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Magnesium in PDB 3q22: X-Ray Crystal Structure of the N4 Mini-Vrnap and P2_7A Promoter Transcription Initiation Complex with Gtp and Magnesium: Substrate Complex I

Enzymatic activity of X-Ray Crystal Structure of the N4 Mini-Vrnap and P2_7A Promoter Transcription Initiation Complex with Gtp and Magnesium: Substrate Complex I

All present enzymatic activity of X-Ray Crystal Structure of the N4 Mini-Vrnap and P2_7A Promoter Transcription Initiation Complex with Gtp and Magnesium: Substrate Complex I:
2.7.7.6;

Protein crystallography data

The structure of X-Ray Crystal Structure of the N4 Mini-Vrnap and P2_7A Promoter Transcription Initiation Complex with Gtp and Magnesium: Substrate Complex I, PDB code: 3q22 was solved by M.L.Gleghorn, K.S.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.11
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.300, 111.787, 276.850, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 21.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Crystal Structure of the N4 Mini-Vrnap and P2_7A Promoter Transcription Initiation Complex with Gtp and Magnesium: Substrate Complex I (pdb code 3q22). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the X-Ray Crystal Structure of the N4 Mini-Vrnap and P2_7A Promoter Transcription Initiation Complex with Gtp and Magnesium: Substrate Complex I, PDB code: 3q22:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3q22

Go back to Magnesium Binding Sites List in 3q22
Magnesium binding site 1 out of 2 in the X-Ray Crystal Structure of the N4 Mini-Vrnap and P2_7A Promoter Transcription Initiation Complex with Gtp and Magnesium: Substrate Complex I


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 the N4 Mini-Vrnap and P2_7A Promoter Transcription Initiation Complex with Gtp and Magnesium: Substrate Complex I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1110

b:22.5
occ:1.00
O2B A:GTP1108 2.3 28.2 1.0
O1G A:GTP1108 2.4 26.9 1.0
O A:GLY560 2.4 20.1 1.0
OD2 A:ASP951 2.5 22.1 1.0
O2A A:GTP1108 2.5 25.9 1.0
OD1 A:ASP559 3.3 30.5 1.0
PB A:GTP1108 3.3 26.5 1.0
C A:GLY560 3.5 19.8 1.0
CG A:ASP951 3.5 20.9 1.0
O A:HOH1431 3.5 45.0 1.0
PG A:GTP1108 3.6 28.0 1.0
PA A:GTP1108 3.7 26.1 1.0
OD2 A:ASP559 3.7 30.6 1.0
CG A:ASP559 3.8 25.8 1.0
O3A A:GTP1108 3.8 27.6 1.0
O3B A:GTP1108 3.8 27.3 1.0
OD1 A:ASP951 3.9 22.1 1.0
N A:GLY560 4.0 20.2 1.0
CA A:GLY560 4.0 19.6 1.0
O2G A:GTP1108 4.2 26.7 1.0
C5' A:GTP1108 4.2 23.3 1.0
O5' A:GTP1108 4.5 24.6 1.0
CB A:ASN563 4.6 17.3 1.0
N A:VAL561 4.6 19.4 1.0
O1B A:GTP1108 4.6 28.5 1.0
N A:THR562 4.7 18.5 1.0
C A:ASP559 4.7 20.7 1.0
O3G A:GTP1108 4.8 26.1 1.0
N A:ASN563 4.8 17.4 1.0
O1A A:GTP1108 4.8 25.7 1.0
CB A:ASP951 4.8 20.0 1.0
CA A:VAL561 5.0 19.0 1.0

Magnesium binding site 2 out of 2 in 3q22

Go back to Magnesium Binding Sites List in 3q22
Magnesium binding site 2 out of 2 in the X-Ray Crystal Structure of the N4 Mini-Vrnap and P2_7A Promoter Transcription Initiation Complex with Gtp and Magnesium: Substrate Complex I


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 the N4 Mini-Vrnap and P2_7A Promoter Transcription Initiation Complex with Gtp and Magnesium: Substrate Complex I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1109

b:27.9
occ:1.00
OD2 B:ASP951 2.2 24.4 1.0
O B:GLY560 2.4 21.7 1.0
O2B B:GTP1107 2.4 34.5 1.0
O1G B:GTP1107 2.7 34.1 1.0
O2A B:GTP1107 2.8 35.2 1.0
CG B:ASP951 3.3 22.0 1.0
OD1 B:ASP559 3.4 31.1 1.0
C B:GLY560 3.4 20.8 1.0
O B:HOH1927 3.5 40.5 1.0
PB B:GTP1107 3.6 34.7 1.0
OD1 B:ASP951 3.8 23.8 1.0
CG B:ASP559 3.8 26.9 1.0
CA B:GLY560 3.9 21.4 1.0
PG B:GTP1107 3.9 33.1 1.0
OD2 B:ASP559 3.9 28.9 1.0
N B:GLY560 3.9 22.1 1.0
PA B:GTP1107 4.0 33.9 1.0
O B:HOH2110 4.0 44.1 1.0
O3A B:GTP1107 4.1 34.7 1.0
O3B B:GTP1107 4.1 34.5 1.0
C5' B:GTP1107 4.4 29.9 1.0
O2G B:GTP1107 4.4 33.7 1.0
CB B:ASN563 4.4 18.3 1.0
CB B:ASP951 4.5 21.0 1.0
N B:VAL561 4.5 20.0 1.0
O B:HOH1869 4.6 34.3 1.0
O B:ASP951 4.6 20.6 1.0
C B:ASP559 4.7 22.5 1.0
N B:ASN563 4.7 18.1 1.0
O5' B:GTP1107 4.8 32.4 1.0
N B:THR562 4.8 18.3 1.0
O1B B:GTP1107 4.9 35.6 1.0
O B:HOH1666 4.9 32.4 1.0
CA B:VAL561 5.0 19.0 1.0
CB B:ASP559 5.0 23.5 1.0

Reference:

M.L.Gleghorn, E.K.Davydova, R.Basu, L.B.Rothman-Denes, K.S.Murakami. X-Ray Crystal Structures Elucidate the Nucleotidyl Transfer Reaction of Transcript Initiation Using Two Nucleotides. Proc.Natl.Acad.Sci.Usa V. 108 3566 2011.
ISSN: ISSN 0027-8424
PubMed: 21321236
DOI: 10.1073/PNAS.1016691108
Page generated: Mon Dec 14 08:41:21 2020

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