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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

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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

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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

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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

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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

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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

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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

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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

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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

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