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Manganese in PDB 1r89: Crystal Structures of An Archaeal Class I Cca-Adding Enzyme and Its Nucleotide Complexes

Enzymatic activity of Crystal Structures of An Archaeal Class I Cca-Adding Enzyme and Its Nucleotide Complexes

All present enzymatic activity of Crystal Structures of An Archaeal Class I Cca-Adding Enzyme and Its Nucleotide Complexes:
2.7.7.25;

Protein crystallography data

The structure of Crystal Structures of An Archaeal Class I Cca-Adding Enzyme and Its Nucleotide Complexes, PDB code: 1r89 was solved by Y.Xiong, F.Li, J.Wang, A.M.Weiner, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.63 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 86.151, 79.954, 78.145, 90.00, 97.53, 90.00
R / Rfree (%) 18.5 / 22.6

Other elements in 1r89:

The structure of Crystal Structures of An Archaeal Class I Cca-Adding Enzyme and Its Nucleotide Complexes also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structures of An Archaeal Class I Cca-Adding Enzyme and Its Nucleotide Complexes (pdb code 1r89). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structures of An Archaeal Class I Cca-Adding Enzyme and Its Nucleotide Complexes, PDB code: 1r89:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 1r89

Go back to Manganese Binding Sites List in 1r89
Manganese binding site 1 out of 3 in the Crystal Structures of An Archaeal Class I Cca-Adding Enzyme and Its Nucleotide Complexes


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structures of An Archaeal Class I Cca-Adding Enzyme and Its Nucleotide Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn600

b:40.4
occ:1.00
O2B A:CTP501 2.1 32.9 1.0
O1A A:CTP501 2.3 39.9 1.0
OD2 A:ASP61 2.3 27.6 1.0
O A:HOH602 2.3 32.6 0.5
O3G A:CTP501 2.3 41.0 1.0
PB A:CTP501 3.2 38.9 1.0
CG A:ASP61 3.3 31.8 1.0
MG A:MG750 3.3 61.5 1.0
OD1 A:ASP61 3.5 30.4 1.0
PA A:CTP501 3.5 45.1 1.0
PG A:CTP501 3.5 42.8 1.0
O3A A:CTP501 3.7 47.4 1.0
O3B A:CTP501 3.8 40.0 1.0
O A:HOH930 3.9 48.1 1.0
OG A:SER47 4.1 27.4 1.0
O1G A:CTP501 4.3 42.4 1.0
N A:SER47 4.4 23.6 1.0
O1B A:CTP501 4.5 37.1 1.0
O5' A:CTP501 4.5 50.2 1.0
O A:HOH697 4.6 88.7 1.0
C5' A:CTP501 4.6 48.8 1.0
O2A A:CTP501 4.6 48.4 1.0
OE1 A:GLU59 4.6 49.1 1.0
O A:GLU59 4.6 31.9 1.0
CB A:ASP61 4.7 30.6 1.0
CA A:GLY46 4.8 25.9 1.0
O2G A:CTP501 4.8 37.0 1.0
CB A:SER47 5.0 25.5 1.0

Manganese binding site 2 out of 3 in 1r89

Go back to Manganese Binding Sites List in 1r89
Manganese binding site 2 out of 3 in the Crystal Structures of An Archaeal Class I Cca-Adding Enzyme and Its Nucleotide Complexes


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structures of An Archaeal Class I Cca-Adding Enzyme and Its Nucleotide Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:18.6
occ:1.00
O1B A:CTP502 1.8 17.6 1.0
NE2 A:HIS398 2.0 20.8 1.0
O3G A:CTP502 2.1 28.3 1.0
ND1 A:HIS396 2.1 14.1 1.0
CE1 A:HIS396 2.9 13.6 1.0
CE1 A:HIS398 2.9 25.6 1.0
CD2 A:HIS398 3.0 22.8 1.0
PB A:CTP502 3.1 22.5 1.0
PG A:CTP502 3.1 25.8 1.0
CG A:HIS396 3.1 12.8 1.0
O3B A:CTP502 3.4 26.1 1.0
CB A:HIS396 3.6 11.6 1.0
O2G A:CTP502 3.7 29.6 1.0
O3A A:CTP502 3.8 19.1 1.0
CA A:HIS396 3.8 11.1 1.0
ND1 A:HIS398 4.1 22.6 1.0
NE2 A:HIS396 4.1 16.4 1.0
CG A:HIS398 4.1 15.8 1.0
CD2 A:HIS396 4.2 18.5 1.0
O2B A:CTP502 4.3 28.1 1.0
O A:THR395 4.4 12.7 1.0
O1G A:CTP502 4.5 31.4 1.0
C A:HIS396 4.8 10.5 1.0
N A:HIS396 4.8 9.9 1.0
C5' A:CTP502 4.8 16.0 1.0
O A:HIS396 4.8 12.8 1.0
C A:THR395 4.9 12.0 1.0

Manganese binding site 3 out of 3 in 1r89

Go back to Manganese Binding Sites List in 1r89
Manganese binding site 3 out of 3 in the Crystal Structures of An Archaeal Class I Cca-Adding Enzyme and Its Nucleotide Complexes


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structures of An Archaeal Class I Cca-Adding Enzyme and Its Nucleotide Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn604

b:71.2
occ:1.00
ND1 A:HIS101 1.8 43.2 1.0
OD1 A:ASP110 2.0 30.1 1.0
O A:HOH862 2.6 52.8 1.0
CG A:HIS101 2.8 37.3 1.0
CE1 A:HIS101 2.8 41.6 1.0
CG A:ASP110 2.8 34.7 1.0
OD2 A:ASP110 3.1 37.5 1.0
CB A:HIS101 3.1 30.8 1.0
OE2 A:GLU59 3.3 53.1 1.0
O A:VAL109 3.8 28.1 1.0
NH1 A:ARG93 3.9 56.8 1.0
NE2 A:HIS101 3.9 44.4 1.0
CD2 A:HIS101 3.9 42.9 1.0
CA A:HIS101 4.0 29.6 1.0
CB A:ASP110 4.1 31.3 1.0
C A:VAL109 4.1 28.6 1.0
N A:ASP110 4.3 28.7 1.0
CD A:GLU59 4.3 47.7 1.0
CA A:ASP110 4.3 29.3 1.0
CZ A:ARG93 4.6 56.0 1.0
CE1 A:TYR99 4.7 33.5 1.0
CD A:ARG93 4.8 51.6 1.0
N A:VAL109 4.8 29.3 1.0
N A:GLY102 4.9 29.3 1.0
C A:HIS101 4.9 30.6 1.0

Reference:

Y.Xiong, F.Li, J.Wang, A.M.Weiner, T.A.Steitz. Crystal Structures of An Archaeal Class I Cca-Adding Enzyme and Its Nucleotide Complexes Mol.Cell V. 12 1165 2003.
ISSN: ISSN 1097-2765
PubMed: 14636575
DOI: 10.1016/S1097-2765(03)00440-4
Page generated: Sat Aug 16 08:55:32 2025

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