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Zinc in PDB 2w4l: Human Dcmp Deaminase

Enzymatic activity of Human Dcmp Deaminase

All present enzymatic activity of Human Dcmp Deaminase:
3.5.4.12;

Protein crystallography data

The structure of Human Dcmp Deaminase, PDB code: 2w4l was solved by M.I.Siponen, M.Moche, C.H.Arrowsmith, H.Berglund, C.Bountra, R.Collins, L.G.Dahlgren, A.M.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, A.Johansson, I.Johansson, T.Karlberg, T.Kotenyova, L.Lehtio, M.E.Nilsson, T.Nyman, C.Persson, J.Sagemark, H.Schuler, A.G.Thorsell, L.Tresaugues, S.Van Den Berg, J.Weigelt, M.Welin, M.Wikstrom, M.Wisniewska, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.70 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 66.230, 80.070, 96.240, 90.00, 94.34, 90.00
R / Rfree (%) 20 / 24.3

Other elements in 2w4l:

The structure of Human Dcmp Deaminase also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Dcmp Deaminase (pdb code 2w4l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Human Dcmp Deaminase, PDB code: 2w4l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2w4l

Go back to Zinc Binding Sites List in 2w4l
Zinc binding site 1 out of 6 in the Human Dcmp Deaminase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Dcmp Deaminase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1170

b:20.0
occ:1.00
ND1 A:HIS84 2.1 19.9 1.0
O A:HOH2049 2.2 22.1 1.0
SG A:CYS113 2.3 18.4 1.0
SG A:CYS110 2.3 18.1 1.0
CE1 A:HIS84 3.0 18.1 1.0
CG A:HIS84 3.1 18.9 1.0
CB A:CYS113 3.2 17.4 1.0
CB A:CYS110 3.4 18.3 1.0
CB A:HIS84 3.5 18.1 1.0
N A:CYS110 3.8 18.5 1.0
N A:CYS113 3.9 17.9 1.0
OE2 A:GLU86 4.0 22.4 1.0
CA A:CYS110 4.1 18.6 1.0
NE2 A:HIS84 4.1 17.8 1.0
CA A:CYS113 4.2 17.8 1.0
CD2 A:HIS84 4.2 19.3 1.0
CD A:GLU86 4.4 20.6 1.0
OE1 A:GLU86 4.4 20.2 1.0
O A:CYS110 4.6 18.9 1.0
C A:CYS110 4.6 18.7 1.0
O A:HOH2028 4.7 37.6 1.0
C A:PRO109 4.9 18.7 1.0
CA A:HIS84 5.0 17.9 1.0

Zinc binding site 2 out of 6 in 2w4l

Go back to Zinc Binding Sites List in 2w4l
Zinc binding site 2 out of 6 in the Human Dcmp Deaminase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Dcmp Deaminase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1171

b:21.0
occ:1.00
ND1 B:HIS84 2.1 19.1 1.0
O B:HOH2035 2.2 17.8 1.0
SG B:CYS113 2.2 18.3 1.0
SG B:CYS110 2.4 20.7 1.0
CE1 B:HIS84 3.0 20.8 1.0
CG B:HIS84 3.2 19.0 1.0
CB B:CYS113 3.2 18.0 1.0
CB B:CYS110 3.5 20.1 1.0
CB B:HIS84 3.5 19.0 1.0
N B:CYS110 3.8 20.0 1.0
N B:CYS113 4.0 18.1 1.0
O B:HOH2016 4.0 46.6 1.0
OE2 B:GLU86 4.1 21.5 1.0
CA B:CYS113 4.2 17.9 1.0
NE2 B:HIS84 4.2 21.2 1.0
OE1 B:GLU86 4.2 19.5 1.0
CA B:CYS110 4.2 20.0 1.0
O B:HOH2007 4.2 22.5 1.0
CD2 B:HIS84 4.3 21.0 1.0
CD B:GLU86 4.3 20.3 1.0
O B:CYS110 4.6 19.8 1.0
C B:CYS110 4.7 19.9 1.0
C B:PRO109 4.9 20.2 1.0

Zinc binding site 3 out of 6 in 2w4l

Go back to Zinc Binding Sites List in 2w4l
Zinc binding site 3 out of 6 in the Human Dcmp Deaminase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Dcmp Deaminase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1170

b:20.7
occ:1.00
ND1 C:HIS84 2.1 20.6 1.0
O C:HOH2037 2.2 18.2 1.0
SG C:CYS113 2.2 18.1 1.0
SG C:CYS110 2.4 20.1 1.0
CE1 C:HIS84 3.0 19.9 1.0
CG C:HIS84 3.1 20.1 1.0
CB C:CYS113 3.1 17.2 1.0
CB C:HIS84 3.4 19.4 1.0
CB C:CYS110 3.6 19.6 1.0
N C:CYS110 3.9 19.3 1.0
N C:CYS113 4.0 17.6 1.0
O C:HOH2008 4.1 28.1 1.0
NE2 C:HIS84 4.1 19.9 1.0
CA C:CYS113 4.2 17.3 1.0
OE1 C:GLU86 4.2 19.4 1.0
CD2 C:HIS84 4.2 19.9 1.0
CA C:CYS110 4.2 19.6 1.0
OE2 C:GLU86 4.3 24.2 1.0
CD C:GLU86 4.4 20.5 1.0
O C:HOH2020 4.4 27.4 1.0
C C:CYS110 4.7 19.4 1.0
O C:CYS110 4.8 19.4 1.0
C C:PRO109 5.0 19.2 1.0
CA C:HIS84 5.0 19.4 1.0

Zinc binding site 4 out of 6 in 2w4l

Go back to Zinc Binding Sites List in 2w4l
Zinc binding site 4 out of 6 in the Human Dcmp Deaminase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Dcmp Deaminase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1170

b:23.2
occ:1.00
ND1 D:HIS84 2.0 22.7 1.0
SG D:CYS113 2.2 19.9 1.0
O D:HOH2036 2.2 20.3 1.0
SG D:CYS110 2.4 20.7 1.0
CE1 D:HIS84 2.9 22.0 1.0
CG D:HIS84 3.1 22.0 1.0
CB D:CYS113 3.1 19.9 1.0
CB D:HIS84 3.5 21.9 1.0
CB D:CYS110 3.5 21.3 1.0
N D:CYS110 3.8 21.0 1.0
N D:CYS113 4.0 20.3 1.0
NE2 D:HIS84 4.1 22.2 1.0
CA D:CYS113 4.2 20.0 1.0
OE1 D:GLU86 4.2 20.8 1.0
CD2 D:HIS84 4.2 22.8 1.0
CA D:CYS110 4.2 21.3 1.0
OE2 D:GLU86 4.4 23.9 1.0
CD D:GLU86 4.5 22.0 1.0
O D:CYS110 4.7 21.2 1.0
C D:CYS110 4.7 21.6 1.0
C D:PRO109 5.0 20.6 1.0
O D:HOH2019 5.0 33.5 1.0

Zinc binding site 5 out of 6 in 2w4l

Go back to Zinc Binding Sites List in 2w4l
Zinc binding site 5 out of 6 in the Human Dcmp Deaminase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human Dcmp Deaminase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1174

b:18.9
occ:1.00
ND1 E:HIS84 2.1 16.9 1.0
O E:HOH2044 2.1 17.2 1.0
SG E:CYS113 2.3 18.1 1.0
SG E:CYS110 2.4 19.4 1.0
CE1 E:HIS84 3.0 16.9 1.0
CG E:HIS84 3.1 16.7 1.0
CB E:CYS113 3.2 18.0 1.0
CB E:HIS84 3.4 16.4 1.0
CB E:CYS110 3.5 19.7 1.0
N E:CYS110 3.9 20.2 1.0
N E:CYS113 4.0 18.8 1.0
OE2 E:GLU86 4.0 21.7 1.0
O E:HOH2025 4.1 43.6 1.0
NE2 E:HIS84 4.1 16.7 1.0
CA E:CYS113 4.2 18.1 1.0
CD2 E:HIS84 4.2 17.8 1.0
CA E:CYS110 4.2 19.8 1.0
OE1 E:GLU86 4.3 18.5 1.0
CD E:GLU86 4.3 19.3 1.0
O E:HOH2006 4.5 31.6 1.0
C E:CYS110 4.7 19.6 1.0
O E:CYS110 4.7 19.2 1.0
CA E:HIS84 4.9 16.1 1.0

Zinc binding site 6 out of 6 in 2w4l

Go back to Zinc Binding Sites List in 2w4l
Zinc binding site 6 out of 6 in the Human Dcmp Deaminase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human Dcmp Deaminase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1171

b:19.2
occ:1.00
O F:HOH2051 2.0 18.1 1.0
ND1 F:HIS84 2.1 21.3 1.0
SG F:CYS113 2.2 16.4 1.0
SG F:CYS110 2.4 16.9 1.0
CE1 F:HIS84 3.0 21.3 1.0
CB F:CYS113 3.1 15.7 1.0
CG F:HIS84 3.1 19.7 1.0
CB F:HIS84 3.5 18.8 1.0
CB F:CYS110 3.5 17.1 1.0
N F:CYS110 3.8 17.3 1.0
OE2 F:GLU86 3.9 20.7 1.0
N F:CYS113 3.9 15.6 1.0
O F:HOH2043 4.0 28.4 1.0
CA F:CYS113 4.1 15.3 1.0
NE2 F:HIS84 4.1 22.0 1.0
CA F:CYS110 4.2 17.1 1.0
CD2 F:HIS84 4.2 20.7 1.0
OE1 F:GLU86 4.2 18.2 1.0
CD F:GLU86 4.3 18.4 1.0
O F:CYS110 4.7 16.6 1.0
C F:CYS110 4.7 16.9 1.0
C F:PRO109 5.0 17.6 1.0

Reference:

M.I.Siponen, M.Moche, C.H.Arrowsmith, H.Berglund, C.Bountra, R.Collins, L.G.Dahlgren, A.M.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, A.Johansson, I.Johansson, T.Karlberg, T.Kotenyova, L.Lehtio, M.E.Nilsson, T.Nyman, C.Persson, J.Sagemark, H.Schuler, A.G.Thorsell, L.Tresaugues, S.Van Den Berg, J.Weigelt, M.Welin, M.Wikstrom, M.Wisniewska, P.Nordlund. The Crystal Structure of Human Dcmp Deaminase To Be Published.
Page generated: Wed Dec 16 03:56:55 2020

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