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Magnesium in PDB 1kxg: The 2.0 Ang Resolution Structure of Blys, B Lymphocyte Stimulator.

Protein crystallography data

The structure of The 2.0 Ang Resolution Structure of Blys, B Lymphocyte Stimulator., PDB code: 1kxg was solved by D.A.Oren, Y.Li, Y.Volovik, T.S.Morris, C.Dharia, K.Das, O.Galperina, R.Gentz, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.64 / 2.00
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 123.580, 123.580, 161.230, 90.00, 90.00, 120.00
R / Rfree (%) 18.9 / 20.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The 2.0 Ang Resolution Structure of Blys, B Lymphocyte Stimulator. (pdb code 1kxg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the The 2.0 Ang Resolution Structure of Blys, B Lymphocyte Stimulator., PDB code: 1kxg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 1kxg

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Magnesium binding site 1 out of 7 in the The 2.0 Ang Resolution Structure of Blys, B Lymphocyte Stimulator.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The 2.0 Ang Resolution Structure of Blys, B Lymphocyte Stimulator. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:27.8
occ:1.00
 OE1 A:GLN234 2.3 27.5 1.0
OE1 C:GLN234 2.5 27.1 1.0
OE1 B:GLN234 2.5 26.9 1.0
O B:HOH1019 2.5 23.8 1.0
O A:HOH504 2.6 26.0 1.0
O C:HOH1017 2.7 26.0 1.0
MG B:MG702 3.2 31.6 1.0
CD A:GLN234 3.3 28.5 1.0
CD C:GLN234 3.4 27.3 1.0
CD B:GLN234 3.4 27.3 1.0
NE2 B:GLN234 3.7 28.2 1.0
NE2 C:GLN234 3.7 25.8 1.0
NE2 A:GLN234 3.7 29.1 1.0
OD1 A:ASN243 4.0 26.0 1.0
OD1 C:ASN243 4.1 28.6 1.0
OD1 B:ASN243 4.1 27.2 1.0
CG A:ASN243 4.4 26.9 1.0
CG B:ASN243 4.5 29.7 1.0
CG C:ASN243 4.5 29.8 1.0
CG A:GLN234 4.6 26.5 1.0
ND2 A:ASN243 4.7 27.8 1.0
CG C:GLN234 4.7 27.2 1.0
CG B:GLN234 4.8 27.1 1.0
CB A:GLN234 4.8 25.4 1.0
ND2 C:ASN243 4.8 30.7 1.0
ND2 B:ASN243 4.9 29.4 1.0

Magnesium binding site 2 out of 7 in 1kxg

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Magnesium binding site 2 out of 7 in the The 2.0 Ang Resolution Structure of Blys, B Lymphocyte Stimulator.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The 2.0 Ang Resolution Structure of Blys, B Lymphocyte Stimulator. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:47.2
occ:1.00
 O4 F:CIT888 2.4 39.7 1.0
O4 A:CIT889 2.4 36.1 1.0
O F:HOH395 2.8 36.1 1.0
O7 F:CIT888 2.8 37.5 1.0
O A:HOH10 2.9 32.0 1.0
O7 A:CIT889 3.0 31.4 1.0
O F:HOH20 3.3 50.1 1.0
C5 A:CIT889 3.4 37.9 1.0
C5 F:CIT888 3.4 40.6 1.0
MG F:MG902 3.9 43.4 1.0
C4 A:CIT889 3.9 35.2 1.0
NZ A:LYS252 3.9 33.7 1.0
C3 F:CIT888 4.0 37.6 1.0
MG A:MG903 4.0 41.1 1.0
C4 F:CIT888 4.0 39.3 1.0
C3 A:CIT889 4.0 33.2 1.0
NZ F:LYS252 4.1 30.8 1.0
OE2 F:GLU254 4.1 36.4 1.0
OE1 A:GLU254 4.1 34.8 1.0
O3 F:CIT888 4.5 42.0 1.0
O5 F:CIT888 4.6 37.6 1.0
O3 A:CIT889 4.6 38.8 1.0
CE A:LYS252 4.7 33.3 1.0
C6 F:CIT888 4.8 37.8 1.0
O5 A:CIT889 4.9 31.8 1.0
CE F:LYS252 4.9 30.6 1.0
C6 A:CIT889 4.9 31.5 1.0

Magnesium binding site 3 out of 7 in 1kxg

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Magnesium binding site 3 out of 7 in the The 2.0 Ang Resolution Structure of Blys, B Lymphocyte Stimulator.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The 2.0 Ang Resolution Structure of Blys, B Lymphocyte Stimulator. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:41.1
occ:1.00
 O A:HOH10 2.7 32.0 1.0
O1 F:CIT888 2.8 37.4 1.0
O7 F:CIT888 2.9 37.5 1.0
NH2 A:ARG214 2.9 24.4 1.0
O A:LYS252 3.1 23.2 1.0
O5 A:CIT889 3.3 31.8 1.0
CG A:LYS252 3.5 27.3 1.0
NH1 A:ARG214 3.5 24.8 1.0
CZ A:ARG214 3.6 25.6 1.0
C1 F:CIT888 3.6 37.1 1.0
C A:LYS252 3.7 22.0 1.0
C6 A:CIT889 3.7 31.5 1.0
O7 A:CIT889 4.0 31.4 1.0
C2 F:CIT888 4.0 35.8 1.0
MG A:MG901 4.0 47.2 1.0
C3 F:CIT888 4.0 37.6 1.0
CB A:LYS252 4.1 23.4 1.0
O4 F:CIT888 4.2 39.7 1.0
C4 A:CIT889 4.2 35.2 1.0
C3 A:CIT889 4.2 33.2 1.0
N A:LEU253 4.2 20.8 1.0
C A:LEU253 4.2 21.8 1.0
CA A:LEU253 4.2 21.2 1.0
N A:GLU254 4.3 22.0 1.0
O6 A:CIT889 4.4 29.7 1.0
CA A:LYS252 4.5 21.5 1.0
O2 F:CIT888 4.6 33.4 1.0
CB A:GLU254 4.6 27.0 1.0
CD A:LYS252 4.6 30.1 1.0
O A:LEU253 4.7 20.8 1.0
C5 F:CIT888 4.7 40.6 1.0
NE A:ARG214 4.7 24.1 1.0
CE A:LYS252 4.7 33.3 1.0
O A:HOH4 4.8 23.9 1.0
OE1 A:GLU254 5.0 34.8 1.0
CA A:GLU254 5.0 24.2 1.0
O5 F:CIT888 5.0 37.6 1.0
OD2 A:ASP257 5.0 27.4 1.0
O4 A:CIT889 5.0 36.1 1.0
C4 F:CIT888 5.0 39.3 1.0

Magnesium binding site 4 out of 7 in 1kxg

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Magnesium binding site 4 out of 7 in the The 2.0 Ang Resolution Structure of Blys, B Lymphocyte Stimulator.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The 2.0 Ang Resolution Structure of Blys, B Lymphocyte Stimulator. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:31.6
occ:1.00
 O B:HOH1019 2.4 23.8 1.0
O C:HOH1017 2.4 26.0 1.0
O A:HOH507 2.5 24.2 1.0
O C:HOH1018 2.5 24.2 1.0
O A:HOH504 2.5 26.0 1.0
O B:HOH1020 2.6 31.3 1.0
MG A:MG701 3.2 27.8 1.0
O A:HOH510 3.8 36.2 1.0
O A:HOH509 4.0 35.0 1.0
O A:HOH511 4.1 35.0 1.0
O B:ASN235 4.1 33.2 1.0
O A:ASN235 4.1 27.7 1.0
O C:ASN235 4.2 29.1 1.0
ND2 A:ASN243 4.3 27.8 1.0
ND2 C:ASN243 4.4 30.7 1.0
ND2 B:ASN243 4.4 29.4 1.0
OD1 A:ASN243 4.5 26.0 1.0
OD1 C:ASN243 4.5 28.6 1.0
OD1 B:ASN243 4.5 27.2 1.0
CG A:ASN243 4.7 26.9 1.0
CG C:ASN243 4.8 29.8 1.0
CG B:ASN243 4.8 29.7 1.0
OE1 B:GLN234 5.0 26.9 1.0
OE1 C:GLN234 5.0 27.1 1.0

Magnesium binding site 5 out of 7 in 1kxg

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Magnesium binding site 5 out of 7 in the The 2.0 Ang Resolution Structure of Blys, B Lymphocyte Stimulator.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The 2.0 Ang Resolution Structure of Blys, B Lymphocyte Stimulator. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg801

b:29.6
occ:1.00
 O E:HOH1021 2.4 24.2 1.0
O E:HOH1020 2.4 20.7 1.0
O F:HOH603 2.4 23.5 1.0
O D:HOH1014 2.5 21.7 1.0
O D:HOH1013 2.5 22.4 1.0
O F:HOH608 2.5 24.1 1.0
MG D:MG802 3.2 28.4 1.0
O D:HOH1015 3.9 28.1 1.0
O F:HOH609 4.0 31.8 1.0
O F:ASN235 4.0 22.3 1.0
O E:HOH1022 4.0 32.9 1.0
O D:ASN235 4.1 25.9 1.0
O E:ASN235 4.2 26.2 1.0
ND2 F:ASN243 4.3 21.1 1.0
ND2 E:ASN243 4.3 27.1 1.0
ND2 D:ASN243 4.4 23.5 1.0
OD1 D:ASN243 4.5 22.5 1.0
OD1 E:ASN243 4.6 24.5 1.0
OD1 F:ASN243 4.6 24.9 1.0
CG F:ASN243 4.8 23.4 1.0
CG D:ASN243 4.8 23.5 1.0
CG E:ASN243 4.8 28.4 1.0

Magnesium binding site 6 out of 7 in 1kxg

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Magnesium binding site 6 out of 7 in the The 2.0 Ang Resolution Structure of Blys, B Lymphocyte Stimulator.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The 2.0 Ang Resolution Structure of Blys, B Lymphocyte Stimulator. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:28.4
occ:1.00
 OE1 E:GLN234 2.3 23.5 1.0
OE1 D:GLN234 2.4 23.5 1.0
OE1 F:GLN234 2.5 24.8 1.0
O F:HOH603 2.5 23.5 1.0
O D:HOH1013 2.6 22.4 1.0
O E:HOH1020 2.6 20.7 1.0
MG D:MG801 3.2 29.6 1.0
CD E:GLN234 3.3 22.3 1.0
CD D:GLN234 3.3 23.0 1.0
CD F:GLN234 3.4 26.5 1.0
NE2 E:GLN234 3.6 21.1 1.0
NE2 D:GLN234 3.7 20.9 1.0
NE2 F:GLN234 3.8 23.9 1.0
OD1 E:ASN243 4.0 24.5 1.0
OD1 F:ASN243 4.1 24.9 1.0
OD1 D:ASN243 4.2 22.5 1.0
CG E:ASN243 4.4 28.4 1.0
CG F:ASN243 4.4 23.4 1.0
CG D:ASN243 4.5 23.5 1.0
CG E:GLN234 4.6 21.9 1.0
CG D:GLN234 4.7 22.6 1.0
CG F:GLN234 4.7 25.3 1.0
ND2 E:ASN243 4.7 27.1 1.0
ND2 F:ASN243 4.7 21.1 1.0
ND2 D:ASN243 4.8 23.5 1.0
CB E:GLN234 4.9 21.5 1.0
CB D:GLN234 4.9 23.2 1.0
CB F:GLN234 5.0 24.1 1.0
O E:HOH1021 5.0 24.2 1.0

Magnesium binding site 7 out of 7 in 1kxg

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Magnesium binding site 7 out of 7 in the The 2.0 Ang Resolution Structure of Blys, B Lymphocyte Stimulator.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The 2.0 Ang Resolution Structure of Blys, B Lymphocyte Stimulator. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg902

b:43.4
occ:1.00
 O F:HOH395 2.7 36.1 1.0
NH2 F:ARG214 2.9 25.0 1.0
O7 A:CIT889 2.9 31.4 1.0
O5 F:CIT888 3.1 37.6 1.0
O F:LYS252 3.2 24.1 1.0
O1 A:CIT889 3.2 35.2 1.0
CG F:LYS252 3.5 25.0 1.0
CZ F:ARG214 3.6 24.1 1.0
C1 A:CIT889 3.7 35.9 1.0
NH1 F:ARG214 3.7 24.0 1.0
C F:LYS252 3.7 20.3 1.0
C6 F:CIT888 3.8 37.8 1.0
MG A:MG901 3.9 47.2 1.0
C3 A:CIT889 4.1 33.2 1.0
C2 A:CIT889 4.1 33.7 1.0
O7 F:CIT888 4.1 37.5 1.0
CB F:LYS252 4.1 21.5 1.0
O4 A:CIT889 4.1 36.1 1.0
N F:LEU253 4.2 18.4 1.0
C F:LEU253 4.2 20.3 1.0
CA F:LEU253 4.3 20.1 1.0
N F:GLU254 4.3 20.0 1.0
C3 F:CIT888 4.4 37.6 1.0
O2 A:CIT889 4.5 33.7 1.0
C5 A:CIT889 4.5 37.9 1.0
CB F:GLU254 4.5 22.6 1.0
O6 F:CIT888 4.6 35.9 1.0
CA F:LYS252 4.6 20.3 1.0
C4 F:CIT888 4.6 39.3 1.0
CD F:LYS252 4.6 27.7 1.0
O F:LEU253 4.7 19.4 1.0
NE F:ARG214 4.7 23.0 1.0
CE F:LYS252 4.8 30.6 1.0
O F:HOH349 4.9 26.5 1.0
O4 F:CIT888 4.9 39.7 1.0
OE2 F:GLU254 4.9 36.4 1.0
CA F:GLU254 4.9 22.3 1.0
C4 A:CIT889 4.9 35.2 1.0
OD1 F:ASP257 5.0 26.0 1.0

Reference:

D.A.Oren, Y.Li, Y.Volovik, T.S.Morris, C.Dharia, K.Das, O.Galperina, R.Gentz, E.Arnold. Structural Basis of Blys Receptor Recognition. Nat.Struct.Biol. V. 9 288 2002.
ISSN: ISSN 1072-8368
PubMed: 11862220
DOI: 10.1038/NSB769
Page generated: Tue Aug 13 08:09:52 2024

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