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Zinc in PDB 2hvw: Crystal Structure of Dcmp Deaminase From Streptococcus Mutans

Enzymatic activity of Crystal Structure of Dcmp Deaminase From Streptococcus Mutans

All present enzymatic activity of Crystal Structure of Dcmp Deaminase From Streptococcus Mutans:
3.5.4.12;

Protein crystallography data

The structure of Crystal Structure of Dcmp Deaminase From Streptococcus Mutans, PDB code: 2hvw was solved by H.F.Hou, Z.Q.Gao, L.F.Li, Y.H.Liang, X.D.Su, Y.H.Dong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 16.00 / 1.67
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 95.498, 99.657, 141.388, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 17.9

Other elements in 2hvw:

The structure of Crystal Structure of Dcmp Deaminase From Streptococcus Mutans also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 6 in 2hvw

Go back to Zinc Binding Sites List in 2hvw
Zinc binding site 1 out of 6 in the Crystal Structure of Dcmp Deaminase From Streptococcus Mutans


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 Dcmp Deaminase From Streptococcus Mutans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:16.0
occ:0.85
 ND1 A:HIS59 2.2 17.5 1.0
SG A:CYS54 2.3 18.1 1.0
SG A:CYS66 2.4 16.6 1.0
SG A:CYS24 2.4 16.5 1.0
CE1 A:HIS59 3.1 18.8 1.0
CB A:CYS54 3.2 17.4 1.0
CG A:HIS59 3.2 19.7 1.0
CB A:CYS66 3.3 16.6 1.0
CB A:CYS24 3.3 16.5 1.0
CB A:HIS59 3.6 18.3 1.0
CA A:HIS59 3.8 18.8 1.0
CA A:CYS24 4.1 16.5 1.0
NE2 A:HIS59 4.2 19.6 1.0
CD2 A:HIS59 4.3 19.0 1.0
CG2 A:THR69 4.3 13.3 1.0
O3' A:DDN1301 4.5 16.1 1.0
CD A:ARG26 4.6 18.5 1.0
CA A:CYS54 4.6 17.8 1.0
N A:HIS59 4.7 18.8 1.0
CA A:CYS66 4.7 16.3 1.0
CB A:ARG68 4.8 15.2 1.0
C A:CYS24 4.8 17.5 1.0
N A:GLU60 4.9 18.8 1.0
C A:HIS59 4.9 19.1 1.0
CG A:ARG26 5.0 18.2 1.0

Zinc binding site 2 out of 6 in 2hvw

Go back to Zinc Binding Sites List in 2hvw
Zinc binding site 2 out of 6 in the Crystal Structure of Dcmp Deaminase From Streptococcus Mutans


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 Dcmp Deaminase From Streptococcus Mutans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:14.1
occ:0.90
 O4 A:DDN1301 2.0 15.7 1.0
ND1 A:HIS71 2.0 15.1 1.0
SG A:CYS102 2.3 13.1 1.0
SG A:CYS99 2.3 13.7 1.0
CE1 A:HIS71 3.0 15.0 1.0
CG A:HIS71 3.0 12.9 1.0
C4 A:DDN1301 3.1 14.9 1.0
CB A:CYS102 3.2 13.4 1.0
CB A:CYS99 3.4 13.9 1.0
N3 A:DDN1301 3.4 15.6 1.0
CB A:HIS71 3.4 12.4 1.0
C5 A:DDN1301 3.5 14.3 1.0
O A:HOH1443 3.7 16.7 1.0
OE2 A:GLU73 3.7 14.8 1.0
N A:CYS99 3.8 13.9 1.0
C2 A:DDN1301 4.0 16.2 1.0
NE2 A:HIS71 4.1 14.5 1.0
N A:CYS102 4.1 13.6 1.0
CD2 A:HIS71 4.1 14.9 1.0
CA A:CYS99 4.1 13.7 1.0
C6 A:DDN1301 4.1 14.3 1.0
CA A:CYS102 4.2 12.9 1.0
CD A:GLU73 4.3 14.0 1.0
OE1 A:GLU73 4.3 14.2 1.0
N1 A:DDN1301 4.4 14.6 1.0
O A:HOH1456 4.6 18.7 1.0
O A:HOH1431 4.7 16.2 1.0
C A:CYS99 4.7 13.5 1.0
O A:CYS99 4.8 12.6 1.0
O2 A:DDN1301 4.8 14.1 1.0
C A:PRO98 4.8 14.1 1.0
CA A:HIS71 4.9 12.2 1.0
CA A:PRO98 5.0 14.4 1.0

Zinc binding site 3 out of 6 in 2hvw

Go back to Zinc Binding Sites List in 2hvw
Zinc binding site 3 out of 6 in the Crystal Structure of Dcmp Deaminase From Streptococcus Mutans


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 Dcmp Deaminase From Streptococcus Mutans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1003

b:15.1
occ:0.90
 ND1 B:HIS59 2.1 16.3 1.0
SG B:CYS54 2.3 15.5 1.0
SG B:CYS24 2.4 14.2 1.0
SG B:CYS66 2.4 15.6 1.0
CE1 B:HIS59 3.0 17.4 1.0
CG B:HIS59 3.2 17.9 1.0
CB B:CYS54 3.2 16.0 1.0
CB B:CYS66 3.3 15.1 1.0
CB B:CYS24 3.3 15.5 1.0
CB B:HIS59 3.6 17.3 1.0
CA B:HIS59 3.8 16.9 1.0
CA B:CYS24 4.1 15.2 1.0
NE2 B:HIS59 4.2 18.8 1.0
CD2 B:HIS59 4.3 18.4 1.0
CG2 B:THR69 4.4 13.4 1.0
O3' B:DDN1302 4.6 12.9 1.0
CA B:CYS54 4.6 15.9 1.0
CD B:ARG26 4.6 16.0 1.0
N B:HIS59 4.6 16.5 1.0
CA B:CYS66 4.7 14.7 1.0
CB B:ARG68 4.8 13.6 1.0
C B:CYS24 4.8 16.0 1.0
N B:GLU60 4.9 16.3 1.0
CG B:ARG26 4.9 16.3 1.0
C B:HIS59 4.9 17.0 1.0

Zinc binding site 4 out of 6 in 2hvw

Go back to Zinc Binding Sites List in 2hvw
Zinc binding site 4 out of 6 in the Crystal Structure of Dcmp Deaminase From Streptococcus Mutans


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 Dcmp Deaminase From Streptococcus Mutans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1004

b:12.5
occ:0.85
 O4 B:DDN1302 2.1 13.9 1.0
ND1 B:HIS71 2.1 14.7 1.0
SG B:CYS102 2.3 12.6 1.0
SG B:CYS99 2.3 13.5 1.0
CE1 B:HIS71 3.0 12.9 1.0
CG B:HIS71 3.1 12.5 1.0
C4 B:DDN1302 3.1 13.4 1.0
CB B:CYS102 3.2 12.1 1.0
CB B:HIS71 3.4 11.4 1.0
CB B:CYS99 3.4 13.2 1.0
N3 B:DDN1302 3.4 12.5 1.0
C5 B:DDN1302 3.6 13.8 1.0
O B:HOH1418 3.6 19.2 1.0
OE2 B:GLU73 3.7 13.2 1.0
N B:CYS99 3.8 13.5 1.0
C2 B:DDN1302 4.1 15.2 1.0
N B:CYS102 4.1 13.0 1.0
NE2 B:HIS71 4.1 13.3 1.0
CA B:CYS99 4.1 13.0 1.0
CD2 B:HIS71 4.2 13.4 1.0
C6 B:DDN1302 4.2 14.2 1.0
CA B:CYS102 4.2 12.1 1.0
CD B:GLU73 4.3 13.6 1.0
OE1 B:GLU73 4.4 14.8 1.0
N1 B:DDN1302 4.4 15.0 1.0
O B:HOH1431 4.6 18.9 1.0
C B:CYS99 4.7 13.3 1.0
O B:HOH1478 4.8 15.9 1.0
O B:CYS99 4.8 12.1 1.0
C B:PRO98 4.8 13.6 1.0
O2 B:DDN1302 4.8 12.4 1.0
CA B:HIS71 4.9 11.4 1.0
CA B:PRO98 5.0 13.9 1.0

Zinc binding site 5 out of 6 in 2hvw

Go back to Zinc Binding Sites List in 2hvw
Zinc binding site 5 out of 6 in the Crystal Structure of Dcmp Deaminase From Streptococcus Mutans


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 Dcmp Deaminase From Streptococcus Mutans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1005

b:16.8
occ:0.90
 ND1 C:HIS59 2.2 18.7 1.0
SG C:CYS54 2.3 16.8 1.0
SG C:CYS66 2.3 16.6 1.0
SG C:CYS24 2.4 16.4 1.0
CE1 C:HIS59 3.1 21.0 1.0
CB C:CYS54 3.2 17.5 1.0
CG C:HIS59 3.2 20.4 1.0
CB C:CYS66 3.3 16.1 1.0
CB C:CYS24 3.4 17.3 1.0
CB C:HIS59 3.6 19.3 1.0
CA C:HIS59 3.8 19.0 1.0
CA C:CYS24 4.2 17.2 1.0
NE2 C:HIS59 4.2 21.1 1.0
CD2 C:HIS59 4.3 20.7 1.0
CG2 C:THR69 4.4 14.0 1.0
O3' C:DDN1303 4.5 14.0 1.0
CD C:ARG26 4.6 18.2 1.0
CA C:CYS54 4.6 17.9 1.0
N C:HIS59 4.7 18.9 1.0
CA C:CYS66 4.7 15.4 1.0
CB C:ARG68 4.8 15.1 1.0
N C:GLU60 4.8 18.4 1.0
C C:CYS24 4.9 17.7 1.0
C C:HIS59 4.9 19.0 1.0
CG C:ARG26 4.9 18.0 1.0

Zinc binding site 6 out of 6 in 2hvw

Go back to Zinc Binding Sites List in 2hvw
Zinc binding site 6 out of 6 in the Crystal Structure of Dcmp Deaminase From Streptococcus Mutans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Dcmp Deaminase From Streptococcus Mutans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1006

b:13.3
occ:0.85
 ND1 C:HIS71 2.0 15.6 1.0
O4 C:DDN1303 2.0 16.0 1.0
SG C:CYS102 2.3 13.8 1.0
SG C:CYS99 2.3 14.2 1.0
CE1 C:HIS71 3.0 15.1 1.0
CG C:HIS71 3.0 13.2 1.0
C4 C:DDN1303 3.1 14.3 1.0
CB C:CYS102 3.2 13.3 1.0
CB C:CYS99 3.4 13.1 1.0
CB C:HIS71 3.4 13.3 1.0
N3 C:DDN1303 3.4 14.3 1.0
C5 C:DDN1303 3.5 14.4 1.0
O C:HOH1452 3.6 18.1 1.0
OE2 C:GLU73 3.7 14.9 1.0
N C:CYS99 3.7 13.7 1.0
C2 C:DDN1303 4.0 15.4 1.0
NE2 C:HIS71 4.0 14.6 1.0
N C:CYS102 4.1 13.7 1.0
CD2 C:HIS71 4.1 13.9 1.0
CA C:CYS99 4.1 13.6 1.0
C6 C:DDN1303 4.2 13.8 1.0
CA C:CYS102 4.2 13.2 1.0
CD C:GLU73 4.3 14.4 1.0
OE1 C:GLU73 4.3 13.9 1.0
N1 C:DDN1303 4.4 15.3 1.0
O C:HOH1426 4.6 22.4 1.0
C C:CYS99 4.7 13.4 1.0
O C:CYS99 4.7 12.9 1.0
O C:HOH1443 4.8 15.8 1.0
O2 C:DDN1303 4.8 14.1 1.0
C C:PRO98 4.8 13.7 1.0
CA C:HIS71 4.9 12.5 1.0
CA C:PRO98 5.0 14.2 1.0

Reference:

H.F.Hou, Y.H.Liang, L.F.Li, X.D.Su, Y.H.Dong. Crystal Structures of Streptococcus Mutans 2'-Deoxycytidylate Deaminase and Its Complex with Substrate Analog and Allosteric Regulator Dctp X MG2+. J.Mol.Biol. V. 377 220 2008.
ISSN: ISSN 0022-2836
PubMed: 18255096
DOI: 10.1016/J.JMB.2007.12.064
Page generated: Thu Oct 17 00:43:24 2024

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