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Magnesium in PDB 1jwy: Crystal Structure of the Dynamin A Gtpase Domain Complexed with Gdp, Determined As Myosin Fusion

Protein crystallography data

The structure of Crystal Structure of the Dynamin A Gtpase Domain Complexed with Gdp, Determined As Myosin Fusion, PDB code: 1jwy was solved by H.H.Niemann, M.L.W.Knetsch, A.Scherer, D.J.Manstein, F.J.Kull, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.40 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.550, 61.950, 181.070, 90.00, 94.52, 90.00
R / Rfree (%) 20.3 / 25.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Dynamin A Gtpase Domain Complexed with Gdp, Determined As Myosin Fusion (pdb code 1jwy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Dynamin A Gtpase Domain Complexed with Gdp, Determined As Myosin Fusion, PDB code: 1jwy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1jwy

Go back to Magnesium Binding Sites List in 1jwy
Magnesium binding site 1 out of 2 in the Crystal Structure of the Dynamin A Gtpase Domain Complexed with Gdp, Determined As Myosin Fusion


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 the Dynamin A Gtpase Domain Complexed with Gdp, Determined As Myosin Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1202

b:15.9
occ:1.00
O A:HOH1326 2.1 11.4 1.0
O A:HOH1409 2.2 11.5 1.0
O2B A:ADP1203 2.2 17.5 1.0
OG A:SER248 2.2 16.9 1.0
O A:HOH1372 2.3 12.0 1.0
OG1 A:THR197 2.3 23.6 1.0
CB A:THR197 3.1 21.5 1.0
PB A:ADP1203 3.3 18.4 1.0
CB A:SER248 3.3 17.8 1.0
O3B A:ADP1203 3.4 14.8 1.0
N A:THR197 3.8 23.9 1.0
N A:SER248 3.9 16.9 1.0
CA A:THR197 4.1 19.4 1.0
OD2 A:ASP465 4.1 25.2 1.0
O2A A:ADP1203 4.1 18.6 1.0
OD1 A:ASP465 4.1 25.5 1.0
O A:HOH1628 4.2 34.1 1.0
CA A:SER248 4.2 16.5 1.0
CG2 A:THR197 4.3 8.2 1.0
O3A A:ADP1203 4.3 15.7 1.0
O A:HOH1353 4.3 21.8 1.0
O A:HOH1386 4.3 31.5 1.0
O1B A:ADP1203 4.4 14.2 1.0
PA A:ADP1203 4.6 20.6 1.0
CG A:ASP465 4.6 26.3 1.0
O A:ASN246 4.7 19.7 1.0
CB A:LYS196 4.7 10.4 1.0
O1A A:ADP1203 4.7 14.5 1.0
CE A:LYS196 4.8 22.8 1.0
NZ A:LYS196 4.8 22.1 1.0
C A:LYS196 4.9 23.8 1.0
OD1 A:ASN244 4.9 20.3 1.0
C A:SER247 5.0 16.2 1.0

Magnesium binding site 2 out of 2 in 1jwy

Go back to Magnesium Binding Sites List in 1jwy
Magnesium binding site 2 out of 2 in the Crystal Structure of the Dynamin A Gtpase Domain Complexed with Gdp, Determined As Myosin Fusion


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 the Dynamin A Gtpase Domain Complexed with Gdp, Determined As Myosin Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1204

b:77.7
occ:1.00
OG A:SER823 2.8 71.5 1.0
O A:HOH1600 2.9 60.9 1.0
NZ A:LYS822 2.9 69.0 1.0
O3B A:GDP1205 3.2 84.0 1.0
O A:HOH1596 3.8 58.2 1.0
OD2 A:ASP922 3.9 68.8 1.0
N A:SER823 3.9 58.7 1.0
CB A:LYS822 4.0 68.5 1.0
CB A:SER823 4.1 62.7 1.0
CE A:LYS822 4.1 68.7 1.0
CA A:SER823 4.3 60.2 1.0
PB A:GDP1205 4.4 78.6 1.0
O A:HOH1334 4.4 58.9 1.0
O1B A:GDP1205 4.4 88.2 1.0
OD1 A:ASP922 4.5 69.0 1.0
CG A:ASP922 4.7 65.2 1.0
C A:LYS822 4.7 62.8 1.0
CG A:LYS822 4.9 71.0 1.0
CA A:LYS822 4.9 67.0 1.0
CD A:LYS822 5.0 68.7 1.0
O2B A:GDP1205 5.0 86.7 1.0

Reference:

H.H.Niemann, M.L.Knetsch, A.Scherer, D.J.Manstein, F.J.Kull. Crystal Structure of A Dynamin Gtpase Domain in Both Nucleotide-Free and Gdp-Bound Forms. Embo J. V. 20 5813 2001.
ISSN: ISSN 0261-4189
PubMed: 11689422
DOI: 10.1093/EMBOJ/20.21.5813
Page generated: Mon Dec 14 06:11:51 2020

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