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Magnesium in PDB 1yfr: Crystal Structure of Alanyl-Trna Synthetase in Complex with Atp and Magnesium

Enzymatic activity of Crystal Structure of Alanyl-Trna Synthetase in Complex with Atp and Magnesium

All present enzymatic activity of Crystal Structure of Alanyl-Trna Synthetase in Complex with Atp and Magnesium:
6.1.1.7;

Protein crystallography data

The structure of Crystal Structure of Alanyl-Trna Synthetase in Complex with Atp and Magnesium, PDB code: 1yfr was solved by M.A.Swairjo, P.R.Schimmel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 173.602, 73.926, 73.976, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 22.5

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 6 in 1yfr

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Magnesium binding site 1 out of 6 in the Crystal Structure of Alanyl-Trna Synthetase in Complex with Atp and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Alanyl-Trna Synthetase in Complex with Atp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1502

b:59.7
occ:1.00
 O1B A:ATP1500 2.3 45.1 1.0
O1A A:ATP1500 2.4 36.2 1.0
OE2 A:GLU174 2.6 29.4 1.0
OD1 A:ASN194 2.8 21.3 1.0
O A:HOH1510 3.0 60.0 1.0
OE1 A:GLU191 3.3 37.4 1.0
MG A:MG1504 3.3 57.6 1.0
PA A:ATP1500 3.5 38.9 1.0
PB A:ATP1500 3.5 47.9 1.0
CD A:GLU174 3.5 28.2 1.0
CG A:ASN194 3.5 21.0 1.0
O3A A:ATP1500 3.7 42.4 1.0
O A:HOH1529 3.7 15.6 1.0
CD A:GLU191 3.9 36.1 1.0
O3B A:ATP1500 4.0 47.5 1.0
OE1 A:GLU174 4.0 21.2 1.0
O2A A:ATP1500 4.0 38.1 1.0
OE2 A:GLU191 4.0 31.1 1.0
ND2 A:ASN194 4.1 21.0 1.0
CB A:ASN194 4.4 21.0 1.0
CG A:GLU174 4.5 26.5 1.0
O2B A:ATP1500 4.8 45.1 1.0
O5' A:ATP1500 4.9 39.9 1.0
O3' A:ATP1500 4.9 25.8 1.0

Magnesium binding site 2 out of 6 in 1yfr

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Magnesium binding site 2 out of 6 in the Crystal Structure of Alanyl-Trna Synthetase in Complex with Atp and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Alanyl-Trna Synthetase in Complex with Atp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1503

b:53.6
occ:1.00
 O2B A:ATP1500 2.3 45.1 1.0
O1G A:ATP1500 2.5 55.0 1.0
O A:HOH1506 2.7 60.0 1.0
O2G A:ATP1500 2.7 46.5 1.0
O A:HOH1505 2.9 50.5 1.0
PG A:ATP1500 3.0 50.8 1.0
PB A:ATP1500 3.3 47.9 1.0
O3B A:ATP1500 3.3 47.5 1.0
O A:HOH1590 3.6 19.7 1.0
O1B A:ATP1500 4.3 45.1 1.0
O3G A:ATP1500 4.4 52.1 1.0
O3A A:ATP1500 4.5 42.4 1.0
CE1 A:HIS86 4.5 27.6 1.0
NH2 A:ARG69 4.7 23.3 1.0
O A:HOH1531 4.8 17.5 1.0

Magnesium binding site 3 out of 6 in 1yfr

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Magnesium binding site 3 out of 6 in the Crystal Structure of Alanyl-Trna Synthetase in Complex with Atp and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Alanyl-Trna Synthetase in Complex with Atp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1504

b:57.6
occ:1.00
 O A:HOH1509 2.5 60.0 1.0
O A:HOH1531 2.7 17.5 1.0
OE1 A:GLU174 3.2 21.2 1.0
MG A:MG1502 3.3 59.7 1.0
O A:HOH1508 3.4 57.6 1.0
O1B A:ATP1500 3.5 45.1 1.0
OE2 A:GLU174 3.5 29.4 1.0
CD A:GLU174 3.8 28.2 1.0
O3B A:ATP1500 3.8 47.5 1.0
OE2 A:GLU191 3.8 31.1 1.0
PB A:ATP1500 4.3 47.9 1.0
CD A:GLU191 4.4 36.1 1.0
O1G A:ATP1500 4.5 55.0 1.0
OH A:TYR176 4.7 15.1 1.0
OE1 A:GLU191 4.8 37.4 1.0
PG A:ATP1500 4.8 50.8 1.0
O A:HOH1507 4.8 60.0 1.0

Magnesium binding site 4 out of 6 in 1yfr

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Magnesium binding site 4 out of 6 in the Crystal Structure of Alanyl-Trna Synthetase in Complex with Atp and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Alanyl-Trna Synthetase in Complex with Atp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2502

b:44.3
occ:1.00
 O1A B:ATP2500 2.4 36.2 1.0
O1B B:ATP2500 2.5 45.1 1.0
OE2 B:GLU174 2.7 32.8 1.0
O B:HOH2506 2.9 59.6 1.0
OD1 B:ASN194 3.0 26.9 1.0
OE1 B:GLU191 3.0 27.6 1.0
MG B:MG2504 3.0 57.3 1.0
CG B:ASN194 3.5 24.6 1.0
PA B:ATP2500 3.5 38.9 1.0
PB B:ATP2500 3.6 47.9 1.0
CD B:GLU174 3.7 29.1 1.0
O3A B:ATP2500 3.8 42.4 1.0
O3B B:ATP2500 4.0 47.5 1.0
CD B:GLU191 4.1 26.1 1.0
ND2 B:ASN194 4.1 27.2 1.0
O2A B:ATP2500 4.1 38.1 1.0
CB B:ASN194 4.2 24.1 1.0
OE1 B:GLU174 4.5 31.9 1.0
CG B:GLU174 4.6 30.7 1.0
O B:HOH2600 4.6 16.5 1.0
OE2 B:GLU191 4.7 25.6 1.0
O3' B:ATP2500 4.8 25.8 1.0
O5' B:ATP2500 4.8 39.9 1.0
O2B B:ATP2500 5.0 45.1 1.0
O B:HOH2507 5.0 60.0 1.0

Magnesium binding site 5 out of 6 in 1yfr

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Magnesium binding site 5 out of 6 in the Crystal Structure of Alanyl-Trna Synthetase in Complex with Atp and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Alanyl-Trna Synthetase in Complex with Atp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2503

b:60.0
occ:1.00
 O2B B:ATP2500 2.0 45.1 1.0
O2G B:ATP2500 2.7 46.5 1.0
O1G B:ATP2500 2.8 55.0 1.0
O B:HOH2505 3.0 45.9 1.0
PG B:ATP2500 3.1 50.8 1.0
PB B:ATP2500 3.2 47.9 1.0
O3B B:ATP2500 3.4 47.5 1.0
NH2 B:ARG69 3.4 21.3 1.0
NH1 B:ARG69 3.7 23.4 1.0
CZ B:ARG69 4.0 22.7 1.0
O1B B:ATP2500 4.2 45.1 1.0
O3A B:ATP2500 4.3 42.4 1.0
OD2 B:ASP76 4.3 30.9 1.0
O3G B:ATP2500 4.6 52.1 1.0
CE1 B:HIS86 5.0 44.0 1.0
OD1 B:ASP76 5.0 32.8 1.0

Magnesium binding site 6 out of 6 in 1yfr

Go back to Magnesium Binding Sites List in 1yfr
Magnesium binding site 6 out of 6 in the Crystal Structure of Alanyl-Trna Synthetase in Complex with Atp and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Alanyl-Trna Synthetase in Complex with Atp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2504

b:57.3
occ:1.00
 OE2 B:GLU174 2.9 32.8 1.0
MG B:MG2502 3.0 44.3 1.0
O1B B:ATP2500 3.2 45.1 1.0
O B:HOH2507 3.3 60.0 1.0
O B:HOH2541 3.3 24.0 1.0
OE1 B:GLU174 3.4 31.9 1.0
CD B:GLU174 3.5 29.1 1.0
O3B B:ATP2500 3.7 47.5 1.0
OE1 B:GLU191 3.7 27.6 1.0
CD B:GLU191 3.9 26.1 1.0
OE2 B:GLU191 4.0 25.6 1.0
PB B:ATP2500 4.1 47.9 1.0
O B:HOH2506 4.5 59.6 1.0
O1G B:ATP2500 4.5 55.0 1.0
CG B:GLU191 4.8 23.5 1.0
PG B:ATP2500 4.8 50.8 1.0
OH B:TYR176 5.0 30.6 1.0
CG B:GLU174 5.0 30.7 1.0

Reference:

M.A.Swairjo, P.R.Schimmel. Breaking Sieve For Steric Exclusion of A Noncognate Amino Acid From Active Site of A Trna Synthetase. Proc.Natl.Acad.Sci.Usa V. 102 988 2005.
ISSN: ISSN 0027-8424
PubMed: 15657145
DOI: 10.1073/PNAS.0409024102
Page generated: Tue Aug 13 18:37:17 2024

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