Atomistry » Magnesium » PDB 5d2k-5dar » 5d5v
Atomistry »
  Magnesium »
    PDB 5d2k-5dar »
      5d5v »

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: Sun Sep 29 02:31:25 2024

Last articles

Cl in 3RVB
Cl in 3RV4
Cl in 3RVF
Cl in 3RUL
Cl in 3RT5
Cl in 3RUU
Cl in 3RUP
Cl in 3RUT
Cl in 3RUO
Cl in 3RUN
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy