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Magnesium in PDB 5hr7: X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna

Enzymatic activity of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna

All present enzymatic activity of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna:
2.1.1.192;

Protein crystallography data

The structure of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna, PDB code: 5hr7 was solved by E.L.Schwalm, T.L.Grove, S.J.Booker, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.717, 70.383, 151.810, 90.00, 90.11, 90.00
R / Rfree (%) 21.6 / 24.8

Other elements in 5hr7:

The structure of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna also contains other interesting chemical elements:

Arsenic (As) 2 atoms
Iron (Fe) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna (pdb code 5hr7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna, PDB code: 5hr7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5hr7

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Magnesium binding site 1 out of 7 in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg101

b:63.6
occ:1.00
 OP2 D:C9 1.9 51.6 1.0
O D:HOH206 2.0 60.1 1.0
OP1 D:U8 2.3 57.8 1.0
O D:HOH211 2.4 54.7 1.0
P D:C9 3.4 56.0 1.0
P D:U8 3.5 57.0 1.0
OP2 D:C12 3.9 58.0 1.0
O5' D:U8 4.0 55.2 1.0
O5' D:C9 4.0 56.0 1.0
OP2 D:U8 4.1 54.6 1.0
OP1 D:C9 4.2 55.9 1.0
OP2 D:U11 4.3 62.0 1.0
O3' D:U8 4.4 57.7 1.0
C3' D:U8 4.4 55.8 1.0
C5' D:C9 4.5 55.0 1.0
C5' D:U8 4.6 55.8 1.0
O3' D:U7 4.8 59.0 1.0

Magnesium binding site 2 out of 7 in 5hr7

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Magnesium binding site 2 out of 7 in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg102

b:49.0
occ:1.00
 O D:HOH204 2.3 50.2 1.0
O D:HOH212 2.4 47.0 1.0
N7 D:G39 2.4 50.4 1.0
O D:HOH210 2.5 51.0 1.0
O2 D:C38 2.5 45.5 1.0
O2' D:C38 2.6 46.7 1.0
C2 D:C38 3.3 46.7 1.0
C8 D:G39 3.4 52.0 1.0
C5 D:G39 3.5 51.1 1.0
C1' D:C38 3.6 46.8 1.0
C2' D:C38 3.6 47.1 1.0
O6 D:G39 3.7 49.8 1.0
N1 D:C38 3.8 45.9 1.0
C6 D:G39 4.0 51.8 1.0
O A:HOH623 4.1 49.9 1.0
O A:ARG206 4.2 52.7 1.0
N3 D:C38 4.2 46.3 1.0
NZ A:LYS305 4.3 53.0 1.0
O3' D:C38 4.3 49.8 1.0
OP2 D:G39 4.3 48.4 1.0
CB A:ARG206 4.5 50.5 1.0
N9 D:G39 4.6 51.9 1.0
C3' D:C38 4.6 47.5 1.0
C4 D:G39 4.7 50.7 1.0
O4' D:C38 4.9 46.3 1.0
C6 D:C38 5.0 44.9 1.0
P D:G39 5.0 51.0 1.0

Magnesium binding site 3 out of 7 in 5hr7

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Magnesium binding site 3 out of 7 in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg103

b:76.4
occ:1.00
 O D:HOH214 2.2 66.5 1.0
OP2 D:G22 3.5 60.8 1.0
N7 D:A45 3.8 53.8 1.0
N3 D:C9 4.2 57.6 1.0
C5 D:A45 4.4 54.3 1.0
C8 D:A45 4.4 56.5 1.0
O2 D:C9 4.4 58.9 1.0
OP2 D:A21 4.5 67.3 1.0
N7 D:A46 4.5 51.8 1.0
N6 D:A46 4.6 52.8 1.0
N6 D:A45 4.6 50.4 1.0
C6 D:A45 4.7 52.8 1.0
C2 D:C9 4.8 57.9 1.0
P D:G22 4.9 58.1 1.0

Magnesium binding site 4 out of 7 in 5hr7

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Magnesium binding site 4 out of 7 in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg101

b:66.1
occ:1.00
 OP2 C:C9 1.9 52.4 1.0
O C:HOH205 1.9 56.5 1.0
OP1 C:U8 2.3 62.8 1.0
P C:C9 3.3 55.9 1.0
P C:U8 3.6 59.9 1.0
OP2 C:C12 3.9 56.2 1.0
O5' C:C9 4.0 56.8 1.0
O5' C:U8 4.0 56.2 1.0
OP1 C:C9 4.1 56.6 1.0
OP2 C:U8 4.2 56.8 1.0
OP2 C:U11 4.3 60.6 1.0
O3' C:U8 4.3 57.8 1.0
C3' C:U8 4.4 55.8 1.0
C5' C:C9 4.4 57.1 1.0
C5' C:U8 4.5 55.3 1.0
O3' C:U7 4.8 62.1 1.0

Magnesium binding site 5 out of 7 in 5hr7

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Magnesium binding site 5 out of 7 in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg102

b:46.1
occ:1.00
 O C:HOH213 2.3 48.6 1.0
O C:HOH206 2.3 51.1 1.0
O C:HOH209 2.4 44.8 1.0
O2 C:C38 2.5 44.0 1.0
N7 C:G39 2.5 46.1 1.0
O2' C:C38 2.6 43.7 1.0
C2 C:C38 3.2 43.8 1.0
C8 C:G39 3.4 48.2 1.0
C1' C:C38 3.5 44.2 1.0
C5 C:G39 3.6 47.5 1.0
C2' C:C38 3.6 44.4 1.0
N1 C:C38 3.7 43.2 1.0
O6 C:G39 3.8 47.6 1.0
C6 C:G39 4.0 48.6 1.0
O B:HOH612 4.1 49.1 1.0
N3 C:C38 4.2 42.5 1.0
O B:ARG206 4.2 51.4 1.0
NZ B:LYS305 4.3 50.0 1.0
OP2 C:G39 4.3 46.0 1.0
O3' C:C38 4.3 46.7 1.0
CB B:ARG206 4.6 50.0 1.0
C3' C:C38 4.6 44.9 1.0
N9 C:G39 4.7 48.3 1.0
C4 C:G39 4.7 47.6 1.0
O4' C:C38 4.9 43.1 1.0
C6 C:C38 4.9 41.6 1.0
P C:G39 5.0 47.5 1.0

Magnesium binding site 6 out of 7 in 5hr7

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Magnesium binding site 6 out of 7 in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg103

b:74.3
occ:1.00
 O C:HOH211 2.1 69.0 1.0
N7 C:A45 3.8 55.2 1.0
OP2 C:G22 3.9 60.1 1.0
OP2 C:A21 4.2 69.8 1.0
C8 C:A45 4.3 56.4 1.0
C5 C:A45 4.5 55.3 1.0
O2 C:C9 4.6 58.9 1.0
N3 C:C9 4.6 59.0 1.0
N7 C:A46 4.6 51.2 1.0
OP2 C:A46 4.8 58.4 1.0
N6 C:A45 5.0 51.4 1.0
N6 C:A46 5.0 52.4 1.0

Magnesium binding site 7 out of 7 in 5hr7

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Magnesium binding site 7 out of 7 in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg104

b:83.5
occ:1.00
 OP1 C:C47 2.8 61.6 1.0
OP1 C:G49 3.0 74.4 1.0
P C:C47 4.0 59.1 1.0
OP2 C:C47 4.3 53.9 1.0
P C:G49 4.4 76.8 1.0

Reference:

E.L.Schwalm, T.L.Grove, S.J.Booker, A.K.Boal. Crystallographic Capture of A Radical S-Adenosylmethionine Enzyme in the Act of Modifying Trna. Science V. 352 309 2016.
ISSN: ESSN 1095-9203
PubMed: 27081063
DOI: 10.1126/SCIENCE.AAD5367
Page generated: Sun Sep 29 16:33:40 2024

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