Magnesium in PDB 6p24: Escherichia Coli Trna Synthetase

Enzymatic activity of Escherichia Coli Trna Synthetase

All present enzymatic activity of Escherichia Coli Trna Synthetase:
6.1.1.20;

Protein crystallography data

The structure of Escherichia Coli Trna Synthetase, PDB code: 6p24 was solved by D.Kahne, V.Baidin, T.W.Owens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 82.04 / 2.12
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.269, 173.583, 251.472, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 26.5

Other elements in 6p24:

The structure of Escherichia Coli Trna Synthetase also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the Escherichia Coli Trna Synthetase (pdb code 6p24). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Escherichia Coli Trna Synthetase, PDB code: 6p24:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in 6p24

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Magnesium binding site 1 out of 13 in the Escherichia Coli Trna Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Escherichia Coli Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:48.1
occ:1.00
 OE2 A:GLU252 2.0 46.4 1.0
OE1 B:GLU463 2.1 39.5 1.0
CD A:GLU252 3.0 46.8 1.0
CD B:GLU463 3.2 40.8 1.0
OE1 A:GLU252 3.3 41.4 1.0
OE2 B:GLU463 4.0 35.0 1.0
O B:HOH1005 4.0 41.6 1.0
CG B:GLU463 4.0 40.0 1.0
CB B:GLU463 4.0 37.0 1.0
OD1 B:ASP460 4.1 51.9 1.0
OD2 B:ASP454 4.2 48.9 1.0
ND2 B:ASN165 4.3 46.4 1.0
O B:HOH924 4.3 38.2 1.0
OE2 B:GLU464 4.3 48.8 1.0
O B:ASP454 4.3 46.2 1.0
CA B:ASP460 4.3 39.7 1.0
O B:ASP460 4.3 38.7 1.0
CG A:GLU252 4.4 40.3 1.0
CB B:ASP460 4.5 40.2 1.0
CG B:ASP460 4.6 46.5 1.0
O A:HOH535 4.8 55.4 1.0
C B:ASP460 4.8 47.2 1.0
CB B:ASP454 4.8 40.0 1.0
CG B:ASP454 4.9 47.2 1.0

Magnesium binding site 2 out of 13 in 6p24

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Magnesium binding site 2 out of 13 in the Escherichia Coli Trna Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Escherichia Coli Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:63.4
occ:1.00
 OD1 A:ASN103 2.1 55.0 1.0
NZ D:LYS505 2.9 40.9 1.0
O B:ASP504 3.0 41.2 1.0
O A:HOH516 3.0 49.1 1.0
CG A:ASN103 3.2 69.0 1.0
O A:ILE101 3.3 50.4 1.0
C B:ASP504 3.3 42.3 1.0
CA A:ASN103 3.4 52.9 1.0
O A:GLU102 3.5 55.5 1.0
CA B:ASP504 3.6 46.4 1.0
CE D:LYS505 3.6 38.7 1.0
N A:ASN103 3.6 52.1 1.0
O B:ASN503 3.6 40.1 1.0
C A:GLU102 3.7 54.9 1.0
CB A:ASN103 3.9 56.7 1.0
N B:GLY506 4.1 36.7 1.0
N B:LYS505 4.2 46.8 1.0
C A:ILE101 4.3 46.8 1.0
CG2 A:ILE101 4.3 41.6 1.0
ND2 A:ASN103 4.3 51.3 1.0
C B:ASN503 4.5 37.7 1.0
N B:ASP504 4.5 44.5 1.0
CB B:ASP504 4.6 45.2 1.0
CA B:LYS505 4.7 43.5 1.0
C A:ASN103 4.7 47.0 1.0
C B:LYS505 4.7 43.2 1.0
CA B:GLY506 4.8 44.4 1.0
OG D:SER623 4.8 41.0 1.0
CA A:GLU102 4.8 53.2 1.0
N A:GLY104 4.9 50.0 1.0
O D:HOH985 4.9 45.4 1.0
OD1 B:ASP504 4.9 41.4 1.0
N A:GLU102 4.9 48.2 1.0

Magnesium binding site 3 out of 13 in 6p24

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Magnesium binding site 3 out of 13 in the Escherichia Coli Trna Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Escherichia Coli Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:56.3
occ:1.00
 OE1 A:GLU268 2.1 57.6 1.0
OE1 B:GLU31 2.3 67.4 1.0
OE1 A:GLU256 2.6 59.3 1.0
CD A:GLU268 2.7 75.5 1.0
OE2 A:GLU268 2.8 60.9 1.0
OE2 A:GLU256 2.9 49.9 1.0
CD A:GLU256 3.1 56.8 1.0
CD B:GLU31 3.2 52.8 1.0
OE2 B:GLU31 3.5 74.3 1.0
O B:HOH969 3.5 55.6 1.0
NH1 A:ARG244 4.0 43.3 1.0
CG A:GLU268 4.2 66.7 1.0
CG A:GLU256 4.5 43.7 1.0
CG B:GLU31 4.6 55.3 1.0
NH2 A:ARG244 4.6 42.8 1.0
CZ A:ARG244 4.8 46.1 1.0
CB B:GLU31 4.9 42.8 1.0
CB A:GLU268 4.9 60.7 1.0

Magnesium binding site 4 out of 13 in 6p24

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Magnesium binding site 4 out of 13 in the Escherichia Coli Trna Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Escherichia Coli Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:68.9
occ:1.00
 O A:GLY308 3.5 52.9 1.0
OG1 A:THR310 3.6 66.8 1.0
N A:THR310 3.7 52.0 1.0
O A:HOH526 3.8 61.5 1.0
CG2 A:THR310 3.8 45.2 1.0
CB D:ALA697 3.9 54.8 1.0
CA A:VAL309 4.1 46.6 1.0
O D:ALA697 4.2 51.7 1.0
CB A:THR310 4.2 51.3 1.0
C D:ALA697 4.3 53.0 1.0
O D:ARG698 4.3 53.6 1.0
C D:ARG698 4.3 64.0 1.0
C A:VAL309 4.4 49.5 1.0
C A:GLY308 4.5 50.9 1.0
N D:GLU699 4.6 64.3 1.0
N D:ARG698 4.6 54.5 1.0
CA A:THR310 4.6 53.2 1.0
CA D:ALA697 4.8 53.2 1.0
CA D:GLU699 4.8 66.8 1.0
CA D:ARG698 4.8 58.0 1.0
N A:VAL309 4.8 48.2 1.0
O D:HOH1110 5.0 62.9 1.0

Magnesium binding site 5 out of 13 in 6p24

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Magnesium binding site 5 out of 13 in the Escherichia Coli Trna Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Escherichia Coli Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:73.7
occ:1.00
 O D:HOH933 2.8 50.5 1.0
O A:LYS327 2.8 76.6 1.0
O D:LEU627 3.1 53.2 1.0
O D:HOH1060 3.2 51.1 1.0
OXT A:LYS327 3.3 78.5 1.0
C A:LYS327 3.4 70.5 1.0
N D:GLY629 3.8 53.4 1.0
C D:LEU627 3.9 46.3 1.0
CA D:GLY629 4.0 41.7 1.0
C D:THR628 4.0 47.5 1.0
O D:VAL693 4.1 59.8 1.0
CB D:ARG692 4.3 42.3 1.0
O D:THR628 4.3 46.7 1.0
CD D:ARG692 4.3 40.8 1.0
O D:ASP626 4.6 40.7 1.0
CA D:THR628 4.6 54.5 1.0
N D:THR628 4.7 54.9 1.0
CA D:LEU627 4.8 50.2 1.0
CG D:ARG692 4.8 52.4 1.0
CA A:LYS327 4.8 65.0 1.0
N D:VAL693 4.9 48.6 1.0
NH1 D:ARG692 4.9 55.1 1.0

Magnesium binding site 6 out of 13 in 6p24

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Magnesium binding site 6 out of 13 in the Escherichia Coli Trna Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Escherichia Coli Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg801

b:69.4
occ:1.00
 OE2 B:GLU31 3.4 74.3 1.0
NH2 A:ARG244 3.8 42.8 1.0
CD B:GLU31 4.1 52.8 1.0
CZ A:ARG244 4.2 46.1 1.0
CG B:GLU31 4.2 55.3 1.0
O A:TRP266 4.4 55.7 1.0
NH2 A:ARG242 4.4 47.3 1.0
OD2 A:ASP258 4.5 52.7 1.0
NE A:ARG244 4.6 51.1 1.0
NH1 A:ARG244 4.7 43.3 1.0
CG2 B:THR26 4.8 43.0 1.0
OE1 A:GLU268 4.9 57.6 1.0
CG A:ASP258 4.9 54.9 1.0
OD1 A:ASP258 4.9 50.0 1.0
CB A:GLU268 5.0 60.7 1.0

Magnesium binding site 7 out of 13 in 6p24

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Magnesium binding site 7 out of 13 in the Escherichia Coli Trna Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Escherichia Coli Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:58.8
occ:1.00
 O A:HOH518 2.6 39.3 1.0
O A:HOH545 2.7 50.9 1.0
OE2 B:GLU459 3.0 53.1 1.0
CG B:GLU459 3.5 43.1 1.0
CD1 B:LEU416 3.5 58.6 1.0
CD B:GLU459 3.6 50.0 1.0
O A:HOH536 3.8 42.2 1.0
NZ B:LYS412 3.8 69.7 1.0
CD A:PRO277 4.0 51.5 1.0
CD2 B:LEU416 4.0 52.0 1.0
O A:VAL275 4.0 46.6 1.0
CG B:LEU416 4.2 59.7 1.0
CB A:PRO277 4.2 44.9 1.0
N A:PRO277 4.3 49.5 1.0
CG A:PRO277 4.3 41.5 1.0
CA A:PRO277 4.5 51.8 1.0
CB A:PRO287 4.5 57.4 1.0
CE B:LYS412 4.7 61.9 1.0
O A:PRO287 4.8 53.5 1.0
CD B:LYS412 4.8 53.0 1.0
OE1 B:GLU459 4.8 51.5 1.0
CB B:GLU459 4.9 40.3 1.0

Magnesium binding site 8 out of 13 in 6p24

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Magnesium binding site 8 out of 13 in the Escherichia Coli Trna Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Escherichia Coli Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:62.5
occ:1.00
 OG1 B:THR253 2.6 58.7 1.0
O B:HOH929 2.8 55.3 1.0
OD1 B:ASN254 2.8 50.8 1.0
O B:MET264 3.2 65.5 1.0
CB B:THR253 3.3 57.6 1.0
CG B:ASN254 3.7 48.9 1.0
C B:THR253 3.8 55.1 1.0
N B:ASN254 3.8 51.9 1.0
O B:THR253 4.1 57.2 1.0
CG2 B:VAL250 4.1 55.7 1.0
CA B:THR253 4.1 57.4 1.0
O B:VAL250 4.2 63.7 1.0
CA B:ASN254 4.2 52.7 1.0
C B:MET264 4.3 65.5 1.0
CG2 B:THR253 4.5 62.0 1.0
ND2 B:ASN254 4.5 43.9 1.0
CB B:ASN254 4.6 54.4 1.0
N B:MET264 4.9 56.2 1.0

Magnesium binding site 9 out of 13 in 6p24

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Magnesium binding site 9 out of 13 in the Escherichia Coli Trna Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Escherichia Coli Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg804

b:78.3
occ:1.00
 O C:HOH526 3.4 39.7 1.0
ND1 B:HIS488 3.5 65.4 1.0
OG C:SER118 3.5 60.0 1.0
CE1 C:PHE119 4.1 52.5 1.0
CG B:HIS488 4.4 61.2 1.0
CE1 B:HIS488 4.4 48.9 1.0
O B:HOH1029 4.4 53.5 1.0
CB B:HIS488 4.4 50.0 1.0
CB C:SER118 4.5 42.5 1.0
CD1 C:PHE119 4.7 51.2 1.0
CZ C:PHE119 4.9 54.7 1.0
CA C:ARG115 4.9 46.4 1.0
O C:ARG115 5.0 43.9 1.0

Magnesium binding site 10 out of 13 in 6p24

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Magnesium binding site 10 out of 13 in the Escherichia Coli Trna Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Escherichia Coli Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:73.3
occ:1.00
 OE2 C:GLU268 2.1 67.2 1.0
OE2 D:GLU31 2.4 70.1 1.0
O2 C:EDO406 2.6 76.4 1.0
O C:HOH543 2.8 70.7 1.0
CD C:GLU268 3.0 78.8 1.0
CD D:GLU31 3.1 55.4 1.0
OE1 D:GLU31 3.2 66.8 1.0
OE1 C:GLU268 3.2 74.4 1.0
OE2 C:GLU256 3.5 68.0 1.0
C2 C:EDO406 3.6 77.7 1.0
OE1 C:GLU256 4.0 63.3 1.0
O D:HOH1065 4.1 59.5 1.0
CD C:GLU256 4.1 62.4 1.0
NH1 C:ARG244 4.3 58.4 1.0
CG C:GLU268 4.4 67.2 1.0
CG D:GLU31 4.6 49.4 1.0
NH2 C:ARG244 4.8 44.9 1.0
C1 C:EDO406 4.9 67.9 1.0
CB C:GLU268 5.0 55.6 1.0

Reference:

D.Kahne, V.Baidin, T.W.Owens. Escherichia Coli Trna Synthetase To Be Published.
Page generated: Mon Dec 14 23:45:51 2020

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