Magnesium in PDB 7yse: Crystal Structure of E. Coli Hetertetrameric Glyrs in Complex with Trna

Enzymatic activity of Crystal Structure of E. Coli Hetertetrameric Glyrs in Complex with Trna

All present enzymatic activity of Crystal Structure of E. Coli Hetertetrameric Glyrs in Complex with Trna:
6.1.1.14;

Protein crystallography data

The structure of Crystal Structure of E. Coli Hetertetrameric Glyrs in Complex with Trna, PDB code: 7yse was solved by L.Han, Y.Ju, H.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.01 / 2.91
Space group P 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 72.71, 162.123, 324.09, 90, 90, 90
R / Rfree (%) 23 / 26

Other elements in 7yse:

The structure of Crystal Structure of E. Coli Hetertetrameric Glyrs in Complex with Trna also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of E. Coli Hetertetrameric Glyrs in Complex with Trna (pdb code 7yse). 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 E. Coli Hetertetrameric Glyrs in Complex with Trna, PDB code: 7yse:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7yse

Go back to Magnesium Binding Sites List in 7yse
Magnesium binding site 1 out of 6 in the Crystal Structure of E. Coli Hetertetrameric Glyrs in Complex with Trna


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 E. Coli Hetertetrameric Glyrs in Complex with Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:58.3
occ:1.00
 OD2 A:ASP119 2.2 57.8 1.0
OE1 A:GLU134 2.7 61.9 1.0
CG A:ASP119 3.5 54.1 1.0
CD A:GLU134 3.7 62.7 1.0
OE1 A:GLU141 3.7 65.8 1.0
OE1 A:GLN144 4.0 52.8 1.0
OD1 A:ASP119 4.1 55.3 1.0
OE2 A:GLU134 4.3 66.2 1.0
CD A:GLU141 4.3 63.1 1.0
OP1 E:A76 4.4 54.5 1.0
OE2 A:GLU141 4.5 65.6 1.0
CG A:GLU134 4.6 61.0 1.0
CB A:ASP119 4.6 51.8 1.0
CB A:GLU134 4.8 58.2 1.0
O2 A:JPO401 4.9 64.2 1.0

Magnesium binding site 2 out of 6 in 7yse

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Magnesium binding site 2 out of 6 in the Crystal Structure of E. Coli Hetertetrameric Glyrs in Complex with Trna


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 E. Coli Hetertetrameric Glyrs in Complex with Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:65.5
occ:1.00
 OD2 B:ASP119 2.1 80.6 1.0
OE2 B:GLU134 2.2 82.2 1.0
CG B:ASP119 3.3 81.9 1.0
CD B:GLU134 3.3 79.0 1.0
OP1 F:A76 3.7 74.4 1.0
OD1 B:ASP119 3.8 81.4 1.0
OE1 B:GLN144 4.1 73.0 1.0
CG B:GLU134 4.2 75.9 1.0
OE1 B:GLU134 4.2 78.5 1.0
OE1 B:GLU141 4.4 93.3 1.0
CB B:ASP119 4.5 81.0 1.0
O2 B:JPO401 4.7 86.0 1.0
P F:A76 4.7 75.5 1.0
OE2 B:GLU141 4.8 96.3 1.0
CD B:GLU141 4.9 92.2 1.0
OP2 F:A76 5.0 75.1 1.0

Magnesium binding site 3 out of 6 in 7yse

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Magnesium binding site 3 out of 6 in the Crystal Structure of E. Coli Hetertetrameric Glyrs in Complex with Trna


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 E. Coli Hetertetrameric Glyrs in Complex with Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg701

b:75.0
occ:1.00
 OE2 A:GLU134 3.7 66.2 1.0
O C:ASP284 4.1 63.5 1.0
CB C:ASP284 4.3 65.1 1.0
CG C:ASP284 4.3 68.4 1.0
OD1 C:ASP284 4.4 72.7 1.0
CD A:GLU134 4.6 62.7 1.0
CA C:ASP284 4.6 63.0 1.0
OE1 A:GLU134 4.7 61.9 1.0
C C:ASP284 4.7 63.0 1.0
OD2 C:ASP284 4.8 71.2 1.0
OE1 C:GLN285 4.9 56.6 1.0
CZ2 A:TRP136 4.9 56.5 1.0

Magnesium binding site 4 out of 6 in 7yse

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Magnesium binding site 4 out of 6 in the Crystal Structure of E. Coli Hetertetrameric Glyrs in Complex with Trna


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 E. Coli Hetertetrameric Glyrs in Complex with Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:64.6
occ:1.00
 OD1 C:ASP425 2.3 73.0 1.0
CG C:ASP425 3.2 72.4 1.0
OD2 C:ASP425 3.5 71.1 1.0
OD1 C:ASN446 3.8 77.2 1.0
CB C:ASP425 4.6 71.5 1.0
CG C:ASN446 4.7 71.8 1.0
ND2 C:ASN446 5.0 69.5 1.0

Magnesium binding site 5 out of 6 in 7yse

Go back to Magnesium Binding Sites List in 7yse
Magnesium binding site 5 out of 6 in the Crystal Structure of E. Coli Hetertetrameric Glyrs in Complex with Trna


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 E. Coli Hetertetrameric Glyrs in Complex with Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg701

b:84.7
occ:1.00
 OD2 D:ASP474 2.1 104.7 1.0
CG D:ASP474 3.3 103.7 1.0
OP2 F:G1 3.5 92.0 1.0
OD1 D:ASP474 3.9 110.1 1.0
CB D:ASP474 4.5 99.9 1.0
OP3 F:G1 4.5 90.5 1.0
OP2 F:U67 4.6 121.3 1.0
P F:G1 4.6 91.3 1.0
OP1 F:U67 4.9 121.9 1.0

Magnesium binding site 6 out of 6 in 7yse

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Magnesium binding site 6 out of 6 in the Crystal Structure of E. Coli Hetertetrameric Glyrs in Complex with Trna


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 E. Coli Hetertetrameric Glyrs in Complex with Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg101

b:68.3
occ:1.00
 OP2 E:U8 3.7 60.2 1.0
OP1 E:U8 3.8 58.3 1.0
OP2 E:A9 3.9 70.4 1.0
OP2 E:U12 3.9 80.9 1.0
OP1 E:A9 4.0 69.7 1.0
P E:U8 4.3 59.6 1.0
OP2 E:C11 4.4 86.9 1.0
P E:A9 4.5 68.2 1.0
C5 E:U12 4.5 81.2 1.0
O5' E:C11 4.8 83.7 1.0

Reference:

L.Han, Y.Ju, H.Zhou. Crystal Structure of E. Coli Hetertetrameric Glyrs in Complex with Trna To Be Published.
Page generated: Fri Apr 7 03:35:53 2023

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