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Magnesium in PDB 7mny: Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 3 in Complex with Ran-Gppnhp

Protein crystallography data

The structure of Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 3 in Complex with Ran-Gppnhp, PDB code: 7mny was solved by C.J.Bley, S.Nie, G.W.Mobbs, S.Petrovic, A.T.Gres, X.Liu, S.Mukherjee, S.Harvey, F.M.Huber, D.H.Lin, B.Brown, A.W.Tang, E.J.Rundlet, A.R.Correia, S.Chen, S.G.Regmi, T.A.Stevens, C.A.Jette, M.Dasso, A.Patke, A.F.Palazzo, A.A.Kossiakoff, A.Hoelz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.93 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 110.2, 136.031, 158.755, 90, 90, 90
R / Rfree (%) 21.4 / 26.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 3 in Complex with Ran-Gppnhp (pdb code 7mny). 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 NUP358/RANBP2 Ran-Binding Domain 3 in Complex with Ran-Gppnhp, PDB code: 7mny:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7mny

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Magnesium binding site 1 out of 6 in the Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 3 in Complex with Ran-Gppnhp


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 NUP358/RANBP2 Ran-Binding Domain 3 in Complex with Ran-Gppnhp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:39.6
occ:1.00
O A:HOH405 2.0 38.3 1.0
OG1 A:THR42 2.0 41.5 1.0
O2B A:GNP301 2.0 37.8 1.0
O2G A:GNP301 2.1 39.7 1.0
OG1 A:THR24 2.1 36.8 1.0
O A:HOH407 2.1 39.1 1.0
HB A:THR42 3.1 51.4 1.0
CB A:THR42 3.1 42.5 1.0
H A:THR42 3.1 50.1 1.0
HB A:THR24 3.1 46.2 1.0
CB A:THR24 3.2 38.1 1.0
PG A:GNP301 3.2 38.4 1.0
PB A:GNP301 3.3 37.6 1.0
H A:THR24 3.3 39.4 1.0
N3B A:GNP301 3.6 38.4 1.0
N A:THR42 3.7 41.4 1.0
O3G A:GNP301 3.9 38.9 1.0
N A:THR24 3.9 34.5 1.0
CA A:THR42 4.0 42.9 1.0
OD2 A:ASP65 4.0 37.8 1.0
HB2 A:LYS23 4.0 44.0 1.0
HG21 A:THR24 4.0 46.0 1.0
HE3 A:LYS23 4.1 46.4 1.0
O2A A:GNP301 4.1 38.2 1.0
O3A A:GNP301 4.1 37.2 1.0
HG21 A:THR42 4.1 52.1 1.0
CA A:THR24 4.1 39.0 1.0
O A:HOH408 4.2 42.8 1.0
CG2 A:THR24 4.2 38.0 1.0
OD1 A:ASP65 4.2 37.0 1.0
CG2 A:THR42 4.2 43.0 1.0
HA A:THR42 4.3 51.9 1.0
O1G A:GNP301 4.4 39.5 1.0
HE1 A:TYR39 4.4 47.6 1.0
HNB3 A:GNP301 4.4 46.5 1.0
HA A:ALA41 4.4 47.6 1.0
CG A:ASP65 4.4 37.3 1.0
PA A:GNP301 4.5 37.2 1.0
HA A:THR24 4.5 47.2 1.0
O1B A:GNP301 4.5 37.2 1.0
O A:VAL40 4.5 40.0 1.0
HG23 A:THR24 4.7 46.0 1.0
O1A A:GNP301 4.7 36.5 1.0
HG23 A:THR42 4.7 52.1 1.0
C A:ALA41 4.7 41.0 1.0
O A:THR66 4.8 39.9 1.0
HA A:ALA67 4.8 51.8 1.0
HE2 A:LYS23 4.8 46.4 1.0
CE A:LYS23 4.9 38.3 1.0
CB A:LYS23 4.9 36.3 1.0
HG22 A:THR42 4.9 52.1 1.0
HG22 A:THR24 4.9 46.0 1.0

Magnesium binding site 2 out of 6 in 7mny

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Magnesium binding site 2 out of 6 in the Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 3 in Complex with Ran-Gppnhp


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 NUP358/RANBP2 Ran-Binding Domain 3 in Complex with Ran-Gppnhp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:45.6
occ:1.00
OG1 C:THR42 2.0 48.8 1.0
O C:HOH405 2.0 46.3 1.0
O2B C:GNP301 2.1 44.5 1.0
O C:HOH402 2.1 46.2 1.0
OG1 C:THR24 2.1 43.7 1.0
O2G C:GNP301 2.2 48.6 1.0
H C:THR42 2.9 60.1 1.0
HB C:THR24 3.1 52.7 1.0
CB C:THR42 3.2 52.1 1.0
CB C:THR24 3.2 43.6 1.0
HB C:THR42 3.2 62.9 1.0
PG C:GNP301 3.3 47.7 1.0
PB C:GNP301 3.3 44.7 1.0
N3B C:GNP301 3.5 47.5 1.0
H C:THR24 3.5 53.1 1.0
N C:THR42 3.5 50.4 1.0
O3G C:GNP301 3.9 50.2 1.0
CA C:THR42 3.9 52.7 1.0
HG21 C:THR24 4.0 53.6 1.0
N C:THR24 4.0 44.0 1.0
OD2 C:ASP65 4.0 43.9 1.0
HB2 C:LYS23 4.0 52.4 1.0
O2A C:GNP301 4.1 45.5 1.0
HA C:ALA41 4.1 60.4 1.0
CA C:THR24 4.2 44.0 1.0
OD1 C:ASP65 4.2 46.5 1.0
CG2 C:THR24 4.2 44.3 1.0
HNB3 C:GNP301 4.2 57.5 1.0
HG21 C:THR42 4.3 66.7 1.0
O3A C:GNP301 4.3 45.4 1.0
CG2 C:THR42 4.3 55.2 1.0
HA C:THR42 4.3 63.7 1.0
HE2 C:LYS23 4.4 56.4 1.0
O1G C:GNP301 4.4 50.9 1.0
HA C:THR24 4.5 53.2 1.0
CG C:ASP65 4.5 46.1 1.0
HA C:ALA67 4.5 67.1 1.0
O1B C:GNP301 4.5 45.2 1.0
C C:ALA41 4.5 51.5 1.0
O C:VAL40 4.6 48.6 1.0
PA C:GNP301 4.6 44.5 1.0
HE1 C:TYR39 4.6 59.7 1.0
O C:THR66 4.7 51.1 1.0
HG23 C:THR42 4.7 66.7 1.0
HG23 C:THR24 4.7 53.6 1.0
HZ3 C:LYS23 4.7 57.3 1.0
HZ1 C:LYS23 4.8 57.3 1.0
CA C:ALA41 4.8 52.0 1.0
HG22 C:THR24 4.9 53.6 1.0
O1A C:GNP301 5.0 43.1 1.0
CB C:LYS23 5.0 43.3 1.0

Magnesium binding site 3 out of 6 in 7mny

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Magnesium binding site 3 out of 6 in the Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 3 in Complex with Ran-Gppnhp


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 NUP358/RANBP2 Ran-Binding Domain 3 in Complex with Ran-Gppnhp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:48.8
occ:1.00
OG1 E:THR42 2.0 51.2 1.0
O E:HOH404 2.0 49.2 1.0
OG1 E:THR24 2.0 47.9 1.0
O E:HOH408 2.1 48.8 1.0
O2B E:GNP301 2.2 47.9 1.0
O2G E:GNP301 2.2 51.2 1.0
H E:THR42 3.0 63.1 1.0
HB E:THR42 3.0 63.9 1.0
HB E:THR24 3.1 56.3 1.0
CB E:THR42 3.1 52.9 1.0
CB E:THR24 3.1 46.8 1.0
PG E:GNP301 3.3 50.3 1.0
H E:THR24 3.3 56.0 1.0
PB E:GNP301 3.4 48.4 1.0
N3B E:GNP301 3.4 49.9 1.0
N E:THR42 3.6 53.2 1.0
O3G E:GNP301 3.9 52.4 1.0
N E:THR24 3.9 46.7 1.0
CA E:THR42 3.9 53.3 1.0
HG21 E:THR24 4.0 55.4 1.0
OD2 E:ASP65 4.0 48.0 1.0
HB2 E:LYS23 4.1 57.8 1.0
CA E:THR24 4.1 46.1 1.0
HNB3 E:GNP301 4.1 60.3 1.0
HG21 E:THR42 4.1 66.5 1.0
CG2 E:THR24 4.1 46.4 1.0
CG2 E:THR42 4.2 55.0 1.0
OD1 E:ASP65 4.3 50.0 1.0
O2A E:GNP301 4.3 49.1 1.0
O3A E:GNP301 4.3 48.0 1.0
HA E:THR42 4.3 64.4 1.0
O1A E:GNP301 4.4 46.9 1.0
HA E:ALA41 4.4 63.2 1.0
HA E:THR24 4.4 55.8 1.0
O1G E:GNP301 4.5 53.8 1.0
HE2 E:LYS23 4.5 61.0 1.0
PA E:GNP301 4.5 47.2 1.0
O1B E:GNP301 4.5 49.0 1.0
CG E:ASP65 4.5 49.9 1.0
HZ3 E:LYS23 4.6 61.3 1.0
HA E:ALA67 4.6 67.8 1.0
HZ1 E:LYS23 4.6 61.3 1.0
O E:VAL40 4.6 51.8 1.0
HG23 E:THR24 4.7 55.4 1.0
C E:ALA41 4.7 54.1 1.0
HG23 E:THR42 4.7 66.5 1.0
O E:THR66 4.8 53.5 1.0
HG22 E:THR24 4.8 55.4 1.0
HG22 E:THR42 4.9 66.5 1.0
NZ E:LYS23 4.9 51.7 1.0

Magnesium binding site 4 out of 6 in 7mny

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Magnesium binding site 4 out of 6 in the Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 3 in Complex with Ran-Gppnhp


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 NUP358/RANBP2 Ran-Binding Domain 3 in Complex with Ran-Gppnhp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg302

b:43.2
occ:1.00
O G:HOH402 2.0 44.4 1.0
OG1 G:THR42 2.0 46.4 1.0
O2G G:GNP301 2.0 45.0 1.0
OG1 G:THR24 2.1 41.9 1.0
O G:HOH405 2.1 42.8 1.0
O2B G:GNP301 2.2 42.3 1.0
HB G:THR24 3.0 50.1 1.0
CB G:THR24 3.1 41.4 1.0
H G:THR42 3.2 56.5 1.0
CB G:THR42 3.2 48.7 1.0
HB G:THR42 3.2 58.8 1.0
PG G:GNP301 3.2 44.8 1.0
H G:THR24 3.3 49.8 1.0
PB G:GNP301 3.3 42.4 1.0
N3B G:GNP301 3.5 43.3 1.0
N G:THR42 3.7 46.7 1.0
OD2 G:ASP65 3.9 41.5 1.0
N G:THR24 3.9 41.1 1.0
HG21 G:THR24 4.0 49.9 1.0
O3G G:GNP301 4.0 47.8 1.0
CA G:THR42 4.0 48.3 1.0
HB2 G:LYS23 4.0 52.1 1.0
CA G:THR24 4.1 40.7 1.0
OD1 G:ASP65 4.1 44.8 1.0
CG2 G:THR24 4.2 41.2 1.0
HG21 G:THR42 4.2 61.3 1.0
HNB3 G:GNP301 4.2 52.4 1.0
CG2 G:THR42 4.3 50.7 1.0
O1G G:GNP301 4.3 46.7 1.0
HA G:THR24 4.3 49.2 1.0
HE2 G:LYS23 4.4 57.2 1.0
HA G:THR42 4.4 58.4 1.0
CG G:ASP65 4.4 44.0 1.0
HA G:ALA41 4.4 54.2 1.0
O3A G:GNP301 4.4 42.0 1.0
O1B G:GNP301 4.4 42.8 1.0
O2A G:GNP301 4.5 42.1 1.0
HA G:ALA67 4.6 67.9 1.0
O G:VAL40 4.6 43.5 1.0
O1A G:GNP301 4.6 41.3 1.0
HG23 G:THR42 4.7 61.3 1.0
PA G:GNP301 4.7 40.8 1.0
O G:THR66 4.7 51.4 1.0
C G:ALA41 4.7 45.9 1.0
HG23 G:THR24 4.7 49.9 1.0
HZ3 G:LYS23 4.8 56.6 1.0
HZ1 G:LYS23 4.8 56.6 1.0
HE1 G:TYR39 4.8 51.5 1.0
HG22 G:THR24 4.8 49.9 1.0
CB G:LYS23 5.0 43.1 1.0

Magnesium binding site 5 out of 6 in 7mny

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Magnesium binding site 5 out of 6 in the Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 3 in Complex with Ran-Gppnhp


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 NUP358/RANBP2 Ran-Binding Domain 3 in Complex with Ran-Gppnhp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:69.7
occ:1.00
O2G I:GNP301 2.0 72.3 1.0
OG1 I:THR24 2.1 68.9 1.0
O I:HOH403 2.1 74.4 1.0
OG1 I:THR42 2.1 71.1 1.0
O2B I:GNP301 2.1 67.3 1.0
O I:HOH401 2.2 65.6 1.0
HB I:THR24 3.0 79.4 1.0
CB I:THR24 3.1 65.8 1.0
CB I:THR42 3.2 75.5 1.0
HB I:THR42 3.2 91.0 1.0
H I:THR42 3.3 84.6 1.0
PG I:GNP301 3.3 71.9 1.0
H I:THR24 3.3 79.7 1.0
PB I:GNP301 3.3 68.8 1.0
N3B I:GNP301 3.6 70.5 1.0
N I:THR42 3.8 70.2 1.0
N I:THR24 3.9 66.0 1.0
OD2 I:ASP65 3.9 72.6 1.0
O2A I:GNP301 3.9 62.0 1.0
HG21 I:THR24 4.0 76.7 1.0
HB2 I:LYS23 4.0 86.1 1.0
O3A I:GNP301 4.0 67.2 1.0
O3G I:GNP301 4.0 78.1 1.0
CA I:THR42 4.1 74.9 1.0
CA I:THR24 4.1 65.1 1.0
CG2 I:THR24 4.1 63.6 1.0
HG21 I:THR42 4.2 97.7 1.0
OD1 I:ASP65 4.2 78.4 1.0
HE2 I:LYS23 4.3 98.9 1.0
CG2 I:THR42 4.3 81.0 1.0
O1G I:GNP301 4.3 71.6 1.0
HA I:ALA41 4.3 80.8 1.0
PA I:GNP301 4.4 63.3 1.0
HA I:THR24 4.4 78.6 1.0
HA I:THR42 4.4 90.3 1.0
CG I:ASP65 4.4 77.8 1.0
HNB3 I:GNP301 4.5 85.0 1.0
HE1 I:TYR39 4.6 77.9 1.0
O I:VAL40 4.6 63.4 1.0
O1B I:GNP301 4.6 69.7 1.0
HG23 I:THR24 4.7 76.7 1.0
HZ1 I:LYS23 4.7 95.6 1.0
HG23 I:THR42 4.7 97.7 1.0
O1A I:GNP301 4.7 63.3 1.0
HZ3 I:LYS23 4.7 95.6 1.0
HA I:ALA67 4.7 111.5 1.0
C I:ALA41 4.7 70.6 1.0
O I:HOH404 4.7 63.3 1.0
HG22 I:THR24 4.8 76.7 1.0
CB I:LYS23 4.9 72.4 1.0
O I:THR66 4.9 86.8 1.0
C I:LYS23 5.0 67.0 1.0

Magnesium binding site 6 out of 6 in 7mny

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Magnesium binding site 6 out of 6 in the Crystal Structure of NUP358/RANBP2 Ran-Binding Domain 3 in Complex with Ran-Gppnhp


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 NUP358/RANBP2 Ran-Binding Domain 3 in Complex with Ran-Gppnhp within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:65.7
occ:1.00
OG1 K:THR24 2.0 64.7 1.0
O K:HOH401 2.0 64.5 1.0
O2G K:GNP301 2.1 69.2 1.0
OG1 K:THR42 2.1 72.5 1.0
O K:HOH402 2.1 70.3 1.0
O2B K:GNP301 2.1 64.0 1.0
HB K:THR42 3.1 93.3 1.0
H K:THR42 3.1 88.7 1.0
CB K:THR42 3.1 77.4 1.0
CB K:THR24 3.1 62.5 1.0
HB K:THR24 3.2 75.4 1.0
PG K:GNP301 3.2 67.7 1.0
H K:THR24 3.3 73.7 1.0
PB K:GNP301 3.3 62.6 1.0
N3B K:GNP301 3.5 63.8 1.0
N K:THR42 3.7 73.5 1.0
O2A K:GNP301 3.8 61.3 1.0
OD2 K:ASP65 3.9 70.8 1.0
N K:THR24 3.9 61.2 1.0
HG21 K:THR24 4.0 75.8 1.0
CA K:THR42 4.0 78.5 1.0
O3G K:GNP301 4.0 68.9 1.0
HB2 K:LYS23 4.1 78.9 1.0
CA K:THR24 4.1 60.5 1.0
CG2 K:THR24 4.2 62.8 1.0
HG21 K:THR42 4.2 100.7 1.0
HNB3 K:GNP301 4.2 77.0 1.0
OD1 K:ASP65 4.2 72.7 1.0
O3A K:GNP301 4.3 61.2 1.0
HE2 K:LYS23 4.3 86.7 1.0
CG2 K:THR42 4.3 83.5 1.0
O1G K:GNP301 4.3 67.4 1.0
HA K:THR42 4.3 94.7 1.0
HA K:ALA41 4.4 80.2 1.0
HA K:THR24 4.4 73.1 1.0
PA K:GNP301 4.4 60.2 1.0
CG K:ASP65 4.5 73.4 1.0
O1B K:GNP301 4.5 62.9 1.0
HA K:ALA67 4.5 98.4 1.0
O K:VAL40 4.6 63.3 1.0
O K:THR66 4.6 79.1 1.0
HG23 K:THR24 4.6 75.8 1.0
HZ2 K:LYS23 4.6 84.2 1.0
HE1 K:TYR39 4.6 74.3 1.0
HZ3 K:LYS23 4.6 84.2 1.0
O1A K:GNP301 4.7 60.2 1.0
C K:ALA41 4.7 72.0 1.0
HG23 K:THR42 4.8 100.7 1.0
HG22 K:THR24 4.9 75.8 1.0
NZ K:LYS23 4.9 69.8 1.0
HG22 K:THR42 5.0 100.7 1.0

Reference:

C.J.Bley, S.Nie, G.W.Mobbs, S.Petrovic, A.T.Gres, X.Liu, S.Mukherjee, S.Harvey, F.M.Huber, D.H.Lin, B.Brown, A.W.Tang, E.J.Rundlet, A.R.Correia, S.Chen, S.G.Regmi, T.A.Stevens, C.A.Jette, M.Dasso, A.Patke, A.F.Palazzo, A.A.Kossiakoff, A.Hoelz. Architecture of the Cytoplasmic Face of the Nuclear Pore. Science V. 376 M9129 2022.
ISSN: ESSN 1095-9203
PubMed: 35679405
DOI: 10.1126/SCIENCE.ABM9129
Page generated: Thu Oct 3 01:03:18 2024

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