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Zinc in PDB 2vr2: Human Dihydropyrimidinase

Enzymatic activity of Human Dihydropyrimidinase

All present enzymatic activity of Human Dihydropyrimidinase:
3.5.2.2;

Protein crystallography data

The structure of Human Dihydropyrimidinase, PDB code: 2vr2 was solved by M.Welin, T.Karlberg, J.Andersson, C.H.Arrowsmith, H.Berglund, R.D.Busam, R.Collins, L.G.Dahlgren, A.M.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, M.D.Herman, I.Johansson, A.Kallas, T.Kotenyova, L.Lehtio, M.Moche, M.E.Nilsson, T.Nyman, C.Persson, J.Sagemark, L.Svensson, A.G.Thorsell, L.Tresaugues, S.Van Den Berg, J.Weigelt, M.Wikstrom, P.Nordlund, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.95 / 2.80
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 89.650, 89.650, 219.100, 90.00, 90.00, 120.00
R / Rfree (%) 20 / 25.1

Other elements in 2vr2:

The structure of Human Dihydropyrimidinase also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Dihydropyrimidinase (pdb code 2vr2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Dihydropyrimidinase, PDB code: 2vr2:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2vr2

Go back to Zinc Binding Sites List in 2vr2
Zinc binding site 1 out of 2 in the Human Dihydropyrimidinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Dihydropyrimidinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1494

b:63.7
occ:0.60
NE2 A:HIS67 2.1 58.6 1.0
NE2 A:HIS69 2.2 60.3 1.0
OD1 A:ASP326 2.3 59.7 1.0
O A:HOH2001 2.9 34.0 1.0
CE1 A:HIS67 3.0 58.8 1.0
NZ A:LYS159 3.0 59.7 1.0
CD2 A:HIS69 3.0 60.2 1.0
CD2 A:HIS67 3.2 58.4 1.0
ZN A:ZN1495 3.2 74.5 0.4
CG A:ASP326 3.2 59.4 1.0
CE1 A:HIS69 3.2 60.4 1.0
OD2 A:ASP326 3.6 60.1 1.0
CD2 A:HIS248 3.7 61.2 1.0
NE2 A:HIS248 3.8 61.5 1.0
ND1 A:HIS67 4.1 58.6 1.0
CG A:HIS69 4.2 60.2 1.0
ND1 A:HIS69 4.2 60.5 1.0
CG A:HIS67 4.2 58.2 1.0
CB A:ASP326 4.4 58.8 1.0
CE A:LYS159 4.4 60.1 1.0
CE1 A:PHE101 4.8 59.5 1.0
CA A:ASP326 4.8 58.6 1.0
CD1 A:PHE101 5.0 59.7 1.0

Zinc binding site 2 out of 2 in 2vr2

Go back to Zinc Binding Sites List in 2vr2
Zinc binding site 2 out of 2 in the Human Dihydropyrimidinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Dihydropyrimidinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1495

b:74.5
occ:0.40
NE2 A:HIS248 2.2 61.5 1.0
NZ A:LYS159 2.6 59.7 1.0
ND1 A:HIS192 2.6 60.6 1.0
CE1 A:HIS248 3.0 61.5 1.0
ZN A:ZN1494 3.2 63.7 0.6
CD2 A:HIS248 3.3 61.2 1.0
CE A:LYS159 3.4 60.1 1.0
CE1 A:HIS192 3.5 61.0 1.0
O A:HOH2001 3.5 34.0 1.0
CG A:HIS192 3.6 59.7 1.0
CB A:HIS192 3.9 59.0 1.0
CE2 A:PHE161 4.2 60.9 1.0
ND1 A:HIS248 4.2 61.0 1.0
O A:GLY298 4.2 59.1 1.0
CG2 A:VAL247 4.3 59.5 1.0
CE1 A:HIS67 4.3 58.8 1.0
CG A:HIS248 4.4 60.8 1.0
NE2 A:HIS67 4.4 58.6 1.0
NE2 A:HIS192 4.6 60.8 1.0
CD2 A:HIS192 4.7 60.3 1.0
CD A:LYS159 4.8 60.3 1.0
OD2 A:ASP326 4.8 60.1 1.0
OD1 A:ASP326 4.9 59.7 1.0
CA A:HIS192 4.9 58.7 1.0
CZ A:PHE161 4.9 61.0 1.0
CD2 A:PHE161 4.9 61.0 1.0

Reference:

M.Welin, T.Karlberg, J.Andersson, C.H.Arrowsmith, H.Berglund, R.D.Busam, R.Collins, L.G.Dahlgren, A.M.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, M.D.Herman, I.Johansson, A.Kallas, T.Kotenyova, L.Lehtio, M.Moche, M.E.Nilsson, T.Nyman, C.Persson, J.Sagemark, L.Svensson, A.G.Thorsell, L.Tresaugues, S.Van Den Berg, J.Weigelt, M.Wikstrom, P.Nordlund. The Crystal Structure of Human Dihydropyrimidinase To Be Published.
Page generated: Wed Dec 16 03:55:59 2020

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