Atomistry » Magnesium » PDB 1kk7-1l3p » 1kxg
Atomistry »
  Magnesium »
    PDB 1kk7-1l3p »
      1kxg »

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

Go back to Magnesium Binding Sites List in 1kxg
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

Go back to Magnesium Binding Sites List in 1kxg
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

Go back to Magnesium Binding Sites List in 1kxg
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

Go back to Magnesium Binding Sites List in 1kxg
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

Go back to Magnesium Binding Sites List in 1kxg
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

Go back to Magnesium Binding Sites List in 1kxg
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

Go back to Magnesium Binding Sites List in 1kxg
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

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy