Magnesium in PDB 6xlj: Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 4-Nt Rna Transcript (Ecmrr-Rpitc-4NT)

Enzymatic activity of Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 4-Nt Rna Transcript (Ecmrr-Rpitc-4NT)

All present enzymatic activity of Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 4-Nt Rna Transcript (Ecmrr-Rpitc-4NT):
2.7.7.6;

Other elements in 6xlj:

The structure of Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 4-Nt Rna Transcript (Ecmrr-Rpitc-4NT) also contains other interesting chemical elements:

Antimony (Sb) 3 atoms
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 4-Nt Rna Transcript (Ecmrr-Rpitc-4NT) (pdb code 6xlj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 4-Nt Rna Transcript (Ecmrr-Rpitc-4NT), PDB code: 6xlj:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6xlj

Go back to Magnesium Binding Sites List in 6xlj
Magnesium binding site 1 out of 2 in the Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 4-Nt Rna Transcript (Ecmrr-Rpitc-4NT)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 4-Nt Rna Transcript (Ecmrr-Rpitc-4NT) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1501

b:62.2
occ:1.00
OD1 D:ASP460 1.9 57.0 1.0
O3' R:G4 1.9 66.7 1.0
OD1 D:ASP464 1.9 57.5 1.0
OD1 D:ASP462 2.1 57.1 1.0
CG D:ASP464 2.7 57.5 1.0
CG D:ASP460 2.7 57.0 1.0
OD2 D:ASP464 2.9 57.5 1.0
O2' R:G4 3.0 66.7 1.0
OD2 D:ASP460 3.0 57.0 1.0
C3' R:G4 3.0 66.7 1.0
CG D:ASP462 3.1 57.1 1.0
OD2 D:ASP462 3.3 57.1 1.0
C2' R:G4 3.5 66.7 1.0
C4' R:G4 3.6 66.7 1.0
O D:ASP460 3.8 57.0 1.0
CB D:ASP464 4.1 57.5 1.0
CB D:ASP460 4.1 57.0 1.0
N D:ASP460 4.3 57.0 1.0
C D:ASP460 4.3 57.0 1.0
C5' R:G4 4.4 66.7 1.0
CB D:ASP462 4.4 57.1 1.0
N D:ASP464 4.5 57.5 1.0
N D:ASP462 4.5 57.1 1.0
CA D:ASP460 4.5 57.0 1.0
CA D:ASP464 4.6 57.5 1.0
O4' R:G4 4.7 66.7 1.0
C1' R:G4 4.7 66.7 1.0
C D:ASP462 4.8 57.1 1.0
CA D:ASP462 4.8 57.1 1.0
NH2 D:ARG425 4.9 54.8 1.0

Magnesium binding site 2 out of 2 in 6xlj

Go back to Magnesium Binding Sites List in 6xlj
Magnesium binding site 2 out of 2 in the Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 4-Nt Rna Transcript (Ecmrr-Rpitc-4NT)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 4-Nt Rna Transcript (Ecmrr-Rpitc-4NT) within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg101

b:85.9
occ:1.00
N7 R:GTP1 2.3 81.5 1.0
C8 R:GTP1 2.9 81.5 1.0
O2B R:GTP1 3.2 81.5 1.0
O3A R:GTP1 3.4 81.5 1.0
O3G R:GTP1 3.4 81.5 1.0
C5 R:GTP1 3.6 81.5 1.0
PB R:GTP1 3.8 81.5 1.0
O6 R:GTP1 4.1 81.5 1.0
N9 R:GTP1 4.2 81.5 1.0
C6 R:GTP1 4.3 81.5 1.0
C4 R:GTP1 4.5 81.5 1.0
O3B R:GTP1 4.5 81.5 1.0
PG R:GTP1 4.5 81.5 1.0
N1 T:DA17 4.6 86.5 1.0
OD1 F:ASP514 4.6 102.0 1.0
PA R:GTP1 4.7 81.5 1.0
NH2 C:ARG540 4.7 77.2 1.0
O1A R:GTP1 4.8 81.5 1.0
C5 R:C2 4.9 74.9 1.0

Reference:

Y.Yang, C.Liu, W.Shi, D.G.Schatz, Y.Hu, B.Liu. Structural Visualization of Bacterial Multidrug-Activated Transcription To Be Published.
Page generated: Sat Apr 17 16:40:49 2021

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