Zinc in PDB 2rgt: Crystal Structure of LHX3 Lim Domains 1 and 2 with the Binding Domain of ISL1

Protein crystallography data

The structure of Crystal Structure of LHX3 Lim Domains 1 and 2 with the Binding Domain of ISL1, PDB code: 2rgt was solved by M.Bhati, M.Lee, J.M.Guss, J.M.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.05
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 119.494, 62.218, 51.885, 90.00, 91.61, 90.00
R / Rfree (%) 21.1 / 25.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of LHX3 Lim Domains 1 and 2 with the Binding Domain of ISL1 (pdb code 2rgt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of LHX3 Lim Domains 1 and 2 with the Binding Domain of ISL1, PDB code: 2rgt:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2rgt

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Zinc binding site 1 out of 8 in the Crystal Structure of LHX3 Lim Domains 1 and 2 with the Binding Domain of ISL1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of LHX3 Lim Domains 1 and 2 with the Binding Domain of ISL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn205

b:60.7
occ:1.00
 ND1 A:HIS55 2.0 40.3 1.0
SG A:CYS34 2.1 44.7 1.0
SG A:CYS58 2.3 49.5 1.0
SG A:CYS37 2.6 47.7 1.0
CE1 A:HIS55 2.9 42.9 1.0
CG A:HIS55 3.0 43.7 1.0
CB A:CYS58 3.1 45.4 1.0
CB A:CYS37 3.4 48.5 1.0
CB A:CYS34 3.4 48.0 1.0
CB A:HIS55 3.4 44.6 1.0
O A:CYS37 3.5 50.0 1.0
N A:CYS37 3.6 48.4 1.0
CA A:CYS37 4.0 48.9 1.0
N A:HIS55 4.0 44.6 1.0
NE2 A:HIS55 4.1 42.0 1.0
CD2 A:HIS55 4.1 41.9 1.0
C A:CYS37 4.2 49.6 1.0
CA A:HIS55 4.3 45.0 1.0
O A:GLN39 4.5 48.6 1.0
C A:GLY36 4.5 48.8 1.0
CA A:CYS58 4.5 46.1 1.0
CA A:GLY36 4.6 48.3 1.0
CA A:CYS34 4.7 48.0 1.0
N A:GLY36 4.8 48.0 1.0
C A:CYS34 4.8 48.3 1.0
O A:HIS55 4.9 45.9 1.0
N A:CYS58 4.9 47.2 1.0

Zinc binding site 2 out of 8 in 2rgt

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Zinc binding site 2 out of 8 in the Crystal Structure of LHX3 Lim Domains 1 and 2 with the Binding Domain of ISL1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of LHX3 Lim Domains 1 and 2 with the Binding Domain of ISL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn206

b:51.9
occ:1.00
 OD1 A:ASP84 2.1 46.3 1.0
SG A:CYS61 2.2 42.8 1.0
SG A:CYS64 2.3 49.1 1.0
SG A:CYS81 2.3 49.1 1.0
CB A:CYS61 2.9 43.8 1.0
CG A:ASP84 3.1 47.6 1.0
CB A:CYS81 3.3 45.9 1.0
CB A:CYS64 3.4 49.2 1.0
CB A:ASP84 3.4 47.7 1.0
N A:CYS64 3.7 49.9 1.0
CG1 A:VAL66 3.9 48.3 1.0
N A:CYS81 4.0 44.0 1.0
CA A:CYS64 4.1 49.5 1.0
CA A:CYS81 4.2 45.8 1.0
OD2 A:ASP84 4.3 45.7 1.0
CA A:CYS61 4.4 44.0 1.0
N A:ASP84 4.5 47.5 1.0
O A:CYS81 4.6 46.5 1.0
CA A:ASP84 4.6 47.3 1.0
C A:CYS81 4.7 46.1 1.0
C A:ASP63 4.8 50.1 1.0
C A:CYS64 4.9 49.4 1.0
CB A:ASP63 4.9 49.3 1.0

Zinc binding site 3 out of 8 in 2rgt

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Zinc binding site 3 out of 8 in the Crystal Structure of LHX3 Lim Domains 1 and 2 with the Binding Domain of ISL1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of LHX3 Lim Domains 1 and 2 with the Binding Domain of ISL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn207

b:31.9
occ:1.00
 ND1 A:HIS115 2.2 26.4 1.0
SG A:CYS118 2.2 33.1 1.0
SG A:CYS93 2.3 37.3 1.0
SG A:CYS96 2.4 38.2 1.0
CB A:CYS93 3.0 36.5 1.0
CG A:HIS115 3.1 27.6 1.0
CE1 A:HIS115 3.2 25.5 1.0
CB A:CYS118 3.2 31.1 1.0
CB A:CYS96 3.3 37.0 1.0
CB A:HIS115 3.4 28.9 1.0
N A:CYS96 3.7 36.8 1.0
O A:HOH295 3.9 33.0 1.0
CA A:CYS96 4.1 37.8 1.0
N A:HIS115 4.1 29.4 1.0
CD2 A:HIS115 4.3 27.4 1.0
NE2 A:HIS115 4.3 28.2 1.0
NE2 A:HIS117 4.4 32.9 1.0
CA A:HIS115 4.4 29.7 1.0
CA A:CYS93 4.5 35.8 1.0
CB A:ALA95 4.5 37.3 1.0
CA A:CYS118 4.7 30.7 1.0
CE1 A:HIS117 4.7 34.0 1.0
C A:ALA95 4.8 37.3 1.0
C A:CYS96 4.8 38.9 1.0
C A:CYS93 5.0 36.4 1.0
N A:GLN97 5.0 39.5 1.0

Zinc binding site 4 out of 8 in 2rgt

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Zinc binding site 4 out of 8 in the Crystal Structure of LHX3 Lim Domains 1 and 2 with the Binding Domain of ISL1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of LHX3 Lim Domains 1 and 2 with the Binding Domain of ISL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn208

b:40.7
occ:1.00
 OD2 A:ASP147 2.2 40.7 1.0
SG A:CYS124 2.3 33.1 1.0
SG A:CYS121 2.3 30.9 1.0
SG A:CYS144 2.4 41.1 1.0
CB A:CYS121 3.0 29.6 1.0
CB A:CYS124 3.2 31.0 1.0
CG A:ASP147 3.3 38.3 1.0
CB A:CYS144 3.5 38.5 1.0
N A:CYS124 3.6 31.4 1.0
CB A:ASP147 3.8 39.2 1.0
CA A:CYS124 4.0 32.4 1.0
N A:CYS144 4.1 37.5 1.0
OD1 A:ASP147 4.3 40.5 1.0
CA A:CYS144 4.4 39.0 1.0
CA A:CYS121 4.5 31.0 1.0
CB A:VAL123 4.6 33.0 1.0
C A:VAL123 4.7 33.0 1.0
C A:CYS124 4.8 31.9 1.0
N A:ASP147 4.9 40.9 1.0
N A:LYS125 4.9 31.8 1.0
CA A:ASP147 5.0 39.5 1.0

Zinc binding site 5 out of 8 in 2rgt

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Zinc binding site 5 out of 8 in the Crystal Structure of LHX3 Lim Domains 1 and 2 with the Binding Domain of ISL1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of LHX3 Lim Domains 1 and 2 with the Binding Domain of ISL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn200

b:59.2
occ:1.00
 SG B:CYS37 2.1 40.7 1.0
ND1 B:HIS55 2.2 41.6 1.0
SG B:CYS34 2.4 42.9 1.0
SG B:CYS58 2.6 44.4 1.0
CB B:CYS34 3.0 42.8 1.0
CE1 B:HIS55 3.2 34.1 1.0
CG B:HIS55 3.2 39.4 1.0
CB B:CYS58 3.2 42.5 1.0
CB B:CYS37 3.3 43.8 1.0
CB B:HIS55 3.5 38.8 1.0
N B:CYS37 3.7 44.1 1.0
CA B:CYS37 4.1 44.4 1.0
N B:HIS55 4.2 38.6 1.0
NE2 B:HIS55 4.3 38.4 1.0
CD2 B:HIS55 4.4 38.8 1.0
CA B:CYS34 4.5 43.1 1.0
CA B:HIS55 4.5 39.1 1.0
CA B:CYS58 4.6 42.5 1.0
C B:GLY36 4.7 44.9 1.0
CA B:GLY36 4.8 44.8 1.0
CE B:LYS57 4.9 49.6 1.0
C B:CYS37 4.9 45.2 1.0
N B:GLY36 4.9 45.0 1.0
N B:CYS58 5.0 42.8 1.0

Zinc binding site 6 out of 8 in 2rgt

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Zinc binding site 6 out of 8 in the Crystal Structure of LHX3 Lim Domains 1 and 2 with the Binding Domain of ISL1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of LHX3 Lim Domains 1 and 2 with the Binding Domain of ISL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:54.6
occ:1.00
 OD2 B:ASP84 2.3 37.2 1.0
SG B:CYS81 2.3 38.0 1.0
SG B:CYS64 2.3 45.6 1.0
SG B:CYS61 2.4 41.6 1.0
CB B:CYS61 3.1 41.5 1.0
CG B:ASP84 3.2 39.6 1.0
CB B:CYS64 3.4 47.2 1.0
CB B:ASP84 3.4 38.5 1.0
CB B:CYS81 3.5 38.5 1.0
N B:CYS64 3.8 46.8 1.0
N B:CYS81 4.0 39.0 1.0
CA B:CYS64 4.2 46.9 1.0
OD1 B:ASP84 4.3 44.8 1.0
CA B:CYS81 4.3 38.6 1.0
CG1 B:VAL66 4.4 47.2 1.0
CB B:ASP63 4.5 47.2 1.0
N B:ASP84 4.5 39.4 1.0
CA B:CYS61 4.6 42.2 1.0
CA B:ASP84 4.6 39.7 1.0
C B:ASP63 4.9 47.0 1.0
C B:CYS64 4.9 47.6 1.0
C B:CYS81 5.0 39.1 1.0
N B:ASP63 5.0 46.8 1.0

Zinc binding site 7 out of 8 in 2rgt

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Zinc binding site 7 out of 8 in the Crystal Structure of LHX3 Lim Domains 1 and 2 with the Binding Domain of ISL1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of LHX3 Lim Domains 1 and 2 with the Binding Domain of ISL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn203

b:32.3
occ:1.00
 ND1 B:HIS115 2.2 26.9 1.0
SG B:CYS96 2.3 30.6 1.0
SG B:CYS93 2.3 26.7 1.0
SG B:CYS118 2.4 25.9 1.0
CB B:CYS93 3.0 29.5 1.0
CE1 B:HIS115 3.1 27.4 1.0
CG B:HIS115 3.3 29.2 1.0
CB B:CYS118 3.3 25.5 1.0
CB B:CYS96 3.5 28.2 1.0
CB B:HIS115 3.6 25.9 1.0
N B:CYS96 3.7 28.5 1.0
O B:HOH298 3.9 26.4 1.0
CA B:CYS96 4.1 27.5 1.0
N B:HIS115 4.2 28.2 1.0
NE2 B:HIS115 4.3 28.1 1.0
CD2 B:HIS115 4.4 25.6 1.0
CA B:CYS93 4.4 29.8 1.0
NE2 B:HIS117 4.4 24.3 1.0
CA B:HIS115 4.5 28.7 1.0
CB B:ALA95 4.6 29.6 1.0
CA B:CYS118 4.7 26.4 1.0
C B:ALA95 4.7 28.9 1.0
CD2 B:HIS117 4.8 26.0 1.0
N B:ALA95 4.8 30.1 1.0
C B:CYS96 4.9 29.2 1.0
C B:CYS93 4.9 29.9 1.0
CA B:ALA95 4.9 30.0 1.0

Zinc binding site 8 out of 8 in 2rgt

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Zinc binding site 8 out of 8 in the Crystal Structure of LHX3 Lim Domains 1 and 2 with the Binding Domain of ISL1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of LHX3 Lim Domains 1 and 2 with the Binding Domain of ISL1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn204

b:30.6
occ:1.00
 OD2 B:ASP147 2.1 28.1 1.0
SG B:CYS144 2.3 28.4 1.0
SG B:CYS121 2.4 23.8 1.0
SG B:CYS124 2.4 25.4 1.0
CG B:ASP147 3.0 29.4 1.0
CB B:CYS121 3.0 26.7 1.0
CB B:CYS124 3.1 19.0 1.0
CB B:CYS144 3.4 27.7 1.0
CB B:ASP147 3.5 28.2 1.0
N B:CYS124 3.8 21.2 1.0
N B:CYS144 3.8 25.6 1.0
CA B:CYS124 4.1 22.5 1.0
OD1 B:ASP147 4.1 23.4 1.0
O B:HOH314 4.1 25.9 1.0
CA B:CYS144 4.2 27.5 1.0
CB B:VAL123 4.3 25.0 1.0
N B:ASP147 4.6 31.4 1.0
CA B:CYS121 4.6 25.4 1.0
CA B:ASP147 4.6 31.0 1.0
CG1 B:VAL123 4.7 20.1 1.0
C B:VAL123 4.8 25.0 1.0
C B:CYS124 4.8 21.9 1.0
N B:VAL123 4.9 25.3 1.0
O B:CYS144 4.9 30.6 1.0
C B:CYS144 5.0 29.1 1.0
C B:VAL143 5.0 27.1 1.0
CA B:VAL123 5.0 21.7 1.0
N B:LYS125 5.0 21.9 1.0
CG1 B:VAL143 5.0 24.5 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: Thu Oct 17 03:48:04 2024

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