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Magnesium in PDB 3i3s: Crystal Structure of H-Ras with THR50 Replaced By Isoleucine

Protein crystallography data

The structure of Crystal Structure of H-Ras with THR50 Replaced By Isoleucine, PDB code: 3i3s was solved by L.Gremer, R.Dvorsky, T.Merbitz-Zahradnik, A.Wittinghofer, M.R.Ahmadian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.86 / 1.36
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 89.210, 89.210, 134.640, 90.00, 90.00, 120.00
R / Rfree (%) 15.9 / 17.8

Other elements in 3i3s:

The structure of Crystal Structure of H-Ras with THR50 Replaced By Isoleucine also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of H-Ras with THR50 Replaced By Isoleucine (pdb code 3i3s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of H-Ras with THR50 Replaced By Isoleucine, PDB code: 3i3s:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3i3s

Go back to Magnesium Binding Sites List in 3i3s
Magnesium binding site 1 out of 3 in the Crystal Structure of H-Ras with THR50 Replaced By Isoleucine


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 H-Ras with THR50 Replaced By Isoleucine within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg168

b:13.6
occ:1.00
O2G R:GNP167 2.0 15.0 1.0
O R:HOH172 2.1 15.3 1.0
O2B R:GNP167 2.1 14.2 1.0
OG1 R:THR35 2.1 14.7 1.0
OG R:SER17 2.1 14.1 1.0
O R:HOH173 2.1 15.1 1.0
CB R:THR35 3.1 14.3 1.0
CB R:SER17 3.2 14.3 1.0
PG R:GNP167 3.2 14.3 1.0
PB R:GNP167 3.2 13.6 1.0
N3B R:GNP167 3.4 14.1 1.0
N R:THR35 3.8 14.9 1.0
N R:SER17 3.9 13.8 1.0
O3G R:GNP167 4.1 15.4 1.0
OD2 R:ASP57 4.1 17.5 1.0
CA R:SER17 4.1 13.7 1.0
CA R:THR35 4.1 15.1 1.0
O2A R:GNP167 4.1 14.5 1.0
OD1 R:ASP57 4.2 16.3 1.0
O R:HOH189 4.2 17.0 1.0
CG2 R:THR35 4.2 16.0 1.0
O3A R:GNP167 4.3 13.5 1.0
O1B R:GNP167 4.3 13.9 1.0
O1G R:GNP167 4.4 14.8 1.0
O R:ASP33 4.5 14.0 1.0
CG R:ASP57 4.5 15.2 1.0
O R:THR58 4.5 15.4 1.0
PA R:GNP167 4.5 13.8 1.0
O1A R:GNP167 4.7 14.6 1.0
C R:PRO34 4.8 15.4 1.0
CB R:LYS16 4.9 13.7 1.0
C R:LYS16 5.0 13.8 1.0
CE R:LYS16 5.0 15.5 1.0

Magnesium binding site 2 out of 3 in 3i3s

Go back to Magnesium Binding Sites List in 3i3s
Magnesium binding site 2 out of 3 in the Crystal Structure of H-Ras with THR50 Replaced By Isoleucine


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 H-Ras with THR50 Replaced By Isoleucine within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg170

b:19.9
occ:0.33
O R:HOH234 2.0 25.5 1.0
O R:HOH218 2.4 22.0 1.0
OE1 R:GLN129 3.9 22.1 0.5
O R:THR124 4.2 17.1 1.0
OE1 R:GLN129 4.3 19.4 0.5
O R:HOH261 4.5 22.0 1.0
NE2 R:GLN129 4.5 20.5 0.5
CD R:GLN129 4.6 19.4 0.5
CD R:GLN129 4.9 18.5 0.5
NE2 R:GLN129 5.0 19.1 0.5

Magnesium binding site 3 out of 3 in 3i3s

Go back to Magnesium Binding Sites List in 3i3s
Magnesium binding site 3 out of 3 in the Crystal Structure of H-Ras with THR50 Replaced By Isoleucine


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 H-Ras with THR50 Replaced By Isoleucine within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg171

b:22.4
occ:0.50
O R:HOH271 1.8 25.9 0.5
OD1 R:ASP105 2.0 22.2 0.5
O R:ARG102 2.2 21.0 0.5
O R:ARG102 2.2 21.3 0.5
O R:HOH273 2.3 22.4 0.5
OD2 R:ASP105 2.5 23.5 0.5
CG R:ASP105 2.5 21.5 0.5
C R:ARG102 3.4 20.9 0.5
C R:ARG102 3.4 20.8 0.5
CB R:ASP105 3.9 21.3 0.5
CB R:ASP105 3.9 21.3 0.5
CA R:ARG102 4.2 20.9 0.5
CA R:ARG102 4.2 21.3 0.5
N R:ASP105 4.3 20.7 1.0
CG R:ARG102 4.3 22.2 0.5
CA R:ASP105 4.3 21.2 0.5
CG R:ASP105 4.3 21.7 0.5
CA R:ASP105 4.3 21.2 0.5
N R:VAL103 4.4 20.1 1.0
OD1 R:ASP105 4.4 22.4 0.5
CA R:VAL103 4.5 20.8 1.0
C R:VAL103 4.5 20.4 1.0
O R:VAL103 4.6 20.6 1.0
CB R:ARG102 4.7 21.2 0.5
CB R:ARG102 4.9 21.6 0.5
NH1 R:ARG73 4.9 31.5 1.0

Reference:

I.C.Cirstea, K.Kutsche, R.Dvorsky, L.Gremer, C.Carta, D.Horn, A.E.Roberts, F.Lepri, T.Merbitz-Zahradnik, R.Konig, C.P.Kratz, F.Pantaleoni, M.L.Dentici, V.A.Joshi, R.S.Kucherlapati, L.Mazzanti, S.Mundlos, M.A.Patton, M.C.Silengo, C.Rossi, G.Zampino, C.Digilio, L.Stuppia, E.Seemanova, L.A.Pennacchio, B.D.Gelb, B.Dallapiccola, A.Wittinghofer, M.R.Ahmadian, M.Tartaglia, M.Zenker. A Restricted Spectrum of Nras Mutations Causes Noonan Syndrome. Nat.Genet. V. 42 27 2010.
ISSN: ISSN 1061-4036
PubMed: 19966803
DOI: 10.1038/NG.497
Page generated: Mon Dec 14 08:15:29 2020

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