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Magnesium in PDB 5d4d: Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Nad and Ctp

Enzymatic activity of Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Nad and Ctp

All present enzymatic activity of Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Nad and Ctp:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Nad and Ctp, PDB code: 5d4d 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) 42.17 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 185.000, 103.510, 296.300, 90.00, 98.27, 90.00
R / Rfree (%) 20.1 / 25.4

Other elements in 5d4d:

The structure of Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Nad 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 Nad and Ctp (pdb code 5d4d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Nad and Ctp, PDB code: 5d4d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 5d4d

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Magnesium binding site 1 out of 10 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Nad 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 Nad and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:17.7
occ:1.00
 O B:ASP191 2.7 29.2 1.0
OD1 B:ASP193 2.9 23.4 1.0
OD2 B:ASP183 3.0 52.8 1.0
O B:LEU192 3.6 25.2 1.0
C B:ASP191 3.8 30.9 1.0
CG B:ARG30 4.1 19.1 1.0
CG B:ASP193 4.1 18.8 1.0
C B:LEU192 4.1 18.5 1.0
CG B:ASP183 4.3 60.7 1.0
CA B:ASP191 4.5 33.6 1.0
N B:LEU192 4.6 28.5 1.0
CA B:ASP183 4.7 29.4 1.0
CA B:LEU192 4.8 22.2 1.0
CB B:ASP191 4.8 36.2 1.0
N B:ASP193 4.8 20.1 1.0
OD2 B:ASP193 4.8 12.8 1.0
CA B:ASP193 4.9 18.1 1.0
CB B:ARG30 4.9 19.5 1.0
CA B:ARG30 4.9 19.2 1.0
CD B:ARG30 5.0 16.4 1.0

Magnesium binding site 2 out of 10 in 5d4d

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Magnesium binding site 2 out of 10 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Nad 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 Nad and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:1.5
occ:1.00
 O3' D:C2005 1.8 6.4 0.8
OD1 D:ASP739 2.0 3.7 1.0
OD1 D:ASP743 2.1 3.3 1.0
OD1 D:ASP741 2.2 3.6 1.0
OD2 D:ASP743 2.8 1.8 1.0
CG D:ASP743 2.8 2.6 1.0
CG D:ASP741 2.9 3.4 1.0
OD2 D:ASP741 3.0 6.0 1.0
CG D:ASP739 3.0 4.2 1.0
C3' D:C2005 3.1 10.3 0.8
OD2 D:ASP739 3.3 11.6 1.0
O2' D:C2005 3.4 8.4 0.8
C2' D:C2005 3.7 10.3 0.8
C4' D:C2005 3.8 13.4 0.8
O D:HOH2302 4.1 2.1 1.0
CB D:ASP743 4.3 1.0 1.0
O D:ASP739 4.3 1.0 1.0
CB D:ASP739 4.3 1.6 1.0
N D:ASP739 4.4 0.5 1.0
CB D:ASP741 4.4 1.3 1.0
C D:ASP739 4.5 0.7 1.0
C5' D:C2005 4.5 18.9 0.8
NH2 D:ARG704 4.6 2.8 1.0
CA D:ASP739 4.6 0.4 1.0
N D:ASP743 4.7 1.5 1.0
N D:ASP741 4.7 0.8 1.0
O D:HOH2118 4.8 15.4 1.0
CA D:ASP743 4.9 1.4 1.0
O4' D:C2005 5.0 14.9 0.8
CA D:ASP741 5.0 1.0 1.0
C1' D:C2005 5.0 13.6 0.8

Magnesium binding site 3 out of 10 in 5d4d

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Magnesium binding site 3 out of 10 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Nad 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 Nad and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2004

b:15.9
occ:1.00
 O D:HOH2101 2.1 13.8 1.0
O D:LYS840 2.3 19.7 1.0
C D:LYS840 3.3 18.4 1.0
O D:LEU839 3.4 27.1 1.0
OE1 B:GLU64 3.9 47.6 1.0
OD2 B:ASP168 3.9 31.5 1.0
CA D:LYS840 4.0 18.1 1.0
OE2 B:GLU64 4.1 48.9 1.0
N D:VAL842 4.1 14.5 1.0
N D:TYR841 4.2 20.1 1.0
CD B:GLU64 4.3 54.9 1.0
C D:LEU839 4.4 25.9 1.0
CA D:TYR841 4.4 16.3 1.0
CB D:VAL842 4.6 12.6 1.0
CG2 D:VAL842 4.6 14.0 1.0
C D:TYR841 4.7 17.5 1.0
N D:LYS840 4.7 21.1 1.0
CG B:ASP168 4.8 30.8 1.0
OD1 B:ASP168 4.9 30.4 1.0
CA D:VAL842 5.0 14.1 1.0

Magnesium binding site 4 out of 10 in 5d4d

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Magnesium binding site 4 out of 10 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Nad 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 Nad and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2007

b:28.8
occ:1.00
 O2A D:CTP2006 2.6 47.9 1.0
O3B D:CTP2006 2.7 26.4 1.0
O5' D:CTP2006 2.9 41.1 1.0
PA D:CTP2006 3.2 80.4 1.0
O D:HOH2118 3.3 15.4 1.0
OD2 D:ASP739 3.3 11.6 1.0
O D:HOH2302 3.4 2.1 1.0
PB D:CTP2006 3.5 42.4 1.0
O1B D:CTP2006 3.5 35.4 1.0
O3A D:CTP2006 3.8 44.3 1.0
O D:HOH2294 3.8 2.1 1.0
OE2 C:GLU685 3.9 9.8 1.0
O D:HOH2139 3.9 15.1 1.0
OE1 C:GLU685 4.1 13.8 1.0
CG D:ASP739 4.2 4.2 1.0
CD C:GLU685 4.3 8.0 1.0
CB D:ASP739 4.4 1.6 1.0
NH2 D:ARG1029 4.4 7.3 1.0
O1A D:CTP2006 4.7 62.8 1.0
NH1 C:ARG879 4.8 4.1 1.0
O2B D:CTP2006 4.9 21.0 1.0

Magnesium binding site 5 out of 10 in 5d4d

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Magnesium binding site 5 out of 10 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Nad 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 Nad and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2001

b:25.3
occ:1.00
 O F:ALA292 2.5 24.8 1.0
O F:GLY296 2.5 33.3 1.0
O F:TRP299 2.6 19.0 1.0
C F:ALA292 3.4 21.3 1.0
C F:GLY296 3.7 35.4 1.0
C F:TRP299 3.7 20.5 1.0
CA F:GLU293 3.8 23.9 1.0
N F:GLU293 3.9 22.6 1.0
N F:TRP299 4.2 23.1 1.0
CB F:TRP299 4.2 22.1 1.0
CA F:TRP299 4.3 23.7 1.0
O F:GLU293 4.3 19.6 1.0
C F:GLU293 4.4 20.1 1.0
CA F:ALA292 4.5 17.2 1.0
N F:GLY296 4.5 31.5 1.0
CA F:GLY296 4.5 32.8 1.0
CB F:ALA292 4.6 16.8 1.0
N F:PRO297 4.6 41.6 1.0
CA F:PRO297 4.7 34.6 1.0
N F:ASP300 4.8 20.8 1.0
N F:GLY298 4.9 28.7 1.0

Magnesium binding site 6 out of 10 in 5d4d

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Magnesium binding site 6 out of 10 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Nad 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 Nad and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg2001

b:41.4
occ:1.00
 OD1 L:ASP193 2.1 43.5 1.0
O L:ASP191 2.9 52.0 1.0
OD1 L:ASP183 3.0 53.1 1.0
CG L:ASP193 3.3 34.7 1.0
O L:LEU192 3.5 38.0 1.0
CG L:ASP183 3.7 50.6 1.0
OD2 L:ASP193 3.9 26.0 1.0
C L:ASP191 4.0 57.5 1.0
C L:LEU192 4.0 39.5 1.0
OD2 L:ASP183 4.1 38.7 1.0
CG L:ARG30 4.3 33.9 1.0
CB L:ASP193 4.4 26.8 1.0
CA L:ASP193 4.4 26.4 1.0
N L:ASP193 4.5 32.5 1.0
CA L:ASP183 4.6 41.3 1.0
N L:GLY31 4.6 30.6 1.0
CA L:ARG30 4.6 35.3 1.0
CB L:ASP183 4.7 40.1 1.0
CA L:LEU192 4.7 42.1 1.0
N L:LEU192 4.8 49.0 1.0
CB L:ARG30 4.9 41.6 1.0
CA L:ASP191 4.9 62.2 1.0

Magnesium binding site 7 out of 10 in 5d4d

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Magnesium binding site 7 out of 10 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Nad 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 Nad and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg2003

b:6.8
occ:1.00
 O3' N:C2005 2.0 26.6 0.8
OD1 N:ASP739 2.1 8.0 1.0
OD1 N:ASP741 2.2 13.3 1.0
OD1 N:ASP743 2.2 8.2 1.0
CG N:ASP741 2.9 11.8 1.0
CG N:ASP743 2.9 6.1 1.0
OD2 N:ASP741 2.9 12.0 1.0
OD2 N:ASP743 3.0 5.4 1.0
CG N:ASP739 3.1 7.7 1.0
C3' N:C2005 3.2 36.0 0.8
OD2 N:ASP739 3.4 12.2 1.0
C4' N:C2005 3.5 33.3 0.8
O N:HOH2115 3.7 8.1 1.0
C5' N:C2005 3.8 40.1 0.8
O2' N:C2005 4.3 22.8 0.8
C2' N:C2005 4.3 34.0 0.8
CB N:ASP741 4.4 5.5 1.0
CB N:ASP743 4.4 3.8 1.0
CB N:ASP739 4.5 6.0 1.0
N N:ASP739 4.5 4.1 1.0
O N:ASP739 4.5 4.2 1.0
N N:ASP741 4.6 5.4 1.0
O N:HOH2131 4.6 17.7 1.0
NH2 N:ARG704 4.7 4.7 1.0
C N:ASP739 4.7 4.0 1.0
O5' N:C2005 4.8 47.1 0.8
CA N:ASP739 4.8 4.4 1.0
N N:ASP743 4.9 5.3 1.0
O4' N:C2005 4.9 36.4 0.8
CA N:ASP741 5.0 5.2 1.0
CA N:ASP743 5.0 5.2 1.0

Magnesium binding site 8 out of 10 in 5d4d

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Magnesium binding site 8 out of 10 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Nad 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 Nad and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg2004

b:27.3
occ:1.00
 O L:HOH2103 2.1 20.1 1.0
O N:HOH2149 2.1 23.3 1.0
O N:HOH2117 2.1 25.3 1.0
O N:HOH2101 2.1 20.6 1.0
O N:LYS840 2.1 21.8 1.0
C N:LYS840 3.3 22.2 1.0
OD2 L:ASP168 3.8 26.0 1.0
OE1 L:GLU64 3.9 51.0 1.0
OD1 L:ASP168 4.0 24.5 1.0
CA N:LYS840 4.2 21.5 1.0
O N:LEU839 4.3 19.1 1.0
N N:TYR841 4.3 22.4 1.0
CG L:ASP168 4.3 20.6 1.0
N N:VAL842 4.3 18.6 1.0
CA N:TYR841 4.4 19.1 1.0
OE2 L:GLU154 4.4 46.1 1.0
OE2 L:GLU64 4.5 45.6 1.0
CD L:GLU64 4.6 57.0 1.0
C N:TYR841 4.9 19.4 1.0
OE1 L:GLU154 4.9 49.9 1.0

Magnesium binding site 9 out of 10 in 5d4d

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Magnesium binding site 9 out of 10 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Nad 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 Nad and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg2006

b:32.8
occ:1.00
 O1A M:CTP1201 2.2 48.9 1.0
O2A M:CTP1201 2.6 50.0 1.0
O3B M:CTP1201 2.6 59.9 1.0
PA M:CTP1201 2.8 69.8 1.0
O M:HOH1368 2.9 17.5 1.0
O N:HOH2242 2.9 12.8 1.0
OD2 N:ASP739 3.3 12.2 1.0
O N:HOH2131 3.3 17.7 1.0
PB M:CTP1201 3.4 73.7 1.0
O1B M:CTP1201 3.5 52.9 1.0
O3A M:CTP1201 3.5 56.3 1.0
O5' M:CTP1201 4.3 55.9 1.0
NH1 M:ARG879 4.3 14.9 1.0
CG N:ASP739 4.5 7.7 1.0
O N:HOH2115 4.8 8.1 1.0
O2B M:CTP1201 4.8 25.9 1.0

Magnesium binding site 10 out of 10 in 5d4d

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Magnesium binding site 10 out of 10 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Nad and Ctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Nad and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg2001

b:51.7
occ:1.00
 O P:GLY296 2.5 70.0 1.0
O P:TRP299 2.9 68.7 1.0
O P:ALA292 3.1 64.6 1.0
C P:GLY296 3.5 73.3 1.0
C P:TRP299 4.0 63.4 1.0
C P:ALA292 4.0 66.6 1.0
CA P:PRO297 4.1 76.3 1.0
N P:PRO297 4.2 80.7 1.0
N P:TRP299 4.3 71.2 1.0
CA P:GLU293 4.3 62.3 1.0
C P:PRO297 4.5 72.6 1.0
N P:GLU293 4.5 69.5 1.0
N P:GLY298 4.6 64.6 1.0
CA P:TRP299 4.6 63.5 1.0
CA P:GLY296 4.6 68.0 1.0
CB P:TRP299 4.7 61.8 1.0
N P:GLY296 4.8 71.7 1.0
O P:GLU293 4.8 71.4 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 02:30:21 2024

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