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Magnesium in PDB 2i4o: Rhodopseudomonas Palustris Prolyl-Trna Synthetase in Complex with Atp

Enzymatic activity of Rhodopseudomonas Palustris Prolyl-Trna Synthetase in Complex with Atp

All present enzymatic activity of Rhodopseudomonas Palustris Prolyl-Trna Synthetase in Complex with Atp:
6.1.1.15;

Protein crystallography data

The structure of Rhodopseudomonas Palustris Prolyl-Trna Synthetase in Complex with Atp, PDB code: 2i4o 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) N/A / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 114.200, 211.210, 148.210, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 26.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Rhodopseudomonas Palustris Prolyl-Trna Synthetase in Complex with Atp (pdb code 2i4o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Rhodopseudomonas Palustris Prolyl-Trna Synthetase in Complex with Atp, PDB code: 2i4o:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2i4o

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Magnesium binding site 1 out of 8 in the Rhodopseudomonas Palustris Prolyl-Trna Synthetase in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rhodopseudomonas Palustris Prolyl-Trna Synthetase in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg439

b:38.6
occ:1.00
 OE1 A:GLN285 2.4 33.4 1.0
OE2 A:GLU282 2.4 35.6 1.0
O2A A:ATP442 2.5 31.4 1.0
O2B A:ATP442 2.5 37.0 1.0
MG A:MG440 2.7 48.6 1.0
CD A:GLU282 3.1 36.5 1.0
OE1 A:GLU282 3.2 38.1 1.0
O3A A:ATP442 3.3 36.1 1.0
PB A:ATP442 3.4 38.9 1.0
PA A:ATP442 3.4 33.5 1.0
CD A:GLN285 3.5 34.5 1.0
CB A:GLN285 3.7 31.9 1.0
O3B A:ATP442 3.9 39.6 1.0
CG A:GLN285 4.1 34.0 1.0
CG A:GLU282 4.5 32.8 1.0
O5' A:ATP442 4.5 32.8 1.0
O3' A:ATP442 4.6 29.7 1.0
O1A A:ATP442 4.6 33.9 1.0
NE2 A:GLN285 4.6 32.4 1.0
CG A:GLU209 4.6 37.9 1.0
C5' A:ATP442 4.6 31.3 1.0
C3' A:ATP442 4.7 29.5 1.0
O1B A:ATP442 4.8 38.9 1.0
CD A:GLU209 4.9 41.7 1.0

Magnesium binding site 2 out of 8 in 2i4o

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Magnesium binding site 2 out of 8 in the Rhodopseudomonas Palustris Prolyl-Trna Synthetase in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rhodopseudomonas Palustris Prolyl-Trna Synthetase in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg440

b:48.6
occ:1.00
 OE1 A:GLU282 2.4 38.1 1.0
MG A:MG439 2.7 38.6 1.0
O2B A:ATP442 2.7 37.0 1.0
CD A:GLU282 3.3 36.5 1.0
OE2 A:GLU282 3.6 35.6 1.0
O3B A:ATP442 3.6 39.6 1.0
O3G A:ATP442 3.6 39.8 1.0
PB A:ATP442 3.8 38.9 1.0
CD A:GLU209 3.9 41.7 1.0
OE2 A:GLU209 3.9 42.0 1.0
OE1 A:GLU209 3.9 44.6 1.0
OE1 A:GLN285 4.1 33.4 1.0
PG A:ATP442 4.3 42.0 1.0
CG A:GLU209 4.5 37.9 1.0
O3A A:ATP442 4.7 36.1 1.0
CG A:GLU282 4.7 32.8 1.0
O2A A:ATP442 5.0 31.4 1.0

Magnesium binding site 3 out of 8 in 2i4o

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Magnesium binding site 3 out of 8 in the Rhodopseudomonas Palustris Prolyl-Trna Synthetase in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rhodopseudomonas Palustris Prolyl-Trna Synthetase in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg441

b:48.9
occ:1.00
 O2G A:ATP442 2.0 40.8 1.0
O1B A:ATP442 2.4 38.9 1.0
O A:HOH448 2.6 24.3 1.0
PG A:ATP442 3.3 42.0 1.0
PB A:ATP442 3.5 38.9 1.0
O3G A:ATP442 3.7 39.8 1.0
O3B A:ATP442 3.8 39.6 1.0
OE1 A:GLU142 3.9 35.3 1.0
O2B A:ATP442 4.2 37.0 1.0
NH1 A:ARG140 4.2 23.4 1.0
OE2 A:GLU92 4.3 38.5 1.0
NH1 A:ARG151 4.4 38.3 1.0
OE1 A:GLU92 4.4 36.7 1.0
O1G A:ATP442 4.6 40.9 1.0
O3A A:ATP442 4.8 36.1 1.0
OE2 A:GLU142 4.8 37.4 1.0
CD A:GLU142 4.8 36.3 1.0
CD A:GLU92 4.8 36.5 1.0
N7 A:ATP442 5.0 24.4 1.0

Magnesium binding site 4 out of 8 in 2i4o

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Magnesium binding site 4 out of 8 in the Rhodopseudomonas Palustris Prolyl-Trna Synthetase in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Rhodopseudomonas Palustris Prolyl-Trna Synthetase in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg439

b:38.2
occ:1.00
 O2A B:ATP442 2.4 29.7 1.0
OE2 B:GLU282 2.4 29.4 1.0
O2B B:ATP442 2.4 30.3 1.0
OE1 B:GLN285 2.6 34.8 1.0
MG B:MG440 3.1 45.1 1.0
O3A B:ATP442 3.4 31.0 1.0
CD B:GLU282 3.4 30.0 1.0
CD B:GLN285 3.4 33.1 1.0
PA B:ATP442 3.5 28.4 1.0
CB B:GLN285 3.5 30.2 1.0
PB B:ATP442 3.5 27.5 1.0
CG B:GLN285 3.6 32.9 1.0
OE1 B:GLU282 3.8 32.4 1.0
O3' B:ATP442 4.2 26.7 1.0
O3B B:ATP442 4.4 33.0 1.0
O5' B:ATP442 4.5 28.9 1.0
C3' B:ATP442 4.6 23.7 1.0
O1A B:ATP442 4.6 29.6 1.0
C5' B:ATP442 4.6 28.0 1.0
OE2 B:GLU209 4.6 35.6 1.0
NE2 B:GLN285 4.7 32.0 1.0
CG B:GLU282 4.7 28.7 1.0
O1B B:ATP442 4.7 31.9 1.0
CD B:GLU209 4.8 36.2 1.0
CG B:GLU209 4.8 31.9 1.0
CA B:GLN285 5.0 29.7 1.0

Magnesium binding site 5 out of 8 in 2i4o

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Magnesium binding site 5 out of 8 in the Rhodopseudomonas Palustris Prolyl-Trna Synthetase in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Rhodopseudomonas Palustris Prolyl-Trna Synthetase in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg440

b:45.1
occ:1.00
 O2B B:ATP442 2.3 30.3 1.0
O3G B:ATP442 2.8 27.0 1.0
OE1 B:GLU282 2.8 32.4 1.0
MG B:MG439 3.1 38.2 1.0
NH2 C:ARG144 3.2 41.0 1.0
PB B:ATP442 3.5 27.5 1.0
OE2 B:GLU282 3.5 29.4 1.0
CD B:GLU282 3.6 30.0 1.0
O3B B:ATP442 3.8 33.0 1.0
OE2 B:GLU209 3.8 35.6 1.0
PG B:ATP442 4.0 35.0 1.0
CD B:GLU209 4.3 36.2 1.0
OE1 B:GLN285 4.4 34.8 1.0
OE1 B:GLU209 4.4 37.9 1.0
CZ C:ARG144 4.5 42.8 1.0
O1B B:ATP442 4.5 31.9 1.0
O3A B:ATP442 4.6 31.0 1.0
O B:HOH510 4.6 28.5 1.0
O1G B:ATP442 4.8 33.0 1.0

Magnesium binding site 6 out of 8 in 2i4o

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Magnesium binding site 6 out of 8 in the Rhodopseudomonas Palustris Prolyl-Trna Synthetase in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Rhodopseudomonas Palustris Prolyl-Trna Synthetase in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg441

b:39.2
occ:1.00
 O2G B:ATP442 2.1 29.8 1.0
O1B B:ATP442 2.2 31.9 1.0
PG B:ATP442 3.2 35.0 1.0
O3B B:ATP442 3.3 33.0 1.0
PB B:ATP442 3.3 27.5 1.0
NH1 B:ARG140 3.8 32.8 1.0
OE2 B:GLU142 3.8 39.5 1.0
O3G B:ATP442 3.9 27.0 1.0
NH1 B:ARG151 4.2 31.5 1.0
OE1 B:GLU92 4.2 40.1 1.0
O3A B:ATP442 4.3 31.0 1.0
N7 B:ATP442 4.3 21.5 1.0
O1G B:ATP442 4.4 33.0 1.0
O2B B:ATP442 4.5 30.3 1.0
OE2 B:GLU92 4.6 42.9 1.0
CD B:ARG140 4.6 29.8 1.0
CD B:GLU142 4.8 35.8 1.0
CZ B:ARG140 4.8 32.8 1.0
CD B:GLU92 4.9 40.0 1.0
C8 B:ATP442 4.9 23.5 1.0
OE1 B:GLU142 4.9 34.8 1.0

Magnesium binding site 7 out of 8 in 2i4o

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Magnesium binding site 7 out of 8 in the Rhodopseudomonas Palustris Prolyl-Trna Synthetase in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Rhodopseudomonas Palustris Prolyl-Trna Synthetase in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg439

b:38.3
occ:1.00
 OE2 C:GLU282 2.2 27.1 1.0
O2A C:ATP441 2.3 28.9 1.0
OE1 C:GLN285 2.4 29.0 1.0
O2B C:ATP441 2.5 36.1 1.0
CD C:GLU282 3.2 27.7 1.0
PA C:ATP441 3.3 25.7 1.0
O3A C:ATP441 3.4 31.9 1.0
PB C:ATP441 3.4 33.9 1.0
OE1 C:GLU282 3.5 35.4 1.0
CD C:GLN285 3.5 28.1 1.0
CB C:GLN285 3.7 24.9 1.0
O3B C:ATP441 4.1 32.6 1.0
CG C:GLN285 4.2 25.6 1.0
O3' C:ATP441 4.4 27.8 1.0
O1A C:ATP441 4.4 27.7 1.0
O5' C:ATP441 4.5 28.2 1.0
CG C:GLU282 4.6 28.7 1.0
NE2 C:GLN285 4.6 26.1 1.0
C3' C:ATP441 4.6 28.9 1.0
CG C:GLU209 4.6 33.3 1.0
C5' C:ATP441 4.7 27.1 1.0
O1B C:ATP441 4.8 34.5 1.0
CD C:GLU209 4.9 33.9 1.0

Magnesium binding site 8 out of 8 in 2i4o

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Magnesium binding site 8 out of 8 in the Rhodopseudomonas Palustris Prolyl-Trna Synthetase in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Rhodopseudomonas Palustris Prolyl-Trna Synthetase in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg440

b:36.9
occ:1.00
 O2G C:ATP441 2.0 33.0 1.0
O1B C:ATP441 2.2 34.5 1.0
O C:HOH497 2.4 25.3 1.0
PG C:ATP441 3.3 35.1 1.0
PB C:ATP441 3.5 33.9 1.0
O3B C:ATP441 3.8 32.6 1.0
O3G C:ATP441 4.0 34.2 1.0
NH1 C:ARG140 4.1 25.6 1.0
OE1 C:GLU92 4.2 37.1 1.0
OE1 C:GLU142 4.3 27.6 1.0
O2B C:ATP441 4.3 36.1 1.0
NH1 C:ARG151 4.4 28.4 1.0
OE2 C:GLU92 4.5 35.6 1.0
O1G C:ATP441 4.5 34.0 1.0
O3A C:ATP441 4.6 31.9 1.0
OE2 C:GLU142 4.7 31.6 1.0
CD C:GLU92 4.7 34.2 1.0
N7 C:ATP441 4.8 24.6 1.0
CD C:GLU142 5.0 29.4 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: Sun Aug 10 11:31:01 2025

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