Magnesium in PDB 6t66: Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4

Enzymatic activity of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4

All present enzymatic activity of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4:
3.6.4.12;

Protein crystallography data

The structure of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4, PDB code: 6t66 was solved by P.Legrand, S.Quevillon-Cheruel, I.Li De La Sierra-Gallay, H.Walbott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.63 / 3.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 118.978, 123.292, 263.493, 90, 90, 90
R / Rfree (%) 25.5 / 27.6

Other elements in 6t66:

The structure of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 also contains other interesting chemical elements:

Fluorine (F) 24 atoms
Aluminium (Al) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 (pdb code 6t66). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4, PDB code: 6t66:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6t66

Go back to Magnesium Binding Sites List in 6t66
Magnesium binding site 1 out of 6 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4


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 the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:63.7
occ:1.00
OG1 A:THR235 1.9 151.9 1.0
F2 A:ALF503 2.3 175.2 1.0
O2B A:GDP501 2.6 151.4 1.0
CE A:MET260 3.2 165.0 1.0
OE1 A:GLU259 3.2 176.5 1.0
CB A:THR235 3.3 152.4 1.0
OD1 A:ASP340 3.4 165.2 1.0
F3 A:ALF503 3.6 175.5 1.0
AL A:ALF503 3.8 175.6 1.0
PB A:GDP501 3.9 152.1 1.0
CD A:GLU259 4.1 184.8 1.0
N A:THR235 4.1 144.9 1.0
CG2 A:THR235 4.1 150.8 1.0
CA A:THR235 4.2 145.0 1.0
O3B A:GDP501 4.2 151.9 1.0
CG A:ASP340 4.3 165.2 1.0
O A:ASP340 4.3 156.7 1.0
OD2 A:ASP340 4.5 171.4 1.0
O3A A:GDP501 4.5 153.0 1.0
O1A A:GDP501 4.5 154.2 1.0
CD1 A:TYR341 4.6 158.3 1.0
OE2 A:GLU259 4.7 177.3 1.0
O2A A:GDP501 4.7 154.4 1.0
SD A:MET260 4.7 168.3 1.0
CB A:GLU259 4.7 159.7 1.0
CE1 A:TYR341 4.8 159.2 1.0
CB A:LYS234 4.8 145.2 1.0
F4 A:ALF503 4.8 176.0 1.0
PA A:GDP501 4.9 154.2 1.0
CG A:GLU259 4.9 168.8 1.0

Magnesium binding site 2 out of 6 in 6t66

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Magnesium binding site 2 out of 6 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4


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 the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:52.1
occ:1.00
OG1 B:THR235 1.9 131.2 1.0
F2 B:ALF503 2.3 160.8 1.0
O2B B:GDP501 2.6 145.8 1.0
CE B:MET260 3.2 155.6 1.0
OE1 B:GLU259 3.2 160.7 1.0
CB B:THR235 3.3 133.0 1.0
OD1 B:ASP340 3.4 147.1 1.0
F3 B:ALF503 3.6 160.5 1.0
AL B:ALF503 3.9 160.6 1.0
PB B:GDP501 3.9 146.1 1.0
CD B:GLU259 4.0 171.8 1.0
N B:THR235 4.1 127.4 1.0
CG2 B:THR235 4.1 131.4 1.0
CA B:THR235 4.2 127.1 1.0
CG B:ASP340 4.3 146.5 1.0
O3B B:GDP501 4.3 146.2 1.0
O B:ASP340 4.3 139.7 1.0
OD2 B:ASP340 4.5 151.6 1.0
O3A B:GDP501 4.5 145.3 1.0
O1A B:GDP501 4.5 144.2 1.0
OE2 B:GLU259 4.6 165.3 1.0
O2A B:GDP501 4.6 145.2 1.0
CD1 B:TYR341 4.7 143.6 1.0
SD B:MET260 4.7 158.9 1.0
CB B:GLU259 4.7 147.7 1.0
CE1 B:TYR341 4.8 144.8 1.0
CB B:LYS234 4.8 129.6 1.0
F4 B:ALF503 4.8 161.0 1.0
PA B:GDP501 4.9 145.0 1.0
CG B:GLU259 4.9 156.5 1.0

Magnesium binding site 3 out of 6 in 6t66

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Magnesium binding site 3 out of 6 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4


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 the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:34.8
occ:1.00
OG1 C:THR235 1.9 139.6 1.0
F2 C:ALF503 2.3 161.8 1.0
O3B C:GDP501 2.6 142.2 1.0
OE1 C:GLU259 3.2 177.6 1.0
CE C:MET260 3.2 172.0 1.0
CB C:THR235 3.3 141.2 1.0
OD1 C:ASP340 3.4 160.9 1.0
F3 C:ALF503 3.6 162.0 1.0
AL C:ALF503 3.9 161.9 1.0
PB C:GDP501 3.9 142.3 1.0
CD C:GLU259 4.1 186.5 1.0
N C:THR235 4.1 134.6 1.0
CG2 C:THR235 4.1 139.7 1.0
CA C:THR235 4.2 134.4 1.0
CG C:ASP340 4.3 161.1 1.0
O1B C:GDP501 4.3 142.9 1.0
O C:ASP340 4.3 154.2 1.0
OD2 C:ASP340 4.5 167.1 1.0
O3A C:GDP501 4.5 142.3 1.0
O2A C:GDP501 4.5 141.6 1.0
OE2 C:GLU259 4.6 178.6 1.0
CD1 C:TYR341 4.6 155.6 1.0
O1A C:GDP501 4.7 142.6 1.0
SD C:MET260 4.7 175.3 1.0
CB C:GLU259 4.8 164.6 1.0
CE1 C:TYR341 4.8 156.3 1.0
CB C:LYS234 4.8 135.5 1.0
F4 C:ALF503 4.8 161.8 1.0
PA C:GDP501 4.9 142.3 1.0
CG C:GLU259 4.9 172.5 1.0

Magnesium binding site 4 out of 6 in 6t66

Go back to Magnesium Binding Sites List in 6t66
Magnesium binding site 4 out of 6 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4


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 the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:74.6
occ:1.00
OG1 D:THR235 1.9 183.2 1.0
F2 D:ALF503 2.3 272.9 1.0
O3B D:GDP501 2.6 220.8 1.0
CE D:MET260 3.1 184.8 1.0
OE1 D:GLU259 3.2 199.3 1.0
CB D:THR235 3.3 183.4 1.0
OD1 D:ASP340 3.4 171.2 1.0
F3 D:ALF503 3.5 272.6 1.0
AL D:ALF503 3.9 272.6 1.0
PB D:GDP501 3.9 220.2 1.0
CD D:GLU259 4.1 206.1 1.0
N D:THR235 4.1 174.9 1.0
CG2 D:THR235 4.1 182.3 1.0
CA D:THR235 4.2 174.8 1.0
CG D:ASP340 4.3 170.7 1.0
O1B D:GDP501 4.3 220.4 1.0
O D:ASP340 4.3 164.1 1.0
OD2 D:ASP340 4.5 175.9 1.0
O3A D:GDP501 4.5 219.1 1.0
O2A D:GDP501 4.6 217.9 1.0
OE2 D:GLU259 4.6 200.4 1.0
CD1 D:TYR341 4.7 165.9 1.0
O1A D:GDP501 4.7 218.1 1.0
SD D:MET260 4.7 188.1 1.0
CB D:GLU259 4.7 177.1 1.0
CE1 D:TYR341 4.8 166.8 1.0
F4 D:ALF503 4.8 272.7 1.0
CB D:LYS234 4.8 176.0 1.0
PA D:GDP501 4.9 218.1 1.0
CG D:GLU259 4.9 186.7 1.0

Magnesium binding site 5 out of 6 in 6t66

Go back to Magnesium Binding Sites List in 6t66
Magnesium binding site 5 out of 6 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4


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 the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg502

b:74.6
occ:1.00
OG1 E:THR235 1.9 198.6 1.0
F2 E:ALF503 2.3 218.7 1.0
O2B E:GDP501 2.6 187.7 1.0
OE1 E:GLU259 3.2 229.7 1.0
CE E:MET260 3.2 204.4 1.0
CB E:THR235 3.3 199.3 1.0
OD1 E:ASP340 3.4 235.3 1.0
F3 E:ALF503 3.6 218.6 1.0
AL E:ALF503 3.9 218.5 1.0
PB E:GDP501 3.9 187.7 1.0
CD E:GLU259 4.1 235.3 1.0
N E:THR235 4.1 192.2 1.0
CG2 E:THR235 4.1 197.9 1.0
CA E:THR235 4.2 191.8 1.0
CG E:ASP340 4.3 235.0 1.0
O3B E:GDP501 4.3 187.7 1.0
O E:ASP340 4.3 228.6 1.0
OD2 E:ASP340 4.5 240.0 1.0
O3A E:GDP501 4.5 187.0 1.0
O2A E:GDP501 4.6 186.2 1.0
CD1 E:TYR341 4.6 229.3 1.0
OE2 E:GLU259 4.6 232.1 1.0
O1A E:GDP501 4.7 186.2 1.0
SD E:MET260 4.7 207.8 1.0
CB E:GLU259 4.7 201.6 1.0
CE1 E:TYR341 4.8 229.9 1.0
CB E:LYS234 4.8 195.7 1.0
F4 E:ALF503 4.8 218.4 1.0
PA E:GDP501 4.9 186.3 1.0
CG E:GLU259 4.9 212.6 1.0

Magnesium binding site 6 out of 6 in 6t66

Go back to Magnesium Binding Sites List in 6t66
Magnesium binding site 6 out of 6 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4


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 the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg502

b:92.1
occ:1.00
OG1 F:THR235 1.9 195.2 1.0
F2 F:ALF503 2.3 287.2 1.0
O2B F:GDP501 2.6 215.6 1.0
CE F:MET260 3.2 197.5 1.0
OE1 F:GLU259 3.2 221.3 1.0
CB F:THR235 3.3 195.9 1.0
OD1 F:ASP340 3.4 204.3 1.0
F3 F:ALF503 3.6 287.9 1.0
AL F:ALF503 3.9 287.8 1.0
PB F:GDP501 3.9 215.3 1.0
CD F:GLU259 4.1 224.9 1.0
N F:THR235 4.1 189.3 1.0
CG2 F:THR235 4.1 194.4 1.0
CA F:THR235 4.2 188.5 1.0
CG F:ASP340 4.3 204.2 1.0
O3B F:GDP501 4.3 216.0 1.0
O F:ASP340 4.3 199.0 1.0
OD2 F:ASP340 4.5 209.8 1.0
O3A F:GDP501 4.5 214.3 1.0
O1A F:GDP501 4.5 213.1 1.0
OE2 F:GLU259 4.6 219.5 1.0
CD1 F:TYR341 4.6 203.1 1.0
O2A F:GDP501 4.6 213.1 1.0
SD F:MET260 4.7 200.8 1.0
CB F:GLU259 4.7 191.1 1.0
CE1 F:TYR341 4.8 204.1 1.0
CB F:LYS234 4.8 193.6 1.0
F4 F:ALF503 4.8 288.0 1.0
PA F:GDP501 4.9 213.3 1.0
CG F:GLU259 4.9 202.5 1.0

Reference:

S.Marsin, Y.Adam, C.Cargemel, J.Andreani, S.Baconnais, P.Legrand, I.Li De La Sierra-Gallay, A.Humbert, M.Aumont-Nicaise, C.Velours, F.Ochsenbein, D.Durand, E.Le Cam, H.Walbott, C.Possoz, S.Quevillon-Cheruel, J.-L.Ferat. Study of the Dnab:Dcia Interplay Reveals Insights Into the Primary Mode of Loading of the Bacterial Replicative Helicase To Be Published.
Page generated: Sun Jul 11 14:56:42 2021

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