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Zinc in PDB 6cme: Structure of Wild-Type ISL2-Lid in Complex with LHX4-LIM1+2

Protein crystallography data

The structure of Structure of Wild-Type ISL2-Lid in Complex with LHX4-LIM1+2, PDB code: 6cme was solved by P.H.Stokes, A.Silva, 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) 25.00 / 1.92
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.488, 88.843, 50.303, 90.00, 111.33, 90.00
R / Rfree (%) 20.1 / 24.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Wild-Type ISL2-Lid in Complex with LHX4-LIM1+2 (pdb code 6cme). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of Wild-Type ISL2-Lid in Complex with LHX4-LIM1+2, PDB code: 6cme:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6cme

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Zinc binding site 1 out of 8 in the Structure of Wild-Type ISL2-Lid in Complex with LHX4-LIM1+2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Wild-Type ISL2-Lid in Complex with LHX4-LIM1+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:21.7
occ:1.00
ND1 A:HIS51 2.2 19.2 1.0
SG A:CYS33 2.3 21.4 1.0
SG A:CYS54 2.3 23.6 1.0
SG A:CYS30 2.4 20.0 1.0
CB A:CYS30 3.0 20.0 1.0
CG A:HIS51 3.2 20.3 1.0
CE1 A:HIS51 3.2 19.0 1.0
CB A:CYS33 3.2 20.9 1.0
CB A:CYS54 3.3 23.4 1.0
CB A:HIS51 3.4 20.5 1.0
N A:CYS33 3.7 21.8 1.0
O A:HOH606 3.9 45.3 1.0
O A:HOH543 4.0 43.1 1.0
CA A:CYS33 4.0 21.9 1.0
N A:HIS51 4.3 20.2 1.0
CD2 A:HIS51 4.3 19.9 1.0
NE2 A:HIS51 4.3 18.9 1.0
CA A:CYS30 4.5 20.8 1.0
CA A:HIS51 4.5 20.9 1.0
CA A:CYS54 4.6 23.8 1.0
C A:GLY32 4.7 21.6 1.0
C A:CYS33 4.8 22.6 1.0
CA A:GLY32 4.9 20.9 1.0
N A:CYS54 4.9 23.8 1.0
N A:ASN34 4.9 22.5 1.0
C A:CYS30 5.0 19.4 1.0

Zinc binding site 2 out of 8 in 6cme

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Zinc binding site 2 out of 8 in the Structure of Wild-Type ISL2-Lid in Complex with LHX4-LIM1+2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Wild-Type ISL2-Lid in Complex with LHX4-LIM1+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:27.8
occ:1.00
OD2 A:ASP80 1.9 29.5 1.0
SG A:CYS77 2.2 27.1 1.0
SG A:CYS60 2.3 32.0 1.0
SG A:CYS57 2.4 25.9 1.0
CG A:ASP80 2.9 32.7 1.0
CB A:CYS57 3.1 24.8 1.0
CB A:CYS60 3.3 31.9 1.0
CB A:ASP80 3.3 32.6 1.0
CB A:CYS77 3.4 25.7 1.0
N A:CYS60 3.7 31.2 1.0
OD1 A:ASP80 3.9 35.2 1.0
N A:CYS77 4.0 23.1 1.0
CA A:CYS60 4.1 33.1 1.0
CA A:CYS77 4.2 25.6 1.0
CB A:ASP59 4.5 34.7 1.0
N A:ASP80 4.5 33.3 1.0
CA A:ASP80 4.5 33.0 1.0
CA A:CYS57 4.6 24.3 1.0
CG A:MET62 4.7 47.4 1.0
C A:ASP59 4.8 32.8 1.0
C A:CYS60 4.8 32.6 1.0
C A:CYS77 4.9 27.9 1.0
O A:CYS77 4.9 25.3 1.0
N A:GLN61 4.9 32.3 1.0
SD A:MET62 4.9 56.2 1.0
CA A:ASP59 5.0 32.7 1.0

Zinc binding site 3 out of 8 in 6cme

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Zinc binding site 3 out of 8 in the Structure of Wild-Type ISL2-Lid in Complex with LHX4-LIM1+2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Wild-Type ISL2-Lid in Complex with LHX4-LIM1+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:27.9
occ:1.00
ND1 A:HIS111 2.0 27.3 1.0
SG A:CYS92 2.2 30.5 1.0
SG A:CYS114 2.4 28.9 1.0
SG A:CYS89 2.4 27.7 1.0
CE1 A:HIS111 2.9 29.2 1.0
CB A:CYS89 2.9 29.9 1.0
CG A:HIS111 3.1 26.4 1.0
CB A:CYS92 3.3 30.1 1.0
CB A:CYS114 3.3 25.8 1.0
O A:HOH557 3.5 43.8 1.0
CB A:HIS111 3.5 24.8 1.0
N A:CYS92 3.8 29.9 1.0
N A:HIS111 4.0 22.7 1.0
NE2 A:HIS111 4.1 30.4 1.0
CA A:CYS92 4.1 31.2 1.0
CD2 A:HIS111 4.2 28.0 1.0
CA A:CYS89 4.4 31.3 1.0
CA A:HIS111 4.4 23.7 1.0
NE2 A:HIS113 4.6 28.7 1.0
CA A:CYS114 4.7 24.1 1.0
CB A:ALA91 4.8 26.0 1.0
C A:CYS92 4.9 33.0 1.0
N A:GLN93 4.9 34.9 1.0
C A:ALA91 5.0 28.7 1.0
C A:CYS89 5.0 29.5 1.0

Zinc binding site 4 out of 8 in 6cme

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Zinc binding site 4 out of 8 in the Structure of Wild-Type ISL2-Lid in Complex with LHX4-LIM1+2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Wild-Type ISL2-Lid in Complex with LHX4-LIM1+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:23.2
occ:1.00
OD2 A:ASP143 2.0 28.1 1.0
SG A:CYS117 2.3 20.6 1.0
SG A:CYS140 2.3 22.8 1.0
SG A:CYS120 2.3 28.3 1.0
CG A:ASP143 3.0 26.1 1.0
CB A:CYS117 3.0 21.9 1.0
CB A:CYS120 3.2 27.9 1.0
CB A:CYS140 3.4 21.0 1.0
CB A:ASP143 3.5 25.3 1.0
N A:CYS120 3.6 26.2 1.0
CA A:CYS120 4.0 26.7 1.0
OD1 A:ASP143 4.0 30.1 1.0
N A:CYS140 4.0 19.1 1.0
O A:HOH556 4.1 53.5 1.0
CA A:CYS140 4.2 20.9 1.0
CA A:CYS117 4.5 22.2 1.0
CB A:ILE119 4.5 24.9 1.0
C A:ILE119 4.7 26.0 1.0
N A:ASP143 4.7 23.6 1.0
CA A:ASP143 4.7 24.2 1.0
NH1 A:ARG122 4.8 45.2 1.0
CG2 A:ILE119 4.8 24.8 1.0
C A:CYS120 4.9 26.2 1.0
C A:CYS140 4.9 20.4 1.0
N A:ILE119 4.9 24.2 1.0
O A:CYS140 4.9 19.9 1.0
CA A:ILE119 4.9 24.9 1.0

Zinc binding site 5 out of 8 in 6cme

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Zinc binding site 5 out of 8 in the Structure of Wild-Type ISL2-Lid in Complex with LHX4-LIM1+2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Wild-Type ISL2-Lid in Complex with LHX4-LIM1+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:21.7
occ:1.00
ND1 B:HIS51 2.1 23.2 1.0
SG B:CYS54 2.2 22.2 1.0
SG B:CYS33 2.3 23.0 1.0
SG B:CYS30 2.4 22.5 1.0
CB B:CYS30 3.0 22.2 1.0
CG B:HIS51 3.1 23.9 1.0
CE1 B:HIS51 3.1 24.3 1.0
CB B:CYS54 3.2 22.6 1.0
CB B:CYS33 3.3 23.0 1.0
CB B:HIS51 3.4 23.6 1.0
N B:CYS33 3.7 22.9 1.0
CA B:CYS33 4.1 23.1 1.0
NE2 B:HIS51 4.2 22.8 1.0
CD2 B:HIS51 4.2 22.3 1.0
N B:HIS51 4.3 21.9 1.0
CA B:HIS51 4.4 23.1 1.0
CA B:CYS30 4.5 22.9 1.0
CA B:CYS54 4.6 23.7 1.0
C B:GLY32 4.7 22.2 1.0
C B:CYS33 4.8 23.4 1.0
CA B:GLY32 4.9 22.5 1.0
N B:CYS54 4.9 23.5 1.0
N B:ASN34 5.0 22.3 1.0

Zinc binding site 6 out of 8 in 6cme

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Zinc binding site 6 out of 8 in the Structure of Wild-Type ISL2-Lid in Complex with LHX4-LIM1+2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Wild-Type ISL2-Lid in Complex with LHX4-LIM1+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:27.9
occ:1.00
OD2 B:ASP80 1.8 29.0 1.0
SG B:CYS77 2.2 27.3 1.0
SG B:CYS60 2.3 29.2 1.0
SG B:CYS57 2.4 24.1 1.0
CG B:ASP80 2.9 32.1 1.0
CB B:CYS57 3.1 23.2 1.0
CB B:CYS60 3.3 30.1 1.0
CB B:CYS77 3.4 26.1 1.0
CB B:ASP80 3.4 29.8 1.0
N B:CYS60 3.7 30.8 1.0
N B:CYS77 3.9 23.2 1.0
OD1 B:ASP80 3.9 32.9 1.0
CA B:CYS60 4.1 31.1 1.0
CA B:CYS77 4.2 25.2 1.0
CB B:ASP59 4.4 34.0 1.0
N B:ASP80 4.5 31.0 1.0
CA B:ASP80 4.6 30.3 1.0
CA B:CYS57 4.6 23.5 1.0
CG B:MET62 4.8 42.5 1.0
C B:CYS60 4.8 30.1 1.0
C B:ASP59 4.8 31.8 1.0
C B:CYS77 4.9 26.1 1.0
N B:GLN61 4.9 30.1 1.0
O B:CYS77 5.0 25.4 1.0

Zinc binding site 7 out of 8 in 6cme

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Zinc binding site 7 out of 8 in the Structure of Wild-Type ISL2-Lid in Complex with LHX4-LIM1+2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Wild-Type ISL2-Lid in Complex with LHX4-LIM1+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:23.2
occ:1.00
ND1 B:HIS111 2.0 21.7 1.0
SG B:CYS92 2.3 25.3 1.0
SG B:CYS114 2.3 23.4 1.0
SG B:CYS89 2.4 23.0 1.0
CE1 B:HIS111 2.9 23.1 1.0
CB B:CYS89 2.9 25.6 1.0
CG B:HIS111 3.1 22.4 1.0
CB B:CYS114 3.2 23.1 1.0
CB B:CYS92 3.3 26.3 1.0
CB B:HIS111 3.5 22.0 1.0
N B:CYS92 3.8 24.4 1.0
N B:HIS111 4.0 21.4 1.0
NE2 B:HIS111 4.1 22.5 1.0
CD2 B:HIS111 4.2 22.6 1.0
CA B:CYS92 4.2 26.3 1.0
CA B:HIS111 4.4 23.1 1.0
CA B:CYS89 4.4 26.8 1.0
CA B:CYS114 4.6 23.8 1.0
CB B:ALA91 4.7 26.7 1.0
C B:ALA91 4.9 25.9 1.0
C B:CYS92 4.9 27.8 1.0
C B:CYS89 5.0 25.8 1.0

Zinc binding site 8 out of 8 in 6cme

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Zinc binding site 8 out of 8 in the Structure of Wild-Type ISL2-Lid in Complex with LHX4-LIM1+2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Wild-Type ISL2-Lid in Complex with LHX4-LIM1+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn404

b:26.1
occ:1.00
OD2 B:ASP143 2.0 25.1 1.0
SG B:CYS140 2.3 22.8 1.0
SG B:CYS117 2.3 22.3 1.0
SG B:CYS120 2.3 28.0 1.0
CG B:ASP143 3.0 24.4 1.0
CB B:CYS117 3.0 21.8 1.0
CB B:CYS120 3.3 27.1 1.0
CB B:CYS140 3.3 21.1 1.0
CB B:ASP143 3.5 22.9 1.0
N B:CYS120 3.7 25.1 1.0
OD1 B:ASP143 4.0 27.9 1.0
CA B:CYS120 4.1 26.1 1.0
N B:CYS140 4.1 20.1 1.0
CA B:CYS140 4.2 20.4 1.0
CA B:CYS117 4.5 21.8 1.0
CB B:ILE119 4.6 23.6 1.0
CA B:ASP143 4.7 22.8 1.0
N B:ASP143 4.7 23.6 1.0
C B:ILE119 4.8 25.1 1.0
O B:CYS140 4.8 19.1 1.0
C B:CYS120 4.9 27.6 1.0
C B:CYS140 4.9 20.4 1.0
CG2 B:ILE119 4.9 23.5 1.0
N B:ILE119 5.0 23.7 1.0

Reference:

P.H.Stokes, N.O.Robertson, A.P.G.Silva, T.Estephan, J.Trewhella, J.M.Guss, J.M.Matthews. Mutation in A Flexible Linker Modulates Binding Affinity For Modular Complexes. Proteins V. 87 425 2019.
ISSN: ESSN 1097-0134
PubMed: 30788856
DOI: 10.1002/PROT.25675
Page generated: Wed Dec 16 11:37:13 2020

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