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Magnesium in PDB 1xmi: Crystal Structure of Human F508A NBD1 Domain with Atp

Enzymatic activity of Crystal Structure of Human F508A NBD1 Domain with Atp

All present enzymatic activity of Crystal Structure of Human F508A NBD1 Domain with Atp:
3.6.3.49;

Protein crystallography data

The structure of Crystal Structure of Human F508A NBD1 Domain with Atp, PDB code: 1xmi was solved by H.A.Lewis, X.Zhao, C.Wang, J.M.Sauder, I.Rooney, B.W.Noland, D.Lorimer, M.C.Kearins, K.Conners, B.Condon, P.C.Maloney, W.B.Guggino, J.F.Hunt, S.Emtage, Structural Genomix, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.20 / 2.25
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 144.461, 154.022, 136.088, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 26.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human F508A NBD1 Domain with Atp (pdb code 1xmi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Human F508A NBD1 Domain with Atp, PDB code: 1xmi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 1xmi

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Magnesium binding site 1 out of 5 in the Crystal Structure of Human F508A NBD1 Domain with Atp


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 Human F508A NBD1 Domain with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg7

b:18.5
occ:1.00
 O2G A:ATP2 1.9 17.5 1.0
O2B A:ATP2 2.0 13.3 1.0
O A:HOH821 2.1 19.8 1.0
O A:HOH828 2.1 10.7 1.0
OG1 A:THR465 2.2 13.5 1.0
OE1 A:GLN493 2.3 35.3 1.0
PG A:ATP2 3.1 17.5 1.0
PB A:ATP2 3.2 15.8 1.0
CD A:GLN493 3.3 29.7 1.0
CB A:THR465 3.3 13.4 1.0
O3B A:ATP2 3.4 19.9 1.0
NE2 A:GLN493 3.7 16.4 1.0
O A:HOH778 3.9 43.7 1.0
O1A A:ATP2 4.0 17.9 1.0
O A:HOH730 4.0 16.8 1.0
O1G A:ATP2 4.0 17.4 1.0
N A:THR465 4.1 13.2 1.0
O A:HOH693 4.1 13.7 1.0
OD1 A:ASP572 4.1 16.2 1.0
OD2 A:ASP572 4.1 20.2 1.0
O3G A:ATP2 4.2 26.2 1.0
O1B A:ATP2 4.2 15.5 1.0
CA A:THR465 4.3 13.3 1.0
O3A A:ATP2 4.3 19.9 1.0
CG2 A:THR465 4.3 12.2 1.0
CG A:GLN493 4.5 27.5 1.0
PA A:ATP2 4.6 15.5 1.0
CG A:ASP572 4.6 19.7 1.0
O A:HOH710 4.7 26.6 1.0
O2A A:ATP2 5.0 18.4 1.0

Magnesium binding site 2 out of 5 in 1xmi

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Magnesium binding site 2 out of 5 in the Crystal Structure of Human F508A NBD1 Domain with Atp


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 Human F508A NBD1 Domain with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg6

b:18.5
occ:1.00
 O2G B:ATP1 1.9 21.9 1.0
O B:HOH833 2.0 11.5 1.0
O2B B:ATP1 2.1 17.4 1.0
O B:HOH840 2.1 17.6 1.0
OG1 B:THR465 2.1 11.3 1.0
OE1 B:GLN493 2.3 34.5 1.0
CD B:GLN493 3.3 30.9 1.0
PG B:ATP1 3.3 17.5 1.0
CB B:THR465 3.3 13.0 1.0
PB B:ATP1 3.4 13.5 1.0
O3B B:ATP1 3.7 17.0 1.0
O B:HOH742 3.8 22.4 1.0
OD2 B:ASP572 3.8 19.1 1.0
NE2 B:GLN493 3.9 16.1 1.0
OD1 B:ASP572 4.0 21.4 1.0
N B:THR465 4.0 15.4 1.0
O1A B:ATP1 4.0 17.2 1.0
O B:HOH702 4.1 12.9 1.0
O1G B:ATP1 4.2 18.5 1.0
CA B:THR465 4.2 13.6 1.0
O3G B:ATP1 4.3 24.4 1.0
O B:HOH835 4.3 34.5 1.0
O1B B:ATP1 4.3 17.4 1.0
CG2 B:THR465 4.3 9.9 1.0
CG B:GLN493 4.4 27.7 1.0
CG B:ASP572 4.4 21.5 1.0
O3A B:ATP1 4.5 16.6 1.0
PA B:ATP1 4.7 15.5 1.0
O B:HOH741 4.8 22.7 1.0
CB B:LYS464 5.0 16.7 1.0

Magnesium binding site 3 out of 5 in 1xmi

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Magnesium binding site 3 out of 5 in the Crystal Structure of Human F508A NBD1 Domain with Atp


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 Human F508A NBD1 Domain with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg8

b:16.1
occ:1.00
 O2G C:ATP3 1.9 21.2 1.0
O C:HOH787 2.1 13.8 1.0
O2B C:ATP3 2.1 15.0 1.0
O C:HOH823 2.1 19.7 1.0
OG1 C:THR465 2.2 8.5 1.0
OE1 C:GLN493 2.3 35.7 1.0
PG C:ATP3 3.3 17.2 1.0
CB C:THR465 3.3 13.4 1.0
CD C:GLN493 3.3 33.2 1.0
PB C:ATP3 3.4 14.1 1.0
O3B C:ATP3 3.7 18.3 1.0
NE2 C:GLN493 3.8 15.1 1.0
O1A C:ATP3 3.9 13.1 1.0
OD2 C:ASP572 3.9 15.0 1.0
O1G C:ATP3 4.1 20.2 1.0
N C:THR465 4.1 12.0 1.0
OD1 C:ASP572 4.1 15.8 1.0
O C:HOH737 4.1 20.7 1.0
O C:HOH711 4.2 17.5 1.0
CA C:THR465 4.2 12.8 1.0
CG2 C:THR465 4.2 9.9 1.0
O C:HOH767 4.3 40.6 1.0
O3G C:ATP3 4.3 22.8 1.0
O C:HOH778 4.3 27.1 1.0
O1B C:ATP3 4.4 12.6 1.0
CG C:GLN493 4.4 25.7 1.0
O3A C:ATP3 4.5 16.3 1.0
CG C:ASP572 4.5 17.6 1.0
PA C:ATP3 4.6 13.7 1.0

Magnesium binding site 4 out of 5 in 1xmi

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Magnesium binding site 4 out of 5 in the Crystal Structure of Human F508A NBD1 Domain with Atp


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 Human F508A NBD1 Domain with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg9

b:13.3
occ:1.00
 O2G D:ATP4 1.9 14.4 1.0
O D:HOH807 2.0 10.3 1.0
O D:HOH810 2.0 12.9 1.0
O2B D:ATP4 2.0 8.3 1.0
OG1 D:THR465 2.2 7.7 1.0
OE1 D:GLN493 2.3 28.9 1.0
PG D:ATP4 3.2 16.2 1.0
CD D:GLN493 3.3 27.1 1.0
CB D:THR465 3.3 13.9 1.0
PB D:ATP4 3.3 12.6 1.0
O3B D:ATP4 3.6 17.5 1.0
O1A D:ATP4 3.8 10.6 1.0
NE2 D:GLN493 3.8 11.3 1.0
O1G D:ATP4 3.9 23.5 1.0
N D:THR465 4.1 10.7 1.0
OD2 D:ASP572 4.1 20.3 1.0
O D:HOH684 4.1 17.2 1.0
O D:HOH691 4.1 14.9 1.0
OD1 D:ASP572 4.1 18.7 1.0
CA D:THR465 4.2 12.3 1.0
CG2 D:THR465 4.3 12.9 1.0
O1B D:ATP4 4.3 10.5 1.0
O3G D:ATP4 4.3 24.4 1.0
O3A D:ATP4 4.4 18.2 1.0
CG D:GLN493 4.4 23.4 1.0
PA D:ATP4 4.6 12.8 1.0
CG D:ASP572 4.6 23.3 1.0
O D:HOH690 4.8 16.9 1.0
O2A D:ATP4 5.0 18.9 1.0

Magnesium binding site 5 out of 5 in 1xmi

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Magnesium binding site 5 out of 5 in the Crystal Structure of Human F508A NBD1 Domain with Atp


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 Human F508A NBD1 Domain with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg10

b:20.9
occ:1.00
 O2G E:ATP5 1.9 23.1 1.0
O E:HOH781 2.1 18.4 1.0
OG1 E:THR465 2.1 18.5 1.0
O2B E:ATP5 2.1 17.8 1.0
O E:HOH785 2.2 19.1 1.0
OE1 E:GLN493 2.3 41.1 1.0
CD E:GLN493 3.2 33.0 1.0
CB E:THR465 3.2 20.0 1.0
PG E:ATP5 3.3 23.2 1.0
PB E:ATP5 3.4 18.9 1.0
O3B E:ATP5 3.7 25.7 1.0
NE2 E:GLN493 3.8 18.2 1.0
O1A E:ATP5 3.9 19.2 1.0
O E:HOH695 4.0 26.4 1.0
OD2 E:ASP572 4.0 23.1 1.0
O1G E:ATP5 4.0 21.9 1.0
N E:THR465 4.1 17.5 1.0
OD1 E:ASP572 4.1 23.9 1.0
CG2 E:THR465 4.2 19.6 1.0
CA E:THR465 4.2 18.9 1.0
O E:HOH721 4.3 30.2 1.0
O3G E:ATP5 4.3 27.2 1.0
O1B E:ATP5 4.4 19.3 1.0
CG E:GLN493 4.4 30.3 1.0
O E:HOH724 4.5 35.3 1.0
O3A E:ATP5 4.5 26.9 1.0
CG E:ASP572 4.5 21.1 1.0
PA E:ATP5 4.7 21.4 1.0

Reference:

H.A.Lewis, X.Zhao, C.Wang, J.M.Sauder, I.Rooney, B.W.Noland, D.Lorimer, M.C.Kearins, K.Conners, B.Condon, P.C.Maloney, W.B.Guggino, J.F.Hunt, S.Emtage. Impact of the Delta-F508 Mutation in First Nucleotide-Binding Domain of Human Cystic Fibrosis Transmembrane Conductance Regulator on Domain Folding and Structure J.Biol.Chem. V. 280 1346 2005.
ISSN: ISSN 0021-9258
PubMed: 15528182
DOI: 10.1074/JBC.M410968200
Page generated: Tue Aug 13 17:44:28 2024

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