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Nickel in PDB 3al6: Crystal Structure of Human TYW5

Protein crystallography data

The structure of Crystal Structure of Human TYW5, PDB code: 3al6 was solved by M.Kato, Y.Araiso, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.02 / 2.80
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 165.871, 165.871, 105.951, 90.00, 90.00, 90.00
R / Rfree (%) 24 / 29.5

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Human TYW5 (pdb code 3al6). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of Human TYW5, PDB code: 3al6:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 3al6

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Nickel binding site 1 out of 4 in the Crystal Structure of Human TYW5


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Human TYW5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni401

b:0.5
occ:1.00
NE2 A:HIS235 2.4 80.3 1.0
OD1 A:ASP162 2.5 81.1 1.0
NE2 A:HIS160 2.5 95.1 1.0
CE1 A:HIS235 3.2 83.2 1.0
CD2 A:HIS160 3.2 87.5 1.0
CG A:ASP162 3.3 80.3 1.0
OD2 A:ASP162 3.3 79.9 1.0
CD2 A:HIS235 3.6 79.2 1.0
CE1 A:HIS160 3.6 93.9 1.0
NH2 A:ARG149 4.0 88.1 1.0
ND2 A:ASN166 4.4 80.1 1.0
ND1 A:HIS235 4.4 84.1 1.0
CG A:HIS160 4.4 93.6 1.0
CZ A:PHE249 4.5 81.6 1.0
CZ A:ARG149 4.6 96.9 1.0
ND1 A:HIS160 4.6 96.0 1.0
NH1 A:ARG149 4.6 0.1 1.0
CG A:HIS235 4.6 80.2 1.0
CB A:ASP162 4.7 80.3 1.0
CE1 A:PHE249 4.9 76.0 1.0

Nickel binding site 2 out of 4 in 3al6

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Nickel binding site 2 out of 4 in the Crystal Structure of Human TYW5


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Human TYW5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni401

b:1.0
occ:1.00
O2 B:AKG501 2.0 63.5 1.0
NE2 B:HIS160 2.0 63.6 1.0
OD1 B:ASP162 2.2 63.9 1.0
O5 B:AKG501 2.6 64.8 1.0
NE2 B:HIS235 2.6 56.9 1.0
C1 B:AKG501 2.9 61.4 1.0
CE1 B:HIS160 3.0 59.6 1.0
CD2 B:HIS160 3.0 60.1 1.0
C2 B:AKG501 3.1 62.8 1.0
CE1 B:HIS235 3.3 58.7 1.0
CG B:ASP162 3.3 62.8 1.0
CD2 B:HIS235 3.8 53.1 1.0
OD2 B:ASP162 3.8 69.2 1.0
O1 B:AKG501 4.0 60.8 1.0
ND1 B:HIS160 4.1 58.5 1.0
CG B:HIS160 4.2 59.1 1.0
NH2 B:ARG149 4.2 57.1 1.0
ND1 B:HIS235 4.5 52.2 1.0
CB B:ASP162 4.6 54.8 1.0
CZ B:PHE249 4.6 59.3 1.0
C3 B:AKG501 4.6 54.6 1.0
NH1 B:ARG149 4.7 62.7 1.0
CG B:HIS235 4.8 55.4 1.0
CZ B:ARG149 4.8 56.2 1.0
ND2 B:ASN166 4.9 52.8 1.0

Nickel binding site 3 out of 4 in 3al6

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Nickel binding site 3 out of 4 in the Crystal Structure of Human TYW5


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Human TYW5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni401

b:0.6
occ:1.00
OD1 C:ASP162 2.5 0.2 1.0
NE2 C:HIS160 2.6 0.8 1.0
NE2 C:HIS235 2.7 1.0 1.0
CE1 C:HIS235 2.7 0.8 1.0
CD2 C:HIS160 2.8 1.0 1.0
CG C:ASP162 3.4 0.8 1.0
OD2 C:ASP162 3.7 0.4 1.0
CE1 C:HIS160 3.7 0.5 1.0
ND1 C:HIS235 4.0 0.0 1.0
CD2 C:HIS235 4.0 0.9 1.0
CG C:HIS160 4.1 0.8 1.0
ND1 C:HIS160 4.5 0.0 1.0
CB C:ASP162 4.6 0.9 1.0
CZ C:PHE249 4.7 0.3 1.0
CG C:HIS235 4.7 0.6 1.0
CE1 C:PHE249 4.7 0.4 1.0
NH1 C:ARG149 4.8 0.9 1.0

Nickel binding site 4 out of 4 in 3al6

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Nickel binding site 4 out of 4 in the Crystal Structure of Human TYW5


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Human TYW5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni401

b:68.9
occ:1.00
NE2 D:HIS160 2.1 52.0 1.0
NE2 D:HIS235 2.2 52.9 1.0
O2 D:AKG501 2.3 62.2 1.0
OD1 D:ASP162 2.4 61.5 1.0
O5 D:AKG501 2.5 49.6 1.0
C1 D:AKG501 3.0 60.3 1.0
C2 D:AKG501 3.0 52.5 1.0
CE1 D:HIS160 3.0 49.2 1.0
CG D:ASP162 3.1 53.4 1.0
OD2 D:ASP162 3.1 60.2 1.0
CD2 D:HIS160 3.2 52.1 1.0
CD2 D:HIS235 3.2 48.8 1.0
CE1 D:HIS235 3.2 52.1 1.0
ND1 D:HIS160 4.2 50.9 1.0
O1 D:AKG501 4.2 61.5 1.0
CG D:HIS160 4.3 57.5 1.0
ND1 D:HIS235 4.3 51.4 1.0
CG D:HIS235 4.4 51.0 1.0
NH2 D:ARG149 4.4 50.9 1.0
C3 D:AKG501 4.5 54.5 1.0
CB D:ASP162 4.6 46.7 1.0
CZ D:PHE249 4.6 59.2 1.0
ND2 D:ASN166 4.7 57.5 1.0

Reference:

M.Kato, Y.Araiso, A.Noma, A.Nagao, T.Suzuki, R.Ishitani, O.Nureki. Crystal Structure of A Novel Jmjc-Domain-Containing Protein, TYW5, Involved in Trna Modification. Nucleic Acids Res. V. 39 1576 2011.
ISSN: ISSN 0305-1048
PubMed: 20972222
DOI: 10.1093/NAR/GKQ919
Page generated: Fri Sep 25 08:19:10 2020
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