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Magnesium in PDB 5d5v: Crystal Structure of Human HSF1 with Satellite III Repeat Dna

Protein crystallography data

The structure of Crystal Structure of Human HSF1 with Satellite III Repeat Dna, PDB code: 5d5v was solved by T.Neudegger, J.Verghese, M.Hayer-Hartl, F.U.Hartl, A.Bracher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 104.813, 112.678, 39.865, 90.00, 92.56, 90.00
R / Rfree (%) 19 / 23.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human HSF1 with Satellite III Repeat Dna (pdb code 5d5v). 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 Human HSF1 with Satellite III Repeat Dna, PDB code: 5d5v:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5d5v

Go back to Magnesium Binding Sites List in 5d5v
Magnesium binding site 1 out of 2 in the Crystal Structure of Human HSF1 with Satellite III Repeat Dna


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 Human HSF1 with Satellite III Repeat Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:31.9
occ:1.00
O B:ASP28 2.3 35.1 1.0
OD1 B:ASP32 2.3 34.9 1.0
O B:ILE35 2.3 25.4 1.0
OG1 B:THR31 2.4 27.1 1.0
O B:VAL26 2.6 30.1 1.0
O B:LEU25 2.9 31.2 1.0
N B:ASP32 3.3 33.4 1.0
C B:VAL26 3.4 32.5 1.0
C B:THR31 3.4 31.5 1.0
CG B:ASP32 3.4 38.9 1.0
C B:ASP28 3.4 37.3 1.0
CA B:ASP32 3.5 35.6 1.0
C B:ILE35 3.5 27.2 1.0
CB B:THR31 3.6 28.9 1.0
O B:THR31 3.8 30.3 1.0
CA B:THR31 3.9 30.9 1.0
CA B:VAL26 4.0 31.2 1.0
N B:ASP28 4.0 37.5 1.0
CB B:ASP32 4.0 36.1 1.0
C B:LEU25 4.0 32.6 1.0
CA B:CYS36 4.1 28.5 1.0
N B:THR31 4.1 32.4 1.0
CA B:ASP28 4.2 36.9 1.0
N B:CYS36 4.2 27.8 1.0
CG2 B:ILE35 4.3 25.1 1.0
C B:SER27 4.3 34.5 1.0
N B:SER27 4.4 33.6 1.0
O B:HOH311 4.4 27.4 1.0
OD2 B:ASP32 4.5 44.3 1.0
N B:PRO29 4.5 37.6 1.0
N B:VAL26 4.5 32.9 1.0
CB B:ASP28 4.5 37.1 1.0
CB B:CYS36 4.6 31.8 1.0
CA B:ILE35 4.7 27.3 1.0
CA B:PRO29 4.7 36.5 1.0
O B:SER27 4.7 35.5 1.0
CG2 B:THR31 4.7 27.7 1.0
C B:ASP32 4.8 37.0 1.0
CA B:SER27 4.9 33.9 1.0
C B:PRO29 4.9 35.4 1.0
CB B:ILE35 4.9 26.1 1.0
N B:ILE35 5.0 30.0 1.0

Magnesium binding site 2 out of 2 in 5d5v

Go back to Magnesium Binding Sites List in 5d5v
Magnesium binding site 2 out of 2 in the Crystal Structure of Human HSF1 with Satellite III Repeat Dna


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 Human HSF1 with Satellite III Repeat Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg201

b:25.4
occ:1.00
OD1 D:ASP32 2.4 31.8 1.0
O D:ILE35 2.4 24.1 1.0
O D:VAL26 2.4 25.5 1.0
OG1 D:THR31 2.5 32.6 1.0
O D:ASP28 2.5 29.2 1.0
O D:LEU25 2.8 30.8 1.0
C D:VAL26 3.2 26.4 1.0
C D:ASP28 3.5 30.9 1.0
CG D:ASP32 3.5 32.1 1.0
C D:ILE35 3.6 25.3 1.0
N D:ASP32 3.6 28.5 1.0
C D:THR31 3.7 29.8 1.0
CB D:THR31 3.7 31.0 1.0
CA D:ASP32 3.7 29.2 1.0
N D:ASP28 3.8 29.5 1.0
CA D:VAL26 3.8 26.9 1.0
C D:LEU25 3.9 28.8 1.0
O D:HOH314 4.0 16.7 1.0
O D:THR31 4.1 28.7 1.0
CA D:CYS36 4.1 27.3 1.0
CA D:ASP28 4.1 31.9 1.0
C D:SER27 4.1 27.2 1.0
N D:SER27 4.1 26.7 1.0
CA D:THR31 4.1 30.5 1.0
CB D:ASP32 4.2 29.8 1.0
N D:CYS36 4.2 25.5 1.0
N D:VAL26 4.3 27.2 1.0
CG2 D:ILE35 4.3 23.7 1.0
N D:THR31 4.3 31.5 1.0
CB D:ASP28 4.5 35.7 1.0
OD2 D:ASP32 4.5 32.3 1.0
CA D:SER27 4.5 28.0 1.0
CB D:CYS36 4.6 29.2 1.0
N D:PRO29 4.6 33.3 1.0
O D:SER27 4.6 25.6 1.0
CA D:ILE35 4.7 25.6 1.0
CG2 D:THR31 4.8 32.1 1.0
CA D:PRO29 4.9 33.6 1.0
CB D:ILE35 5.0 23.7 1.0

Reference:

T.Neudegger, J.Verghese, M.Hayer-Hartl, F.U.Hartl, A.Bracher. Structure of Human Heat-Shock Transcription Factor 1 in Complex with Dna. Nat.Struct.Mol.Biol. V. 23 140 2016.
ISSN: ESSN 1545-9985
PubMed: 26727489
DOI: 10.1038/NSMB.3149
Page generated: Mon Dec 14 20:10:12 2020

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