Magnesium in PDB 6om1: Crystal Structure of An Atypical Integrin

Protein crystallography data

The structure of Crystal Structure of An Atypical Integrin, PDB code: 6om1 was solved by J.C.Wang, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.07 / 2.66
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 144.240, 55.070, 175.070, 90.37, 107.00, 90.01
R / Rfree (%) 24.8 / 28

Other elements in 6om1:

The structure of Crystal Structure of An Atypical Integrin also contains other interesting chemical elements:

Calcium (Ca) 20 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of An Atypical Integrin (pdb code 6om1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of An Atypical Integrin, PDB code: 6om1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6om1

Go back to Magnesium Binding Sites List in 6om1
Magnesium binding site 1 out of 4 in the Crystal Structure of An Atypical Integrin


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 An Atypical Integrin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:57.9
occ:1.00
HG B:SER114 1.3 0.4 1.0
O1S B:MES2014 2.0 73.3 1.0
OE1 B:GLU212 2.1 0.8 1.0
OG B:SER114 2.1 0.3 1.0
O B:HOH2105 2.2 52.5 1.0
O B:HOH2109 2.3 72.3 1.0
HG B:SER116 2.8 0.0 1.0
HB2 B:SER114 2.9 0.3 1.0
CB B:SER114 3.0 0.6 1.0
HB3 B:SER114 3.2 0.3 1.0
CD B:GLU212 3.2 0.5 1.0
OG B:SER116 3.3 0.3 1.0
HG3 B:GLU212 3.4 0.6 1.0
S B:MES2014 3.5 89.3 1.0
H B:SER116 3.7 0.3 1.0
CG B:GLU212 3.7 0.1 1.0
OD2 B:ASP112 3.8 99.0 1.0
HG2 B:GLU212 3.8 0.6 1.0
HB3 B:SER116 4.0 0.6 1.0
O B:THR210 4.2 82.7 1.0
C8 B:MES2014 4.2 98.6 1.0
OD1 B:ASP243 4.2 0.1 1.0
CB B:SER116 4.2 0.1 1.0
H B:ALA115 4.2 0.0 1.0
OE2 B:GLU212 4.3 0.6 1.0
O3S B:MES2014 4.3 92.9 1.0
CA B:SER114 4.4 0.3 1.0
HD21 B:ASN207 4.4 0.8 1.0
O2S B:MES2014 4.4 90.6 1.0
N B:SER116 4.5 0.5 1.0
HG3 B:GLN244 4.5 0.5 1.0
N B:ALA115 4.6 0.1 1.0
HB2 B:GLN244 4.6 0.8 1.0
CG B:ASP112 4.6 0.7 1.0
HG2 B:MET117 4.6 0.9 1.0
OD1 B:ASP112 4.7 0.1 1.0
C B:SER114 4.7 0.4 1.0
OD2 B:ASP243 4.7 0.2 1.0
H B:SER114 4.8 0.5 1.0
C7 B:MES2014 4.8 0.8 1.0
CG B:ASP243 4.9 0.4 1.0
HA B:THR210 4.9 96.7 1.0
HA B:SER114 4.9 0.5 1.0
HB2 B:SER116 5.0 0.6 1.0
HG2 B:GLN244 5.0 0.5 1.0

Magnesium binding site 2 out of 4 in 6om1

Go back to Magnesium Binding Sites List in 6om1
Magnesium binding site 2 out of 4 in the Crystal Structure of An Atypical Integrin


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 An Atypical Integrin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:66.1
occ:1.00
HG D:SER114 1.3 0.5 1.0
OE1 D:GLU212 2.1 0.4 1.0
OG D:SER114 2.1 0.2 1.0
O2S D:MES507 2.1 82.3 1.0
O D:HOH603 2.1 75.4 1.0
O D:HOH602 2.2 60.9 1.0
HB2 D:SER114 2.5 0.5 1.0
CB D:SER114 2.7 0.9 1.0
HG D:SER116 2.7 0.7 1.0
HB3 D:SER114 2.9 0.5 1.0
CD D:GLU212 3.2 0.8 1.0
O1S D:MES507 3.3 91.2 1.0
OG D:SER116 3.3 0.9 1.0
S D:MES507 3.3 87.3 1.0
HG3 D:GLU212 3.6 0.1 1.0
H D:SER116 3.7 0.1 1.0
OD2 D:ASP112 3.8 95.5 1.0
CG D:GLU212 3.9 0.7 1.0
OD1 D:ASP243 4.1 0.5 1.0
HD21 D:ASN207 4.1 0.1 1.0
HG2 D:GLU212 4.1 0.1 1.0
H D:ALA115 4.1 0.2 1.0
CA D:SER114 4.1 0.3 1.0
O3S D:MES507 4.2 88.0 1.0
OE2 D:GLU212 4.2 0.4 1.0
HB3 D:SER116 4.3 0.0 1.0
CB D:SER116 4.4 0.5 1.0
O D:THR210 4.4 82.7 1.0
N D:ALA115 4.4 0.5 1.0
N D:SER116 4.5 0.1 1.0
C D:SER114 4.5 0.2 1.0
HG2 D:MET117 4.5 0.8 1.0
OD1 D:ASP112 4.6 97.4 1.0
C7 D:MES507 4.6 89.1 1.0
CG D:ASP112 4.6 96.3 1.0
H D:SER114 4.6 1.0 1.0
OD2 D:ASP243 4.6 0.3 1.0
HG3 D:GLN244 4.6 1.0 1.0
HA D:SER114 4.7 0.8 1.0
HB2 D:GLN244 4.7 0.4 1.0
C8 D:MES507 4.7 86.9 1.0
CG D:ASP243 4.8 0.6 1.0
ND2 D:ASN207 4.8 98.9 1.0
N D:SER114 4.9 0.1 1.0

Magnesium binding site 3 out of 4 in 6om1

Go back to Magnesium Binding Sites List in 6om1
Magnesium binding site 3 out of 4 in the Crystal Structure of An Atypical Integrin


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 An Atypical Integrin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg505

b:82.1
occ:1.00
HG F:SER114 1.3 0.0 1.0
O F:HOH601 2.1 99.7 1.0
OG F:SER114 2.1 0.5 1.0
O3S F:MES510 2.1 89.2 1.0
O F:HOH604 2.1 87.7 1.0
OE1 F:GLU212 2.1 0.6 1.0
HG F:SER116 2.9 0.9 1.0
CB F:SER114 3.0 0.3 1.0
HB2 F:SER114 3.0 0.8 1.0
CD F:GLU212 3.1 0.8 1.0
HB3 F:SER114 3.2 0.8 1.0
HG3 F:GLU212 3.3 1.0 1.0
OG F:SER116 3.4 0.4 1.0
OD2 F:ASP112 3.5 97.6 1.0
S F:MES510 3.6 90.5 1.0
CG F:GLU212 3.6 0.1 1.0
HD21 F:ASN207 3.8 0.9 1.0
HG2 F:GLU212 3.8 1.0 1.0
OE2 F:GLU212 4.0 0.6 1.0
H F:SER116 4.0 1.0 1.0
OD1 F:ASP243 4.1 0.6 1.0
O2S F:MES510 4.2 99.5 1.0
O1S F:MES510 4.2 99.7 1.0
OD1 F:ASP112 4.2 98.8 1.0
O F:THR210 4.3 95.7 1.0
CG F:ASP112 4.3 96.4 1.0
CA F:SER114 4.4 0.9 1.0
HB2 F:GLN244 4.4 0.8 1.0
HB3 F:SER116 4.5 0.5 1.0
CB F:SER116 4.5 0.1 1.0
HG2 F:MET117 4.5 0.4 1.0
ND2 F:ASN207 4.6 0.0 1.0
H F:SER114 4.6 0.2 1.0
H F:ALA115 4.6 0.3 1.0
C8 F:MES510 4.7 96.4 1.0
C F:SER114 4.8 0.2 1.0
N F:SER116 4.8 0.8 1.0
HD22 F:ASN207 4.8 0.9 1.0
HG3 F:GLN244 4.8 0.9 1.0
N F:ALA115 4.9 0.2 1.0
C7 F:MES510 4.9 97.2 1.0
HA F:SER114 5.0 0.7 1.0

Magnesium binding site 4 out of 4 in 6om1

Go back to Magnesium Binding Sites List in 6om1
Magnesium binding site 4 out of 4 in the Crystal Structure of An Atypical Integrin


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 An Atypical Integrin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg505

b:60.2
occ:1.00
HG H:SER114 1.3 0.1 1.0
O3S H:MES510 2.0 75.8 1.0
O H:HOH601 2.1 56.8 1.0
OG H:SER114 2.1 0.4 1.0
OE1 H:GLU212 2.1 0.3 1.0
O H:HOH607 2.2 62.1 1.0
HG H:SER116 2.8 0.3 1.0
HB2 H:SER114 3.0 0.1 1.0
CB H:SER114 3.0 0.6 1.0
CD H:GLU212 3.1 0.4 1.0
HG3 H:GLU212 3.2 1.0 1.0
HB3 H:SER114 3.2 0.1 1.0
OG H:SER116 3.3 0.9 1.0
OD2 H:ASP112 3.4 90.5 1.0
S H:MES510 3.5 82.8 1.0
CG H:GLU212 3.5 0.1 1.0
OD1 H:ASP243 3.6 0.3 1.0
HG2 H:GLU212 3.6 1.0 1.0
HD21 H:ASN207 3.8 0.4 1.0
H H:SER116 4.0 0.3 1.0
O H:THR210 4.1 95.1 1.0
OD2 H:ASP243 4.1 0.7 1.0
OE2 H:GLU212 4.1 0.0 1.0
O1S H:MES510 4.2 85.0 1.0
CG H:ASP112 4.3 91.4 1.0
OD1 H:ASP112 4.3 93.2 1.0
HG2 H:MET117 4.3 0.5 1.0
CG H:ASP243 4.3 0.8 1.0
O2S H:MES510 4.3 89.3 1.0
HB3 H:SER116 4.3 0.9 1.0
C8 H:MES510 4.4 85.5 1.0
CA H:SER114 4.4 1.0 1.0
CB H:SER116 4.4 0.9 1.0
HB2 H:GLN244 4.5 0.6 1.0
HG3 H:GLN244 4.6 0.5 1.0
H H:ALA115 4.6 0.4 1.0
ND2 H:ASN207 4.6 0.1 1.0
H H:SER114 4.7 0.6 1.0
C H:SER114 4.7 0.1 1.0
N H:SER116 4.7 0.5 1.0
N H:ALA115 4.8 0.5 1.0
HD22 H:ASN207 4.9 0.4 1.0
HA H:THR210 5.0 0.9 1.0
HG2 H:GLN244 5.0 0.5 1.0
HG3 H:MET117 5.0 0.5 1.0

Reference:

J.C.Wang, R.E.Iacob, J.R.Engen, T.A.Springer. Crystal Structure of Atypical Integrin Alphav BETA8 Nat Commun 2019.
ISSN: ESSN 2041-1723
Page generated: Mon Dec 14 23:43:50 2020

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