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Magnesium in PDB 1gki: Plasmid Coupling Protein Trwb in Complex with Adp and MG2+.

Protein crystallography data

The structure of Plasmid Coupling Protein Trwb in Complex with Adp and MG2+., PDB code: 1gki was solved by F.X.Gomis-Ruth, G.Moncalian, F.De La Cruz, M.Coll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50 / 3.0
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 151.100, 151.100, 251.600, 90.00, 90.00, 120.00
R / Rfree (%) 21 / 23.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Plasmid Coupling Protein Trwb in Complex with Adp and MG2+. (pdb code 1gki). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Plasmid Coupling Protein Trwb in Complex with Adp and MG2+., PDB code: 1gki:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 1gki

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Magnesium binding site 1 out of 5 in the Plasmid Coupling Protein Trwb in Complex with Adp and MG2+.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Plasmid Coupling Protein Trwb in Complex with Adp and MG2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:57.5
occ:0.69
O3B A:ADP701 2.2 53.4 0.8
OG A:SER137 2.5 61.0 1.0
O1B A:ADP701 3.2 54.6 0.8
PB A:ADP701 3.2 52.5 0.8
CB A:SER137 3.8 55.6 1.0
O1A A:ADP701 3.9 53.6 0.8
O3A A:ADP701 3.9 51.3 0.8
N A:SER137 4.2 52.1 1.0
CE A:LYS136 4.3 43.2 1.0
O2B A:ADP701 4.4 53.6 0.8
CA A:SER137 4.5 52.3 1.0
NZ A:LYS136 4.5 43.1 1.0
CB A:LYS136 4.6 47.6 1.0
PA A:ADP701 4.6 51.0 0.8

Magnesium binding site 2 out of 5 in 1gki

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Magnesium binding site 2 out of 5 in the Plasmid Coupling Protein Trwb in Complex with Adp and MG2+.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Plasmid Coupling Protein Trwb in Complex with Adp and MG2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:57.4
occ:0.78
O3B B:ADP701 2.1 54.9 1.0
OG B:SER137 2.5 56.6 1.0
O1B B:ADP701 2.9 53.8 1.0
PB B:ADP701 3.1 47.4 1.0
O B:HOH2010 3.7 41.4 1.0
CB B:SER137 3.8 54.6 1.0
O3A B:ADP701 4.0 48.1 1.0
O1A B:ADP701 4.2 56.3 1.0
N B:SER137 4.2 50.6 1.0
O2B B:ADP701 4.2 51.4 1.0
CA B:SER137 4.5 51.1 1.0
NZ B:LYS136 4.5 30.3 1.0
CB B:LYS136 4.6 40.4 1.0
PA B:ADP701 4.8 52.5 1.0

Magnesium binding site 3 out of 5 in 1gki

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Magnesium binding site 3 out of 5 in the Plasmid Coupling Protein Trwb in Complex with Adp and MG2+.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Plasmid Coupling Protein Trwb in Complex with Adp and MG2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg702

b:62.6
occ:1.00
O3B D:ADP701 2.3 56.5 1.0
OG D:SER137 2.5 56.4 1.0
O1B D:ADP701 2.9 56.0 1.0
PB D:ADP701 3.1 50.8 1.0
CB D:SER137 3.8 53.1 1.0
O3A D:ADP701 3.8 54.3 1.0
O1A D:ADP701 4.0 55.1 1.0
N D:SER137 4.1 50.6 1.0
CE D:LYS136 4.4 37.3 1.0
O2B D:ADP701 4.4 59.0 1.0
CA D:SER137 4.4 49.6 1.0
NZ D:LYS136 4.5 34.6 1.0
CB D:LYS136 4.5 44.3 1.0
PA D:ADP701 4.6 54.3 1.0

Magnesium binding site 4 out of 5 in 1gki

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Magnesium binding site 4 out of 5 in the Plasmid Coupling Protein Trwb in Complex with Adp and MG2+.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Plasmid Coupling Protein Trwb in Complex with Adp and MG2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg702

b:61.2
occ:0.89
O3B E:ADP701 2.1 59.1 1.0
OG E:SER137 2.6 59.4 1.0
PB E:ADP701 3.2 57.4 1.0
O1B E:ADP701 3.3 58.6 1.0
O E:HOH2057 3.7 38.8 1.0
CB E:SER137 3.9 54.5 1.0
O E:HOH2054 3.9 33.6 1.0
O2B E:ADP701 4.1 56.6 1.0
N E:SER137 4.2 47.7 1.0
O3A E:ADP701 4.3 60.2 1.0
CE E:LYS136 4.4 32.5 1.0
O E:HOH2012 4.4 33.0 1.0
NZ E:LYS136 4.5 31.0 1.0
CA E:SER137 4.6 51.9 1.0
CB E:LYS136 4.6 39.2 1.0
O1A E:ADP701 4.7 62.0 1.0

Magnesium binding site 5 out of 5 in 1gki

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Magnesium binding site 5 out of 5 in the Plasmid Coupling Protein Trwb in Complex with Adp and MG2+.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Plasmid Coupling Protein Trwb in Complex with Adp and MG2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg702

b:59.2
occ:0.73
OG G:SER137 2.1 61.1 1.0
O3B G:ADP701 2.7 56.8 0.8
CB G:SER137 3.5 57.0 1.0
N G:SER137 3.8 55.8 1.0
PB G:ADP701 3.8 56.5 0.8
O1B G:ADP701 3.9 56.1 0.8
CA G:SER137 4.0 57.2 1.0
O3A G:ADP701 4.3 58.2 0.8
CB G:LYS136 4.4 50.8 1.0
CE G:LYS136 4.5 46.5 1.0
O1A G:ADP701 4.6 59.8 0.8
C G:LYS136 4.7 54.5 1.0
NZ G:LYS136 4.9 46.4 1.0
O G:ASP356 5.0 53.4 1.0

Reference:

F.X.Gomis-Ruth, G.Moncalian, R.Perez-Luque, A.Gonzalez, E.Cabezon, F.De La Cruz, M.Coll. The Bacterial Conjugation Protein Trwb Resembles Ring Helicases and F1-Atpase Nature V. 409 637 2001.
ISSN: ISSN 0028-0836
PubMed: 11214325
DOI: 10.1038/35054586
Page generated: Mon Dec 14 05:57:57 2020

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