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Magnesium in PDB 6gkd: Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A

Enzymatic activity of Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A

All present enzymatic activity of Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A:
3.6.3.49;

Protein crystallography data

The structure of Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A, PDB code: 6gkd was solved by M.Sigoillot, M.Overtus, M.Grodecka, D.Scholl, A.Garcia-Pino, T.Laeremans, L.He, E.Pardon, E.Hildebrandt, I.Urbatsch, J.Steyaert, J.R.Riordan, C.Govaerts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.43 / 2.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 116.940, 146.830, 188.340, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 23.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A (pdb code 6gkd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A, PDB code: 6gkd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 6gkd

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Magnesium binding site 1 out of 10 in the Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:46.5
occ:1.00
 OG1 A:THR465 1.9 62.9 1.0
O2B A:ATP701 2.1 67.8 1.0
O2G A:ATP701 2.1 70.2 1.0
O A:HOH801 2.8 41.2 1.0
NE2 A:GLN493 2.8 88.7 1.0
OE1 A:GLN493 2.8 81.5 1.0
CD A:GLN493 3.0 83.9 1.0
OD1 A:ASP572 3.2 88.4 1.0
CB A:THR465 3.2 64.0 1.0
PB A:ATP701 3.4 66.9 1.0
PG A:ATP701 3.5 71.3 1.0
OD2 A:ASP572 3.6 89.9 1.0
N A:THR465 3.8 59.3 1.0
O3B A:ATP701 3.8 69.3 1.0
CG A:ASP572 3.8 84.9 1.0
O1G A:ATP701 3.9 71.3 1.0
CA A:THR465 4.0 59.4 1.0
O1B A:ATP701 4.0 63.2 1.0
CG2 A:THR465 4.3 60.4 1.0
CG A:GLN493 4.3 57.4 1.0
NZ A:LYS464 4.6 74.0 1.0
CB A:LYS464 4.6 63.7 1.0
O3A A:ATP701 4.6 67.3 1.0
O3G A:ATP701 4.6 73.5 1.0
O2A A:ATP701 4.8 68.1 1.0
C A:LYS464 4.8 62.5 1.0
CB A:GLN493 4.8 54.2 1.0
CG1 A:VAL603 4.8 56.3 1.0
O1A A:ATP701 4.9 68.8 1.0

Magnesium binding site 2 out of 10 in 6gkd

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Magnesium binding site 2 out of 10 in the Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg703

b:67.0
occ:1.00
 O O:HOH806 1.9 82.4 1.0
OE1 A:GLU504 3.1 98.8 1.0
OE1 O:GLU504 3.4 0.2 1.0
O O:HOH808 3.6 58.1 1.0
OE1 L:GLU504 3.6 0.4 1.0
CD A:GLU504 4.1 89.6 1.0
O A:PRO499 4.4 58.7 1.0
OE2 A:GLU504 4.5 83.0 1.0
CD O:GLU504 4.5 98.8 1.0
CD L:GLU504 4.7 92.6 1.0
O L:PRO499 4.7 55.5 1.0
O O:PRO499 4.8 55.6 1.0
OE2 O:GLU504 4.8 88.7 1.0

Magnesium binding site 3 out of 10 in 6gkd

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Magnesium binding site 3 out of 10 in the Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg702

b:52.0
occ:1.00
 OG1 F:THR465 1.9 89.2 1.0
OE1 F:GLN493 1.9 0.5 1.0
O1G F:ATP701 2.0 0.4 1.0
CD F:GLN493 2.6 0.6 1.0
O F:HOH802 2.7 58.8 1.0
O1B F:ATP701 2.8 0.0 1.0
NE2 F:GLN493 2.9 0.3 1.0
CB F:THR465 3.0 93.2 1.0
PG F:ATP701 3.4 98.4 1.0
O2G F:ATP701 3.7 0.3 1.0
CG2 F:THR465 3.7 92.0 1.0
OD1 F:ASP572 3.7 80.9 1.0
O F:HOH804 3.7 66.4 1.0
O1A F:ATP701 3.9 0.3 1.0
PB F:ATP701 4.0 99.9 1.0
CG F:GLN493 4.0 87.4 1.0
OD2 F:ASP572 4.0 93.8 1.0
O3B F:ATP701 4.1 97.3 1.0
CA F:THR465 4.2 88.9 1.0
CG F:ASP572 4.2 82.5 1.0
CB F:GLN493 4.3 72.2 1.0
N F:THR465 4.3 88.9 1.0
O3G F:ATP701 4.5 92.5 1.0
O3A F:ATP701 4.7 0.7 1.0
PA F:ATP701 4.8 0.8 1.0
CE2 F:PHE494 4.9 82.9 1.0

Magnesium binding site 4 out of 10 in 6gkd

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Magnesium binding site 4 out of 10 in the Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg703

b:66.4
occ:1.00
 O I:HOH812 2.2 71.2 1.0
OE1 I:GLU504 3.2 75.5 1.0
OE1 F:GLU504 3.4 85.6 1.0
OE1 R:GLU504 3.6 71.5 1.0
CD I:GLU504 4.2 79.0 1.0
CD F:GLU504 4.4 78.2 1.0
O I:PRO499 4.5 58.2 1.0
OE2 I:GLU504 4.5 80.5 1.0
OE2 F:GLU504 4.6 63.7 1.0
O R:PRO499 4.7 59.6 1.0
CD R:GLU504 4.7 78.7 1.0

Magnesium binding site 5 out of 10 in 6gkd

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Magnesium binding site 5 out of 10 in the Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg704

b:53.7
occ:1.00
 O F:PHE508 3.8 72.4 1.0
C F:PHE508 4.2 70.5 1.0
CA F:GLY509 4.2 63.3 1.0
CA R:GLY509 4.3 71.9 1.0
N F:GLY509 4.3 64.0 1.0
N R:GLY509 4.3 71.4 1.0
O I:PHE508 4.3 75.3 1.0
CA I:GLY509 4.4 69.0 1.0
N I:GLY509 4.4 68.9 1.0
C I:PHE508 4.4 73.4 1.0
C R:PHE508 5.0 74.7 1.0

Magnesium binding site 6 out of 10 in 6gkd

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Magnesium binding site 6 out of 10 in the Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg702

b:55.2
occ:1.00
 O2G I:ATP701 2.2 75.0 1.0
OG1 I:THR465 2.2 68.9 1.0
NE2 I:GLN493 2.3 62.2 1.0
O2B I:ATP701 2.4 65.4 1.0
CB I:THR465 2.9 66.8 1.0
O1A I:ATP701 3.1 68.3 1.0
CD I:GLN493 3.4 72.0 1.0
PG I:ATP701 3.4 73.6 1.0
PB I:ATP701 3.5 65.7 1.0
CG2 I:THR465 3.6 65.3 1.0
O3A I:ATP701 3.7 64.7 1.0
O3G I:ATP701 3.8 75.8 1.0
O3B I:ATP701 3.9 69.3 1.0
PA I:ATP701 3.9 65.8 1.0
OE1 I:GLN493 4.0 61.0 1.0
CA I:THR465 4.2 59.9 1.0
OD2 I:ASP572 4.4 0.1 1.0
CG I:GLN493 4.4 68.9 1.0
N I:THR465 4.4 59.9 1.0
O2A I:ATP701 4.6 67.8 1.0
O1G I:ATP701 4.6 75.4 1.0
O1B I:ATP701 4.8 67.2 1.0
OD1 I:ASP572 4.9 93.6 1.0

Magnesium binding site 7 out of 10 in 6gkd

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Magnesium binding site 7 out of 10 in the Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg702

b:64.5
occ:1.00
 OG1 L:THR465 1.9 54.2 1.0
O3G L:ATP701 1.9 83.2 1.0
O2B L:ATP701 2.0 69.9 1.0
O L:HOH802 2.1 74.0 1.0
NE2 L:GLN493 2.1 51.2 1.0
O L:HOH801 2.5 50.1 1.0
CB L:THR465 2.8 57.0 1.0
PG L:ATP701 3.3 81.3 1.0
PB L:ATP701 3.3 73.1 1.0
O2A L:ATP701 3.3 72.2 1.0
CD L:GLN493 3.4 72.7 1.0
O3B L:ATP701 3.5 76.7 1.0
CG2 L:THR465 3.7 50.9 1.0
CA L:THR465 3.9 58.7 1.0
N L:THR465 3.9 59.8 1.0
OD2 L:ASP572 4.0 69.3 1.0
OE1 L:GLN493 4.1 68.1 1.0
O1G L:ATP701 4.2 79.1 1.0
O2G L:ATP701 4.2 84.6 1.0
OD1 L:ASP572 4.2 67.6 1.0
PA L:ATP701 4.3 74.6 1.0
O3A L:ATP701 4.3 73.2 1.0
O1B L:ATP701 4.3 73.1 1.0
CG L:GLN493 4.3 70.7 1.0
CG L:ASP572 4.5 66.7 1.0
O1A L:ATP701 4.7 73.2 1.0

Magnesium binding site 8 out of 10 in 6gkd

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Magnesium binding site 8 out of 10 in the Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mg702

b:53.8
occ:1.00
 OG1 O:THR465 2.0 61.4 1.0
O3B O:ATP701 2.0 70.7 1.0
OE1 O:GLN493 2.5 90.7 1.0
NE2 O:GLN493 2.8 92.1 1.0
CD O:GLN493 2.9 93.9 1.0
O2G O:ATP701 2.9 73.6 1.0
PG O:ATP701 3.0 71.6 1.0
CB O:THR465 3.2 61.6 1.0
O O:HOH801 3.3 39.9 1.0
PB O:ATP701 3.3 66.9 1.0
O1B O:ATP701 3.5 69.6 1.0
OD1 O:ASP572 3.8 75.1 1.0
O3G O:ATP701 3.8 69.9 1.0
OD2 O:ASP572 3.9 84.1 1.0
O3A O:ATP701 4.0 61.5 1.0
N O:THR465 4.0 54.5 1.0
CA O:THR465 4.1 54.6 1.0
O1G O:ATP701 4.2 73.0 1.0
CG2 O:THR465 4.2 58.4 1.0
CG O:ASP572 4.3 75.1 1.0
CG O:GLN493 4.3 70.4 1.0
O2B O:ATP701 4.4 66.9 1.0
O2A O:ATP701 4.5 61.1 1.0
PA O:ATP701 4.7 59.8 1.0
NZ O:LYS464 4.7 52.5 1.0
CB O:GLN493 4.8 62.0 1.0
O1A O:ATP701 4.9 56.5 1.0
CB O:LYS464 4.9 55.5 1.0

Magnesium binding site 9 out of 10 in 6gkd

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Magnesium binding site 9 out of 10 in the Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mg703

b:52.8
occ:1.00
 O O:HOH803 2.3 60.0 1.0
N O:GLY509 3.9 63.1 1.0
CA O:GLY509 4.1 63.5 1.0
N A:GLY509 4.2 66.2 1.0
CA A:GLY509 4.3 66.3 1.0
O L:PHE508 4.5 73.6 1.0
C O:PHE508 4.6 69.0 1.0
C A:PHE508 4.6 69.1 1.0
CA L:GLY509 4.7 66.3 1.0
C L:PHE508 4.7 71.7 1.0
N L:GLY509 4.8 66.3 1.0
CD1 O:PHE508 4.9 70.8 1.0
CE1 O:PHE508 4.9 72.1 1.0

Magnesium binding site 10 out of 10 in 6gkd

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Magnesium binding site 10 out of 10 in the Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Human NBD1 of Cftr in Complex with Nanobodies D12 and G3A within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg702

b:88.7
occ:1.00
 OG1 R:THR465 1.9 72.0 1.0
O1B R:ATP701 2.0 82.9 1.0
NE2 R:GLN493 2.1 75.6 1.0
O1G R:ATP701 2.7 77.3 1.0
PB R:ATP701 3.2 83.8 1.0
CB R:THR465 3.2 76.0 1.0
CD R:GLN493 3.3 89.5 1.0
OD1 R:ASP572 3.3 79.8 1.0
N R:THR465 3.4 69.8 1.0
O3G R:ATP701 3.4 77.0 1.0
O2B R:ATP701 3.5 82.2 1.0
PG R:ATP701 3.6 78.6 1.0
OD2 R:ASP572 3.7 86.5 1.0
CA R:THR465 3.7 69.4 1.0
O3B R:ATP701 3.8 80.4 1.0
OE1 R:GLN493 3.9 81.3 1.0
CG R:ASP572 3.9 79.8 1.0
CB R:LYS464 4.1 77.6 1.0
NZ R:LYS464 4.2 82.2 1.0
CG R:GLN493 4.3 75.8 1.0
CG2 R:THR465 4.3 77.6 1.0
C R:LYS464 4.4 75.3 1.0
O3A R:ATP701 4.5 84.2 1.0
CG1 R:VAL603 4.5 72.2 1.0
CA R:LYS464 4.7 75.0 1.0
O2A R:ATP701 4.8 85.3 1.0
O1A R:ATP701 4.8 84.8 1.0
O2G R:ATP701 4.9 79.1 1.0
PA R:ATP701 5.0 85.8 1.0

Reference:

M.Sigoillot, M.Overtus, M.Grodecka, D.Scholl, A.Garcia-Pino, T.Laeremans, L.He, E.Pardon, E.Hildebrandt, I.Urbatsch, J.Steyaert, J.R.Riordan, C.Govaerts. Domain-Interface Dynamics of Cftr Revealed By Stabilizing Nanobodies. Nat Commun V. 10 2636 2019.
ISSN: ESSN 2041-1723
PubMed: 31201318
DOI: 10.1038/S41467-019-10714-Y
Page generated: Tue Oct 1 01:14:15 2024

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