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Yttrium in PDB 6mi5: uc(Nmr) Solution Structure of Lanmodulin (Lanm) Complexed with Yttrium(III) Ions

Yttrium Binding Sites:

The binding sites of Yttrium atom in the uc(Nmr) Solution Structure of Lanmodulin (Lanm) Complexed with Yttrium(III) Ions (pdb code 6mi5). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 3 binding sites of Yttrium where determined in the uc(Nmr) Solution Structure of Lanmodulin (Lanm) Complexed with Yttrium(III) Ions, PDB code: 6mi5:
Jump to Yttrium binding site number: 1; 2; 3;

Yttrium binding site 1 out of 3 in 6mi5

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Yttrium binding site 1 out of 3 in the uc(Nmr) Solution Structure of Lanmodulin (Lanm) Complexed with Yttrium(III) Ions


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of uc(Nmr) Solution Structure of Lanmodulin (Lanm) Complexed with Yttrium(III) Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Y200

b:0.0
occ:1.00
OD2 X:ASP35 2.2 0.0 1.0
OE1 X:GLU46 2.3 0.0 1.0
OE2 X:GLU46 2.3 0.0 1.0
OD1 X:ASP39 2.3 0.0 1.0
OD1 X:ASP37 2.4 0.0 1.0
OD2 X:ASP37 2.4 0.0 1.0
OD2 X:ASP39 2.4 0.0 1.0
O X:THR41 2.5 0.0 1.0
CD X:GLU46 2.8 0.0 1.0
CG X:ASP39 2.8 0.0 1.0
CG X:ASP37 2.8 0.0 1.0
CG X:ASP35 3.4 0.0 1.0
H X:ASP39 3.6 0.0 1.0
C X:THR41 3.6 0.0 1.0
HA X:ASP35 3.6 0.0 1.0
HA X:ILE42 4.0 0.0 1.0
OD1 X:ASP35 4.0 0.0 1.0
O X:PHE34 4.0 0.0 1.0
H X:THR41 4.1 0.0 1.0
H X:GLY40 4.1 0.0 1.0
CB X:ASP39 4.3 0.0 1.0
HG12 X:ILE42 4.3 0.0 1.0
CG X:GLU46 4.3 0.0 1.0
CB X:ASP37 4.3 0.0 1.0
N X:ILE42 4.3 0.0 1.0
N X:ASP39 4.5 0.0 1.0
OD1 X:ASP43 4.5 0.0 1.0
CB X:ASP35 4.5 0.0 1.0
CA X:ASP35 4.5 0.0 1.0
HA X:LYS38 4.5 0.0 1.0
H X:ASP43 4.6 0.0 1.0
HB2 X:ASP37 4.6 0.0 1.0
N X:THR41 4.6 0.0 1.0
HB3 X:ASP39 4.7 0.0 1.0
CA X:ILE42 4.7 0.0 1.0
H X:LYS38 4.7 0.0 1.0
CA X:THR41 4.7 0.0 1.0
HG3 X:GLU46 4.7 0.0 1.0
HG2 X:GLU46 4.8 0.0 1.0
HB2 X:ASP35 4.8 0.0 1.0
HB3 X:ASP37 4.8 0.0 1.0
HB2 X:GLU46 4.9 0.0 1.0
CA X:ASP39 5.0 0.0 1.0
HB2 X:ASP39 5.0 0.0 1.0
N X:GLY40 5.0 0.0 1.0

Yttrium binding site 2 out of 3 in 6mi5

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Yttrium binding site 2 out of 3 in the uc(Nmr) Solution Structure of Lanmodulin (Lanm) Complexed with Yttrium(III) Ions


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of uc(Nmr) Solution Structure of Lanmodulin (Lanm) Complexed with Yttrium(III) Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Y201

b:0.0
occ:1.00
OD1 X:ASP67 2.2 0.0 1.0
OD1 X:ASP61 2.2 0.0 1.0
OD2 X:ASP61 2.3 0.0 1.0
OD2 X:ASP63 2.3 0.0 1.0
OE2 X:GLU70 2.3 0.0 1.0
O X:THR65 2.4 0.0 1.0
OE1 X:GLU70 2.4 0.0 1.0
OD1 X:ASP63 2.5 0.0 1.0
CG X:ASP61 2.7 0.0 1.0
CD X:GLU70 2.8 0.0 1.0
CG X:ASP63 2.9 0.0 1.0
CG X:ASP67 3.4 0.0 1.0
C X:THR65 3.6 0.0 1.0
H X:THR65 3.6 0.0 1.0
HA X:LEU66 3.9 0.0 1.0
HB3 X:ASP67 4.1 0.0 1.0
OD2 X:ASP67 4.2 0.0 1.0
HB2 X:GLU70 4.3 0.0 1.0
CB X:ASP61 4.3 0.0 1.0
H X:ASP67 4.3 0.0 1.0
CG X:GLU70 4.3 0.0 1.0
CB X:ASP63 4.4 0.0 1.0
N X:THR65 4.4 0.0 1.0
CB X:ASP67 4.4 0.0 1.0
H X:ASP63 4.5 0.0 1.0
CA X:THR65 4.5 0.0 1.0
N X:LEU66 4.5 0.0 1.0
HD21 X:LEU66 4.5 0.0 1.0
OD1 X:ASP59 4.6 0.0 1.0
HB3 X:ASP61 4.6 0.0 1.0
CA X:LEU66 4.7 0.0 1.0
H X:ASP61 4.7 0.0 1.0
HB X:THR65 4.7 0.0 1.0
OG1 X:THR65 4.8 0.0 1.0
HB3 X:ASP63 4.8 0.0 1.0
HB2 X:ASP61 4.8 0.0 1.0
HG2 X:GLU70 4.8 0.0 1.0
CB X:GLU70 4.9 0.0 1.0
CB X:THR65 4.9 0.0 1.0
N X:ASP67 4.9 0.0 1.0
HB2 X:ASP63 5.0 0.0 1.0
HG3 X:GLU70 5.0 0.0 1.0
H X:GLY64 5.0 0.0 1.0

Yttrium binding site 3 out of 3 in 6mi5

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Yttrium binding site 3 out of 3 in the uc(Nmr) Solution Structure of Lanmodulin (Lanm) Complexed with Yttrium(III) Ions


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 3 of uc(Nmr) Solution Structure of Lanmodulin (Lanm) Complexed with Yttrium(III) Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Y202

b:0.0
occ:1.00
OD1 X:ASP84 2.2 0.0 1.0
OD1 X:ASP88 2.2 0.0 1.0
OE2 X:GLU95 2.3 0.0 1.0
OD1 X:ASP92 2.3 0.0 1.0
OD1 X:ASP86 2.3 0.0 1.0
OE1 X:GLU95 2.3 0.0 1.0
OD2 X:ASP88 2.4 0.0 1.0
CG X:ASP88 2.7 0.0 1.0
CD X:GLU95 2.8 0.0 1.0
O X:THR90 3.2 0.0 1.0
CG X:ASP86 3.4 0.0 1.0
CG X:ASP84 3.4 0.0 1.0
CG X:ASP92 3.5 0.0 1.0
HD2 X:PRO85 3.5 0.0 1.0
OD2 X:ASP86 3.7 0.0 1.0
HA X:LEU91 3.7 0.0 1.0
H X:ASP86 3.8 0.0 1.0
OD2 X:ASP92 4.1 0.0 1.0
H X:ASP88 4.1 0.0 1.0
CB X:ASP88 4.1 0.0 1.0
OD2 X:ASP84 4.2 0.0 1.0
HB2 X:ASP88 4.3 0.0 1.0
CG X:GLU95 4.3 0.0 1.0
HB2 X:ASP84 4.3 0.0 1.0
C X:THR90 4.4 0.0 1.0
CB X:ASP84 4.5 0.0 1.0
HB2 X:ASP92 4.5 0.0 1.0
HG2 X:PRO85 4.6 0.0 1.0
CA X:LEU91 4.6 0.0 1.0
CB X:ASP92 4.6 0.0 1.0
CD X:PRO85 4.6 0.0 1.0
C X:LEU91 4.6 0.0 1.0
HG3 X:GLU95 4.7 0.0 1.0
CB X:ASP86 4.7 0.0 1.0
HB2 X:GLU95 4.7 0.0 1.0
HD23 X:LEU91 4.7 0.0 1.0
N X:ASP86 4.8 0.0 1.0
N X:ASP92 4.8 0.0 1.0
H X:ASP92 4.8 0.0 1.0
HB3 X:ASP88 4.8 0.0 1.0
N X:ASP88 4.8 0.0 1.0
HG2 X:GLU95 4.9 0.0 1.0
HA X:ASP84 4.9 0.0 1.0
N X:LEU91 4.9 0.0 1.0
H X:THR90 5.0 0.0 1.0

Reference:

E.C.Cook, E.R.Featherston, S.A.Showalter, J.A.Cotruvo Jr.. Structural Basis For Rare Earth Element Recognition By Methylobacterium Extorquens Lanmodulin. Biochemistry V. 58 120 2019.
ISSN: ISSN 1520-4995
PubMed: 30352145
DOI: 10.1021/ACS.BIOCHEM.8B01019
Page generated: Wed Dec 16 02:41:19 2020

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