Atomistry » Zinc » PDB 2w22-2wfr » 2w4l
Atomistry »
  Zinc »
    PDB 2w22-2wfr »
      2w4l »

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: Thu Oct 17 04:44:13 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy