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Manganese in PDB 2j3m: Prolyl-Trna Synthetase From Enterococcus Faecalis Complexed with Atp, Manganese and Prolinol

Enzymatic activity of Prolyl-Trna Synthetase From Enterococcus Faecalis Complexed with Atp, Manganese and Prolinol

All present enzymatic activity of Prolyl-Trna Synthetase From Enterococcus Faecalis Complexed with Atp, Manganese and Prolinol:
6.1.1.15;

Protein crystallography data

The structure of Prolyl-Trna Synthetase From Enterococcus Faecalis Complexed with Atp, Manganese and Prolinol, PDB code: 2j3m was solved by T.Crepin, A.Yaremchuk, M.Tukalo, S.Cusack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.49 / 2.3
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.583, 92.679, 101.223, 90.00, 106.11, 90.00
R / Rfree (%) 19.6 / 26

Manganese Binding Sites:

The binding sites of Manganese atom in the Prolyl-Trna Synthetase From Enterococcus Faecalis Complexed with Atp, Manganese and Prolinol (pdb code 2j3m). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Prolyl-Trna Synthetase From Enterococcus Faecalis Complexed with Atp, Manganese and Prolinol, PDB code: 2j3m:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 2j3m

Go back to Manganese Binding Sites List in 2j3m
Manganese binding site 1 out of 6 in the Prolyl-Trna Synthetase From Enterococcus Faecalis Complexed with Atp, Manganese and Prolinol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Prolyl-Trna Synthetase From Enterococcus Faecalis Complexed with Atp, Manganese and Prolinol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1567

b:17.6
occ:1.00
 O2B A:ATP701 1.9 15.1 1.0
ND1 A:HIS410 2.2 16.1 1.0
OE2 A:GLU407 2.3 7.2 1.0
O A:HOH2200 2.3 12.0 1.0
O1A A:ATP701 2.3 20.6 1.0
CD A:GLU407 3.1 9.7 1.0
CE1 A:HIS410 3.1 15.4 1.0
CG A:HIS410 3.2 14.3 1.0
OE1 A:GLU407 3.2 14.3 1.0
PA A:ATP701 3.2 16.1 1.0
PB A:ATP701 3.2 15.7 1.0
MN A:MN1568 3.3 22.1 1.0
O3A A:ATP701 3.4 16.3 1.0
CB A:HIS410 3.5 16.0 1.0
CZ A:PHE412 4.0 13.1 0.7
O2A A:ATP701 4.2 19.2 1.0
O3B A:ATP701 4.2 15.0 1.0
O A:HOH2077 4.2 12.7 1.0
NE2 A:HIS410 4.2 11.4 1.0
CD2 A:HIS410 4.3 11.4 1.0
O3' A:ATP701 4.3 11.0 1.0
O1B A:ATP701 4.4 15.5 1.0
O5' A:ATP701 4.5 15.7 1.0
CG A:GLU407 4.5 11.3 1.0
O A:HOH2199 4.5 24.1 1.0
OE1 A:GLU209 4.6 17.4 1.0
C5' A:ATP701 4.6 13.8 1.0
CG A:GLU209 4.7 13.5 1.0
CE1 A:PHE412 4.7 10.0 0.7
C3' A:ATP701 4.7 11.8 1.0
O A:HOH2201 4.8 7.9 1.0
O1G A:ATP701 4.8 18.5 1.0
CE2 A:PHE412 4.9 13.3 0.7
CA A:HIS410 5.0 15.1 1.0

Manganese binding site 2 out of 6 in 2j3m

Go back to Manganese Binding Sites List in 2j3m
Manganese binding site 2 out of 6 in the Prolyl-Trna Synthetase From Enterococcus Faecalis Complexed with Atp, Manganese and Prolinol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Prolyl-Trna Synthetase From Enterococcus Faecalis Complexed with Atp, Manganese and Prolinol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1568

b:22.1
occ:1.00
 O1G A:ATP701 2.1 18.5 1.0
O A:HOH2201 2.3 7.9 1.0
OE1 A:GLU407 2.3 14.3 1.0
O2B A:ATP701 2.3 15.1 1.0
PB A:ATP701 3.2 15.7 1.0
MN A:MN1567 3.3 17.6 1.0
O3B A:ATP701 3.3 15.0 1.0
PG A:ATP701 3.4 18.2 1.0
CD A:GLU407 3.4 9.7 1.0
OE2 A:GLU407 3.8 7.2 1.0
OE1 A:GLU209 3.9 17.4 1.0
O1B A:ATP701 3.9 15.5 1.0
O A:HOH2200 4.0 12.0 1.0
O A:HOH2084 4.0 14.7 1.0
O B:HOH2161 4.1 10.2 1.0
O3G A:ATP701 4.2 17.9 1.0
O A:HOH2077 4.4 12.7 1.0
O3A A:ATP701 4.5 16.3 1.0
O2G A:ATP701 4.5 12.6 1.0
OD2 A:ASP219 4.5 17.1 1.0
OD1 A:ASP219 4.6 22.1 1.0
CG A:GLU407 4.6 11.3 1.0
ND1 A:HIS410 4.7 16.1 1.0
CB A:GLU407 4.8 12.5 1.0
CD A:GLU209 4.8 14.8 1.0
CG A:ASP219 5.0 19.5 1.0
MN B:MN1570 5.0 24.2 1.0

Manganese binding site 3 out of 6 in 2j3m

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Manganese binding site 3 out of 6 in the Prolyl-Trna Synthetase From Enterococcus Faecalis Complexed with Atp, Manganese and Prolinol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Prolyl-Trna Synthetase From Enterococcus Faecalis Complexed with Atp, Manganese and Prolinol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1567

b:23.3
occ:1.00
 O B:HOH2157 2.0 14.4 1.0
O1A B:ATP701 2.2 19.1 1.0
ND1 B:HIS410 2.2 15.1 1.0
O2B B:ATP701 2.2 23.1 1.0
OE2 B:GLU407 2.3 15.6 1.0
CE1 B:HIS410 3.2 17.7 1.0
CG B:HIS410 3.2 15.4 1.0
CD B:GLU407 3.2 17.2 1.0
PA B:ATP701 3.2 14.2 1.0
O3A B:ATP701 3.4 18.3 1.0
PB B:ATP701 3.4 15.1 1.0
OE1 B:GLU407 3.4 22.1 1.0
CB B:HIS410 3.5 14.3 1.0
MN B:MN1568 3.5 28.2 1.0
O B:HOH2084 4.0 19.2 1.0
O2A B:ATP701 4.1 15.6 1.0
OE1 B:GLU209 4.2 19.2 1.0
NE2 B:HIS410 4.3 16.0 1.0
CD2 B:HIS410 4.3 13.6 1.0
O3' B:ATP701 4.3 12.9 1.0
O3B B:ATP701 4.4 18.7 1.0
O5' B:ATP701 4.4 15.5 1.0
O1B B:ATP701 4.5 19.4 1.0
CG B:GLU407 4.5 15.4 1.0
C3' B:ATP701 4.5 14.6 1.0
O B:HOH2155 4.6 29.2 1.0
O B:HOH2158 4.6 12.7 1.0
C5' B:ATP701 4.6 15.8 1.0
CG B:GLU209 4.6 17.7 1.0
CD B:GLU209 4.9 20.3 1.0
O1G B:ATP701 4.9 19.0 1.0
CA B:HIS410 5.0 14.9 1.0

Manganese binding site 4 out of 6 in 2j3m

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Manganese binding site 4 out of 6 in the Prolyl-Trna Synthetase From Enterococcus Faecalis Complexed with Atp, Manganese and Prolinol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Prolyl-Trna Synthetase From Enterococcus Faecalis Complexed with Atp, Manganese and Prolinol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1568

b:28.2
occ:1.00
 O1G B:ATP701 1.9 19.0 1.0
OE1 B:GLU407 2.2 22.1 1.0
O B:HOH2158 2.2 12.7 1.0
O2B B:ATP701 2.3 23.1 1.0
PG B:ATP701 3.2 19.8 1.0
CD B:GLU407 3.3 17.2 1.0
PB B:ATP701 3.3 15.1 1.0
O3B B:ATP701 3.4 18.7 1.0
MN B:MN1567 3.5 23.3 1.0
OE1 B:GLU209 3.6 19.2 1.0
OE2 B:GLU407 3.7 15.6 1.0
O B:HOH2084 3.9 19.2 1.0
O B:HOH2093 4.0 20.5 1.0
O B:HOH2159 4.1 20.8 1.0
O1B B:ATP701 4.2 19.4 1.0
O3G B:ATP701 4.2 16.7 1.0
O B:HOH2157 4.2 14.4 1.0
O2G B:ATP701 4.2 19.2 1.0
OD1 B:ASP219 4.2 22.5 1.0
O B:HOH2088 4.3 15.7 1.0
O B:HOH2155 4.3 29.2 1.0
CG B:GLU407 4.5 15.4 1.0
O3A B:ATP701 4.5 18.3 1.0
CD B:GLU209 4.6 20.3 1.0
OD2 B:ASP219 4.7 24.6 1.0
CB B:GLU407 4.7 14.3 1.0
CG B:ASP219 4.8 21.4 1.0
MN B:MN1569 4.9 29.6 1.0

Manganese binding site 5 out of 6 in 2j3m

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Manganese binding site 5 out of 6 in the Prolyl-Trna Synthetase From Enterococcus Faecalis Complexed with Atp, Manganese and Prolinol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Prolyl-Trna Synthetase From Enterococcus Faecalis Complexed with Atp, Manganese and Prolinol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1569

b:29.6
occ:1.00
 O2G B:ATP701 2.2 19.2 1.0
O B:HOH2160 2.2 6.9 1.0
O1B B:ATP701 2.3 19.4 1.0
O B:HOH2159 2.4 20.8 1.0
PG B:ATP701 3.3 19.8 1.0
PB B:ATP701 3.4 15.1 1.0
O3B B:ATP701 3.6 18.7 1.0
NH1 B:ARG151 3.8 16.2 1.0
O1G B:ATP701 3.9 19.0 1.0
NH1 B:ARG140 4.0 11.4 1.0
OE1 B:GLU142 4.0 17.3 1.0
O B:HOH2155 4.2 29.2 1.0
OE2 B:GLU142 4.2 17.7 1.0
O2B B:ATP701 4.3 23.1 1.0
O B:HOH2158 4.3 12.7 1.0
O B:HOH2038 4.4 13.8 1.0
O B:HOH2154 4.4 25.2 1.0
N7 B:ATP701 4.5 9.5 1.0
CD B:GLU142 4.6 16.3 1.0
O3G B:ATP701 4.6 16.7 1.0
O3A B:ATP701 4.6 18.3 1.0
OD1 B:ASN92 4.8 25.1 1.0
MN B:MN1568 4.9 28.2 1.0
CZ B:ARG151 5.0 17.8 1.0

Manganese binding site 6 out of 6 in 2j3m

Go back to Manganese Binding Sites List in 2j3m
Manganese binding site 6 out of 6 in the Prolyl-Trna Synthetase From Enterococcus Faecalis Complexed with Atp, Manganese and Prolinol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Prolyl-Trna Synthetase From Enterococcus Faecalis Complexed with Atp, Manganese and Prolinol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1570

b:24.2
occ:1.00
 O1B A:ATP701 2.1 15.5 1.0
O B:HOH2162 2.3 7.9 1.0
O B:HOH2161 2.4 10.2 1.0
O2G A:ATP701 2.5 12.6 1.0
PB A:ATP701 3.3 15.7 1.0
PG A:ATP701 3.4 18.2 1.0
O3B A:ATP701 3.5 15.0 1.0
O1G A:ATP701 3.7 18.5 1.0
NH1 A:ARG151 3.8 7.2 1.0
NH1 A:ARG140 4.1 9.9 1.0
OE1 A:GLU142 4.1 10.4 1.0
O A:HOH2201 4.3 7.9 1.0
O3A A:ATP701 4.4 16.3 1.0
OE2 A:GLU142 4.4 11.0 1.0
O2B A:ATP701 4.5 15.1 1.0
N7 A:ATP701 4.6 8.2 1.0
CD A:GLU142 4.7 12.1 1.0
ND2 A:ASN92 4.7 16.6 1.0
O3G A:ATP701 4.7 17.9 1.0
CZ A:ARG151 4.9 13.7 1.0
MN A:MN1568 5.0 22.1 1.0

Reference:

T.Crepin, A.Yaremchuk, M.Tukalo, S.Cusack. Structures of Two Bacterial Prolyl-Trna Synthetases with and Without A Cis-Editing Domain. Structure V. 14 1511 2006.
ISSN: ISSN 0969-2126
PubMed: 17027500
DOI: 10.1016/J.STR.2006.08.007
Page generated: Sat Oct 5 14:31:04 2024

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