Zinc in PDB 4rdt: Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Flexible Conformation Bound to A Zinc Ion)

The structure of Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Flexible Conformation Bound to A Zinc Ion), PDB code: 4rdt was solved by C.Calmettes, M.El Bakkouri, T.F.Moraes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.93 / 3.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.340, 156.227, 158.075, 90.00, 90.00, 90.00
R / Rfree (%)	27 / 30.5

The binding sites of Zinc atom in the Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Flexible Conformation Bound to A Zinc Ion) (pdb code 4rdt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Flexible Conformation Bound to A Zinc Ion), PDB code: 4rdt:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Flexible Conformation Bound to A Zinc Ion)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Flexible Conformation Bound to A Zinc Ion) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:0.1 occ:1.00 NE2 A:HIS499 1.9 57.5 1.0 OE2 A:GLU340 1.9 0.4 1.0 NE2 A:HIS100 2.1 73.5 1.0 CE1 A:HIS499 2.3 69.6 1.0 OD1 A:ASP99 2.4 58.4 1.0 OD2 A:ASP99 2.7 72.6 1.0 CD2 A:HIS100 2.7 64.9 1.0 CG A:ASP99 2.8 55.9 1.0 CD A:GLU340 3.0 0.4 1.0 CD2 A:HIS499 3.2 61.5 1.0 CE1 A:HIS100 3.3 77.3 1.0 OE1 A:GLU340 3.4 0.8 1.0 OG A:SER97 3.5 98.3 1.0 ND1 A:HIS499 3.6 74.1 1.0 CG A:HIS100 3.9 63.8 1.0 CB A:ALA501 3.9 65.1 1.0 CG A:HIS499 4.0 58.1 1.0 NE2 A:HIS338 4.2 66.6 1.0 ND1 A:HIS100 4.2 65.4 1.0 CG A:GLU340 4.3 0.1 1.0 CB A:ASP99 4.3 54.2 1.0 CZ A:PHE350 4.4 89.4 1.0 CE1 A:PHE350 4.4 79.5 1.0 CD1 A:ILE304 4.4 84.2 1.0 CE1 A:HIS338 4.6 62.1 1.0 CB A:SER97 4.8 81.8 1.0 N A:HIS100 4.9 55.9 1.0 OG1 A:THR502 5.0 0.6 1.0 C A:ASP99 5.0 58.2 1.0

Zinc binding site 2 out of 2 in the Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Flexible Conformation Bound to A Zinc Ion)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Flexible Conformation Bound to A Zinc Ion) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:82.1 occ:1.00 NE2 B:HIS499 1.8 0.9 1.0 OE2 B:GLU340 1.8 0.3 1.0 NE2 B:HIS100 2.1 92.6 1.0 CE1 B:HIS499 2.4 0.4 1.0 OD1 B:ASP99 2.5 94.4 1.0 CD2 B:HIS100 2.7 94.0 1.0 OD2 B:ASP99 2.8 94.7 1.0 CD B:GLU340 2.9 0.8 1.0 CG B:ASP99 3.0 95.2 1.0 CD2 B:HIS499 3.1 0.0 1.0 CE1 B:HIS100 3.3 92.6 1.0 OE1 B:GLU340 3.3 0.8 1.0 ND1 B:HIS499 3.6 0.2 1.0 OG B:SER97 3.6 94.8 1.0 CB B:ALA501 4.0 0.1 1.0 CG B:HIS499 4.0 0.6 1.0 CG B:HIS100 4.0 94.7 1.0 NE2 B:HIS338 4.1 0.6 1.0 CG B:GLU340 4.2 0.7 1.0 ND1 B:HIS100 4.2 93.8 1.0 CE1 B:PHE350 4.3 0.2 1.0 CZ B:PHE350 4.3 0.4 1.0 CD1 B:ILE304 4.5 0.5 1.0 CB B:ASP99 4.5 96.8 1.0 CE1 B:HIS338 4.6 0.4 1.0 CB B:SER97 4.9 95.5 1.0 CD1 B:PHE350 5.0 0.8 1.0

C.Calmettes, C.Ing, C.M.Buckwalter, M.El Bakkouri, C.Chieh-Lin Lai, A.Pogoutse, S.D.Gray-Owen, R.Pomes, T.F.Moraes. The Molecular Mechanism of Zinc Acquisition By the Neisserial Outer-Membrane Transporter Znud. Nat Commun V. 6 7996 2015.
ISSN: ESSN 2041-1723
PubMed: 26282243
DOI: 10.1038/NCOMMS8996