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Manganese in PDB 3q23: X-Ray Crystal Structure of the N4 Mini-Vrnap and P2_7A Promoter Transcription Initiation Complex with Gmpcpp and Manganese: Sustrate Complex II

Enzymatic activity of X-Ray Crystal Structure of the N4 Mini-Vrnap and P2_7A Promoter Transcription Initiation Complex with Gmpcpp and Manganese: Sustrate Complex II

All present enzymatic activity of X-Ray Crystal Structure of the N4 Mini-Vrnap and P2_7A Promoter Transcription Initiation Complex with Gmpcpp and Manganese: Sustrate Complex II:
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 Gmpcpp and Manganese: Sustrate Complex II, PDB code: 3q23 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 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.834, 111.861, 276.093, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 23.1

Manganese Binding Sites:

The binding sites of Manganese atom in the X-Ray Crystal Structure of the N4 Mini-Vrnap and P2_7A Promoter Transcription Initiation Complex with Gmpcpp and Manganese: Sustrate Complex II (pdb code 3q23). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the X-Ray Crystal Structure of the N4 Mini-Vrnap and P2_7A Promoter Transcription Initiation Complex with Gmpcpp and Manganese: Sustrate Complex II, PDB code: 3q23:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3q23

Go back to Manganese Binding Sites List in 3q23
Manganese binding site 1 out of 4 in the X-Ray Crystal Structure of the N4 Mini-Vrnap and P2_7A Promoter Transcription Initiation Complex with Gmpcpp and Manganese: Sustrate Complex II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Crystal Structure of the N4 Mini-Vrnap and P2_7A Promoter Transcription Initiation Complex with Gmpcpp and Manganese: Sustrate Complex II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1107

b:16.3
occ:1.00
 OD1 A:ASP951 2.0 15.8 1.0
O3G A:G2P1111 2.1 22.7 1.0
OD1 A:ASP559 2.1 16.4 1.0
O2A A:G2P1108 2.3 16.0 1.0
O A:HOH2284 2.4 18.0 1.0
O3' A:G2P1111 2.4 20.1 1.0
CG A:ASP951 3.0 14.9 1.0
CG A:ASP559 3.0 15.7 1.0
PG A:G2P1111 3.3 24.8 1.0
OD2 A:ASP559 3.3 17.0 1.0
OD2 A:ASP951 3.3 14.8 1.0
PA A:G2P1108 3.5 17.2 1.0
O1G A:G2P1111 3.5 23.5 1.0
MN A:MN1109 3.6 17.2 1.0
C3' A:G2P1111 3.8 20.6 1.0
O1A A:G2P1108 3.8 16.4 1.0
O2' A:G2P1111 4.0 21.4 1.0
O A:HOH1221 4.1 22.3 1.0
O3B A:G2P1111 4.1 26.2 1.0
N A:GLY952 4.1 13.9 1.0
O5' A:G2P1108 4.2 17.7 1.0
C5' A:G2P1108 4.2 16.5 1.0
C A:ASP951 4.3 14.0 1.0
CB A:ASP951 4.3 14.2 1.0
CB A:ASP559 4.4 15.4 1.0
O2G A:G2P1111 4.4 25.3 1.0
C2' A:G2P1111 4.5 20.1 1.0
C4' A:G2P1111 4.5 21.2 1.0
OE1 A:GLU557 4.5 21.0 1.0
CA A:GLY952 4.5 13.9 1.0
O A:ILE949 4.6 13.7 1.0
O A:ASP951 4.6 14.4 1.0
CA A:ASP951 4.7 14.0 1.0
N A:ASP951 4.7 13.7 1.0
O1G A:G2P1108 4.8 18.4 1.0
O1B A:G2P1108 5.0 17.7 1.0
C3A A:G2P1108 5.0 17.9 1.0

Manganese binding site 2 out of 4 in 3q23

Go back to Manganese Binding Sites List in 3q23
Manganese binding site 2 out of 4 in the X-Ray Crystal Structure of the N4 Mini-Vrnap and P2_7A Promoter Transcription Initiation Complex with Gmpcpp and Manganese: Sustrate Complex II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Crystal Structure of the N4 Mini-Vrnap and P2_7A Promoter Transcription Initiation Complex with Gmpcpp and Manganese: Sustrate Complex II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1109

b:17.2
occ:1.00
 O1B A:G2P1108 2.1 17.7 1.0
O A:GLY560 2.1 14.4 1.0
OD2 A:ASP559 2.2 17.0 1.0
O1G A:G2P1108 2.2 18.4 1.0
OD2 A:ASP951 2.3 14.8 1.0
O2A A:G2P1108 2.3 16.0 1.0
CG A:ASP559 3.2 15.7 1.0
PB A:G2P1108 3.2 18.8 1.0
C A:GLY560 3.3 14.4 1.0
CG A:ASP951 3.3 14.9 1.0
PG A:G2P1108 3.4 19.0 1.0
PA A:G2P1108 3.5 17.2 1.0
OD1 A:ASP559 3.5 16.4 1.0
MN A:MN1107 3.6 16.3 1.0
O3B A:G2P1108 3.7 19.1 1.0
C3A A:G2P1108 3.7 17.9 1.0
OD1 A:ASP951 3.7 15.8 1.0
N A:GLY560 3.8 15.0 1.0
O A:HOH1221 3.9 22.3 1.0
CA A:GLY560 3.9 14.5 1.0
C5' A:G2P1108 4.0 16.5 1.0
O A:HOH1418 4.1 28.2 1.0
O3G A:G2P1108 4.2 18.0 1.0
O5' A:G2P1108 4.2 17.7 1.0
CB A:ASN563 4.2 13.7 1.0
N A:VAL561 4.4 13.9 1.0
C A:ASP559 4.4 15.1 1.0
CB A:ASP559 4.4 15.4 1.0
O3G A:G2P1111 4.5 22.7 1.0
N A:ASN563 4.5 13.6 1.0
N A:THR562 4.5 13.8 1.0
O2B A:G2P1108 4.6 18.0 1.0
CB A:ASP951 4.6 14.2 1.0
O2G A:G2P1108 4.6 18.4 1.0
CA A:VAL561 4.7 14.1 1.0
O1A A:G2P1108 4.7 16.4 1.0
C A:VAL561 4.9 13.9 1.0
O A:ASP559 4.9 15.1 1.0
CA A:ASP559 5.0 15.2 1.0
O A:ASP951 5.0 14.4 1.0

Manganese binding site 3 out of 4 in 3q23

Go back to Manganese Binding Sites List in 3q23
Manganese binding site 3 out of 4 in the X-Ray Crystal Structure of the N4 Mini-Vrnap and P2_7A Promoter Transcription Initiation Complex with Gmpcpp and Manganese: Sustrate Complex II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Crystal Structure of the N4 Mini-Vrnap and P2_7A Promoter Transcription Initiation Complex with Gmpcpp and Manganese: Sustrate Complex II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1107

b:20.4
occ:1.00
 OD1 B:ASP951 2.1 16.0 1.0
O3G B:G2P1108 2.1 31.3 1.0
OD1 B:ASP559 2.2 20.1 1.0
O2A B:G2P1109 2.3 19.7 1.0
O B:HOH1767 2.3 18.1 1.0
O3' B:G2P1108 2.4 24.7 1.0
CG B:ASP951 3.0 16.1 1.0
CG B:ASP559 3.1 18.9 1.0
PG B:G2P1108 3.3 32.8 1.0
OD2 B:ASP951 3.3 16.6 1.0
OD2 B:ASP559 3.3 19.7 1.0
PA B:G2P1109 3.4 21.4 1.0
O1G B:G2P1108 3.5 31.9 1.0
MN B:MN1110 3.5 19.6 1.0
O1A B:G2P1109 3.8 21.7 1.0
C3' B:G2P1108 3.8 24.5 1.0
O5' B:G2P1109 4.0 21.7 1.0
O B:HOH1968 4.1 31.9 1.0
C5' B:G2P1109 4.1 20.8 1.0
O2' B:G2P1108 4.1 24.4 1.0
N B:GLY952 4.1 15.5 1.0
O3B B:G2P1108 4.2 33.5 1.0
C B:ASP951 4.3 15.4 1.0
CB B:ASP951 4.3 15.6 1.0
O2G B:G2P1108 4.4 31.9 1.0
O B:ILE949 4.5 14.9 1.0
C2' B:G2P1108 4.5 24.1 1.0
CA B:GLY952 4.5 15.3 1.0
C4' B:G2P1108 4.5 25.0 1.0
CB B:ASP559 4.5 18.1 1.0
O B:ASP951 4.6 15.5 1.0
OE1 B:GLU557 4.6 22.7 1.0
CA B:ASP951 4.7 15.5 1.0
N B:ASP951 4.7 15.4 1.0
O3G B:G2P1109 4.7 22.2 1.0
O2B B:G2P1109 4.9 19.5 1.0
C3A B:G2P1109 5.0 20.6 1.0

Manganese binding site 4 out of 4 in 3q23

Go back to Manganese Binding Sites List in 3q23
Manganese binding site 4 out of 4 in the X-Ray Crystal Structure of the N4 Mini-Vrnap and P2_7A Promoter Transcription Initiation Complex with Gmpcpp and Manganese: Sustrate Complex II


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of X-Ray Crystal Structure of the N4 Mini-Vrnap and P2_7A Promoter Transcription Initiation Complex with Gmpcpp and Manganese: Sustrate Complex II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1110

b:19.6
occ:1.00
 O B:GLY560 2.1 16.1 1.0
O2B B:G2P1109 2.1 19.5 1.0
OD2 B:ASP951 2.2 16.6 1.0
O2A B:G2P1109 2.2 19.7 1.0
O3G B:G2P1109 2.2 22.2 1.0
OD2 B:ASP559 2.3 19.7 1.0
PB B:G2P1109 3.2 21.7 1.0
C B:GLY560 3.2 16.0 1.0
CG B:ASP559 3.2 18.9 1.0
CG B:ASP951 3.3 16.1 1.0
PA B:G2P1109 3.4 21.4 1.0
PG B:G2P1109 3.5 22.4 1.0
MN B:MN1107 3.5 20.4 1.0
OD1 B:ASP559 3.6 20.1 1.0
O3B B:G2P1109 3.7 21.1 1.0
OD1 B:ASP951 3.7 16.0 1.0
C3A B:G2P1109 3.7 20.6 1.0
N B:GLY560 3.8 16.7 1.0
CA B:GLY560 3.8 16.2 1.0
O B:HOH1968 3.9 31.9 1.0
C5' B:G2P1109 3.9 20.8 1.0
O B:HOH2074 4.1 37.3 1.0
O1G B:G2P1109 4.1 21.0 1.0
O5' B:G2P1109 4.2 21.7 1.0
CB B:ASN563 4.2 15.2 1.0
N B:VAL561 4.4 15.4 1.0
C B:ASP559 4.4 17.1 1.0
N B:ASN563 4.5 14.9 1.0
CB B:ASP559 4.5 18.1 1.0
O3G B:G2P1108 4.5 31.3 1.0
CB B:ASP951 4.6 15.6 1.0
O1B B:G2P1109 4.6 20.7 1.0
N B:THR562 4.6 15.3 1.0
O2G B:G2P1109 4.7 22.3 1.0
O1A B:G2P1109 4.7 21.7 1.0
CA B:VAL561 4.7 15.4 1.0
O B:ASP951 4.9 15.5 1.0
C B:VAL561 4.9 15.3 1.0
O B:ASP559 5.0 16.8 1.0
CA B:ASP559 5.0 17.5 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: Sat Oct 5 17:35:31 2024

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