Manganese in PDB 1ucg: Crystal Structure of Ribonuclease MC1 N71T Mutant

All present enzymatic activity of Crystal Structure of Ribonuclease MC1 N71T Mutant:
3.1.27.1;

The structure of Crystal Structure of Ribonuclease MC1 N71T Mutant, PDB code: 1ucg was solved by A.Suzuki, T.Numata, M.Yao, I.Tanaka, M.Kimura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.65
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.790, 135.900, 52.390, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 19.6

The binding sites of Manganese atom in the Crystal Structure of Ribonuclease MC1 N71T Mutant (pdb code 1ucg). 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 Ribonuclease MC1 N71T Mutant, PDB code: 1ucg:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Ribonuclease MC1 N71T Mutant


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 Ribonuclease MC1 N71T Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:39.8 occ:1.00 O A:HOH419 1.8 31.2 1.0 O A:HOH420 1.9 38.4 1.0 O A:HOH418 1.9 33.6 1.0 O A:HOH416 2.0 39.7 1.0 O A:HOH417 2.2 42.3 1.0 OE2 A:GLU84 3.6 19.9 1.0 NZ A:LYS87 3.7 23.6 1.0 NE2 A:HIS88 3.7 17.8 1.0 NE2 A:HIS34 3.7 19.6 1.0 NE2 A:HIS83 3.8 22.0 1.0 CD A:LYS87 4.0 19.8 1.0 CE A:LYS87 4.2 22.7 1.0 CZ2 A:TRP37 4.4 20.4 1.0 CD2 A:HIS83 4.4 19.5 1.0 CD2 A:HIS88 4.4 16.4 1.0 CE1 A:HIS34 4.4 20.8 1.0 CD A:GLU84 4.6 17.9 1.0 CD2 A:HIS34 4.7 17.4 1.0 CE1 A:HIS88 4.7 17.1 1.0 OE1 A:GLU84 4.7 17.6 1.0 CE1 A:HIS83 4.9 20.0 1.0 CE2 A:TRP37 4.9 16.9 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Ribonuclease MC1 N71T Mutant


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 Ribonuclease MC1 N71T Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:60.1 occ:1.00 CE1 A:HIS83 3.7 20.0 1.0 NZ B:LYS87 3.8 21.2 1.0 NZ A:LYS87 4.0 23.6 1.0 CE1 B:HIS83 4.0 19.8 1.0 O A:HOH338 4.1 40.4 1.0 CD A:LYS87 4.3 19.8 1.0 CE A:LYS87 4.3 22.7 1.0 CE B:LYS87 4.5 19.9 1.0 O B:HOH425 4.5 31.1 1.0 NE2 A:HIS83 4.5 22.0 1.0 CD B:LYS87 4.6 18.6 1.0 NE2 B:HIS83 4.6 24.1 1.0 ND1 A:HIS83 4.7 21.4 1.0 O A:HOH419 4.7 31.2 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Ribonuclease MC1 N71T Mutant


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 Ribonuclease MC1 N71T Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn503 b:36.7 occ:1.00 O B:HOH421 1.8 30.1 1.0 O B:HOH425 1.8 31.1 1.0 O B:HOH424 1.8 30.7 1.0 O B:HOH422 1.8 31.0 1.0 O B:HOH423 2.5 44.0 1.0 OE2 B:GLU84 3.6 20.3 1.0 NE2 B:HIS34 3.6 18.7 1.0 NZ B:LYS87 3.7 21.2 1.0 NE2 B:HIS88 3.7 17.3 1.0 NE2 B:HIS83 3.9 24.1 1.0 CD B:LYS87 4.1 18.6 1.0 CZ2 B:TRP37 4.2 21.0 1.0 CE B:LYS87 4.3 19.9 1.0 CE1 B:HIS34 4.3 19.7 1.0 CD2 B:HIS88 4.4 17.2 1.0 CD B:GLU84 4.5 18.0 1.0 CD2 B:HIS83 4.6 20.2 1.0 CD2 B:HIS34 4.6 18.2 1.0 OE1 B:GLU84 4.6 17.3 1.0 CE1 B:HIS88 4.7 16.8 1.0 CE2 B:TRP37 4.8 16.9 1.0 O B:HOH401 4.9 53.9 1.0 NE1 B:TRP37 4.9 17.1 1.0 CH2 B:TRP37 5.0 19.8 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Ribonuclease MC1 N71T Mutant


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 Ribonuclease MC1 N71T Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn504 b:32.2 occ:1.00 O B:HOH427 1.7 28.2 1.0 O B:HOH428 1.8 33.8 1.0 O B:HOH429 1.8 32.3 1.0 O B:HOH426 1.9 37.2 1.0 O B:HOH430 2.0 43.9 1.0 NE B:ARG132 3.7 24.8 1.0 NZ B:LYS136 3.8 18.4 1.0 NH2 B:ARG132 3.9 27.3 1.0 CZ B:ARG132 4.2 25.9 1.0 CA B:GLN133 4.3 16.6 1.0 CB B:GLN133 4.3 17.7 1.0 CD B:LYS136 4.4 23.7 1.0 CE B:LYS136 4.4 24.1 1.0 N B:GLN133 4.6 17.2 1.0 CD B:ARG132 4.7 22.3 1.0 CG B:ARG132 4.9 20.4 1.0

T.Numata, A.Suzuki, Y.Kakuta, K.Kimura, M.Yao, I.Tanaka, Y.Yoshida, T.Ueda, M.Kimura. Crystal Structures of the Ribonuclease MC1 Mutants N71T and N71S in Complex with 5'-Gmp: Structural Basis For Alterations in Substrate Specificity Biochemistry V. 42 5270 2003.
ISSN: ISSN 0006-2960
PubMed: 12731868
DOI: 10.1021/BI034103G