Atomistry » Zinc » PDB 6dit-6dxq » 6dnl
Atomistry »
  Zinc »
    PDB 6dit-6dxq »
      6dnl »

Zinc in PDB 6dnl: Crystal Structure of Neisseria Meningitidis Dsbd C-Terminal Domain in the Reduced Form

Enzymatic activity of Crystal Structure of Neisseria Meningitidis Dsbd C-Terminal Domain in the Reduced Form

All present enzymatic activity of Crystal Structure of Neisseria Meningitidis Dsbd C-Terminal Domain in the Reduced Form:
1.8.1.8;

Protein crystallography data

The structure of Crystal Structure of Neisseria Meningitidis Dsbd C-Terminal Domain in the Reduced Form, PDB code: 6dnl was solved by R.P.Smith, B.Heras, J.J.Paxman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.30 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.250, 28.060, 45.800, 90.00, 100.96, 90.00
R / Rfree (%) 17.7 / 21.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Neisseria Meningitidis Dsbd C-Terminal Domain in the Reduced Form (pdb code 6dnl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Neisseria Meningitidis Dsbd C-Terminal Domain in the Reduced Form, PDB code: 6dnl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6dnl

Go back to Zinc Binding Sites List in 6dnl
Zinc binding site 1 out of 8 in the Crystal Structure of Neisseria Meningitidis Dsbd C-Terminal Domain in the Reduced Form


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 Neisseria Meningitidis Dsbd C-Terminal Domain in the Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:24.8
occ:0.93
 O A:HOH366 1.9 28.3 1.0
O A:HOH358 2.1 34.1 1.0
ZN A:ZN205 3.1 23.3 0.9
ZN A:ZN204 3.3 19.6 1.0
O A:HOH346 3.3 22.6 1.0
OXT A:ACT210 3.6 21.9 1.0
C A:ACT210 4.0 17.9 1.0
O A:ACT210 4.0 20.4 1.0
OD2 A:ASP4 4.2 19.5 1.0
OE2 A:GLU69 4.3 22.6 1.0
OD1 A:ASP4 4.4 19.2 1.0
OE1 A:GLU69 4.4 20.9 1.0
CG A:ASP4 4.5 18.3 1.0
CD A:GLU69 4.7 22.0 1.0
H2 A:ACT210 4.9 27.7 0.5

Zinc binding site 2 out of 8 in 6dnl

Go back to Zinc Binding Sites List in 6dnl
Zinc binding site 2 out of 8 in the Crystal Structure of Neisseria Meningitidis Dsbd C-Terminal Domain in the Reduced Form


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 Neisseria Meningitidis Dsbd C-Terminal Domain in the Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:24.8
occ:0.95
 OD2 A:ASP21 1.8 29.9 1.0
NE2 A:HIS19 2.0 39.2 1.0
O A:HOH350 2.1 26.8 1.0
CG A:ASP21 2.7 21.8 1.0
OD1 A:ASP21 3.0 24.4 1.0
CE1 A:HIS19 3.0 44.0 1.0
CD2 A:HIS19 3.1 30.8 1.0
ND1 A:HIS19 4.1 37.6 1.0
CB A:ASP21 4.1 22.2 1.0
CG A:HIS19 4.2 26.5 1.0
O A:HOH339 4.4 35.6 1.0
N A:LYS22 4.9 19.7 1.0
C A:ASP21 4.9 21.8 1.0
CA A:ASP21 5.0 18.5 1.0

Zinc binding site 3 out of 8 in 6dnl

Go back to Zinc Binding Sites List in 6dnl
Zinc binding site 3 out of 8 in the Crystal Structure of Neisseria Meningitidis Dsbd C-Terminal Domain in the Reduced Form


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 Neisseria Meningitidis Dsbd C-Terminal Domain in the Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:33.5
occ:0.68
 OD2 A:ASP62 2.1 23.5 1.0
O A:HOH356 2.2 37.5 1.0
ZN A:ZN208 2.5 0.1 1.0
OD1 A:ASP31 2.6 85.2 1.0
CG A:ASP62 2.9 24.3 1.0
OD1 A:ASP62 3.0 19.5 1.0
OD2 A:ASP31 3.1 0.3 1.0
CG A:ASP31 3.1 71.5 1.0
OG1 A:THR64 3.6 23.7 1.0
CE2 A:TYR29 4.0 25.9 1.0
CB A:THR64 4.2 21.7 1.0
CB A:ASP62 4.3 18.1 1.0
O A:HOH338 4.3 39.2 1.0
CB A:ASP31 4.4 37.1 1.0
N A:ASP31 4.6 17.7 1.0
CD2 A:TYR29 4.6 18.2 1.0
O A:HOH303 4.8 44.0 1.0
CA A:ASP31 4.9 19.8 1.0
CG2 A:THR64 4.9 24.9 1.0
CE A:MET1 4.9 56.4 1.0
O A:ACT211 5.0 51.3 1.0

Zinc binding site 4 out of 8 in 6dnl

Go back to Zinc Binding Sites List in 6dnl
Zinc binding site 4 out of 8 in the Crystal Structure of Neisseria Meningitidis Dsbd C-Terminal Domain in the Reduced Form


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 Neisseria Meningitidis Dsbd C-Terminal Domain in the Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:19.6
occ:1.00
 OD2 A:ASP4 2.0 19.5 1.0
O A:ACT210 2.1 20.4 1.0
OXT A:ACT210 2.6 21.9 1.0
C A:ACT210 2.7 17.9 1.0
CG A:ASP4 2.8 18.3 1.0
OD1 A:ASP4 2.9 19.2 1.0
ZN A:ZN201 3.3 24.8 0.9
O A:HOH366 3.4 28.3 1.0
O A:HOH358 4.1 34.1 1.0
CB A:ASP4 4.2 16.4 1.0
CH3 A:ACT210 4.2 23.1 1.0
O A:HOH346 4.2 22.6 1.0
H1 A:ACT210 4.5 27.7 1.0
CB A:ALA6 4.6 16.3 1.0
H2 A:ACT210 4.6 27.7 0.5
H2 A:ACT210 4.7 27.7 0.5
N A:ALA7 4.8 13.7 1.0

Zinc binding site 5 out of 8 in 6dnl

Go back to Zinc Binding Sites List in 6dnl
Zinc binding site 5 out of 8 in the Crystal Structure of Neisseria Meningitidis Dsbd C-Terminal Domain in the Reduced Form


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 Neisseria Meningitidis Dsbd C-Terminal Domain in the Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn205

b:23.3
occ:0.89
 O A:HOH366 1.9 28.3 1.0
OE2 A:GLU69 2.0 22.6 1.0
CD A:GLU69 2.8 22.0 1.0
OE1 A:GLU69 2.9 20.9 1.0
ZN A:ZN201 3.1 24.8 0.9
CG A:GLU69 4.2 17.5 1.0
O A:HOH358 4.3 34.1 1.0
O A:HOH321 4.3 20.3 1.0
O A:HOH346 4.3 22.6 1.0
NZ A:LYS67 4.3 31.7 1.0
CD A:LYS67 4.4 24.1 1.0
CA A:ASP4 4.8 14.9 1.0
CG A:ASP4 4.9 18.3 1.0
CB A:GLU69 5.0 18.8 1.0
CE A:LYS67 5.0 29.1 1.0

Zinc binding site 6 out of 8 in 6dnl

Go back to Zinc Binding Sites List in 6dnl
Zinc binding site 6 out of 8 in the Crystal Structure of Neisseria Meningitidis Dsbd C-Terminal Domain in the Reduced Form


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 Neisseria Meningitidis Dsbd C-Terminal Domain in the Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn206

b:18.1
occ:0.79
 OD2 A:ASP27 2.0 26.1 1.0
O A:ACT209 2.1 22.9 1.0
O A:HOH364 2.2 20.4 1.0
SG A:CYS36 2.3 24.1 1.0
CG A:ASP27 2.8 21.5 1.0
O A:HOH323 2.9 25.4 1.0
OD1 A:ASP27 3.0 18.5 1.0
C A:ACT209 3.1 21.3 1.0
CB A:CYS36 3.3 24.2 1.0
OXT A:ACT209 3.4 23.7 1.0
ZN A:ZN207 3.5 19.4 0.8
CA A:CYS36 3.5 21.9 1.0
O A:HOH307 3.9 20.1 1.0
CB A:ASP27 4.2 14.3 1.0
OE1 A:GLN60 4.2 40.9 1.0
N A:CYS36 4.4 21.1 1.0
CH3 A:ACT209 4.5 24.5 1.0
C A:CYS36 4.6 25.0 1.0
O A:CYS36 4.6 22.5 1.0
H2 A:ACT209 4.6 29.4 0.5
CB A:MET39 4.7 20.7 1.0
CG2 A:VAL85 4.8 15.6 1.0
H1 A:ACT209 4.9 29.4 1.0
CD1 A:TYR29 4.9 23.1 1.0
O A:SER35 4.9 20.3 1.0
CG A:MET39 4.9 20.4 1.0
CD1 A:LEU44 5.0 26.5 1.0
C A:SER35 5.0 20.0 1.0

Zinc binding site 7 out of 8 in 6dnl

Go back to Zinc Binding Sites List in 6dnl
Zinc binding site 7 out of 8 in the Crystal Structure of Neisseria Meningitidis Dsbd C-Terminal Domain in the Reduced Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Neisseria Meningitidis Dsbd C-Terminal Domain in the Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn207

b:19.4
occ:0.84
 OXT A:ACT209 2.0 23.7 1.0
O A:HOH307 2.2 20.1 1.0
SG A:CYS36 2.2 24.1 1.0
SG A:CYS33 2.3 20.8 1.0
C A:ACT209 3.1 21.3 1.0
CB A:CYS36 3.1 24.2 1.0
N A:CYS36 3.3 21.1 1.0
CB A:CYS33 3.3 23.2 1.0
O A:ACT209 3.4 22.9 1.0
ZN A:ZN206 3.5 18.1 0.8
CA A:CYS36 3.5 21.9 1.0
CB A:PRO83 3.8 26.2 1.0
O A:PHE28 4.0 20.4 1.0
C A:SER35 4.1 20.0 1.0
CA A:PRO83 4.1 23.4 1.0
OD1 A:ASP27 4.1 18.5 1.0
CH3 A:ACT209 4.4 24.5 1.0
CB A:SER35 4.4 25.7 1.0
H2 A:ACT209 4.4 29.4 0.5
CA A:CYS33 4.6 22.1 1.0
CA A:SER35 4.7 21.8 1.0
O A:CYS33 4.7 27.0 1.0
C A:CYS33 4.8 28.0 1.0
N A:SER35 4.8 23.2 1.0
O A:SER35 4.8 20.3 1.0
H1 A:ACT209 4.8 29.4 1.0
CB A:PRO82 4.9 22.9 1.0
OD2 A:ASP27 4.9 26.1 1.0
N A:GLY84 4.9 18.6 1.0
CA A:TYR29 4.9 15.2 1.0
C A:PHE28 4.9 19.1 1.0
CG A:ASP27 4.9 21.5 1.0

Zinc binding site 8 out of 8 in 6dnl

Go back to Zinc Binding Sites List in 6dnl
Zinc binding site 8 out of 8 in the Crystal Structure of Neisseria Meningitidis Dsbd C-Terminal Domain in the Reduced Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Neisseria Meningitidis Dsbd C-Terminal Domain in the Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn208

b:0.1
occ:1.00
 OD2 A:ASP31 2.1 0.3 1.0
ZN A:ZN203 2.5 33.5 0.7
OD1 A:ASP31 2.5 85.2 1.0
CG A:ASP31 2.6 71.5 1.0
O A:ACT211 3.0 51.3 1.0
O A:HOH356 3.1 37.5 1.0
O A:HOH303 3.7 44.0 1.0
C A:ACT211 3.9 50.7 1.0
O A:HOH361 3.9 42.0 1.0
OXT A:ACT211 4.0 51.1 1.0
CB A:ASP31 4.1 37.1 1.0
OD2 A:ASP62 4.5 23.5 1.0
O A:HOH389 4.7 42.2 1.0

Reference:

R.P.Smith, B.Mohanty, S.Mowlaboccus, J.J.Paxman, M.L.Williams, S.J.Headey, G.Wang, P.Subedi, B.C.Doak, C.M.Kahler, M.J.Scanlon, B.Heras. Structural and Biochemical Insights Into the Disulfide Reductase Mechanism of Dsbd, An Essential Enzyme For Neisserial Pathogens. J. Biol. Chem. V. 293 16559 2018.
ISSN: ESSN 1083-351X
PubMed: 30181210
DOI: 10.1074/JBC.RA118.004847
Page generated: Mon Oct 28 19:42:36 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy