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Zinc in PDB 4lcs: The Crystal Structure of Di-Zn Dihydropyrimidinase in Complex with Hydantoin

Protein crystallography data

The structure of The Crystal Structure of Di-Zn Dihydropyrimidinase in Complex with Hydantoin, PDB code: 4lcs was solved by Y.C.Hsieh, M.C.Chen, C.C.Hsu, S.I.Chan, Y.S.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.20
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 161.026, 161.026, 93.438, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 20.2

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystal Structure of Di-Zn Dihydropyrimidinase in Complex with Hydantoin (pdb code 4lcs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The Crystal Structure of Di-Zn Dihydropyrimidinase in Complex with Hydantoin, PDB code: 4lcs:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4lcs

Go back to Zinc Binding Sites List in 4lcs
Zinc binding site 1 out of 2 in the The Crystal Structure of Di-Zn Dihydropyrimidinase in Complex with Hydantoin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Di-Zn Dihydropyrimidinase in Complex with Hydantoin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:49.9
occ:1.00
OQ2 A:KCX155 2.0 27.9 0.5
NE2 A:HIS244 2.2 20.9 1.0
ND1 A:HIS188 2.4 27.5 1.0
CX A:KCX155 3.0 27.0 0.5
CD2 A:HIS244 3.0 21.1 1.0
N A:HYN603 3.0 68.3 1.0
CE1 A:HIS188 3.1 28.1 1.0
C1 A:HYN603 3.1 72.4 1.0
CE1 A:HIS244 3.3 21.8 1.0
OQ1 A:KCX155 3.3 25.8 0.5
CG A:HIS188 3.5 25.9 1.0
ZN A:ZN602 3.5 39.2 1.0
O A:GLY294 3.9 30.4 1.0
CB A:HIS188 3.9 23.7 1.0
NZ A:KCX155 4.1 31.7 1.0
CE1 A:PHE157 4.1 26.7 1.0
CG A:HIS244 4.2 21.9 1.0
NE2 A:HIS188 4.3 33.0 1.0
C2 A:HYN603 4.3 81.2 1.0
ND1 A:HIS244 4.3 20.9 1.0
CG2 A:VAL243 4.4 17.6 1.0
C A:HYN603 4.5 77.2 1.0
CD2 A:HIS188 4.5 27.6 1.0
CE A:KCX155 4.6 29.2 1.0
OD2 A:ASP322 4.7 31.9 1.0
CE1 A:HIS63 4.8 26.4 1.0
NE2 A:HIS63 4.8 25.5 1.0
CA A:HIS188 4.8 23.6 1.0
CD1 A:PHE157 4.9 25.5 1.0
OH A:TYR160 4.9 58.1 1.0
CZ A:PHE157 4.9 23.2 1.0
C A:GLY294 5.0 30.1 1.0
CE2 A:TYR160 5.0 36.9 1.0

Zinc binding site 2 out of 2 in 4lcs

Go back to Zinc Binding Sites List in 4lcs
Zinc binding site 2 out of 2 in the The Crystal Structure of Di-Zn Dihydropyrimidinase in Complex with Hydantoin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Di-Zn Dihydropyrimidinase in Complex with Hydantoin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:39.2
occ:1.00
OQ1 A:KCX155 2.0 25.8 0.5
NE2 A:HIS63 2.1 25.5 1.0
NE2 A:HIS65 2.2 27.3 1.0
OD1 A:ASP322 2.4 32.6 1.0
N A:HYN603 2.9 68.3 1.0
C1 A:HYN603 3.0 72.4 1.0
CE1 A:HIS63 3.1 26.4 1.0
CX A:KCX155 3.1 27.0 0.5
CG A:ASP322 3.1 29.8 1.0
CE1 A:HIS65 3.2 23.8 1.0
CD2 A:HIS63 3.2 24.5 1.0
CD2 A:HIS65 3.2 23.8 1.0
OD2 A:ASP322 3.5 31.9 1.0
ZN A:ZN601 3.5 49.9 1.0
OQ2 A:KCX155 3.6 27.9 0.5
C2 A:HYN603 3.9 81.2 1.0
CD2 A:HIS244 4.0 21.1 1.0
C A:HYN603 4.1 77.2 1.0
NZ A:KCX155 4.2 31.7 1.0
ND1 A:HIS63 4.3 22.8 1.0
ND1 A:HIS65 4.3 24.8 1.0
CB A:ASP322 4.3 26.7 1.0
CG A:HIS63 4.3 24.7 1.0
CG A:HIS65 4.3 24.5 1.0
NE2 A:HIS244 4.4 20.9 1.0
CA A:ASP322 4.7 23.5 1.0
CE2 A:PHE97 4.7 22.2 1.0
N1 A:HYN603 4.7 73.7 1.0
CD2 A:PHE97 4.8 21.9 1.0
O1 A:HYN603 4.8 65.4 1.0

Reference:

Y.C.Hsieh, M.C.Chen, C.C.Hsu, S.I.Chan, Y.S.Yang, C.J.Chen. Crystal Structures of Vertebrate Dihydropyrimidinase and Complexes From Tetraodon Nigroviridis with Lysine Carbamylation: Metal and Structural Requirements For Post-Translational Modification and Function. J.Biol.Chem. V. 288 30645 2013.
ISSN: ISSN 0021-9258
PubMed: 24005677
DOI: 10.1074/JBC.M113.496778
Page generated: Wed Dec 16 05:31:48 2020

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