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Zinc in PDB 4wco: Crystal Structure of Extracellular Domain of Human Lectin-Like Transcript 1 (LLT1), the Ligand For Natural Killer Receptor-P1A

Protein crystallography data

The structure of Crystal Structure of Extracellular Domain of Human Lectin-Like Transcript 1 (LLT1), the Ligand For Natural Killer Receptor-P1A, PDB code: 4wco was solved by S.Kita, H.Matsubara, Y.Kasai, T.Tamaoki, Y.Okabe, H.Fukuhara, J.Kamishikiryo, T.Ose, K.Kuroki, K.Maenaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.65 / 2.46
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 82.379, 84.658, 53.422, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 25.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Extracellular Domain of Human Lectin-Like Transcript 1 (LLT1), the Ligand For Natural Killer Receptor-P1A (pdb code 4wco). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of Extracellular Domain of Human Lectin-Like Transcript 1 (LLT1), the Ligand For Natural Killer Receptor-P1A, PDB code: 4wco:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 4wco

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Zinc binding site 1 out of 7 in the Crystal Structure of Extracellular Domain of Human Lectin-Like Transcript 1 (LLT1), the Ligand For Natural Killer Receptor-P1A


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 Extracellular Domain of Human Lectin-Like Transcript 1 (LLT1), the Ligand For Natural Killer Receptor-P1A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:86.3
occ:1.00
OD1 A:ASP109 2.4 52.2 1.0
O A:HOH703 2.4 45.8 1.0
CG A:ASP109 3.1 50.6 1.0
OD1 A:ASP104 3.2 73.7 1.0
OD2 A:ASP109 3.2 54.5 1.0
O A:ALA108 3.7 47.0 1.0
NE2 A:GLN100 4.3 44.5 1.0
CG A:ASP104 4.3 72.9 1.0
C A:ALA108 4.5 46.9 1.0
CB A:ASP109 4.5 45.7 1.0
CB A:ASP104 4.8 61.3 1.0
CA A:ASP104 4.9 53.0 1.0
CA A:ASP109 4.9 44.8 1.0

Zinc binding site 2 out of 7 in 4wco

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Zinc binding site 2 out of 7 in the Crystal Structure of Extracellular Domain of Human Lectin-Like Transcript 1 (LLT1), the Ligand For Natural Killer Receptor-P1A


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 Extracellular Domain of Human Lectin-Like Transcript 1 (LLT1), the Ligand For Natural Killer Receptor-P1A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:80.0
occ:1.00
O3 B:SO4503 2.5 37.4 1.0
OD2 B:ASP92 2.9 40.3 1.0
S B:SO4503 3.5 32.5 1.0
O2 B:SO4503 3.6 39.5 1.0
O B:THR93 3.8 33.1 1.0
CG B:ASP92 3.8 41.9 1.0
O4 B:SO4503 3.9 32.7 1.0
OD1 B:ASP92 3.9 43.5 1.0
NZ B:LYS94 4.7 39.0 1.0
O1 B:SO4503 4.8 38.6 1.0
CG B:LYS94 4.9 32.3 1.0

Zinc binding site 3 out of 7 in 4wco

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Zinc binding site 3 out of 7 in the Crystal Structure of Extracellular Domain of Human Lectin-Like Transcript 1 (LLT1), the Ligand For Natural Killer Receptor-P1A


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 Extracellular Domain of Human Lectin-Like Transcript 1 (LLT1), the Ligand For Natural Killer Receptor-P1A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:30.5
occ:1.00
OD1 C:ASP109 1.9 36.4 1.0
OE2 B:GLU179 2.0 49.4 1.0
O C:HOH813 2.0 17.9 1.0
O2 B:SO4503 2.0 39.5 1.0
OE1 B:GLU179 2.4 46.3 1.0
CD B:GLU179 2.4 43.9 1.0
OD2 C:ASP109 2.5 30.1 1.0
CG C:ASP109 2.5 28.5 1.0
S B:SO4503 3.2 32.5 1.0
O1 B:SO4503 3.4 38.6 1.0
O4 B:SO4503 3.7 32.7 1.0
CG B:GLU179 3.9 40.5 1.0
O C:ALA108 4.0 32.5 1.0
CB C:ASP109 4.0 23.3 1.0
NE2 C:GLN100 4.1 33.5 1.0
OD1 C:ASP104 4.1 32.0 1.0
O3 B:SO4503 4.4 37.4 1.0
C C:ALA108 4.6 32.2 1.0
CG2 C:ILE146 4.7 25.5 1.0
CA C:ASP109 4.7 30.4 1.0
CB B:GLU179 4.9 39.4 1.0
N C:ASP109 5.0 29.6 1.0

Zinc binding site 4 out of 7 in 4wco

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Zinc binding site 4 out of 7 in the Crystal Structure of Extracellular Domain of Human Lectin-Like Transcript 1 (LLT1), the Ligand For Natural Killer Receptor-P1A


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 Extracellular Domain of Human Lectin-Like Transcript 1 (LLT1), the Ligand For Natural Killer Receptor-P1A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:79.1
occ:1.00
OD1 B:ASP109 2.4 47.9 1.0
OD2 B:ASP109 3.0 48.6 1.0
CG B:ASP109 3.1 44.4 1.0
OD2 B:ASP104 3.7 53.5 1.0
O B:ALA108 4.2 28.9 1.0
CB B:ASP109 4.5 39.7 1.0
NE2 B:GLN100 4.6 28.1 1.0
CG2 B:ILE146 4.7 56.1 1.0
CG B:ASP104 4.9 47.8 1.0
C B:ALA108 4.9 27.1 1.0

Zinc binding site 5 out of 7 in 4wco

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Zinc binding site 5 out of 7 in the Crystal Structure of Extracellular Domain of Human Lectin-Like Transcript 1 (LLT1), the Ligand For Natural Killer Receptor-P1A


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 Extracellular Domain of Human Lectin-Like Transcript 1 (LLT1), the Ligand For Natural Killer Receptor-P1A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:62.3
occ:1.00
OE1 C:GLU179 1.9 63.0 1.0
O C:HOH808 2.5 33.8 1.0
O C:ACT204 2.7 32.0 1.0
CD C:GLU179 2.9 59.9 1.0
OE2 C:GLU179 3.2 64.6 1.0
OXT C:ACT204 3.6 32.2 1.0
C C:ACT204 3.6 26.9 1.0
CG C:GLU179 4.2 53.7 1.0
CB C:GLU179 4.9 46.2 1.0

Zinc binding site 6 out of 7 in 4wco

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Zinc binding site 6 out of 7 in the Crystal Structure of Extracellular Domain of Human Lectin-Like Transcript 1 (LLT1), the Ligand For Natural Killer Receptor-P1A


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 Extracellular Domain of Human Lectin-Like Transcript 1 (LLT1), the Ligand For Natural Killer Receptor-P1A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:50.7
occ:1.00
OD2 C:ASP130 2.1 32.3 1.0
O C:HOH805 2.1 51.9 1.0
OXT C:ACT205 2.4 49.0 1.0
O C:HOH807 2.7 48.6 1.0
CG C:ASP130 3.1 35.1 1.0
OD1 C:ASP130 3.3 37.1 1.0
C C:ACT205 3.5 47.9 1.0
OH C:TYR165 4.0 43.3 1.0
NH1 C:ARG180 4.1 37.0 1.0
CH3 C:ACT205 4.3 45.8 1.0
CE1 C:TYR165 4.3 41.0 1.0
O C:ACT205 4.3 46.6 1.0
CB C:ASP130 4.4 31.9 1.0
CZ C:TYR165 4.5 43.2 1.0

Zinc binding site 7 out of 7 in 4wco

Go back to Zinc Binding Sites List in 4wco
Zinc binding site 7 out of 7 in the Crystal Structure of Extracellular Domain of Human Lectin-Like Transcript 1 (LLT1), the Ligand For Natural Killer Receptor-P1A


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 Extracellular Domain of Human Lectin-Like Transcript 1 (LLT1), the Ligand For Natural Killer Receptor-P1A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn203

b:0.7
occ:1.00
OD1 C:ASP107 2.5 50.4 1.0
O C:HOH812 2.7 37.7 1.0
OD2 C:ASP107 3.1 50.8 1.0
CG C:ASP107 3.2 49.4 1.0
O3 B:SO4503 3.8 37.4 1.0
CB C:ASP107 4.7 44.2 1.0
O1 B:SO4503 4.9 38.6 1.0
S B:SO4503 4.9 32.5 1.0

Reference:

S.Kita, H.Matsubara, Y.Kasai, T.Tamaoki, Y.Okabe, H.Fukuhara, J.Kamishikiryo, E.Krayukhina, S.Uchiyama, T.Ose, K.Kuroki, K.Maenaka. Crystal Structure of Extracellular Domain of Human Lectin-Like Transcript 1 (LLT1), the Ligand For Natural Killer Receptor-P1A Eur.J.Immunol. V. 45 1605 2015.
ISSN: ISSN 0014-2980
PubMed: 25826155
DOI: 10.1002/EJI.201545509
Page generated: Wed Dec 16 05:50:50 2020

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