Zinc in PDB 6dps: Crystal Structure of Neisseria Meningitidis Dsbd N-Terminal Domain in the Oxidised Form

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

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

Resolution Low / High (Å)	35.81 / 2.56
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	147.643, 147.643, 147.643, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 23.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Neisseria Meningitidis Dsbd N-Terminal Domain in the Oxidised Form (pdb code 6dps). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 32 binding sites of Zinc where determined in the Crystal Structure of Neisseria Meningitidis Dsbd N-Terminal Domain in the Oxidised Form, PDB code: 6dps:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 32 in the Crystal Structure of Neisseria Meningitidis Dsbd N-Terminal Domain in the Oxidised 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 N-Terminal Domain in the Oxidised Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:43.4 occ:1.00 NE2 A:HIS72 2.0 43.4 1.0 OE1 C:GLU74 2.1 51.0 1.0 OE2 A:GLU100 2.2 47.2 1.0 NZ A:LYS60 2.2 51.8 1.0 OE1 A:GLU100 2.8 42.4 1.0 CE1 A:HIS72 2.8 37.7 1.0 CD A:GLU100 2.8 38.0 1.0 CD C:GLU74 2.8 47.3 1.0 OE2 C:GLU74 3.0 52.0 1.0 CE A:LYS60 3.0 65.0 1.0 CD2 A:HIS72 3.1 35.8 1.0 CB C:HIS73 3.8 29.8 1.0 ND1 A:HIS72 4.0 39.5 1.0 CD1 A:TYR33 4.1 52.9 1.0 CG A:HIS72 4.1 53.7 1.0 CG C:GLU74 4.2 34.7 1.0 CG A:GLU100 4.3 43.0 1.0 CG A:TYR33 4.4 45.1 1.0 CD A:LYS60 4.5 59.4 1.0 CB A:TYR33 4.5 32.3 1.0 CG C:HIS73 4.6 50.5 1.0 CE1 A:TYR33 4.6 41.5 1.0 CB C:GLU74 4.8 28.4 1.0 C C:HIS73 4.9 43.6 1.0 CA C:HIS73 5.0 35.5 1.0

Zinc binding site 2 out of 32 in the Crystal Structure of Neisseria Meningitidis Dsbd N-Terminal Domain in the Oxidised 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 N-Terminal Domain in the Oxidised Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:0.9 occ:1.00 NE2 A:HIS121 2.4 70.3 1.0 O F:HOH303 2.9 74.2 1.0 CD2 A:HIS121 3.0 68.4 1.0 OG1 A:THR119 3.4 81.2 1.0 CE1 A:HIS121 3.5 65.7 1.0 CG A:HIS121 4.3 67.7 1.0 O F:HOH305 4.3 63.0 1.0 ND1 A:HIS121 4.5 66.3 1.0 CB A:THR119 4.5 68.8 1.0 O A:THR119 4.6 80.5 1.0 OE2 F:GLU63 4.6 0.0 1.0 C A:THR119 5.0 68.2 1.0

Zinc binding site 3 out of 32 in the Crystal Structure of Neisseria Meningitidis Dsbd N-Terminal Domain in the Oxidised 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 N-Terminal Domain in the Oxidised Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:62.8 occ:1.00 O A:THR124 1.9 78.2 1.0 OE2 A:GLU8 1.9 99.8 1.0 NE2 D:HIS121 2.1 68.8 1.0 CD A:GLU8 2.7 80.5 1.0 OE1 A:GLU8 2.9 77.6 1.0 CE1 D:HIS121 2.9 63.5 1.0 C A:THR124 3.0 61.9 1.0 CD2 D:HIS121 3.2 61.0 1.0 O D:HOH315 3.9 45.9 1.0 ND1 D:HIS121 4.0 66.4 1.0 CG A:GLU8 4.1 74.1 1.0 CG D:HIS121 4.2 62.1 1.0 CA A:THR124 4.3 66.1 1.0 CB A:THR124 4.6 66.5 1.0 NE2 D:GLN123 4.7 78.3 1.0

Zinc binding site 4 out of 32 in the Crystal Structure of Neisseria Meningitidis Dsbd N-Terminal Domain in the Oxidised 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 N-Terminal Domain in the Oxidised Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:62.8 occ:1.00 OE2 B:GLU8 1.9 1.0 1.0 NE2 C:HIS121 2.0 53.8 1.0 O B:THR124 2.1 52.0 1.0 CD B:GLU8 2.6 0.5 1.0 OE1 B:GLU8 2.8 0.7 1.0 CE1 C:HIS121 2.8 48.8 1.0 C B:THR124 3.1 47.8 1.0 CD2 C:HIS121 3.2 44.3 1.0 ND1 C:HIS121 4.0 45.6 1.0 CG B:GLU8 4.1 81.1 1.0 CG C:HIS121 4.2 42.4 1.0 O C:HOH306 4.2 47.2 1.0 CA B:THR124 4.5 69.3 1.0 O B:HOH346 4.7 64.7 1.0 CB B:THR124 5.0 72.7 1.0

Zinc binding site 5 out of 32 in the Crystal Structure of Neisseria Meningitidis Dsbd N-Terminal Domain in the Oxidised 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 N-Terminal Domain in the Oxidised Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:44.1 occ:0.55 CE1 D:HIS73 1.9 51.6 1.0 NE2 B:HIS73 2.0 41.8 1.0 OD2 E:ASP30 2.0 46.4 1.0 CE1 B:HIS73 2.5 50.1 1.0 ZN D:ZN204 2.5 40.6 0.6 O D:HOH305 2.5 51.6 1.0 NE2 D:HIS73 2.7 50.0 1.0 CG E:ASP30 2.8 39.0 1.0 OD1 E:ASP30 2.9 46.1 1.0 ND1 D:HIS73 3.1 44.0 1.0 CD2 B:HIS73 3.2 36.8 1.0 ND1 B:HIS73 3.7 49.9 1.0 CD2 D:HIS73 3.9 48.0 1.0 CG B:HIS73 4.1 37.9 1.0 CG D:HIS73 4.1 41.7 1.0 CB E:ASP30 4.2 41.1 1.0 C E:ASP30 4.5 52.0 1.0 N E:GLY31 4.5 47.7 1.0 O E:ASP30 4.6 49.5 1.0 OD1 D:ASP30 4.7 87.1 1.0 CA E:GLY31 4.9 35.5 1.0 CA E:ASP30 5.0 41.2 1.0 CB D:HIS72 5.0 31.6 1.0 O B:HOH316 5.0 46.9 1.0

Zinc binding site 6 out of 32 in the Crystal Structure of Neisseria Meningitidis Dsbd N-Terminal Domain in the Oxidised 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 N-Terminal Domain in the Oxidised Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:43.0 occ:1.00 OE1 D:GLU74 2.0 44.3 1.0 OE2 B:GLU100 2.0 48.6 1.0 NE2 B:HIS72 2.0 40.9 1.0 NZ B:LYS60 2.2 40.2 1.0 CD B:GLU100 2.8 36.9 1.0 OE1 B:GLU100 2.9 45.0 1.0 CE B:LYS60 2.9 39.8 1.0 CE1 B:HIS72 3.0 38.4 1.0 CD2 B:HIS72 3.0 43.3 1.0 CD D:GLU74 3.0 51.6 1.0 OE2 D:GLU74 3.5 74.9 1.0 CD1 B:TYR33 3.9 34.0 1.0 CB D:HIS73 4.0 31.3 1.0 ND1 B:HIS72 4.1 60.1 1.0 CG B:HIS72 4.2 51.8 1.0 CG B:GLU100 4.2 43.1 1.0 CG D:GLU74 4.3 33.3 1.0 CD B:LYS60 4.3 53.7 1.0 CG B:TYR33 4.3 37.8 1.0 CE1 B:TYR33 4.4 37.9 1.0 CB B:TYR33 4.5 44.9 1.0 CB D:GLU74 4.6 29.3 1.0 C D:HIS73 4.8 29.5 1.0 CG D:HIS73 4.8 41.7 1.0 CA D:HIS73 5.0 29.7 1.0

Zinc binding site 7 out of 32 in the Crystal Structure of Neisseria Meningitidis Dsbd N-Terminal Domain in the Oxidised 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 N-Terminal Domain in the Oxidised Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:58.6 occ:1.00 NE2 B:HIS121 2.0 55.5 1.0 OE1 E:GLU63 2.0 68.8 1.0 O B:HOH329 2.4 49.2 1.0 CD E:GLU63 2.9 67.4 1.0 CD2 B:HIS121 2.9 45.5 1.0 CE1 B:HIS121 3.0 43.0 1.0 OE2 E:GLU63 3.1 65.0 1.0 OG1 B:THR119 3.5 85.3 1.0 CG B:HIS121 4.1 48.7 1.0 ND1 B:HIS121 4.1 57.2 1.0 CG E:GLU63 4.3 67.0 1.0 CB B:THR119 4.8 54.6 1.0 O B:THR119 4.8 44.6 1.0 CZ E:PHE64 5.0 72.9 1.0

Zinc binding site 8 out of 32 in the Crystal Structure of Neisseria Meningitidis Dsbd N-Terminal Domain in the Oxidised 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 N-Terminal Domain in the Oxidised Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn205 b:0.3 occ:1.00 ZN B:ZN206 2.5 0.2 1.0 O B:HOH325 2.9 63.3 1.0 OE2 B:GLU63 3.8 95.4 1.0 OE1 B:GLU63 4.0 95.9 1.0 CD B:GLU63 4.1 80.4 1.0 O B:GLU63 4.9 51.9 1.0 CA B:GLU63 5.0 46.1 1.0

Zinc binding site 9 out of 32 in the Crystal Structure of Neisseria Meningitidis Dsbd N-Terminal Domain in the Oxidised Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Neisseria Meningitidis Dsbd N-Terminal Domain in the Oxidised Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn206 b:0.2 occ:1.00 OE2 B:GLU63 2.4 95.4 1.0 ZN B:ZN205 2.5 0.3 1.0 OE1 B:GLU63 2.9 95.9 1.0 CD B:GLU63 3.0 80.4 1.0 CG B:GLU63 4.4 59.9 1.0 O B:HOH325 4.5 63.3 1.0 NH1 D:ARG25 4.7 73.0 0.6

Zinc binding site 10 out of 32 in the Crystal Structure of Neisseria Meningitidis Dsbd N-Terminal Domain in the Oxidised Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Neisseria Meningitidis Dsbd N-Terminal Domain in the Oxidised Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn207 b:0.6 occ:1.00 NE2 B:GLN123 3.4 91.0 1.0 N B:HIS121 3.5 45.9 1.0 O B:HIS121 3.9 64.6 1.0 CA B:TYR120 3.9 48.7 1.0 CD2 B:TYR120 4.2 55.6 1.0 CB B:TYR120 4.2 46.3 1.0 C B:TYR120 4.2 56.6 1.0 O B:HOH329 4.4 49.2 1.0 CA B:HIS121 4.5 45.2 1.0 CG B:TYR120 4.5 60.5 1.0 CD2 B:HIS121 4.5 45.5 1.0 CD B:GLN123 4.5 91.3 1.0 O B:THR119 4.5 44.6 1.0 C B:HIS121 4.6 57.2 1.0 CB B:HIS121 4.6 38.9 1.0 CG B:HIS121 4.9 48.7 1.0

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