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Zinc in PDB 2jtn: uc(Nmr) Solution Structure of A LDB1-Lid:LHX3-Lim Complex

Zinc Binding Sites:

The binding sites of Zinc atom in the uc(Nmr) Solution Structure of A LDB1-Lid:LHX3-Lim Complex (pdb code 2jtn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the uc(Nmr) Solution Structure of A LDB1-Lid:LHX3-Lim Complex, PDB code: 2jtn:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2jtn

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Zinc binding site 1 out of 4 in the uc(Nmr) Solution Structure of A LDB1-Lid:LHX3-Lim Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of uc(Nmr) Solution Structure of A LDB1-Lid:LHX3-Lim Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn183

b:0.0
occ:1.00
ND1 A:HIS84 2.0 0.0 1.0
SG A:CYS66 2.3 0.0 1.0
SG A:CYS87 2.3 0.0 1.0
SG A:CYS63 2.3 0.0 1.0
HB2 A:HIS84 2.5 0.0 1.0
HB2 A:CYS66 2.8 0.0 1.0
CG A:HIS84 2.9 0.0 1.0
CE1 A:HIS84 3.1 0.0 1.0
CB A:HIS84 3.1 0.0 1.0
CB A:CYS66 3.2 0.0 1.0
HB3 A:CYS63 3.4 0.0 1.0
HE1 A:HIS84 3.4 0.0 1.0
HB2 A:CYS87 3.4 0.0 1.0
HB3 A:HIS84 3.5 0.0 1.0
CB A:CYS87 3.5 0.0 1.0
CB A:CYS63 3.5 0.0 1.0
HB3 A:CYS87 3.8 0.0 1.0
HB3 A:CYS66 3.9 0.0 1.0
HB2 A:CYS63 3.9 0.0 1.0
HD12 A:ILE70 3.9 0.0 1.0
CD2 A:HIS84 4.1 0.0 1.0
H A:HIS84 4.1 0.0 1.0
NE2 A:HIS84 4.2 0.0 1.0
CA A:CYS66 4.3 0.0 1.0
HA A:CYS66 4.4 0.0 1.0
O A:ALA64 4.4 0.0 1.0
CA A:HIS84 4.5 0.0 1.0
O A:GLY65 4.6 0.0 1.0
HD11 A:ILE70 4.6 0.0 1.0
N A:CYS66 4.6 0.0 1.0
H A:CYS87 4.7 0.0 1.0
N A:HIS84 4.7 0.0 1.0
C A:GLY65 4.7 0.0 1.0
CD1 A:ILE70 4.8 0.0 1.0
CA A:CYS63 4.8 0.0 1.0
CA A:CYS87 4.8 0.0 1.0
C A:CYS63 4.9 0.0 1.0
HA A:HIS84 4.9 0.0 1.0

Zinc binding site 2 out of 4 in 2jtn

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Zinc binding site 2 out of 4 in the uc(Nmr) Solution Structure of A LDB1-Lid:LHX3-Lim Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of uc(Nmr) Solution Structure of A LDB1-Lid:LHX3-Lim Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn184

b:0.0
occ:1.00
OD2 A:ASP113 2.0 0.0 1.0
SG A:CYS90 2.3 0.0 1.0
SG A:CYS110 2.3 0.0 1.0
SG A:CYS93 2.3 0.0 1.0
H A:CYS110 2.8 0.0 1.0
CG A:ASP113 2.8 0.0 1.0
HB2 A:CYS93 3.0 0.0 1.0
H A:CYS93 3.3 0.0 1.0
CB A:CYS90 3.3 0.0 1.0
HB2 A:CYS90 3.3 0.0 1.0
CB A:CYS93 3.3 0.0 1.0
HB3 A:CYS90 3.4 0.0 1.0
HB3 A:CYS110 3.5 0.0 1.0
OD1 A:ASP113 3.5 0.0 1.0
HB3 A:ASP113 3.5 0.0 1.0
CB A:CYS110 3.5 0.0 1.0
N A:CYS110 3.7 0.0 1.0
CB A:ASP113 3.8 0.0 1.0
H A:ASP113 3.8 0.0 1.0
HB3 A:ASP92 4.0 0.0 1.0
HB3 A:CYS93 4.0 0.0 1.0
N A:CYS93 4.1 0.0 1.0
CA A:CYS110 4.1 0.0 1.0
CA A:CYS93 4.3 0.0 1.0
HA A:TYR109 4.3 0.0 1.0
HB2 A:CYS110 4.4 0.0 1.0
HG22 A:VAL95 4.4 0.0 1.0
HB2 A:ASP113 4.4 0.0 1.0
HB3 A:TYR109 4.5 0.0 1.0
HB3 A:ASP112 4.6 0.0 1.0
HD2 A:TYR109 4.6 0.0 1.0
N A:ASP113 4.7 0.0 1.0
O A:CYS110 4.7 0.0 1.0
CA A:CYS90 4.7 0.0 1.0
H A:ASP92 4.7 0.0 1.0
C A:TYR109 4.7 0.0 1.0
C A:CYS110 4.7 0.0 1.0
CD2 A:TYR109 4.8 0.0 1.0
HG21 A:VAL95 4.8 0.0 1.0
CA A:ASP113 4.9 0.0 1.0
HD22 A:LEU97 4.9 0.0 1.0
CA A:TYR109 4.9 0.0 1.0
HA A:CYS90 4.9 0.0 1.0
CG A:TYR109 4.9 0.0 1.0
H A:HIS94 5.0 0.0 1.0
HA A:CYS93 5.0 0.0 1.0
HD12 A:LEU97 5.0 0.0 1.0

Zinc binding site 3 out of 4 in 2jtn

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Zinc binding site 3 out of 4 in the uc(Nmr) Solution Structure of A LDB1-Lid:LHX3-Lim Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of uc(Nmr) Solution Structure of A LDB1-Lid:LHX3-Lim Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn185

b:0.0
occ:1.00
ND1 A:HIS144 2.0 0.0 1.0
SG A:CYS122 2.3 0.0 1.0
SG A:CYS125 2.3 0.0 1.0
SG A:CYS147 2.3 0.0 1.0
HB3 A:ALA124 2.5 0.0 1.0
HB2 A:HIS144 2.6 0.0 1.0
H A:CYS125 2.6 0.0 1.0
CG A:HIS144 3.0 0.0 1.0
CE1 A:HIS144 3.0 0.0 1.0
HB3 A:CYS122 3.2 0.0 1.0
CB A:HIS144 3.2 0.0 1.0
HE1 A:HIS144 3.3 0.0 1.0
CB A:CYS122 3.3 0.0 1.0
N A:CYS125 3.4 0.0 1.0
HB2 A:CYS147 3.5 0.0 1.0
CB A:ALA124 3.5 0.0 1.0
CB A:CYS125 3.5 0.0 1.0
CB A:CYS147 3.5 0.0 1.0
HB2 A:CYS122 3.6 0.0 1.0
HB3 A:CYS125 3.6 0.0 1.0
HB3 A:HIS144 3.7 0.0 1.0
HB1 A:ALA124 3.8 0.0 1.0
H A:ALA124 3.9 0.0 1.0
HB3 A:CYS147 3.9 0.0 1.0
CA A:CYS125 4.0 0.0 1.0
CD2 A:HIS144 4.1 0.0 1.0
NE2 A:HIS144 4.2 0.0 1.0
HB2 A:ALA124 4.2 0.0 1.0
H A:HIS144 4.2 0.0 1.0
C A:ALA124 4.2 0.0 1.0
CA A:ALA124 4.3 0.0 1.0
H A:LEU127 4.3 0.0 1.0
HB3 A:LEU127 4.3 0.0 1.0
N A:ALA124 4.4 0.0 1.0
HB2 A:CYS125 4.4 0.0 1.0
CA A:HIS144 4.5 0.0 1.0
H A:CYS147 4.5 0.0 1.0
HB2 A:LEU127 4.5 0.0 1.0
H A:GLN126 4.6 0.0 1.0
N A:HIS144 4.7 0.0 1.0
CA A:CYS122 4.7 0.0 1.0
C A:CYS125 4.8 0.0 1.0
HA A:HIS144 4.8 0.0 1.0
CA A:CYS147 4.9 0.0 1.0
HA A:CYS125 4.9 0.0 1.0
CB A:LEU127 4.9 0.0 1.0
N A:GLN126 5.0 0.0 1.0

Zinc binding site 4 out of 4 in 2jtn

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Zinc binding site 4 out of 4 in the uc(Nmr) Solution Structure of A LDB1-Lid:LHX3-Lim Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of uc(Nmr) Solution Structure of A LDB1-Lid:LHX3-Lim Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn186

b:0.0
occ:1.00
OD2 A:ASP176 2.0 0.0 1.0
SG A:CYS150 2.3 0.0 1.0
SG A:CYS173 2.3 0.0 1.0
SG A:CYS153 2.3 0.0 1.0
CG A:ASP176 2.9 0.0 1.0
H A:CYS173 3.0 0.0 1.0
HB2 A:CYS173 3.0 0.0 1.0
HB2 A:CYS153 3.1 0.0 1.0
H A:CYS153 3.1 0.0 1.0
HB2 A:CYS150 3.2 0.0 1.0
CB A:CYS150 3.2 0.0 1.0
CB A:CYS173 3.3 0.0 1.0
HB3 A:CYS150 3.3 0.0 1.0
CB A:CYS153 3.4 0.0 1.0
OD1 A:ASP176 3.5 0.0 1.0
HB2 A:ASP176 3.8 0.0 1.0
N A:CYS173 3.8 0.0 1.0
CB A:ASP176 3.9 0.0 1.0
HB A:VAL152 4.0 0.0 1.0
N A:CYS153 4.0 0.0 1.0
HB3 A:CYS173 4.1 0.0 1.0
HB3 A:CYS153 4.1 0.0 1.0
CA A:CYS173 4.2 0.0 1.0
H A:VAL152 4.3 0.0 1.0
CA A:CYS153 4.3 0.0 1.0
HB3 A:ASP176 4.4 0.0 1.0
HA A:VAL172 4.4 0.0 1.0
CA A:CYS150 4.7 0.0 1.0
H A:ASP176 4.7 0.0 1.0
HA A:CYS173 4.8 0.0 1.0
HG21 A:VAL172 4.9 0.0 1.0
HA A:CYS150 4.9 0.0 1.0
HD12 A:LEU157 4.9 0.0 1.0
HA A:CYS153 4.9 0.0 1.0
C A:VAL172 5.0 0.0 1.0
H A:LYS154 5.0 0.0 1.0
CB A:VAL152 5.0 0.0 1.0

Reference:

M.Bhati, C.Lee, A.L.Nancarrow, M.Lee, V.J.Craig, I.Bach, J.M.Guss, J.P.Mackay, J.M.Matthews. Implementing the Lim Code: the Structural Basis For Cell Type-Specific Assembly of Lim-Homeodomain Complexes Embo J. V. 27 2018 2008.
ISSN: ISSN 0261-4189
PubMed: 18583962
DOI: 10.1038/EMBOJ.2008.123
Page generated: Wed Dec 16 03:33:12 2020

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