Atomistry » Manganese » PDB 1r2m-1sfy » 1r8c
Atomistry »
  Manganese »
    PDB 1r2m-1sfy »
      1r8c »

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

Go back to Manganese Binding Sites List in 1r8c
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

Go back to Manganese Binding Sites List in 1r8c
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

Go back to Manganese Binding Sites List in 1r8c
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy