Atomistry » Zinc » PDB 6cll-6cvr » 6cme
Atomistry »
  Zinc »
    PDB 6cll-6cvr »
      6cme »

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

Go back to Zinc Binding Sites List in 6cme
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

Go back to Zinc Binding Sites List in 6cme
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

Go back to Zinc Binding Sites List in 6cme
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

Go back to Zinc Binding Sites List in 6cme
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

Go back to Zinc Binding Sites List in 6cme
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

Go back to Zinc Binding Sites List in 6cme
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

Go back to Zinc Binding Sites List in 6cme
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

Go back to Zinc Binding Sites List in 6cme
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: Mon Oct 28 19:00:45 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy