Atomistry » Magnesium » PDB 5y4n-5ylu » 5yjg
Atomistry »
  Magnesium »
    PDB 5y4n-5ylu »
      5yjg »

Magnesium in PDB 5yjg: Structural Insights Into Periostin Functions

Protein crystallography data

The structure of Structural Insights Into Periostin Functions, PDB code: 5yjg was solved by H.Liu, J.Liu, F.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.14 / 2.40
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 105.605, 105.605, 331.225, 90.00, 90.00, 120.00
R / Rfree (%) 21.2 / 24.8

Other elements in 5yjg:

The structure of Structural Insights Into Periostin Functions also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Calcium (Ca) 6 atoms
Chlorine (Cl) 16 atoms
Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structural Insights Into Periostin Functions (pdb code 5yjg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structural Insights Into Periostin Functions, PDB code: 5yjg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5yjg

Go back to Magnesium Binding Sites List in 5yjg
Magnesium binding site 1 out of 8 in the Structural Insights Into Periostin Functions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Insights Into Periostin Functions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg725

b:48.6
occ:1.00
 O A:PRO137 2.6 41.0 1.0
OD1 A:ASN139 2.9 47.7 1.0
N A:THR113 3.0 40.5 1.0
OG1 A:THR113 3.1 39.5 1.0
C A:SER138 3.2 39.9 1.0
CA A:ALA110 3.3 46.0 1.0
N A:ASN139 3.3 38.0 1.0
C A:ALA110 3.4 44.0 1.0
CB A:ALA110 3.4 41.5 1.0
O A:SER138 3.5 38.6 1.0
CB A:THR113 3.5 41.9 1.0
CD1 A:TRP142 3.6 44.1 1.0
N A:THR112 3.6 43.1 1.0
O A:ALA110 3.7 45.7 1.0
C A:PRO137 3.7 40.5 1.0
CB A:THR112 3.7 42.0 1.0
CA A:SER138 3.8 44.9 1.0
CA A:ASN139 3.8 44.4 1.0
CA A:THR113 3.9 40.6 1.0
NE1 A:TRP142 3.9 41.7 1.0
C A:THR112 3.9 43.8 1.0
CA A:THR112 3.9 44.0 1.0
CG A:ASN139 4.0 48.7 1.0
N A:THR111 4.0 44.5 1.0
N A:SER138 4.2 40.7 1.0
O A:HOH904 4.2 47.1 1.0
CB A:ASN139 4.5 42.9 1.0
C A:THR111 4.5 43.1 1.0
OG1 A:THR112 4.6 45.3 1.0
N A:ALA110 4.7 42.2 1.0
CG2 A:THR112 4.7 37.8 1.0
CG A:TRP142 4.8 46.0 1.0
O A:GLY109 4.9 47.5 1.0
CA A:THR111 4.9 41.5 1.0
CA A:PRO137 4.9 41.9 1.0
CG2 A:THR113 5.0 37.0 1.0

Magnesium binding site 2 out of 8 in 5yjg

Go back to Magnesium Binding Sites List in 5yjg
Magnesium binding site 2 out of 8 in the Structural Insights Into Periostin Functions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Insights Into Periostin Functions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg726

b:72.6
occ:1.00
 O A:PRO274 2.7 55.7 1.0
N A:PHE250 3.0 73.4 1.0
OD1 A:ASN276 3.0 67.5 1.0
C A:THR275 3.2 66.1 1.0
CE1 A:PHE279 3.3 64.2 1.0
N A:ASN276 3.4 71.0 1.0
CB A:PHE250 3.4 69.9 1.0
O A:THR275 3.4 62.3 1.0
CA A:LEU247 3.5 72.8 1.0
CD1 A:PHE279 3.5 67.7 1.0
O A:ASP246 3.6 72.7 1.0
CA A:THR275 3.6 67.5 1.0
C A:LEU247 3.7 74.3 1.0
CB A:SER249 3.7 67.3 1.0
C A:PRO274 3.7 53.1 1.0
N A:SER249 3.8 70.5 1.0
CA A:PHE250 3.8 69.8 1.0
CA A:ASN276 3.9 68.2 1.0
C A:SER249 4.0 72.2 1.0
CA A:SER249 4.0 68.8 1.0
CG A:ASN276 4.0 68.0 1.0
O A:LEU247 4.1 69.7 1.0
N A:SER248 4.1 77.5 1.0
N A:THR275 4.1 54.5 1.0
CD2 A:LEU247 4.1 64.2 1.0
CB A:LEU247 4.4 72.9 1.0
C A:ASP246 4.4 76.1 1.0
N A:LEU247 4.4 74.2 1.0
OG A:SER249 4.4 68.1 1.0
CZ A:PHE279 4.5 67.6 1.0
C A:SER248 4.5 70.0 1.0
CB A:ASN276 4.6 61.0 1.0
CG A:PHE250 4.8 67.0 1.0
CG A:PHE279 4.8 67.0 1.0
CG A:LEU247 4.9 69.5 1.0
CA A:SER248 5.0 74.3 1.0
C A:PHE250 5.0 69.6 1.0
CB A:THR275 5.0 68.0 1.0

Magnesium binding site 3 out of 8 in 5yjg

Go back to Magnesium Binding Sites List in 5yjg
Magnesium binding site 3 out of 8 in the Structural Insights Into Periostin Functions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Insights Into Periostin Functions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg727

b:52.8
occ:1.00
 OD1 A:ASN410 2.6 46.8 1.0
O A:PRO408 2.7 40.9 1.0
CA A:GLN381 3.1 48.9 1.0
O A:GLN380 3.1 46.1 1.0
N A:PHE384 3.1 47.1 1.0
C A:GLN381 3.2 47.7 1.0
O A:GLN381 3.3 50.1 1.0
CB A:PHE384 3.4 42.4 1.0
N A:ASN410 3.4 45.4 1.0
C A:VAL409 3.5 45.3 1.0
CG A:ASN410 3.7 43.6 1.0
CA A:ASN410 3.8 44.8 1.0
CE2 A:PHE413 3.8 47.9 1.0
CB A:THR383 3.8 47.1 1.0
C A:PRO408 3.8 49.6 1.0
C A:GLN380 3.8 45.2 1.0
O A:VAL409 3.8 40.5 1.0
CA A:PHE384 3.9 44.6 1.0
N A:GLN381 3.9 41.6 1.0
N A:THR383 3.9 38.5 1.0
N A:THR382 4.0 42.5 1.0
CA A:VAL409 4.0 44.1 1.0
C A:THR383 4.1 52.1 1.0
CB A:GLN381 4.1 43.8 1.0
CA A:THR383 4.2 49.5 1.0
CD2 A:PHE413 4.3 47.5 1.0
CB A:ASN410 4.4 40.6 1.0
N A:VAL409 4.4 44.5 1.0
OG1 A:THR383 4.5 43.7 1.0
C A:THR382 4.6 48.5 1.0
CG A:GLN381 4.7 44.5 1.0
ND2 A:ASN410 4.7 46.4 1.0
CG A:PHE384 4.8 42.4 1.0
CG2 A:THR383 4.8 44.5 1.0
CZ A:PHE413 4.8 44.1 1.0
CA A:THR382 4.9 47.1 1.0

Magnesium binding site 4 out of 8 in 5yjg

Go back to Magnesium Binding Sites List in 5yjg
Magnesium binding site 4 out of 8 in the Structural Insights Into Periostin Functions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Insights Into Periostin Functions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg728

b:86.5
occ:1.00
 N A:PHE512 2.3 83.7 1.0
CB A:PHE512 2.8 85.0 1.0
OD1 A:ASN538 2.9 84.8 1.0
O A:PHE509 3.0 80.2 1.0
CA A:PHE512 3.1 84.9 1.0
CE2 A:PHE541 3.3 98.5 1.0
O A:PRO536 3.3 78.0 1.0
C A:THR511 3.4 86.6 1.0
C A:PHE509 3.4 85.0 1.0
CB A:THR511 3.5 91.0 1.0
CD2 A:PHE541 3.5 0.8 1.0
N A:THR511 3.5 80.5 1.0
CA A:THR511 3.6 88.7 1.0
CA A:PHE509 3.8 85.3 1.0
CG A:ASN538 4.0 89.0 1.0
O A:ARG508 4.1 89.0 1.0
N A:ASN538 4.1 95.0 1.0
C A:THR537 4.1 93.8 1.0
C A:SER510 4.1 82.5 1.0
N A:SER510 4.1 84.7 1.0
CG A:PHE512 4.2 87.3 1.0
O A:THR537 4.2 92.2 1.0
CA A:ASN538 4.3 94.5 1.0
C A:PHE512 4.3 83.9 1.0
CZ A:PHE541 4.4 96.9 1.0
OG1 A:THR511 4.4 97.3 1.0
CG2 A:THR511 4.5 93.3 1.0
C A:PRO536 4.5 83.6 1.0
O A:THR511 4.5 82.4 1.0
N A:LEU513 4.5 83.0 1.0
O A:SER510 4.7 85.0 1.0
CG A:PHE541 4.7 0.4 1.0
N A:PHE509 4.7 82.0 1.0
CA A:THR537 4.7 88.2 1.0
CB A:ASN538 4.8 90.6 1.0
CA A:SER510 4.8 86.2 1.0
C A:ARG508 4.8 84.8 1.0
ND2 A:ASN538 4.8 88.5 1.0
CB A:PHE509 4.9 79.8 1.0
CD1 A:PHE512 4.9 87.2 1.0

Magnesium binding site 5 out of 8 in 5yjg

Go back to Magnesium Binding Sites List in 5yjg
Magnesium binding site 5 out of 8 in the Structural Insights Into Periostin Functions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structural Insights Into Periostin Functions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg729

b:48.1
occ:1.00
 OD2 A:ASP350 2.6 42.9 1.0
O A:CYS208 2.8 40.1 1.0
N A:GLU313 2.8 44.7 1.0
OG A:SER312 3.2 48.4 1.0
N A:SER312 3.2 41.9 1.0
CG A:ASP350 3.2 46.0 1.0
CG A:GLU313 3.3 42.4 1.0
CB A:GLU313 3.3 46.9 1.0
OD1 A:ASP350 3.3 45.9 1.0
CB A:CYS311 3.4 41.4 1.0
NH2 A:ARG228 3.6 47.1 1.0
CA A:GLU313 3.7 41.8 1.0
CB A:CYS208 3.8 38.2 1.0
C A:SER312 3.8 45.4 1.0
C A:CYS311 3.8 42.1 1.0
CA A:SER312 3.8 41.8 1.0
C A:CYS208 3.9 44.2 1.0
NH1 A:ARG228 4.0 40.8 1.0
CB A:SER312 4.0 45.2 1.0
CA A:CYS311 4.1 42.6 1.0
CZ A:ARG228 4.1 49.1 1.0
CA A:CYS208 4.2 44.1 1.0
CB A:ASP350 4.5 46.0 1.0
SG A:CYS311 4.5 48.3 1.0
SG A:CYS208 4.6 47.1 1.0
O A:CYS311 4.7 44.4 1.0
CD A:GLU313 4.7 46.6 1.0
C A:GLU313 4.7 42.3 1.0
N A:SER314 4.9 42.6 1.0
CG2 A:THR205 4.9 38.4 1.0
O A:SER312 5.0 45.9 1.0

Magnesium binding site 6 out of 8 in 5yjg

Go back to Magnesium Binding Sites List in 5yjg
Magnesium binding site 6 out of 8 in the Structural Insights Into Periostin Functions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structural Insights Into Periostin Functions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg730

b:70.3
occ:1.00
 O A:HOH830 3.1 53.1 1.0
CB A:MET473 4.1 47.5 1.0
N A:VAL466 4.2 44.6 1.0
O A:HOH914 4.3 51.4 1.0
CG2 A:VAL466 4.3 45.4 1.0
CB A:VAL466 4.4 45.8 1.0
O A:MET473 4.5 49.5 1.0
CE A:MET473 4.7 34.2 1.0
O A:GLU474 4.7 52.0 1.0
C A:MET473 4.7 50.9 1.0
CA A:ALA465 4.8 48.5 1.0
C A:ALA465 4.8 47.7 1.0
CA A:VAL466 4.9 42.0 1.0
CD1 A:LEU440 4.9 43.9 1.0
SD A:MET473 4.9 61.7 1.0
CL A:CL713 5.0 82.0 1.0

Magnesium binding site 7 out of 8 in 5yjg

Go back to Magnesium Binding Sites List in 5yjg
Magnesium binding site 7 out of 8 in the Structural Insights Into Periostin Functions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structural Insights Into Periostin Functions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg731

b:70.6
occ:1.00
 OD2 A:ASP613 2.8 61.3 1.0
OG A:SER612 2.8 60.1 1.0
OE2 A:GLU597 3.1 71.4 1.0
OE1 A:GLU597 3.1 68.1 1.0
CA A:GLY574 3.5 54.7 1.0
CG A:ASP613 3.5 58.2 1.0
CD A:GLU597 3.5 71.6 1.0
CB A:SER612 3.6 59.7 1.0
O A:HOH816 3.6 59.1 1.0
OD1 A:ASP613 3.7 52.2 1.0
CB A:LEU602 3.7 60.0 1.0
N A:GLY574 4.0 52.3 1.0
C A:GLY574 4.0 57.3 1.0
N A:LYS575 4.1 54.5 1.0
N A:LEU602 4.3 71.2 1.0
O A:HOH898 4.3 72.0 1.0
CA A:LEU602 4.5 69.0 1.0
O A:ASP600 4.5 77.2 1.0
CB A:ASP613 4.7 51.8 1.0
CG A:LEU602 4.7 61.7 1.0
CD2 A:LEU602 4.7 64.1 1.0
O A:GLY574 4.7 55.8 1.0
C A:SER612 4.8 62.7 1.0
CA A:SER612 4.8 64.0 1.0
C A:THR601 4.9 75.9 1.0
N A:ASP613 4.9 57.5 1.0
CG A:GLU597 5.0 68.4 1.0

Magnesium binding site 8 out of 8 in 5yjg

Go back to Magnesium Binding Sites List in 5yjg
Magnesium binding site 8 out of 8 in the Structural Insights Into Periostin Functions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structural Insights Into Periostin Functions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg732

b:48.5
occ:1.00
 OD1 A:ASN197 2.6 47.9 1.0
O A:PHE195 2.8 43.9 1.0
N A:CYS208 3.0 35.7 1.0
OG1 A:THR205 3.0 40.6 1.0
N A:ASN207 3.3 39.8 1.0
O A:THR205 3.4 44.1 1.0
CG A:ASN197 3.5 41.8 1.0
C A:THR205 3.6 41.6 1.0
CB A:ASN197 3.6 41.9 1.0
N A:ASN197 3.7 43.0 1.0
CA A:CYS208 3.8 44.1 1.0
CA A:ASN207 3.8 42.1 1.0
CB A:THR205 3.8 40.0 1.0
C A:PHE195 3.8 42.4 1.0
SG A:CYS311 3.8 48.3 1.0
C A:ASN207 3.9 43.5 1.0
C A:VAL206 3.9 42.6 1.0
C A:ILE196 4.0 49.2 1.0
N A:VAL206 4.0 42.0 1.0
CA A:VAL206 4.0 38.6 1.0
CA A:ASN197 4.3 42.0 1.0
CA A:ILE196 4.3 41.1 1.0
CA A:THR205 4.4 41.6 1.0
N A:ILE196 4.4 42.0 1.0
SG A:CYS208 4.5 47.1 1.0
O A:ILE196 4.5 42.5 1.0
CB A:PHE195 4.6 47.8 1.0
CB A:CYS208 4.7 38.2 1.0
ND2 A:ASN197 4.7 39.1 1.0
O A:VAL206 4.8 44.5 1.0
CA A:PHE195 4.8 43.1 1.0
O A:HOH919 4.9 61.9 1.0
C A:CYS208 4.9 44.2 1.0

Reference:

J.Liu, J.Zhang, F.Xu, Z.Lin, Z.Li, H.Liu. Structural Characterizations of Human Periostin Dimerization and Cysteinylation. Febs Lett. V. 592 1789 2018.
ISSN: ISSN 1873-3468
PubMed: 29754429
DOI: 10.1002/1873-3468.13091
Page generated: Mon Sep 30 11:12:58 2024

Last articles

Fe in 6M2I
Fe in 6M1W
Fe in 6LY5
Fe in 6M0A
Fe in 6LVV
Fe in 6LU1
Fe in 6LY4
Fe in 6LVC
Fe in 6LVB
Fe in 6LS3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy