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Zinc in PDB 5hee: Crystal Structure of the TK2203 Protein

Protein crystallography data

The structure of Crystal Structure of the TK2203 Protein, PDB code: 5hee was solved by Y.Nishitani, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.69 / 1.41
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 74.373, 42.543, 143.506, 90.00, 94.47, 90.00
R / Rfree (%) 16.3 / 18.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the TK2203 Protein (pdb code 5hee). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of the TK2203 Protein, PDB code: 5hee:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 5hee

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Zinc binding site 1 out of 5 in the Crystal Structure of the TK2203 Protein


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 the TK2203 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:18.4
occ:0.32
NE2 A:HIS10 2.0 17.3 1.0
OD2 A:ASP222 2.1 19.5 1.0
NE2 A:HIS48 2.2 19.6 1.0
O A:HOH1219 2.3 31.8 1.0
O A:HOH1235 2.6 26.8 1.0
O A:HOH1120 2.8 25.0 1.0
CD2 A:HIS10 2.9 12.6 1.0
CD2 A:HIS48 3.0 14.4 1.0
CE1 A:HIS10 3.1 15.4 1.0
CG A:ASP222 3.1 16.6 1.0
CE1 A:HIS48 3.3 22.9 1.0
OD1 A:ASP222 3.8 15.1 1.0
NE2 A:HIS175 3.9 24.1 1.0
OD2 A:ASP172 4.0 17.0 1.0
CB A:ASP222 4.0 16.4 1.0
CB A:ASP172 4.0 14.2 1.0
CG A:HIS10 4.1 15.0 1.0
CE1 A:HIS175 4.1 19.9 1.0
ND1 A:HIS10 4.1 16.9 1.0
CG A:HIS48 4.2 13.8 1.0
O A:HOH1300 4.3 36.5 1.0
CG A:ASP172 4.3 15.7 1.0
ND1 A:HIS48 4.3 18.9 1.0
NE1 A:TRP119 4.7 15.7 1.0
N A:ASP172 4.8 13.5 1.0
CA A:ASP172 5.0 12.7 1.0
CG A:PRO47 5.0 13.5 1.0

Zinc binding site 2 out of 5 in 5hee

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Zinc binding site 2 out of 5 in the Crystal Structure of the TK2203 Protein


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 the TK2203 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:28.5
occ:0.45
OE2 A:GLU198 2.3 46.5 1.0
OE2 A:GLU202 2.9 39.3 1.0
OE1 A:GLU202 3.0 32.9 1.0
CD A:GLU202 3.3 35.6 1.0
O A:HOH1104 3.4 19.4 1.0
CD A:GLU198 3.5 51.9 1.0
NH2 A:ARG204 3.7 40.2 1.0
CG A:GLU198 4.2 41.6 1.0
OE1 A:GLU198 4.4 47.9 1.0
CG A:GLU202 4.8 33.3 1.0
CZ A:ARG204 4.9 29.2 1.0

Zinc binding site 3 out of 5 in 5hee

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Zinc binding site 3 out of 5 in the Crystal Structure of the TK2203 Protein


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 the TK2203 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:21.9
occ:0.32
O B:HOH1264 2.0 25.2 1.0
NE2 B:HIS55 2.0 14.9 1.0
O A:HOH1236 2.0 23.5 1.0
NE2 A:HIS55 2.0 14.1 1.0
CE1 B:HIS55 2.7 13.4 1.0
CE1 A:HIS55 2.8 14.1 1.0
CD2 A:HIS55 3.2 15.7 1.0
CD2 B:HIS55 3.2 14.7 1.0
O A:HOH1312 3.6 43.2 1.0
ND1 B:HIS55 3.9 14.1 1.0
ND1 A:HIS55 4.0 15.7 1.0
O B:HOH1363 4.0 38.9 1.0
CG A:HIS55 4.2 16.0 1.0
CG B:HIS55 4.2 14.8 1.0
O B:HOH1300 4.2 22.2 1.0
O A:HOH1271 4.3 20.1 1.0
O B:HOH1212 4.9 28.6 1.0
O A:HOH1194 4.9 25.9 1.0

Zinc binding site 4 out of 5 in 5hee

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Zinc binding site 4 out of 5 in the Crystal Structure of the TK2203 Protein


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 the TK2203 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:17.3
occ:0.33
O B:HOH1157 2.0 25.4 1.0
NE2 B:HIS10 2.0 17.0 1.0
OD2 B:ASP222 2.1 17.3 1.0
NE2 B:HIS48 2.2 17.8 1.0
O B:HOH1258 2.5 27.7 1.0
O B:HOH1113 2.7 22.8 1.0
CD2 B:HIS10 2.9 13.5 1.0
CD2 B:HIS48 2.9 14.0 1.0
CE1 B:HIS10 3.1 13.8 1.0
CG B:ASP222 3.1 14.9 1.0
CE1 B:HIS48 3.3 21.9 1.0
NE2 B:HIS175 3.8 20.9 1.0
OD1 B:ASP222 3.9 14.4 1.0
CB B:ASP222 4.0 13.3 1.0
OD2 B:ASP172 4.0 15.4 1.0
CB B:ASP172 4.1 12.5 1.0
CG B:HIS10 4.1 13.2 1.0
CE1 B:HIS175 4.1 19.4 1.0
ND1 B:HIS10 4.1 14.3 1.0
CG B:HIS48 4.2 15.8 1.0
ND1 B:HIS48 4.3 18.9 1.0
CG B:ASP172 4.3 13.3 1.0
NE1 B:TRP119 4.5 18.6 1.0
N B:ASP172 4.9 10.9 1.0

Zinc binding site 5 out of 5 in 5hee

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Zinc binding site 5 out of 5 in the Crystal Structure of the TK2203 Protein


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 the TK2203 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:16.4
occ:0.58
OE2 B:GLU198 2.3 17.0 1.0
O B:HOH1291 2.3 22.8 1.0
OE2 B:GLU202 2.4 16.9 1.0
O B:HOH1315 2.4 19.1 1.0
OE1 B:GLU202 2.6 16.6 1.0
CD B:GLU202 2.8 14.6 1.0
CD B:GLU198 3.4 21.2 1.0
CG B:GLU198 3.8 16.4 1.0
NH1 B:ARG204 4.0 16.6 1.0
O B:HOH1309 4.1 40.1 1.0
CG B:GLU202 4.3 14.6 1.0
O B:HOH1146 4.4 32.9 1.0
OE1 B:GLU198 4.5 22.9 1.0
O B:HOH1128 4.6 25.6 1.0
O B:HOH1343 4.9 43.4 1.0
CZ B:ARG204 4.9 16.9 1.0
NE B:ARG204 5.0 18.7 1.0

Reference:

Y.Nishitani, J.R.Simons, T.Kanai, H.Atomi, K.Miki. Crystal Structure of the TK2203 Protein From Thermococcus Kodakarensis, A Putative Extradiol Dioxygenase Acta Crystallogr.,Sect.F V. 72 427 2016.
ISSN: ESSN 2053-230X
PubMed: 27303894
DOI: 10.1107/S2053230X16006920
Page generated: Wed Dec 16 06:20:16 2020

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