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Magnesium in PDB 6uk1: Crystal Structure of Nucleotide-Binding Domain 2 (NBD2) of the Human Cystic Fibrosis Transmembrane Conductance Regulator (Cftr)

Enzymatic activity of Crystal Structure of Nucleotide-Binding Domain 2 (NBD2) of the Human Cystic Fibrosis Transmembrane Conductance Regulator (Cftr)

All present enzymatic activity of Crystal Structure of Nucleotide-Binding Domain 2 (NBD2) of the Human Cystic Fibrosis Transmembrane Conductance Regulator (Cftr):
5.6.1.6;

Protein crystallography data

The structure of Crystal Structure of Nucleotide-Binding Domain 2 (NBD2) of the Human Cystic Fibrosis Transmembrane Conductance Regulator (Cftr), PDB code: 6uk1 was solved by C.Wang, S.M.Vorobiev, R.M.Vernon, N.Khazanov, H.Senderowitz, J.D.Forman-Kay, J.F.Hunt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.41 / 2.69
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 95.063, 60.132, 105.160, 90.00, 99.57, 90.00
R / Rfree (%) 27.3 / 30.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Nucleotide-Binding Domain 2 (NBD2) of the Human Cystic Fibrosis Transmembrane Conductance Regulator (Cftr) (pdb code 6uk1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Nucleotide-Binding Domain 2 (NBD2) of the Human Cystic Fibrosis Transmembrane Conductance Regulator (Cftr), PDB code: 6uk1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6uk1

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Magnesium binding site 1 out of 4 in the Crystal Structure of Nucleotide-Binding Domain 2 (NBD2) of the Human Cystic Fibrosis Transmembrane Conductance Regulator (Cftr)


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 Nucleotide-Binding Domain 2 (NBD2) of the Human Cystic Fibrosis Transmembrane Conductance Regulator (Cftr) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1502

b:20.9
occ:1.00
 O1G A:ATP1501 2.0 19.8 1.0
O A:HOH1601 2.1 22.3 1.0
O D:HOH1612 2.1 22.3 1.0
O A:HOH1605 2.1 19.4 1.0
OG A:SER1251 2.1 22.2 1.0
O1B A:ATP1501 2.4 17.0 1.0
O3G D:ATP1501 2.8 43.6 1.0
CB A:SER1251 3.2 15.6 1.0
PG A:ATP1501 3.3 28.1 1.0
PB A:ATP1501 3.7 25.3 1.0
O3G A:ATP1501 3.7 34.8 1.0
O3B A:ATP1501 3.9 32.4 1.0
O2A A:ATP1501 4.0 25.0 1.0
PG D:ATP1501 4.1 32.6 1.0
OE1 A:GLU1371 4.2 28.7 1.0
OD2 A:ASP1370 4.2 35.2 1.0
O1G D:ATP1501 4.2 38.4 1.0
CA A:SER1251 4.4 19.5 1.0
N A:SER1251 4.4 15.6 1.0
OD1 A:ASP1370 4.4 29.4 1.0
O2G A:ATP1501 4.5 43.8 1.0
O2B A:ATP1501 4.6 5.0 1.0
O2G D:ATP1501 4.7 15.7 1.0
CG A:ASP1370 4.7 25.2 1.0
O3A A:ATP1501 4.7 20.4 1.0
PA A:ATP1501 4.8 33.0 1.0
O A:HOH1610 4.8 20.1 1.0
O1A A:ATP1501 4.9 41.2 1.0
OG1 D:THR1246 5.0 39.5 1.0

Magnesium binding site 2 out of 4 in 6uk1

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Magnesium binding site 2 out of 4 in the Crystal Structure of Nucleotide-Binding Domain 2 (NBD2) of the Human Cystic Fibrosis Transmembrane Conductance Regulator (Cftr)


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 Nucleotide-Binding Domain 2 (NBD2) of the Human Cystic Fibrosis Transmembrane Conductance Regulator (Cftr) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1502

b:69.7
occ:1.00
 O B:HOH1601 2.1 48.7 1.0
OG B:SER1251 2.1 79.0 1.0
O C:HOH1605 2.1 38.8 1.0
OD1 B:ASP1370 2.2 82.3 1.0
OE2 B:GLU1371 2.3 74.5 1.0
OD2 B:ASP1370 2.3 72.5 1.0
CG B:ASP1370 2.6 69.2 1.0
O1G B:ATP1501 2.8 49.9 1.0
O1B B:ATP1501 2.9 37.3 1.0
CB B:SER1251 3.5 48.9 1.0
CD B:GLU1371 3.5 62.0 1.0
N B:SER1251 4.0 49.0 1.0
O B:HOH1603 4.0 37.4 1.0
CB B:ASP1370 4.1 59.4 1.0
CA B:SER1251 4.1 49.0 1.0
CG B:GLU1371 4.2 58.2 1.0
O1G C:ATP1501 4.2 61.0 1.0
PG B:ATP1501 4.2 30.3 1.0
PB B:ATP1501 4.3 33.8 1.0
O C:HOH1609 4.4 25.6 1.0
OE1 B:GLU1371 4.4 57.8 1.0
CE1 B:HIS1375 4.5 57.8 1.0
O B:HOH1608 4.7 26.5 1.0
ND1 B:HIS1375 4.8 58.0 1.0
CB B:LYS1250 4.8 48.8 1.0
O3B B:ATP1501 4.8 33.6 1.0
O2G B:ATP1501 4.9 44.1 1.0
CE B:LYS1250 4.9 48.3 1.0
O2B B:ATP1501 4.9 31.8 1.0
CA B:ASP1370 4.9 59.3 1.0
C B:LYS1250 4.9 49.1 1.0
C B:ASP1370 5.0 58.9 1.0
CB B:GLU1371 5.0 58.1 1.0

Magnesium binding site 3 out of 4 in 6uk1

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Magnesium binding site 3 out of 4 in the Crystal Structure of Nucleotide-Binding Domain 2 (NBD2) of the Human Cystic Fibrosis Transmembrane Conductance Regulator (Cftr)


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 Nucleotide-Binding Domain 2 (NBD2) of the Human Cystic Fibrosis Transmembrane Conductance Regulator (Cftr) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1502

b:42.2
occ:1.00
 O C:HOH1608 2.1 30.6 1.0
O C:HOH1601 2.1 25.4 1.0
OG C:SER1251 2.2 63.1 1.0
O2G C:ATP1501 2.2 77.7 1.0
O1B C:ATP1501 2.4 30.3 1.0
O3B C:ATP1501 2.5 63.8 1.0
PG C:ATP1501 2.9 54.5 1.0
O1A C:ATP1501 2.9 12.8 1.0
PB C:ATP1501 3.0 41.0 1.0
O3G B:ATP1501 3.0 24.6 1.0
CB C:SER1251 3.1 63.3 1.0
O1G C:ATP1501 3.8 61.0 1.0
O3A C:ATP1501 3.9 50.3 1.0
PA C:ATP1501 3.9 43.0 1.0
O3G C:ATP1501 4.1 47.2 1.0
O2B C:ATP1501 4.2 27.8 1.0
N C:SER1251 4.3 63.3 1.0
CA C:SER1251 4.3 63.4 1.0
PG B:ATP1501 4.4 30.3 1.0
O2A C:ATP1501 4.5 32.1 1.0
OD2 C:ASP1370 4.7 48.1 1.0
O C:HOH1609 4.7 25.6 1.0
O2G B:ATP1501 4.7 44.1 1.0
O B:HOH1603 4.8 37.4 1.0
OE1 C:GLU1371 4.9 47.1 1.0

Magnesium binding site 4 out of 4 in 6uk1

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Magnesium binding site 4 out of 4 in the Crystal Structure of Nucleotide-Binding Domain 2 (NBD2) of the Human Cystic Fibrosis Transmembrane Conductance Regulator (Cftr)


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 Nucleotide-Binding Domain 2 (NBD2) of the Human Cystic Fibrosis Transmembrane Conductance Regulator (Cftr) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1502

b:13.3
occ:1.00
 O1B D:ATP1501 2.1 17.3 1.0
O2G D:ATP1501 2.1 15.7 1.0
O D:HOH1602 2.1 9.9 1.0
O D:HOH1610 2.1 15.1 1.0
OG D:SER1251 2.2 17.8 1.0
O1A D:ATP1501 3.0 22.7 1.0
O3G A:ATP1501 3.0 34.8 1.0
CB D:SER1251 3.1 17.6 1.0
PG D:ATP1501 3.2 32.6 1.0
PB D:ATP1501 3.3 29.6 1.0
O3B D:ATP1501 3.5 26.6 1.0
O3G D:ATP1501 3.8 43.6 1.0
PA D:ATP1501 4.0 30.3 1.0
O3A D:ATP1501 4.2 16.5 1.0
N D:SER1251 4.2 25.1 1.0
CA D:SER1251 4.3 27.8 1.0
PG A:ATP1501 4.3 28.1 1.0
O2B D:ATP1501 4.4 8.3 1.0
O2G A:ATP1501 4.4 43.8 1.0
O2A D:ATP1501 4.5 54.4 1.0
O1G D:ATP1501 4.5 38.4 1.0
OD2 D:ASP1370 4.6 34.9 1.0
OE1 D:GLU1371 4.7 35.4 1.0
OD1 D:ASP1370 4.9 30.0 1.0

Reference:

C.Wang, S.Vorobiev, R.M.Vernon, N.Khazanov, H.Senderowitz, J.D.Forman-Kay, J.F.Hunt. A Thermodynamically Stabilized Form of the Second Nucleotide Binding Domain From Human Cftr Shows A Catalytically Inactive Conformation To Be Published.
Page generated: Tue Oct 1 21:06:19 2024

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