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Manganese in PDB 1b8a: Aspartyl-Trna Synthetase

Enzymatic activity of Aspartyl-Trna Synthetase

All present enzymatic activity of Aspartyl-Trna Synthetase:
6.1.1.12;

Protein crystallography data

The structure of Aspartyl-Trna Synthetase, PDB code: 1b8a was solved by E.Schmitt, L.Moulinier, J.-C.Thierry, D.Moras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 124.800, 125.000, 87.160, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 20.2

Manganese Binding Sites:

The binding sites of Manganese atom in the Aspartyl-Trna Synthetase (pdb code 1b8a). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Aspartyl-Trna Synthetase, PDB code: 1b8a:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 1b8a

Go back to Manganese Binding Sites List in 1b8a
Manganese binding site 1 out of 6 in the Aspartyl-Trna Synthetase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Aspartyl-Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn600

b:19.6
occ:1.00
 O2B A:ATP500 2.2 24.2 1.0
O3G A:ATP500 2.2 24.9 1.0
O A:HOH2199 2.3 19.5 1.0
O A:HOH2201 2.3 16.5 1.0
O A:HOH2198 2.3 20.4 1.0
O A:HOH2200 2.4 15.8 1.0
PB A:ATP500 3.2 26.5 1.0
O3B A:ATP500 3.3 23.7 1.0
PG A:ATP500 3.4 27.2 1.0
O2G A:ATP500 3.9 25.8 1.0
NE2 A:HIS223 4.0 18.5 1.0
O A:HOH2241 4.0 38.8 1.0
O A:HOH3071 4.1 39.9 1.0
O A:HOH2644 4.2 31.4 1.0
O1B A:ATP500 4.3 24.1 1.0
OE2 A:GLU216 4.3 18.6 1.0
O3A A:ATP500 4.3 24.9 1.0
O A:HOH3114 4.3 37.0 1.0
OE1 A:GLU174 4.4 38.2 1.0
CD2 A:HIS223 4.4 17.4 1.0
OE1 A:GLU216 4.4 20.9 1.0
O1G A:ATP500 4.5 26.0 1.0
O A:HOH2581 4.6 37.7 1.0
NH1 A:ARG214 4.6 26.2 1.0
O A:HOH2832 4.6 39.2 1.0
N7 A:ATP500 4.6 15.9 1.0
CD A:GLU216 4.8 20.5 1.0

Manganese binding site 2 out of 6 in 1b8a

Go back to Manganese Binding Sites List in 1b8a
Manganese binding site 2 out of 6 in the Aspartyl-Trna Synthetase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Aspartyl-Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:39.0
occ:1.00
 O1B A:ATP500 2.2 24.1 1.0
OG A:SER364 2.4 20.4 1.0
O A:HOH2250 2.4 18.9 1.0
OE2 A:GLU361 2.4 15.5 1.0
O1A A:ATP500 2.6 25.1 1.0
O A:HOH2251 2.6 25.3 1.0
MN A:MN602 3.1 31.8 1.0
CD A:GLU361 3.1 17.2 1.0
CB A:SER364 3.3 14.6 1.0
OE1 A:GLU361 3.3 17.6 1.0
PB A:ATP500 3.3 26.5 1.0
O3A A:ATP500 3.4 24.9 1.0
PA A:ATP500 3.6 24.7 1.0
OD1 A:ASP354 3.8 19.6 1.0
OD2 A:ASP354 4.1 21.5 1.0
O3B A:ATP500 4.1 23.7 1.0
O A:HOH2249 4.2 23.2 1.0
NZ A:LYS336 4.3 22.3 1.0
CG A:ASP354 4.3 18.1 1.0
CG A:GLU361 4.5 15.5 1.0
O3' A:ATP500 4.5 13.8 1.0
O2B A:ATP500 4.5 24.2 1.0
CA A:SER364 4.5 12.9 1.0
O2A A:ATP500 4.5 25.2 1.0
O A:HOH2517 4.6 27.8 1.0
O A:HOH2880 4.7 36.1 1.0
O5' A:ATP500 4.7 21.6 1.0
O2G A:ATP500 4.8 25.8 1.0
O A:HOH2644 4.8 31.4 1.0
C3' A:ATP500 4.8 14.1 1.0
C5' A:ATP500 4.9 17.9 1.0
N A:SER364 4.9 12.3 1.0

Manganese binding site 3 out of 6 in 1b8a

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Manganese binding site 3 out of 6 in the Aspartyl-Trna Synthetase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Aspartyl-Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:31.8
occ:1.00
 OE1 A:GLU361 2.2 17.6 1.0
O2G A:ATP500 2.3 25.8 1.0
O1B A:ATP500 2.3 24.1 1.0
O A:HOH2249 2.4 23.2 1.0
O A:HOH2250 2.5 18.9 1.0
O A:HOH2248 2.5 27.3 1.0
MN A:MN601 3.1 39.0 1.0
CD A:GLU361 3.2 17.2 1.0
PG A:ATP500 3.3 27.2 1.0
O3B A:ATP500 3.4 23.7 1.0
PB A:ATP500 3.4 26.5 1.0
OE2 A:GLU361 3.5 15.5 1.0
OD2 A:ASP354 4.0 21.5 1.0
O A:HOH2517 4.1 27.8 1.0
O A:HOH3114 4.1 37.0 1.0
O A:HOH2239 4.1 19.5 1.0
O A:HOH2644 4.2 31.4 1.0
O1G A:ATP500 4.3 26.0 1.0
O2B A:ATP500 4.4 24.2 1.0
CG A:GLU361 4.5 15.5 1.0
O3G A:ATP500 4.5 24.9 1.0
O3A A:ATP500 4.6 24.9 1.0
CB A:GLU361 4.8 13.0 1.0
O A:HOH2251 4.8 25.3 1.0
O A:HOH2201 5.0 16.5 1.0
OG A:SER364 5.0 20.4 1.0
O A:HOH2903 5.0 39.7 1.0

Manganese binding site 4 out of 6 in 1b8a

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Manganese binding site 4 out of 6 in the Aspartyl-Trna Synthetase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Aspartyl-Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1600

b:18.6
occ:1.00
 O2G B:ATP1500 2.2 21.4 1.0
O B:HOH2197 2.2 18.7 1.0
O B:HOH2194 2.2 15.5 1.0
O B:HOH2196 2.3 15.5 1.0
O2B B:ATP1500 2.3 23.2 1.0
O B:HOH2195 2.4 17.7 1.0
PG B:ATP1500 3.3 24.0 1.0
PB B:ATP1500 3.3 23.2 1.0
O3B B:ATP1500 3.4 22.2 1.0
O1G B:ATP1500 3.9 24.0 1.0
NH1 B:ARG1214 4.1 15.8 1.0
O B:HOH2831 4.1 41.5 1.0
CE1 B:HIS1223 4.1 13.9 1.0
O B:HOH2987 4.2 41.1 1.0
OE2 B:GLU1216 4.3 16.7 1.0
O1B B:ATP1500 4.3 23.0 1.0
OE1 B:GLU1216 4.3 20.1 1.0
O3A B:ATP1500 4.5 23.3 1.0
N7 B:ATP1500 4.5 13.6 1.0
O3G B:ATP1500 4.6 22.9 1.0
ND1 B:HIS1223 4.6 15.9 1.0
CD B:GLU1216 4.7 18.9 1.0

Manganese binding site 5 out of 6 in 1b8a

Go back to Manganese Binding Sites List in 1b8a
Manganese binding site 5 out of 6 in the Aspartyl-Trna Synthetase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Aspartyl-Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1601

b:28.6
occ:1.00
 O1G B:ATP1500 2.2 24.0 1.0
OE1 B:GLU1361 2.2 16.2 1.0
O1B B:ATP1500 2.3 23.0 1.0
O B:HOH2252 2.5 27.4 1.0
O B:HOH2254 2.5 22.6 1.0
O B:HOH2293 2.7 32.5 1.0
MN B:MN1602 3.0 39.8 1.0
CD B:GLU1361 3.1 15.3 1.0
PG B:ATP1500 3.3 24.0 1.0
O3B B:ATP1500 3.3 22.2 1.0
PB B:ATP1500 3.4 23.2 1.0
OE2 B:GLU1361 3.4 13.9 1.0
O3G B:ATP1500 4.1 22.9 1.0
OD2 B:ASP1354 4.1 20.6 1.0
O B:HOH2677 4.2 32.9 1.0
O B:HOH2488 4.4 23.1 1.0
O3A B:ATP1500 4.4 23.3 1.0
O2B B:ATP1500 4.5 23.2 1.0
O2G B:ATP1500 4.5 21.4 1.0
CG B:GLU1361 4.5 12.4 1.0
O B:HOH2253 4.6 26.9 1.0
OD2 B:ASP1304 4.6 29.2 1.0
CB B:GLU1361 4.8 11.8 1.0
O B:HOH2195 4.9 17.7 1.0
O B:HOH2045 4.9 21.0 1.0

Manganese binding site 6 out of 6 in 1b8a

Go back to Manganese Binding Sites List in 1b8a
Manganese binding site 6 out of 6 in the Aspartyl-Trna Synthetase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Aspartyl-Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1602

b:39.8
occ:1.00
 O1B B:ATP1500 2.3 23.0 1.0
O B:HOH2254 2.3 22.6 1.0
OE2 B:GLU1361 2.5 13.9 1.0
O1A B:ATP1500 2.6 21.5 1.0
O B:HOH2253 2.6 26.9 1.0
OG B:SER1364 2.6 17.6 1.0
MN B:MN1601 3.0 28.6 1.0
CB B:SER1364 3.1 12.4 1.0
CD B:GLU1361 3.2 15.3 1.0
OE1 B:GLU1361 3.3 16.2 1.0
O3A B:ATP1500 3.4 23.3 1.0
PB B:ATP1500 3.4 23.2 1.0
PA B:ATP1500 3.6 21.9 1.0
OD1 B:ASP1354 4.0 17.2 1.0
O3B B:ATP1500 4.1 22.2 1.0
OD2 B:ASP1354 4.1 20.6 1.0
O B:HOH2677 4.2 32.9 1.0
CG B:ASP1354 4.4 15.8 1.0
CA B:SER1364 4.4 10.8 1.0
O B:HOH2252 4.4 27.4 1.0
NZ B:LYS1336 4.4 20.8 1.0
O3' B:ATP1500 4.5 12.1 1.0
CG B:GLU1361 4.5 12.4 1.0
O2A B:ATP1500 4.6 21.5 1.0
O2B B:ATP1500 4.6 23.2 1.0
O5' B:ATP1500 4.6 18.5 1.0
O1G B:ATP1500 4.7 24.0 1.0
C3' B:ATP1500 4.8 12.3 1.0
C5' B:ATP1500 4.8 15.8 1.0
N B:SER1364 4.9 10.4 1.0

Reference:

E.Schmitt, L.Moulinier, S.Fujiwara, T.Imanaka, J.C.Thierry, D.Moras. Crystal Structure of Aspartyl-Trna Synthetase From Pyrococcus Kodakaraensis Kod: Archaeon Specificity and Catalytic Mechanism of Adenylate Formation. Embo J. V. 17 5227 1998.
ISSN: ISSN 0261-4189
PubMed: 9724658
DOI: 10.1093/EMBOJ/17.17.5227
Page generated: Sat Oct 5 09:46:29 2024

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