Zinc in PDB 6jkw: Seleno-Methionine Pngm-1 From Deep-Sea Sediment Metagenome

The structure of Seleno-Methionine Pngm-1 From Deep-Sea Sediment Metagenome, PDB code: 6jkw was solved by M.K.Hong, K.S.Park, J.H.Jeon, J.H.Lee, Y.S.Park, S.H.Lee, L.W.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.93 / 2.29
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	121.857, 83.124, 162.833, 90.00, 110.18, 90.00
R / Rfree (%)	21.1 / 27.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Seleno-Methionine Pngm-1 From Deep-Sea Sediment Metagenome (pdb code 6jkw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Seleno-Methionine Pngm-1 From Deep-Sea Sediment Metagenome, PDB code: 6jkw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Seleno-Methionine Pngm-1 From Deep-Sea Sediment Metagenome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Seleno-Methionine Pngm-1 From Deep-Sea Sediment Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:30.9 occ:1.00 OD2 A:ASP210 2.1 14.6 1.0 NE2 A:HIS279 2.2 26.5 1.0 NE2 A:HIS96 2.4 12.4 1.0 OD1 A:ASP95 2.5 19.3 1.0 CG A:ASP210 2.9 18.1 1.0 CD2 A:HIS96 3.0 11.7 1.0 CE1 A:HIS279 3.0 25.2 1.0 OD1 A:ASP210 3.0 20.1 1.0 ZN A:ZN402 3.0 21.5 1.0 CD2 A:HIS279 3.4 25.5 1.0 CG A:ASP95 3.5 18.2 1.0 CE1 A:HIS96 3.6 12.4 1.0 OD2 A:ASP95 3.9 19.6 1.0 NE2 A:HIS91 3.9 10.6 1.0 ND1 A:HIS279 4.2 26.0 1.0 CE1 A:HIS91 4.2 10.7 1.0 CG A:HIS96 4.2 12.5 1.0 CB A:ASP210 4.4 18.2 1.0 CG A:HIS279 4.4 24.1 1.0 ND1 A:HIS96 4.5 12.7 1.0 ND1 A:HIS93 4.7 16.4 1.0 CB A:ASP95 4.8 16.1 1.0 NE2 A:HIS188 4.9 17.9 1.0 CE1 A:HIS188 4.9 17.8 1.0

Zinc binding site 2 out of 16 in the Seleno-Methionine Pngm-1 From Deep-Sea Sediment Metagenome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Seleno-Methionine Pngm-1 From Deep-Sea Sediment Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:21.5 occ:1.00 OD2 A:ASP210 2.0 14.6 1.0 ND1 A:HIS93 2.1 16.4 1.0 NE2 A:HIS188 2.2 17.9 1.0 NE2 A:HIS91 2.3 10.6 1.0 CE1 A:HIS93 2.8 16.6 1.0 CE1 A:HIS188 2.9 17.8 1.0 ZN A:ZN401 3.0 30.9 1.0 CD2 A:HIS91 3.1 10.8 1.0 CG A:ASP210 3.2 18.1 1.0 CG A:HIS93 3.2 15.5 1.0 CD2 A:HIS188 3.3 17.7 1.0 CE1 A:HIS91 3.4 10.7 1.0 CB A:HIS93 3.7 16.3 1.0 CB A:ASP210 3.8 18.2 1.0 NE2 A:HIS93 4.0 15.9 1.0 ND1 A:HIS188 4.0 19.1 1.0 CD2 A:HIS93 4.2 16.2 1.0 CD2 A:HIS96 4.2 11.7 1.0 OD1 A:ASP210 4.2 20.1 1.0 CG A:HIS188 4.3 17.6 1.0 NE2 A:HIS96 4.3 12.4 1.0 CG A:HIS91 4.3 11.0 1.0 ND1 A:HIS91 4.5 11.4 1.0 OD2 A:ASP95 4.5 19.6 1.0 OD1 A:ASP95 4.6 19.3 1.0

Zinc binding site 3 out of 16 in the Seleno-Methionine Pngm-1 From Deep-Sea Sediment Metagenome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Seleno-Methionine Pngm-1 From Deep-Sea Sediment Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:33.2 occ:1.00 OD2 B:ASP210 2.1 17.3 1.0 NE2 B:HIS279 2.2 24.5 1.0 NE2 B:HIS96 2.4 9.7 1.0 OD1 B:ASP95 2.6 25.1 1.0 CG B:ASP210 2.9 18.9 1.0 CD2 B:HIS96 2.9 9.7 1.0 CE1 B:HIS279 3.0 24.9 1.0 OD1 B:ASP210 3.1 22.2 1.0 ZN B:ZN402 3.2 19.8 1.0 CD2 B:HIS279 3.4 23.5 1.0 CG B:ASP95 3.6 17.6 1.0 CE1 B:HIS96 3.6 10.5 1.0 OD2 B:ASP95 3.9 18.8 1.0 NE2 B:HIS91 4.1 9.3 1.0 ND1 B:HIS279 4.2 26.4 1.0 CG B:HIS96 4.2 10.2 1.0 CE1 B:HIS91 4.3 9.1 1.0 CB B:ASP210 4.3 17.7 1.0 CG B:HIS279 4.4 23.1 1.0 ND1 B:HIS96 4.5 10.9 1.0 ND1 B:HIS93 4.8 12.6 1.0 CB B:ASP95 4.8 16.2 1.0 NE2 B:HIS188 5.0 18.3 1.0

Zinc binding site 4 out of 16 in the Seleno-Methionine Pngm-1 From Deep-Sea Sediment Metagenome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Seleno-Methionine Pngm-1 From Deep-Sea Sediment Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:19.8 occ:1.00 ND1 B:HIS93 2.1 12.6 1.0 OD2 B:ASP210 2.2 17.3 1.0 NE2 B:HIS91 2.3 9.3 1.0 NE2 B:HIS188 2.3 18.3 1.0 CE1 B:HIS93 2.8 13.4 1.0 CD2 B:HIS91 3.1 9.6 1.0 CE1 B:HIS188 3.1 17.8 1.0 ZN B:ZN401 3.2 33.2 1.0 CG B:HIS93 3.2 12.8 1.0 CG B:ASP210 3.2 18.9 1.0 CD2 B:HIS188 3.3 17.7 1.0 CE1 B:HIS91 3.3 9.1 1.0 CB B:ASP210 3.6 17.7 1.0 CB B:HIS93 3.7 13.7 1.0 NE2 B:HIS93 4.0 13.3 1.0 CD2 B:HIS96 4.1 9.7 1.0 CD2 B:HIS93 4.2 13.8 1.0 NE2 B:HIS96 4.3 9.7 1.0 ND1 B:HIS188 4.3 17.9 1.0 OD1 B:ASP210 4.3 22.2 1.0 CG B:HIS91 4.3 9.4 1.0 ND1 B:HIS91 4.4 9.3 1.0 CG B:HIS188 4.4 17.9 1.0 OD2 B:ASP95 4.6 18.8 1.0 OD1 B:ASP95 4.9 25.1 1.0

Zinc binding site 5 out of 16 in the Seleno-Methionine Pngm-1 From Deep-Sea Sediment Metagenome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Seleno-Methionine Pngm-1 From Deep-Sea Sediment Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:39.2 occ:1.00 OD2 C:ASP210 2.3 22.0 1.0 NE2 C:HIS279 2.3 27.9 1.0 NE2 C:HIS96 2.3 18.6 1.0 OD1 C:ASP95 2.4 29.4 1.0 CD2 C:HIS96 2.8 19.0 1.0 CE1 C:HIS279 3.0 31.4 1.0 CG C:ASP210 3.0 25.8 1.0 ZN C:ZN402 3.1 28.2 1.0 OD1 C:ASP210 3.1 27.7 1.0 CG C:ASP95 3.3 24.4 1.0 CD2 C:HIS279 3.4 27.0 1.0 CE1 C:HIS96 3.5 17.6 1.0 OD2 C:ASP95 3.7 29.2 1.0 NE2 C:HIS91 4.0 17.4 1.0 CG C:HIS96 4.1 18.3 1.0 ND1 C:HIS279 4.2 31.0 1.0 CE1 C:HIS91 4.3 17.6 1.0 ND1 C:HIS96 4.4 17.0 1.0 CG C:HIS279 4.4 28.1 1.0 CB C:ASP210 4.5 25.0 1.0 CB C:ASP95 4.6 21.9 1.0 ND1 C:HIS93 4.6 21.7 1.0 CB C:HIS93 4.9 22.5 1.0 NE2 C:HIS188 4.9 27.5 1.0 O C:ASP95 4.9 20.6 1.0

Zinc binding site 6 out of 16 in the Seleno-Methionine Pngm-1 From Deep-Sea Sediment Metagenome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Seleno-Methionine Pngm-1 From Deep-Sea Sediment Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:28.2 occ:1.00 OD2 C:ASP210 2.0 22.0 1.0 ND1 C:HIS93 2.1 21.7 1.0 NE2 C:HIS188 2.2 27.5 1.0 NE2 C:HIS91 2.3 17.4 1.0 CE1 C:HIS93 3.0 22.2 1.0 CD2 C:HIS91 3.0 16.8 1.0 ZN C:ZN401 3.1 39.2 1.0 CE1 C:HIS188 3.1 26.3 1.0 CD2 C:HIS188 3.1 25.1 1.0 CG C:HIS93 3.1 20.5 1.0 CG C:ASP210 3.2 25.8 1.0 CE1 C:HIS91 3.5 17.6 1.0 CB C:HIS93 3.5 22.5 1.0 CB C:ASP210 3.7 25.0 1.0 CD2 C:HIS96 4.1 19.0 1.0 NE2 C:HIS93 4.1 21.4 1.0 NE2 C:HIS96 4.1 18.6 1.0 ND1 C:HIS188 4.2 26.7 1.0 OD1 C:ASP210 4.2 27.7 1.0 CG C:HIS188 4.2 25.4 1.0 CD2 C:HIS93 4.2 20.8 1.0 CG C:HIS91 4.3 17.0 1.0 OD2 C:ASP95 4.4 29.2 1.0 ND1 C:HIS91 4.5 17.5 1.0 OD1 C:ASP95 4.7 29.4 1.0 CA C:HIS93 4.9 20.9 1.0 CG C:ASP95 5.0 24.4 1.0

Zinc binding site 7 out of 16 in the Seleno-Methionine Pngm-1 From Deep-Sea Sediment Metagenome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Seleno-Methionine Pngm-1 From Deep-Sea Sediment Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:37.7 occ:1.00 NE2 D:HIS279 2.1 31.1 1.0 OD2 D:ASP210 2.3 25.4 1.0 NE2 D:HIS96 2.3 16.0 1.0 OD1 D:ASP95 2.6 28.6 1.0 OD1 D:ASP210 2.8 22.0 1.0 CD2 D:HIS96 2.9 16.0 1.0 CG D:ASP210 2.9 23.6 1.0 CE1 D:HIS279 3.0 32.3 1.0 ZN D:ZN402 3.2 25.5 1.0 CD2 D:HIS279 3.2 29.7 1.0 CG D:ASP95 3.4 24.9 1.0 CE1 D:HIS96 3.5 15.0 1.0 OD2 D:ASP95 3.6 28.9 1.0 NE2 D:HIS91 4.0 19.0 1.0 ND1 D:HIS279 4.2 31.3 1.0 CG D:HIS96 4.2 15.6 1.0 CG D:HIS279 4.3 29.9 1.0 CE1 D:HIS91 4.3 18.9 1.0 CB D:ASP210 4.4 24.2 1.0 ND1 D:HIS96 4.5 14.7 1.0 CB D:ASP95 4.7 22.2 1.0 NE2 D:HIS188 4.8 24.7 1.0 ND1 D:HIS93 4.8 20.2 1.0 CB D:HIS93 4.9 21.1 1.0

Zinc binding site 8 out of 16 in the Seleno-Methionine Pngm-1 From Deep-Sea Sediment Metagenome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Seleno-Methionine Pngm-1 From Deep-Sea Sediment Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn402 b:25.5 occ:1.00 OD2 D:ASP210 2.0 25.4 1.0 ND1 D:HIS93 2.1 20.2 1.0 NE2 D:HIS188 2.2 24.7 1.0 NE2 D:HIS91 2.3 19.0 1.0 CE1 D:HIS93 3.0 20.6 1.0 CD2 D:HIS188 3.0 25.8 1.0 CD2 D:HIS91 3.1 17.8 1.0 CG D:HIS93 3.1 20.7 1.0 CG D:ASP210 3.1 23.6 1.0 ZN D:ZN401 3.2 37.7 1.0 CE1 D:HIS188 3.3 25.2 1.0 CB D:HIS93 3.4 21.1 1.0 CE1 D:HIS91 3.4 18.9 1.0 CB D:ASP210 3.7 24.2 1.0 OD1 D:ASP210 4.1 22.0 1.0 CD2 D:HIS96 4.1 16.0 1.0 NE2 D:HIS93 4.1 21.9 1.0 CD2 D:HIS93 4.2 23.2 1.0 NE2 D:HIS96 4.2 16.0 1.0 CG D:HIS188 4.2 24.5 1.0 ND1 D:HIS188 4.3 27.5 1.0 CG D:HIS91 4.3 16.6 1.0 OD2 D:ASP95 4.3 28.9 1.0 ND1 D:HIS91 4.5 18.0 1.0 CA D:HIS93 4.8 20.7 1.0 OD1 D:ASP95 4.9 28.6 1.0

Zinc binding site 9 out of 16 in the Seleno-Methionine Pngm-1 From Deep-Sea Sediment Metagenome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Seleno-Methionine Pngm-1 From Deep-Sea Sediment Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn401 b:33.8 occ:1.00 NE2 E:HIS279 2.2 29.6 1.0 NE2 E:HIS96 2.2 14.1 1.0 OD1 E:ASP95 2.3 28.0 1.0 OD2 E:ASP210 2.3 26.0 1.0 CE1 E:HIS279 2.8 31.3 1.0 CD2 E:HIS96 2.9 13.8 1.0 CG E:ASP210 3.1 26.1 1.0 OD1 E:ASP210 3.1 24.4 1.0 ZN E:ZN402 3.1 24.2 1.0 CG E:ASP95 3.2 24.3 1.0 CD2 E:HIS279 3.4 29.6 1.0 CE1 E:HIS96 3.4 14.0 1.0 OD2 E:ASP95 3.5 29.4 1.0 O E:HOH523 3.9 20.8 1.0 ND1 E:HIS279 4.1 33.6 1.0 NE2 E:HIS91 4.1 13.9 1.0 CG E:HIS96 4.1 14.2 1.0 CG E:HIS279 4.3 29.4 1.0 ND1 E:HIS96 4.4 14.0 1.0 CE1 E:HIS91 4.4 14.4 1.0 CB E:ASP95 4.5 21.2 1.0 CB E:ASP210 4.6 26.5 1.0 ND1 E:HIS93 4.6 18.8 1.0 NE2 E:HIS188 4.9 29.8 1.0 CB E:HIS93 4.9 15.5 1.0

Zinc binding site 10 out of 16 in the Seleno-Methionine Pngm-1 From Deep-Sea Sediment Metagenome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Seleno-Methionine Pngm-1 From Deep-Sea Sediment Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn402 b:24.2 occ:1.00 OD2 E:ASP210 1.9 26.0 1.0 ND1 E:HIS93 2.1 18.8 1.0 NE2 E:HIS188 2.2 29.8 1.0 NE2 E:HIS91 2.3 13.9 1.0 CE1 E:HIS93 2.9 17.5 1.0 CG E:ASP210 3.0 26.1 1.0 CD2 E:HIS91 3.1 14.2 1.0 ZN E:ZN401 3.1 33.8 1.0 CD2 E:HIS188 3.1 26.8 1.0 CG E:HIS93 3.2 15.1 1.0 CE1 E:HIS188 3.2 27.9 1.0 CE1 E:HIS91 3.4 14.4 1.0 CB E:ASP210 3.6 26.5 1.0 CB E:HIS93 3.6 15.5 1.0 OD1 E:ASP210 4.0 24.4 1.0 NE2 E:HIS93 4.0 17.6 1.0 NE2 E:HIS96 4.0 14.1 1.0 CD2 E:HIS96 4.1 13.8 1.0 CD2 E:HIS93 4.2 16.9 1.0 CG E:HIS188 4.3 29.6 1.0 ND1 E:HIS188 4.3 30.1 1.0 CG E:HIS91 4.3 13.9 1.0 OD2 E:ASP95 4.4 29.4 1.0 ND1 E:HIS91 4.4 14.2 1.0 OD1 E:ASP95 4.7 28.0 1.0 CG E:ASP95 5.0 24.3 1.0 CE1 E:HIS96 5.0 14.0 1.0

L.W.Kang, S.H.Lee. Pngm 1 A Novel Subclass B3 Metallo Beta Lactamase From A Deep Sea Sediment Metagenome Journal of Global V. 14 302 2018ANTIMICROBIAL Resistance.
ISSN: ISSN 2213-7165
PubMed: 29842976
DOI: 10.1016/J.JGAR.2018.05.021.