.Hillerich, R.Foti, R.D.Seidel, W.D.Zencheck, R.Toro, H.J.Imker, F.M.Raushel, J.A.Gerlt, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.04 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.958, 46.765, 130.785, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 20.7

The binding sites of Manganese atom in the Structure of An Amidohydrolase From Chromobacterium Violaceum (Efi Target Efi-500202) with Bound Mn, Amp and Phosphate. (pdb code 2yb1). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Structure of An Amidohydrolase From Chromobacterium Violaceum (Efi Target Efi-500202) with Bound Mn, Amp and Phosphate., PDB code: 2yb1:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Structure of An Amidohydrolase From Chromobacterium Violaceum (Efi Target Efi-500202) with Bound Mn, Amp and Phosphate.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of An Amidohydrolase From Chromobacterium Violaceum (Efi Target Efi-500202) with Bound Mn, Amp and Phosphate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1289 b:8.8 occ:1.00 OD2 A:ASP14 2.2 3.8 1.0 O2 A:PO41293 2.2 9.3 1.0 NE2 A:HIS39 2.2 4.5 1.0 NE2 A:HIS250 2.3 7.8 1.0 O2' A:AMP1292 2.4 9.9 1.0 O3' A:AMP1292 2.5 13.8 1.0 CG A:ASP14 2.9 5.6 1.0 OD1 A:ASP14 2.9 6.3 1.0 CE1 A:HIS39 3.2 4.7 1.0 CD2 A:HIS39 3.2 4.4 1.0 CE1 A:HIS250 3.2 7.9 1.0 CD2 A:HIS250 3.3 6.2 1.0 C2' A:AMP1292 3.3 9.7 1.0 C3' A:AMP1292 3.4 11.9 1.0 P A:PO41293 3.5 9.3 1.0 O4 A:PO41293 3.9 6.7 1.0 CE1 A:HIS9 3.9 5.4 1.0 NE2 A:HIS9 3.9 5.8 1.0 O1 A:PO41293 4.1 8.0 1.0 OG1 A:THR135 4.1 10.1 1.0 C4' A:AMP1292 4.1 11.7 1.0 ND1 A:HIS9 4.3 5.9 1.0 ND1 A:HIS39 4.3 4.0 1.0 CB A:ASP14 4.3 5.8 1.0 CD2 A:HIS9 4.3 6.5 1.0 CG A:HIS39 4.3 5.2 1.0 ND1 A:HIS250 4.4 7.1 1.0 MN A:MN1290 4.4 7.5 1.0 CG A:HIS250 4.4 6.0 1.0 O A:HOH2268 4.5 11.7 1.0 O A:HOH2141 4.5 15.2 1.0 CG A:HIS9 4.5 6.3 1.0 C1' A:AMP1292 4.6 11.0 1.0 O3 A:PO41293 4.6 9.1 1.0 O4' A:AMP1292 4.9 11.8 1.0

Manganese binding site 2 out of 3 in the Structure of An Amidohydrolase From Chromobacterium Violaceum (Efi Target Efi-500202) with Bound Mn, Amp and Phosphate.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of An Amidohydrolase From Chromobacterium Violaceum (Efi Target Efi-500202) with Bound Mn, Amp and Phosphate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1290 b:7.5 occ:1.00 O3 A:PO41293 2.1 9.1 1.0 NE2 A:HIS9 2.2 5.8 1.0 NE2 A:HIS7 2.2 4.9 1.0 OE1 A:GLU64 2.3 3.8 1.0 OD1 A:ASP248 2.5 6.7 1.0 O2 A:PO41293 2.5 9.3 1.0 P A:PO41293 2.9 9.3 1.0 CE1 A:HIS9 3.1 5.4 1.0 CE1 A:HIS7 3.1 6.1 1.0 CD A:GLU64 3.1 6.6 1.0 CD2 A:HIS9 3.2 6.5 1.0 CD2 A:HIS7 3.2 6.8 1.0 OE2 A:GLU64 3.3 6.9 1.0 CG A:ASP248 3.4 11.1 1.0 MN A:MN1291 3.6 10.7 1.0 OD2 A:ASP248 3.9 16.6 1.0 O1 A:PO41293 3.9 8.0 1.0 O4 A:PO41293 4.0 6.7 1.0 CE1 A:HIS39 4.1 4.7 1.0 CE1 A:HIS250 4.2 7.9 1.0 ND1 A:HIS9 4.2 5.9 1.0 NE2 A:HIS39 4.2 4.5 1.0 ND1 A:HIS7 4.2 6.7 1.0 CG A:HIS9 4.3 6.3 1.0 CG A:HIS7 4.3 7.6 1.0 MN A:MN1289 4.4 8.8 1.0 CG A:GLU64 4.5 7.2 1.0 NE2 A:HIS250 4.6 7.8 1.0 CB A:ASP248 4.6 8.4 1.0 CB A:GLU64 4.8 6.8 1.0 O A:THR37 4.9 4.8 1.0 ND1 A:HIS39 4.9 4.0 1.0 CA A:ASP248 4.9 6.8 1.0 CD2 A:HIS191 4.9 7.8 1.0

Manganese binding site 3 out of 3 in the Structure of An Amidohydrolase From Chromobacterium Violaceum (Efi Target Efi-500202) with Bound Mn, Amp and Phosphate.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of An Amidohydrolase From Chromobacterium Violaceum (Efi Target Efi-500202) with Bound Mn, Amp and Phosphate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1291 b:10.7 occ:1.00 OE2 A:GLU64 2.1 6.9 1.0 O3 A:PO41293 2.1 9.1 1.0 NE2 A:HIS191 2.1 7.8 1.0 ND1 A:HIS75 2.2 10.2 1.0 O4 A:PO41293 2.3 6.7 1.0 P A:PO41293 2.7 9.3 1.0 CD2 A:HIS191 3.0 7.8 1.0 CD A:GLU64 3.0 6.6 1.0 CG A:HIS75 3.2 8.5 1.0 CE1 A:HIS75 3.2 10.7 1.0 CE1 A:HIS191 3.2 8.4 1.0 OE1 A:GLU64 3.4 3.8 1.0 CB A:HIS75 3.5 7.2 1.0 MN A:MN1290 3.6 7.5 1.0 O2 A:PO41293 3.8 9.3 1.0 O1 A:PO41293 3.8 8.0 1.0 CG A:HIS191 4.2 7.5 1.0 CE1 A:HIS39 4.2 4.7 1.0 CG A:GLU64 4.2 7.2 1.0 ND1 A:HIS191 4.3 7.0 1.0 NE2 A:HIS75 4.3 10.5 1.0 CD2 A:HIS75 4.3 9.1 1.0 CE1 A:HIS7 4.4 6.1 1.0 NH2 A:ARG194 4.5 38.6 1.0 O A:HOH2177 4.6 29.7 1.0 O3' A:AMP1292 4.6 13.8 1.0 NE2 A:HIS7 4.7 4.9 1.0 CB A:ALA190 4.7 4.6 1.0 NH1 A:ARG194 4.9 38.8 1.0 CA A:HIS75 5.0 7.6 1.0 CZ A:ARG194 5.0 38.8 1.0 OD2 A:ASP248 5.0 16.6 1.0

J.A.Cummings, M.W.Vetting, S.V.Ghodge, C.Xu, B.Hillerich, R.D.Seidel, S.C.Almo, F.M.Raushel. Prospecting For Unannotated Enzymes: Discovery of A 3',5'-Nucleotide Bisphosphate Phosphatase Within the Amidohydrolase Superfamily. Biochemistry V. 53 591 2014.
ISSN: ISSN 0006-2960
PubMed: 24401123
DOI: 10.1021/BI401640R