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Manganese in PDB 1r8c: Crystal Structures of An Archaeal Class I Cca-Adding Enzyme and Its Nucleotide

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

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

Protein crystallography data

The structure of Crystal Structures of An Archaeal Class I Cca-Adding Enzyme and Its Nucleotide, PDB code: 1r8c 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) 35.58 / 1.90
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 (%) 18.1 / 21.5

Other elements in 1r8c:

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

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 (pdb code 1r8c). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Crystal Structures of An Archaeal Class I Cca-Adding Enzyme and Its Nucleotide, PDB code: 1r8c:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 1r8c

Go back to Manganese Binding Sites List in 1r8c
Manganese binding site 1 out of 5 in the Crystal Structures of An Archaeal Class I Cca-Adding Enzyme and Its Nucleotide


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn600

b:41.6
occ:1.00
 O2B A:UTP501 2.1 31.4 1.0
OD2 A:ASP61 2.3 28.3 1.0
O1A A:UTP501 2.3 37.1 1.0
O3G A:UTP501 2.3 45.5 1.0
OE1 A:GLU59 2.3 46.4 1.0
PB A:UTP501 3.2 37.9 1.0
CG A:ASP61 3.3 29.9 1.0
CD A:GLU59 3.5 47.6 1.0
PA A:UTP501 3.5 48.5 1.0
MN A:MN604 3.5 80.8 1.0
OD1 A:ASP61 3.5 27.8 1.0
PG A:UTP501 3.6 40.6 1.0
O3A A:UTP501 3.7 46.3 1.0
O3B A:UTP501 3.7 37.5 1.0
CG A:GLU59 4.0 43.0 1.0
OG A:SER47 4.0 28.4 1.0
O A:HOH778 4.1 81.0 1.0
O1G A:UTP501 4.3 45.0 1.0
O A:GLU59 4.3 31.1 1.0
N A:SER47 4.4 28.1 1.0
O5' A:UTP501 4.5 51.1 1.0
OE2 A:GLU59 4.5 46.5 1.0
CB A:GLU59 4.6 36.6 1.0
O1B A:UTP501 4.6 38.6 1.0
C5' A:UTP501 4.6 53.8 1.0
O2A A:UTP501 4.7 49.8 1.0
CB A:ASP61 4.7 28.0 1.0
O2G A:UTP501 4.8 39.7 1.0
CA A:GLY46 4.8 29.4 1.0
CB A:SER47 4.9 25.4 1.0
C A:GLU59 5.0 33.9 1.0

Manganese binding site 2 out of 5 in 1r8c

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Manganese binding site 2 out of 5 in the Crystal Structures of An Archaeal Class I Cca-Adding Enzyme and Its Nucleotide


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:33.1
occ:1.00
 O1B A:UTP502 2.1 38.5 1.0
ND1 A:HIS396 2.1 26.6 1.0
O3G A:UTP502 2.2 37.4 1.0
NE2 A:HIS398 2.3 30.7 1.0
CE1 A:HIS396 3.1 23.5 1.0
CG A:HIS396 3.1 16.0 1.0
PB A:UTP502 3.2 40.8 1.0
CD2 A:HIS398 3.2 28.5 1.0
PG A:UTP502 3.2 43.7 1.0
CE1 A:HIS398 3.3 29.8 1.0
O3B A:UTP502 3.4 39.8 1.0
CB A:HIS396 3.4 13.4 1.0
O3A A:UTP502 3.8 33.5 1.0
O2G A:UTP502 3.8 44.5 1.0
CA A:HIS396 3.8 12.6 1.0
NE2 A:HIS396 4.2 22.3 1.0
CD2 A:HIS396 4.2 24.6 1.0
CG A:HIS398 4.4 22.5 1.0
ND1 A:HIS398 4.4 29.4 1.0
O A:THR395 4.4 14.4 1.0
O2B A:UTP502 4.5 41.0 1.0
O1G A:UTP502 4.5 42.6 1.0
N A:HIS396 4.8 11.8 1.0
C A:HIS396 4.8 12.2 1.0
C5' A:UTP502 4.8 44.6 1.0
O A:HIS396 4.9 9.7 1.0
C A:THR395 4.9 13.2 1.0

Manganese binding site 3 out of 5 in 1r8c

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Manganese binding site 3 out of 5 in the Crystal Structures of An Archaeal Class I Cca-Adding Enzyme and Its Nucleotide


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:83.1
occ:1.00
 ND1 A:HIS101 2.2 43.9 1.0
OD1 A:ASP110 2.4 28.9 1.0
OD2 A:ASP110 2.8 34.9 1.0
O A:HOH908 2.9 71.0 1.0
CE1 A:HIS101 2.9 45.5 1.0
CG A:ASP110 3.0 35.1 1.0
CG A:HIS101 3.4 38.4 1.0
NH1 A:ARG93 3.5 49.1 1.0
O A:HOH719 3.6 69.7 1.0
OE2 A:GLU59 3.8 46.5 1.0
CB A:HIS101 4.0 34.5 1.0
NE2 A:HIS101 4.1 42.1 1.0
CD2 A:HIS101 4.4 41.4 1.0
CB A:ASP110 4.4 29.4 1.0
O A:VAL109 4.6 29.6 1.0
CD A:GLU59 4.6 47.6 1.0
OE1 A:GLU108 4.7 44.4 1.0
CZ A:ARG93 4.7 47.8 1.0
C A:VAL109 4.7 29.6 1.0
MN A:MN604 4.7 80.8 1.0
N A:ASP110 4.8 28.5 1.0
CB A:GLU108 4.8 32.6 1.0
CG A:GLU59 4.9 43.0 1.0
CA A:ASP110 4.9 29.0 1.0
CA A:HIS101 5.0 33.5 1.0

Manganese binding site 4 out of 5 in 1r8c

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Manganese binding site 4 out of 5 in the Crystal Structures of An Archaeal Class I Cca-Adding Enzyme and Its Nucleotide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structures of An Archaeal Class I Cca-Adding Enzyme and Its Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn603

b:92.2
occ:1.00
 OD2 A:ASP218 2.1 22.6 1.0
NE2 A:HIS133 2.3 30.4 1.0
O A:HOH896 2.6 84.4 1.0
CE1 A:HIS133 3.2 34.7 1.0
CG A:ASP218 3.2 20.7 1.0
CD2 A:HIS133 3.3 35.4 1.0
CB A:ARG129 3.5 62.4 1.0
OD1 A:ASP218 3.8 20.2 1.0
CG A:ARG129 4.1 65.1 1.0
CG A:ARG224 4.1 25.0 1.0
CB A:ASP218 4.3 18.0 1.0
ND1 A:HIS133 4.3 34.3 1.0
CG A:HIS133 4.4 29.0 1.0
O A:HOH691 4.6 43.2 1.0
CG1 A:VAL220 4.6 31.2 1.0
CB A:ASP221 4.7 24.1 1.0
CB A:ARG224 4.7 20.9 1.0
CB A:VAL220 4.8 25.7 1.0
O A:HOH915 4.8 83.2 1.0
CA A:ARG129 4.8 61.4 1.0
O A:ARG129 4.8 58.6 1.0
C A:ARG129 4.8 57.7 1.0
CD A:ARG224 5.0 33.7 1.0
CE2 A:TYR173 5.0 23.8 1.0

Manganese binding site 5 out of 5 in 1r8c

Go back to Manganese Binding Sites List in 1r8c
Manganese binding site 5 out of 5 in the Crystal Structures of An Archaeal Class I Cca-Adding Enzyme and Its Nucleotide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structures of An Archaeal Class I Cca-Adding Enzyme and Its Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn604

b:80.8
occ:1.00
 OD1 A:ASP61 2.1 27.8 1.0
OD2 A:ASP110 2.4 34.9 1.0
OE1 A:GLU59 2.5 46.4 1.0
O A:HOH750 2.5 68.9 1.0
CD A:GLU59 2.9 47.6 1.0
O1A A:UTP501 3.1 37.1 1.0
CG A:ASP61 3.2 29.9 1.0
OE2 A:GLU59 3.3 46.5 1.0
O A:HOH778 3.5 81.0 1.0
OD2 A:ASP61 3.5 28.3 1.0
MN A:MN600 3.5 41.6 1.0
CG A:ASP110 3.6 35.1 1.0
CG A:GLU59 3.7 43.0 1.0
CB A:ASP110 4.2 29.4 1.0
PA A:UTP501 4.4 48.5 1.0
CB A:ASP61 4.4 28.0 1.0
O5' A:UTP501 4.5 51.1 1.0
OD1 A:ASP110 4.6 28.9 1.0
MN A:MN602 4.7 83.1 1.0
C5' A:UTP501 4.9 53.8 1.0
O3G A:UTP501 5.0 45.5 1.0
CA A:ASP61 5.0 28.1 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 Oct 5 12:19:11 2024

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