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Magnesium in PDB 3d2f: Crystal Structure of A Complex of SSE1P and HSP70

Protein crystallography data

The structure of Crystal Structure of A Complex of SSE1P and HSP70, PDB code: 3d2f was solved by S.Polier, A.Bracher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 129.500, 141.902, 151.680, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 24.4

Other elements in 3d2f:

The structure of Crystal Structure of A Complex of SSE1P and HSP70 also contains other interesting chemical elements:

Potassium (K) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Complex of SSE1P and HSP70 (pdb code 3d2f). 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 A Complex of SSE1P and HSP70, PDB code: 3d2f:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3d2f

Go back to Magnesium Binding Sites List in 3d2f
Magnesium binding site 1 out of 6 in the Crystal Structure of A Complex of SSE1P and HSP70


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 A Complex of SSE1P and HSP70 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2001

b:40.6
occ:1.00
 O A:HOH3003 2.0 42.0 1.0
O A:HOH3005 2.1 39.4 1.0
O3G A:ATP1001 2.1 47.1 1.0
O A:HOH3004 2.1 40.3 1.0
O2B A:ATP1001 2.2 41.7 1.0
O A:HOH3006 2.2 39.1 1.0
PB A:ATP1001 3.4 42.8 1.0
PG A:ATP1001 3.4 43.9 1.0
O3B A:ATP1001 3.7 43.0 1.0
O2A A:ATP1001 4.0 45.2 1.0
OD2 A:ASP203 4.0 55.1 1.0
O3A A:ATP1001 4.1 40.3 1.0
OD1 A:ASP8 4.1 47.3 1.0
O1G A:ATP1001 4.1 45.6 1.0
O A:HOH3108 4.1 58.3 1.0
K A:K3001 4.2 44.1 1.0
O A:HOH3010 4.2 52.3 1.0
O A:HOH3189 4.3 56.4 1.0
O A:HOH3011 4.3 43.6 1.0
OD1 A:ASP203 4.4 52.3 1.0
OD2 A:ASP8 4.4 46.9 1.0
OD2 A:ASP174 4.4 47.4 1.0
CD1 A:ILE372 4.5 38.6 1.0
PA A:ATP1001 4.5 41.0 1.0
O2G A:ATP1001 4.6 46.2 1.0
CG A:ASP203 4.6 49.0 1.0
O1B A:ATP1001 4.6 41.4 1.0
NZ A:LYS69 4.6 45.8 1.0
CA A:GLY10 4.7 42.2 1.0
CG A:ASP8 4.7 46.2 1.0
O A:HOH3099 4.8 49.3 1.0
CA A:GLY205 4.9 41.1 1.0

Magnesium binding site 2 out of 6 in 3d2f

Go back to Magnesium Binding Sites List in 3d2f
Magnesium binding site 2 out of 6 in the Crystal Structure of A Complex of SSE1P and HSP70


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 A Complex of SSE1P and HSP70 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2002

b:42.3
occ:1.00
 O A:SER384 2.5 56.1 1.0
O A:ALA381 2.6 45.9 1.0
O A:LEU387 2.7 63.5 1.0
O A:ILE382 3.0 49.2 1.0
C A:ILE382 3.5 49.0 1.0
C A:SER384 3.6 56.5 1.0
N A:SER384 3.7 53.5 1.0
C A:ALA381 3.7 45.9 1.0
C A:LEU387 3.8 63.5 1.0
CA A:ILE382 3.9 48.6 1.0
CA A:SER384 4.0 55.3 1.0
CB A:SER384 4.1 55.4 1.0
N A:ILE382 4.2 47.4 1.0
N A:HIS383 4.4 49.7 1.0
C A:HIS383 4.5 51.8 1.0
N A:ARG388 4.6 62.9 1.0
N A:LEU387 4.6 63.3 1.0
CA A:ARG388 4.6 62.6 1.0
CA A:LEU387 4.7 63.6 1.0
N A:PRO385 4.8 58.0 1.0
N A:VAL389 4.8 61.7 1.0
OG A:SER384 4.9 56.7 1.0
CA A:HIS383 4.9 50.6 1.0

Magnesium binding site 3 out of 6 in 3d2f

Go back to Magnesium Binding Sites List in 3d2f
Magnesium binding site 3 out of 6 in the Crystal Structure of A Complex of SSE1P and HSP70


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 A Complex of SSE1P and HSP70 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:37.7
occ:1.00
 O B:GLY189 2.6 46.3 1.0
O B:HOH2084 2.6 30.6 1.0
O B:GLY191 2.7 47.8 1.0
OG1 B:THR188 2.9 45.0 1.0
O B:THR188 3.0 45.1 1.0
O B:LYS190 3.2 46.5 1.0
C B:GLY189 3.5 46.0 1.0
C B:THR188 3.6 45.2 1.0
C B:LYS190 3.7 46.7 1.0
C B:GLY191 3.7 47.5 1.0
CB B:THR188 3.9 45.0 1.0
CG B:ARG193 4.0 45.0 1.0
N B:GLY189 4.2 45.3 1.0
N B:GLY191 4.2 46.9 1.0
CA B:GLY191 4.2 47.2 1.0
N B:LYS190 4.3 46.3 1.0
CA B:THR188 4.3 45.0 1.0
CA B:GLY189 4.4 45.6 1.0
CA B:LYS190 4.5 46.5 1.0
O B:ILE212 4.7 47.1 1.0
O B:HOH2071 4.8 41.4 1.0
N B:GLU192 4.9 47.2 1.0
CD B:ARG193 4.9 45.5 1.0
N B:ARG193 5.0 45.7 1.0
N B:ASP214 5.0 49.4 1.0

Magnesium binding site 4 out of 6 in 3d2f

Go back to Magnesium Binding Sites List in 3d2f
Magnesium binding site 4 out of 6 in the Crystal Structure of A Complex of SSE1P and HSP70


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 A Complex of SSE1P and HSP70 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2001

b:40.7
occ:1.00
 O C:HOH3006 2.0 37.1 1.0
O1G C:ATP1001 2.0 41.8 1.0
O2B C:ATP1001 2.0 42.8 1.0
O C:HOH3004 2.0 38.3 1.0
O C:HOH3005 2.1 38.3 1.0
O C:HOH3003 2.1 36.6 1.0
PG C:ATP1001 3.3 43.3 1.0
PB C:ATP1001 3.3 41.5 1.0
O3B C:ATP1001 3.6 41.1 1.0
O2G C:ATP1001 3.8 43.8 1.0
O2A C:ATP1001 4.0 44.7 1.0
O3A C:ATP1001 4.0 42.5 1.0
OD1 C:ASP8 4.0 41.0 1.0
K C:K3001 4.1 45.8 1.0
O C:HOH3107 4.2 50.6 1.0
O C:HOH3010 4.3 37.5 1.0
OD2 C:ASP8 4.3 41.0 1.0
OD2 C:ASP203 4.3 51.4 1.0
O C:HOH3011 4.3 46.7 1.0
CA C:GLY10 4.5 43.4 1.0
O3G C:ATP1001 4.5 41.3 1.0
PA C:ATP1001 4.5 42.4 1.0
O1B C:ATP1001 4.5 42.6 1.0
OD1 C:ASP203 4.6 48.7 1.0
OD2 C:ASP174 4.6 47.2 1.0
CG C:ASP8 4.6 42.0 1.0
CD1 C:ILE372 4.7 41.0 1.0
NZ C:LYS69 4.7 44.0 1.0
O C:HOH3098 4.9 43.0 1.0
CG C:ASP203 4.9 47.4 1.0
CA C:GLY205 5.0 42.3 1.0

Magnesium binding site 5 out of 6 in 3d2f

Go back to Magnesium Binding Sites List in 3d2f
Magnesium binding site 5 out of 6 in the Crystal Structure of A Complex of SSE1P and HSP70


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 A Complex of SSE1P and HSP70 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2002

b:29.2
occ:1.00
 O C:LEU387 2.6 51.7 1.0
O C:SER384 2.7 48.6 1.0
O C:ALA381 2.7 43.9 1.0
O C:ILE382 3.0 46.2 1.0
C C:ILE382 3.5 46.0 1.0
C C:SER384 3.8 48.7 1.0
CA C:ILE382 3.8 45.4 1.0
C C:ALA381 3.8 43.8 1.0
C C:LEU387 3.8 51.8 1.0
N C:SER384 3.9 47.5 1.0
CA C:SER384 4.2 47.8 1.0
CB C:SER384 4.2 47.8 1.0
N C:ILE382 4.3 44.4 1.0
N C:HIS383 4.4 46.7 1.0
CA C:ARG388 4.5 52.8 1.0
C C:HIS383 4.6 47.5 1.0
N C:ARG388 4.6 52.0 1.0
CA C:LEU387 4.9 51.6 1.0
N C:VAL389 4.9 52.8 1.0
N C:LEU387 4.9 51.5 1.0
N C:PRO385 5.0 49.4 1.0
CA C:HIS383 5.0 47.4 1.0

Magnesium binding site 6 out of 6 in 3d2f

Go back to Magnesium Binding Sites List in 3d2f
Magnesium binding site 6 out of 6 in the Crystal Structure of A Complex of SSE1P and HSP70


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 A Complex of SSE1P and HSP70 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2001

b:33.0
occ:1.00
 O D:GLY191 2.4 45.1 1.0
O D:GLY189 2.7 42.5 1.0
OG1 D:THR188 2.9 39.2 1.0
O D:LYS190 2.9 44.6 1.0
O D:THR188 3.4 41.0 1.0
C D:GLY191 3.5 45.3 1.0
C D:LYS190 3.5 44.1 1.0
C D:GLY189 3.6 43.0 1.0
C D:THR188 3.8 41.1 1.0
CB D:THR188 3.9 40.3 1.0
CA D:GLY191 3.9 44.8 1.0
N D:GLY191 3.9 44.5 1.0
N D:GLY189 4.3 41.8 1.0
N D:LYS190 4.3 43.3 1.0
CA D:LYS190 4.4 43.9 1.0
CA D:THR188 4.5 40.1 1.0
CA D:GLY189 4.5 42.6 1.0
N D:GLU192 4.6 45.6 1.0
CD D:ARG193 4.7 46.5 1.0
CG D:ARG193 5.0 45.4 1.0

Reference:

S.Polier, Z.Dragovic, F.U.Hartl, A.Bracher. Structural Basis For the Cooperation of HSP70 and HSP110 Chaperones in Protein Folding. Cell(Cambridge,Mass.) V. 133 1068 2008.
ISSN: ISSN 0092-8674
PubMed: 18555782
DOI: 10.1016/J.CELL.2008.05.022
Page generated: Wed Aug 14 12:19:59 2024

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