Atomistry » Magnesium » PDB 5d1f-5d9c » 5d4e
Atomistry »
  Magnesium »
    PDB 5d1f-5d9c »
      5d4e »

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

Go back to Magnesium Binding Sites List in 5d4e
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

Go back to Magnesium Binding Sites List in 5d4e
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

Go back to Magnesium Binding Sites List in 5d4e
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

Go back to Magnesium Binding Sites List in 5d4e
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

Go back to Magnesium Binding Sites List in 5d4e
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

Go back to Magnesium Binding Sites List in 5d4e
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

Go back to Magnesium Binding Sites List in 5d4e
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

Go back to Magnesium Binding Sites List in 5d4e
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

Go back to Magnesium Binding Sites List in 5d4e
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: Mon Dec 14 20:10:06 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy