Atomistry » Magnesium » PDB 4um5-4uuw » 4um9
Atomistry »
  Magnesium »
    PDB 4um5-4uuw »
      4um9 »

Magnesium in PDB 4um9: Crystal Structure of Alpha V Beta 6 with Peptide

Protein crystallography data

The structure of Crystal Structure of Alpha V Beta 6 with Peptide, PDB code: 4um9 was solved by X.Dong, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 185.020, 168.090, 101.800, 90.00, 98.95, 90.00
R / Rfree (%) 22.2 / 26.6

Other elements in 4um9:

The structure of Crystal Structure of Alpha V Beta 6 with Peptide also contains other interesting chemical elements:

Calcium (Ca) 12 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Alpha V Beta 6 with Peptide (pdb code 4um9). 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 Alpha V Beta 6 with Peptide, PDB code: 4um9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4um9

Go back to Magnesium Binding Sites List in 4um9
Magnesium binding site 1 out of 2 in the Crystal Structure of Alpha V Beta 6 with Peptide


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 Alpha V Beta 6 with Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:62.0
occ:1.00
O B:HOH4014 2.1 44.6 1.0
O B:HOH4027 2.1 48.1 1.0
OE2 B:GLU223 2.1 52.5 1.0
O B:HOH4013 2.1 36.5 1.0
OG B:SER125 2.1 85.1 1.0
OD1 E:ASP243 2.2 58.8 1.0
CB B:SER125 2.2 50.5 1.0
CG E:ASP243 3.0 57.3 1.0
CD B:GLU223 3.3 38.2 1.0
OG B:SER127 3.6 72.7 1.0
OD2 E:ASP243 3.6 61.7 1.0
CA B:SER125 3.7 39.3 1.0
CG B:GLU223 3.9 32.6 1.0
CB E:ASP243 4.0 55.6 1.0
OD1 B:ASP123 4.2 67.6 1.0
OD2 B:ASP123 4.2 56.0 1.0
C B:SER125 4.2 42.7 1.0
OE1 B:GLU223 4.3 53.2 1.0
N B:ALA126 4.4 52.0 1.0
O B:HOH4015 4.4 68.3 1.0
CA E:ASP243 4.5 46.9 1.0
O B:THR221 4.5 48.2 1.0
ND2 B:ASN218 4.5 39.5 1.0
CG B:ASP123 4.6 63.9 1.0
N B:SER125 4.6 42.8 1.0
N B:SER127 4.6 84.3 1.0
CB B:SER127 4.7 58.3 1.0
OD1 B:ASP254 4.7 59.8 1.0
O E:ASP243 4.8 69.7 1.0
CB B:ALA255 4.9 28.0 1.0

Magnesium binding site 2 out of 2 in 4um9

Go back to Magnesium Binding Sites List in 4um9
Magnesium binding site 2 out of 2 in the Crystal Structure of Alpha V Beta 6 with Peptide


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 Alpha V Beta 6 with Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2001

b:81.6
occ:1.00
O D:HOH4005 2.1 91.3 1.0
O D:HOH4011 2.1 66.0 1.0
O D:HOH4004 2.1 49.8 1.0
OG D:SER125 2.1 80.4 1.0
OD1 F:ASP243 2.1 62.5 1.0
OE2 D:GLU223 2.1 56.3 1.0
CB D:SER125 2.4 61.2 1.0
CD D:GLU223 3.2 48.1 1.0
CG F:ASP243 3.4 44.8 1.0
OG D:SER127 3.4 76.2 1.0
OD2 D:ASP123 3.6 79.7 1.0
CG D:GLU223 3.7 47.8 1.0
CA D:SER125 3.9 49.2 1.0
OD2 F:ASP243 4.2 49.9 1.0
OD1 D:ASP254 4.3 76.8 1.0
OE1 D:GLU223 4.3 44.5 1.0
CB F:ASP243 4.3 38.8 1.0
CG D:ASP123 4.4 64.0 1.0
OD1 D:ASP123 4.4 69.8 1.0
CB D:ALA255 4.4 38.0 1.0
C D:SER125 4.5 49.6 1.0
O D:THR221 4.5 57.3 1.0
CB D:SER127 4.6 67.4 1.0
N D:SER125 4.7 52.5 1.0
N D:ALA126 4.7 53.6 1.0
CA F:ASP243 4.7 46.9 1.0
N D:SER127 4.8 76.2 1.0
O F:ASP243 5.0 68.5 1.0

Reference:

X.Dong, N.E.Hudson, C.Lu, T.A.Springer. Structural Determinants of Integrin Beta-Subunit Specificity For Latent Tgf-Beta Nat.Struct.Mol.Biol. 2014.
ISSN: ESSN 1545-9985
PubMed: 25383667
DOI: 10.1038/NSMB.2905
Page generated: Mon Dec 14 19:37:29 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy