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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

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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

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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

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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

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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

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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

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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

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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

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