Magnesium in PDB 6om2: Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide
Protein crystallography data
The structure of Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide, PDB code: 6om2
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)
|
47.43 /
2.77
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
161.190,
53.850,
176.620,
90.00,
111.47,
90.00
|
R / Rfree (%)
|
25.1 /
28.2
|
Other elements in 6om2:
The structure of Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide
(pdb code 6om2). 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 Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide, PDB code: 6om2:
Jump to Magnesium binding site number:
1;
2;
Magnesium binding site 1 out
of 2 in 6om2
Go back to
Magnesium Binding Sites List in 6om2
Magnesium binding site 1 out
of 2 in the Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand 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 Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg2001
b:0.3
occ:1.00
|
OE2
|
B:GLU212
|
2.1
|
89.0
|
1.0
|
OD1
|
E:ASP217
|
2.1
|
1.0
|
1.0
|
OG
|
B:SER114
|
2.1
|
0.1
|
1.0
|
OG
|
B:SER116
|
2.1
|
0.1
|
1.0
|
O
|
B:HOH3203
|
2.1
|
0.8
|
1.0
|
O
|
B:HOH3206
|
2.2
|
91.2
|
1.0
|
HG
|
B:SER116
|
2.5
|
0.9
|
1.0
|
HB2
|
B:SER114
|
2.6
|
0.9
|
1.0
|
HG
|
B:SER114
|
2.8
|
0.5
|
1.0
|
CB
|
B:SER114
|
2.8
|
0.3
|
1.0
|
H
|
B:SER116
|
3.0
|
0.3
|
1.0
|
CD
|
B:GLU212
|
3.2
|
87.0
|
1.0
|
CG
|
E:ASP217
|
3.2
|
0.6
|
1.0
|
HB3
|
B:SER114
|
3.2
|
0.9
|
1.0
|
CB
|
B:SER116
|
3.3
|
1.0
|
1.0
|
HG3
|
B:GLU212
|
3.4
|
0.2
|
1.0
|
HB3
|
B:SER116
|
3.4
|
0.2
|
1.0
|
CG
|
B:GLU212
|
3.7
|
87.7
|
1.0
|
N
|
B:SER116
|
3.8
|
0.4
|
1.0
|
HG2
|
B:GLU212
|
3.9
|
0.2
|
1.0
|
OD2
|
B:ASP112
|
3.9
|
0.8
|
1.0
|
HB2
|
B:SER116
|
4.0
|
0.2
|
1.0
|
CB
|
E:ASP217
|
4.0
|
0.3
|
1.0
|
OD2
|
E:ASP217
|
4.1
|
0.1
|
1.0
|
HD21
|
B:ASN207
|
4.1
|
0.5
|
1.0
|
CA
|
B:SER116
|
4.1
|
0.1
|
1.0
|
HG2
|
B:MET117
|
4.1
|
1.0
|
1.0
|
CA
|
B:SER114
|
4.1
|
0.0
|
1.0
|
H
|
B:ALA115
|
4.2
|
0.9
|
1.0
|
HG3
|
B:GLN244
|
4.2
|
0.7
|
1.0
|
OE1
|
B:GLU212
|
4.2
|
84.9
|
1.0
|
OD1
|
B:ASP243
|
4.2
|
84.3
|
1.0
|
O
|
B:THR210
|
4.2
|
94.2
|
1.0
|
HB2
|
B:GLN244
|
4.3
|
0.4
|
1.0
|
N
|
B:ALA115
|
4.3
|
0.3
|
1.0
|
C
|
B:SER114
|
4.3
|
0.0
|
1.0
|
CA
|
E:ASP217
|
4.4
|
0.6
|
1.0
|
H
|
B:MET117
|
4.4
|
0.1
|
1.0
|
H
|
B:SER114
|
4.7
|
0.1
|
1.0
|
HA
|
B:SER114
|
4.7
|
0.6
|
1.0
|
CG
|
B:ASP112
|
4.8
|
0.2
|
1.0
|
OD1
|
B:ASP112
|
4.8
|
0.3
|
1.0
|
ND2
|
B:ASN207
|
4.8
|
90.4
|
1.0
|
N
|
B:MET117
|
4.8
|
0.8
|
1.0
|
C
|
B:SER116
|
4.8
|
0.1
|
1.0
|
HA
|
B:THR210
|
4.9
|
0.8
|
1.0
|
C
|
B:ALA115
|
4.9
|
0.4
|
1.0
|
CG
|
B:GLN244
|
4.9
|
94.8
|
1.0
|
HA
|
B:SER116
|
4.9
|
0.9
|
1.0
|
HD22
|
B:ASN207
|
5.0
|
0.5
|
1.0
|
N
|
B:SER114
|
5.0
|
0.4
|
1.0
|
O
|
E:ASP217
|
5.0
|
1.0
|
1.0
|
|
Magnesium binding site 2 out
of 2 in 6om2
Go back to
Magnesium Binding Sites List in 6om2
Magnesium binding site 2 out
of 2 in the Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand 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 Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg3208
b:0.6
occ:1.00
|
OD1
|
F:ASP217
|
2.1
|
0.9
|
1.0
|
HG
|
D:SER114
|
2.1
|
0.6
|
1.0
|
OE2
|
D:GLU212
|
2.1
|
0.4
|
1.0
|
OG
|
D:SER114
|
2.1
|
0.5
|
1.0
|
OG
|
D:SER116
|
2.1
|
0.3
|
1.0
|
O
|
D:HOH3303
|
2.2
|
0.1
|
1.0
|
O
|
D:HOH3309
|
2.3
|
85.4
|
1.0
|
HG
|
D:SER116
|
2.5
|
0.1
|
1.0
|
HB2
|
D:SER114
|
2.7
|
0.8
|
1.0
|
CB
|
D:SER114
|
2.9
|
99.0
|
1.0
|
H
|
D:SER116
|
3.2
|
0.3
|
1.0
|
CD
|
D:GLU212
|
3.2
|
0.2
|
1.0
|
CG
|
F:ASP217
|
3.2
|
0.3
|
1.0
|
HB3
|
D:SER114
|
3.3
|
0.8
|
1.0
|
HG3
|
D:GLU212
|
3.3
|
0.2
|
1.0
|
CB
|
D:SER116
|
3.4
|
0.6
|
1.0
|
HB3
|
D:SER116
|
3.5
|
0.9
|
1.0
|
CG
|
D:GLU212
|
3.7
|
0.7
|
1.0
|
OD2
|
D:ASP112
|
3.8
|
0.4
|
1.0
|
HG2
|
D:GLU212
|
3.8
|
0.2
|
1.0
|
N
|
D:SER116
|
3.9
|
1.0
|
1.0
|
OD1
|
D:ASP243
|
4.0
|
95.3
|
1.0
|
HB2
|
D:SER116
|
4.0
|
0.9
|
1.0
|
OD2
|
F:ASP217
|
4.0
|
0.2
|
1.0
|
CB
|
F:ASP217
|
4.1
|
0.7
|
1.0
|
HG3
|
D:GLN244
|
4.2
|
0.8
|
1.0
|
HB2
|
D:GLN244
|
4.2
|
0.8
|
1.0
|
CA
|
D:SER116
|
4.2
|
0.2
|
1.0
|
CA
|
D:SER114
|
4.2
|
97.3
|
1.0
|
OE1
|
D:GLU212
|
4.3
|
0.9
|
1.0
|
HD21
|
D:ASN207
|
4.3
|
0.6
|
1.0
|
O
|
D:THR210
|
4.3
|
85.1
|
1.0
|
HG2
|
D:MET117
|
4.3
|
0.0
|
1.0
|
H
|
D:ALA115
|
4.3
|
0.4
|
1.0
|
H
|
D:MET117
|
4.5
|
0.9
|
1.0
|
C
|
D:SER114
|
4.5
|
98.8
|
1.0
|
N
|
D:ALA115
|
4.5
|
0.0
|
1.0
|
CA
|
F:ASP217
|
4.6
|
0.0
|
1.0
|
CG
|
D:ASP112
|
4.7
|
0.6
|
1.0
|
H
|
D:SER114
|
4.7
|
0.7
|
1.0
|
OD1
|
D:ASP112
|
4.8
|
0.5
|
1.0
|
OD2
|
D:ASP243
|
4.8
|
99.2
|
1.0
|
CG
|
D:ASP243
|
4.8
|
97.5
|
1.0
|
CG
|
D:GLN244
|
4.8
|
0.1
|
1.0
|
HA
|
D:SER114
|
4.8
|
0.8
|
1.0
|
N
|
D:MET117
|
4.9
|
98.3
|
1.0
|
C
|
D:SER116
|
4.9
|
0.5
|
1.0
|
CB
|
D:GLN244
|
4.9
|
99.0
|
1.0
|
HG2
|
D:GLN244
|
4.9
|
0.8
|
1.0
|
HA
|
D:THR210
|
5.0
|
1.0
|
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: Tue Oct 1 13:26:14 2024
|