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Magnesium in PDB 5d4e: Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp

Enzymatic activity of Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp

All present enzymatic activity of Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp, PDB code: 5d4e was solved by Y.Zhang, R.H.Ebright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.68 / 3.08
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 185.811, 103.948, 297.143, 90.00, 98.47, 90.00
R / Rfree (%) 21 / 24.6

Other elements in 5d4e:

The structure of Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp (pdb code 5d4e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp, PDB code: 5d4e:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 5d4e

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Magnesium binding site 1 out of 9 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp


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 Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:71.1
occ:1.00
 O B:ASP191 2.6 67.5 1.0
OD2 B:ASP183 3.3 82.7 1.0
OD1 B:ASP193 3.3 62.4 1.0
CG B:ARG30 3.4 46.6 1.0
C B:ASP191 3.6 71.6 1.0
CA B:ASP191 4.0 76.1 1.0
CB B:ASP191 4.0 76.8 1.0
CD B:ARG30 4.1 44.0 1.0
CB B:ARG30 4.2 50.2 1.0
CG B:ASP183 4.4 79.8 1.0
CG B:ASP193 4.5 55.2 1.0
CA B:ARG30 4.5 48.3 1.0
O B:LEU192 4.5 52.0 1.0
N B:LEU192 4.7 70.4 1.0
C B:LEU192 4.8 51.8 1.0
OD2 B:ASP193 4.9 52.1 1.0
OD1 B:ASP183 4.9 79.3 1.0

Magnesium binding site 2 out of 9 in 5d4e

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Magnesium binding site 2 out of 9 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp


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 Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:22.6
occ:1.00
 O3' D:C2005 1.9 43.6 0.8
OD1 D:ASP741 2.0 37.3 1.0
OD1 D:ASP739 2.1 25.0 1.0
OD1 D:ASP743 2.1 33.6 1.0
CG D:ASP741 2.7 34.6 1.0
OD2 D:ASP743 2.7 19.1 1.0
CG D:ASP743 2.8 25.7 1.0
OD2 D:ASP741 2.8 32.9 1.0
C3' D:C2005 3.1 53.9 0.8
CG D:ASP739 3.2 28.7 1.0
C4' D:C2005 3.5 51.2 0.8
OD2 D:ASP739 3.5 38.8 1.0
C5' D:C2005 3.8 54.8 0.8
O2' D:C2005 4.0 47.4 0.8
CB D:ASP741 4.1 24.0 1.0
C2' D:C2005 4.1 51.7 0.8
O D:ASP739 4.2 20.4 1.0
CB D:ASP743 4.3 24.6 1.0
N D:ASP741 4.4 27.9 1.0
N D:ASP739 4.4 25.8 1.0
CB D:ASP739 4.5 28.1 1.0
C D:ASP739 4.6 22.2 1.0
NH2 D:ARG704 4.7 25.0 1.0
CA D:ASP739 4.8 25.0 1.0
CA D:ASP741 4.8 21.1 1.0
O4' D:C2005 4.8 53.4 0.8
N D:ASP743 4.9 23.3 1.0
CA D:ASP743 4.9 23.7 1.0

Magnesium binding site 3 out of 9 in 5d4e

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Magnesium binding site 3 out of 9 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp


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 Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2004

b:27.5
occ:1.00
 O D:LYS840 2.0 37.6 1.0
C D:LYS840 3.2 35.5 1.0
OD2 B:ASP168 3.5 39.4 1.0
OD1 B:ASP168 3.5 47.6 1.0
CG B:ASP168 3.9 38.3 1.0
OE2 B:GLU154 4.1 64.7 1.0
N D:TYR841 4.1 34.6 1.0
CA D:LYS840 4.2 38.5 1.0
CA D:TYR841 4.2 35.3 1.0
OE1 B:GLU64 4.3 83.7 1.0
O D:LEU839 4.3 31.9 1.0
N D:VAL842 4.4 32.0 1.0
OE2 B:GLU64 4.6 75.1 1.0
C D:TYR841 4.8 31.6 1.0
OE1 B:GLU154 4.9 74.2 1.0
CD B:GLU64 4.9 86.7 1.0
CD B:GLU154 4.9 73.3 1.0
CG D:LYS840 5.0 37.4 1.0

Magnesium binding site 4 out of 9 in 5d4e

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Magnesium binding site 4 out of 9 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp


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 Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2007

b:49.5
occ:1.00
 OD2 D:ASP739 2.1 38.8 1.0
O6 D:DPO2006 2.2 69.6 1.0
O3 D:DPO2006 2.3 68.7 1.0
CG D:ASP739 3.0 28.7 1.0
CB D:ASP739 3.3 28.1 1.0
O4 D:DPO2006 3.3 84.1 1.0
P2 D:DPO2006 3.3 70.4 1.0
P1 D:DPO2006 3.3 98.5 1.0
NH1 C:ARG879 3.6 37.2 1.0
OE1 C:GLU685 3.8 37.7 1.0
OD2 C:ASP686 3.8 39.4 1.0
OD1 D:ASP739 4.1 25.0 1.0
O2 D:DPO2006 4.2 65.3 1.0
O5 D:DPO2006 4.2 58.0 1.0
NH2 D:ARG1029 4.4 34.4 1.0
O7 D:DPO2006 4.4 45.6 1.0
O1 D:DPO2006 4.6 83.6 1.0
CA D:ASP739 4.7 25.0 1.0
CD C:GLU685 4.7 33.5 1.0
OD2 D:ASP741 4.8 32.9 1.0
CZ C:ARG879 4.8 24.9 1.0
CG C:ASP686 5.0 35.8 1.0

Magnesium binding site 5 out of 9 in 5d4e

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Magnesium binding site 5 out of 9 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp


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 Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2001

b:92.7
occ:1.00
 O F:ALA292 2.1 90.7 1.0
O F:TRP299 2.3 98.5 1.0
O F:GLY296 2.3 98.6 1.0
C F:ALA292 3.1 93.6 1.0
C F:TRP299 3.4 99.1 1.0
C F:GLY296 3.5 95.7 1.0
N F:TRP299 3.9 99.0 1.0
CA F:TRP299 3.9 96.2 1.0
CB F:TRP299 3.9 98.3 1.0
CA F:ALA292 4.0 83.6 1.0
N F:GLU293 4.0 98.9 1.0
CB F:ALA292 4.1 81.8 1.0
CA F:GLU293 4.2 94.1 1.0
N F:GLY296 4.3 0.2 1.0
N F:PRO297 4.4 0.9 1.0
CA F:PRO297 4.4 0.3 1.0
CA F:GLY296 4.4 96.2 1.0
N F:ASP300 4.5 93.4 1.0
C F:PRO297 4.6 98.6 1.0
N F:GLY298 4.7 97.8 1.0
O F:GLU293 4.7 94.7 1.0
C F:GLU293 4.7 93.6 1.0
CA F:ASP300 4.9 87.2 1.0

Magnesium binding site 6 out of 9 in 5d4e

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Magnesium binding site 6 out of 9 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp


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 Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg1601

b:25.2
occ:1.00
 O N:LYS840 2.1 35.4 1.0
OD2 L:ASP168 3.3 46.9 1.0
C N:LYS840 3.3 32.5 1.0
OD1 L:ASP168 3.5 57.0 1.0
CG L:ASP168 3.8 44.7 1.0
CA N:TYR841 4.2 37.1 1.0
N N:TYR841 4.2 34.7 1.0
CA N:LYS840 4.3 30.0 1.0
N N:VAL842 4.4 34.5 1.0
OE1 L:GLU154 4.4 68.2 1.0
O N:LEU839 4.5 34.5 1.0
OE1 L:GLU64 4.6 67.4 1.0
OE2 L:GLU64 4.7 68.0 1.0
C N:TYR841 4.8 34.8 1.0
OE2 L:GLU154 4.8 58.3 1.0
CB L:ALA153 4.9 42.0 1.0

Magnesium binding site 7 out of 9 in 5d4e

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Magnesium binding site 7 out of 9 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg1604

b:13.9
occ:1.00
 O3' N:C1605 1.8 25.2 0.7
OD1 N:ASP739 2.0 19.5 1.0
OD1 N:ASP743 2.1 20.0 1.0
OD1 N:ASP741 2.1 16.6 1.0
OD2 N:ASP741 2.8 25.2 1.0
CG N:ASP741 2.8 14.8 1.0
CG N:ASP743 2.9 15.3 1.0
OD2 N:ASP743 3.0 14.8 1.0
C3' N:C1605 3.0 32.1 0.7
CG N:ASP739 3.1 23.4 1.0
O2' N:C1605 3.3 24.8 0.7
OD2 N:ASP739 3.4 36.6 1.0
C4' N:C1605 3.6 31.8 0.7
C2' N:C1605 3.7 31.4 0.7
CB N:ASP741 4.3 10.0 1.0
O N:HOH2140 4.3 25.6 1.0
C5' N:C1605 4.3 31.0 0.7
O N:ASP739 4.3 14.4 1.0
CB N:ASP743 4.3 12.8 1.0
CB N:ASP739 4.4 16.4 1.0
N N:ASP739 4.5 16.7 1.0
C N:ASP739 4.6 11.1 1.0
N N:ASP743 4.6 13.5 1.0
NH2 N:ARG704 4.6 24.4 1.0
CA N:ASP739 4.7 9.7 1.0
N N:ASP741 4.7 12.6 1.0
O4' N:C1605 4.8 33.7 0.7
CA N:ASP743 4.9 15.2 1.0
CA N:ASP741 4.9 10.5 1.0
C1' N:C1605 4.9 33.9 0.7

Magnesium binding site 8 out of 9 in 5d4e

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Magnesium binding site 8 out of 9 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg1607

b:36.6
occ:1.00
 OD2 N:ASP739 2.1 36.6 1.0
O6 N:DPO1606 2.2 51.3 1.0
O1 N:DPO1606 2.4 58.4 1.0
O M:HOH1216 2.8 28.9 1.0
CG N:ASP739 3.1 23.4 1.0
CB N:ASP739 3.3 16.4 1.0
P2 N:DPO1606 3.4 61.7 1.0
P1 N:DPO1606 3.4 84.5 1.0
O4 N:DPO1606 3.4 74.5 1.0
OE1 M:GLU685 3.6 26.4 1.0
O N:HOH2140 4.0 25.6 1.0
OD2 M:ASP686 4.0 26.6 1.0
NH1 M:ARG879 4.2 19.6 1.0
O N:HOH2284 4.2 33.2 1.0
OD1 N:ASP739 4.2 19.5 1.0
O2 N:DPO1606 4.2 43.4 1.0
O7 N:DPO1606 4.3 47.4 1.0
O5 N:DPO1606 4.4 26.2 1.0
CD M:GLU685 4.4 26.5 1.0
NH2 N:ARG1029 4.4 25.0 1.0
O3 N:DPO1606 4.6 62.1 1.0
OE2 M:GLU685 4.7 28.9 1.0
CA N:ASP739 4.8 9.7 1.0
OD2 N:ASP741 4.9 25.2 1.0

Magnesium binding site 9 out of 9 in 5d4e

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Magnesium binding site 9 out of 9 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg2001

b:39.0
occ:1.00
 O P:GLY296 2.3 49.3 1.0
O P:ALA292 2.3 45.8 1.0
O P:TRP299 2.9 33.7 1.0
C P:ALA292 3.3 42.1 1.0
C P:GLY296 3.4 49.8 1.0
CA P:GLU293 3.7 43.8 1.0
N P:GLU293 3.9 43.9 1.0
C P:TRP299 4.0 38.4 1.0
O P:GLU293 4.1 38.2 1.0
N P:GLY296 4.1 50.2 1.0
CA P:GLY296 4.2 47.7 1.0
CB P:TRP299 4.2 37.4 1.0
C P:GLU293 4.2 40.4 1.0
N P:PRO297 4.3 55.0 1.0
N P:TRP299 4.3 41.1 1.0
CA P:ALA292 4.4 37.1 1.0
CA P:TRP299 4.4 39.4 1.0
CA P:PRO297 4.5 50.1 1.0
CB P:ALA292 4.6 41.5 1.0
C P:PRO297 4.9 49.1 1.0

Reference:

J.G.Bird, Y.Zhang, Y.Tian, N.Panova, I.Barvik, L.Greene, M.Liu, B.Buckley, L.Krasny, J.K.Lee, C.D.Kaplan, R.H.Ebright, B.E.Nickels. The Mechanism of Rna 5' Capping with Nad(+), Nadh and Desphospho-Coa. Nature V. 535 444 2016.
ISSN: ESSN 1476-4687
PubMed: 27383794
DOI: 10.1038/NATURE18622
Page generated: Sun Sep 29 02:30:56 2024

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