Zinc in PDB 6xbf: Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1G

The structure of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1G, PDB code: 6xbf was solved by L.J.Worrall, T.Sun, V.K.Mulligan, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.71 / 2.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	42.615, 74.19, 76.65, 95.75, 103.46, 106.43
R / Rfree (%)	19.4 / 24.5

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>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1G (pdb code 6xbf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1G, PDB code: 6xbf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1G


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1G within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:34.5 occ:1.00 ND1 A:HIS122 2.0 30.8 1.0 NE2 A:HIS189 2.2 42.5 1.0 NE2 A:HIS120 2.2 30.5 1.0 SG F:DCY1004 2.3 37.2 1.0 CD2 A:HIS189 2.9 36.6 1.0 CE1 A:HIS122 3.0 34.4 1.0 CG A:HIS122 3.0 35.0 1.0 CD2 A:HIS120 3.1 30.4 1.0 CB F:DCY1004 3.1 42.1 1.0 CE1 A:HIS120 3.2 32.5 1.0 CE1 A:HIS189 3.3 38.6 1.0 CB A:HIS122 3.4 33.4 1.0 ZN A:ZN302 3.8 27.8 1.0 NE2 A:HIS122 4.1 38.7 1.0 CD2 A:HIS122 4.1 35.5 1.0 CG A:HIS189 4.2 37.6 1.0 OD1 A:ASP124 4.2 41.1 1.0 SG A:CYS208 4.2 30.9 1.0 ND1 A:HIS120 4.3 30.5 1.0 CG A:HIS120 4.3 26.1 1.0 CB A:CYS208 4.3 28.9 1.0 ND1 A:HIS189 4.3 36.7 1.0 CG2 A:THR190 4.6 29.2 1.0 CA F:DCY1004 4.6 37.4 1.0 OD2 A:ASP124 4.7 35.4 1.0 CG A:ASP124 4.8 38.3 1.0 O A:HOH504 4.8 39.8 1.0 CA A:HIS122 4.9 33.4 1.0 O F:DCY1004 5.0 36.4 1.0

Zinc binding site 2 out of 12 in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1G


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1G within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:27.8 occ:1.00 OD2 A:ASP124 2.0 35.4 1.0 SG F:DCY1004 2.1 37.2 1.0 NE2 A:HIS250 2.1 27.9 1.0 SG A:CYS208 2.4 30.9 1.0 O A:HOH504 3.0 39.8 1.0 CE1 A:HIS250 3.1 29.4 1.0 CG A:ASP124 3.1 38.3 1.0 CD2 A:HIS250 3.2 29.9 1.0 CB F:DCY1004 3.4 42.1 1.0 CB A:CYS208 3.5 28.9 1.0 OD1 A:ASP124 3.6 41.1 1.0 ZN A:ZN301 3.8 34.5 1.0 CA F:DCY1004 3.8 37.4 1.0 CD F:PRO1005 4.1 40.5 1.0 ND1 A:HIS250 4.2 28.9 1.0 CG A:HIS250 4.3 30.7 1.0 C F:DCY1004 4.3 38.5 1.0 NE2 A:HIS189 4.3 42.5 1.0 CB A:SER249 4.3 38.8 1.0 CB A:ASP124 4.4 35.7 1.0 N F:PRO1005 4.4 38.2 1.0 CE1 A:HIS189 4.6 38.6 1.0 CA A:CYS208 4.6 31.0 1.0 CE1 A:HIS120 4.7 32.5 1.0 NE2 A:HIS120 4.7 30.5 1.0 OG A:SER249 4.7 38.3 1.0 CE A:LYS125 5.0 35.0 1.0

Zinc binding site 3 out of 12 in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1G


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1G within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:84.9 occ:1.00 O F:HOH1102 2.3 74.9 1.0 OE1 A:GLU152 2.8 44.7 1.0 OE2 A:GLU152 2.8 53.4 1.0 OD2 A:ASP223 3.0 67.0 1.0 CD A:GLU152 3.1 44.9 1.0 NH2 F:DAR1002 3.6 68.9 1.0 O A:HOH437 3.6 81.5 1.0 NE F:DAR1002 3.9 68.7 1.0 CG A:ASP223 4.0 85.0 1.0 NE2 A:HIS122 4.1 38.7 1.0 CZ F:DAR1002 4.2 77.2 1.0 CG A:GLU152 4.6 44.9 1.0 O A:HOH425 4.7 37.0 1.0 CB A:ASP223 4.7 80.2 1.0 O A:HOH432 4.7 60.0 1.0 OD1 A:ASP223 4.7 82.5 1.0 CD2 A:HIS122 4.8 35.5 1.0 CG F:DAR1002 4.8 63.1 1.0 CD F:DAR1002 4.9 66.1 1.0

Zinc binding site 4 out of 12 in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1G


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1G within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:34.8 occ:1.00 NE2 B:HIS120 2.0 29.0 1.0 ND1 B:HIS122 2.1 33.6 1.0 NE2 B:HIS189 2.2 31.2 1.0 SG G:DCY1004 2.4 46.1 1.0 CD2 B:HIS189 2.9 32.3 1.0 CD2 B:HIS120 3.0 31.3 1.0 CE1 B:HIS120 3.0 31.7 1.0 CE1 B:HIS122 3.0 35.7 1.0 CG B:HIS122 3.1 31.6 1.0 CB G:DCY1004 3.2 49.8 1.0 CE1 B:HIS189 3.4 38.2 1.0 CB B:HIS122 3.4 30.4 1.0 ZN B:ZN302 3.8 28.5 1.0 ND1 B:HIS120 4.1 31.3 1.0 OD1 B:ASP124 4.1 32.1 1.0 CG B:HIS120 4.1 32.5 1.0 CG B:HIS189 4.1 34.8 1.0 SG B:CYS208 4.1 32.9 1.0 NE2 B:HIS122 4.1 36.5 1.0 CD2 B:HIS122 4.2 31.2 1.0 CB B:CYS208 4.2 30.7 1.0 O B:HOH455 4.3 30.9 1.0 ND1 B:HIS189 4.3 37.7 1.0 CG2 B:THR190 4.5 30.3 1.0 OD2 B:ASP124 4.6 32.2 1.0 CA G:DCY1004 4.7 51.0 1.0 CG B:ASP124 4.8 33.5 1.0 CA B:HIS122 4.8 33.6 1.0

Zinc binding site 5 out of 12 in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1G


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1G within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:28.5 occ:1.00 OD2 B:ASP124 2.0 32.2 1.0 NE2 B:HIS250 2.1 34.6 1.0 SG G:DCY1004 2.1 46.1 1.0 O B:HOH455 2.2 30.9 1.0 SG B:CYS208 2.4 32.9 1.0 CE1 B:HIS250 3.1 36.5 1.0 CG B:ASP124 3.1 33.5 1.0 CD2 B:HIS250 3.2 33.0 1.0 CB G:DCY1004 3.4 49.8 1.0 CB B:CYS208 3.4 30.7 1.0 OD1 B:ASP124 3.6 32.1 1.0 ZN B:ZN301 3.8 34.8 1.0 CA G:DCY1004 3.8 51.0 1.0 CD G:PRO1005 4.0 53.2 1.0 ND1 B:HIS250 4.2 34.8 1.0 N G:PRO1005 4.2 52.2 1.0 C G:DCY1004 4.2 55.9 1.0 CG B:HIS250 4.3 34.6 1.0 CB B:SER249 4.3 33.7 1.0 NE2 B:HIS189 4.3 31.2 1.0 CB B:ASP124 4.4 33.0 1.0 CA B:CYS208 4.6 37.5 1.0 CE1 B:HIS189 4.6 38.2 1.0 CE1 B:HIS120 4.6 31.7 1.0 OG B:SER249 4.7 29.9 1.0 NE2 B:HIS120 4.7 29.0 1.0 CG G:PRO1005 4.9 53.4 1.0 CE B:LYS125 5.0 38.5 1.0

Zinc binding site 6 out of 12 in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1G


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1G within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:28.6 occ:1.00 O C:HOH454 2.2 25.2 1.0 OE2 C:GLU227 2.3 61.8 1.0 OE2 B:GLU152 2.3 35.6 1.0 OD2 B:ASP223 2.4 47.0 1.0 OE1 B:GLU152 2.5 37.4 1.0 OE1 C:GLU227 2.5 67.8 1.0 CD C:GLU227 2.7 63.8 1.0 CD B:GLU152 2.7 38.0 1.0 OD1 B:ASP223 2.8 51.4 1.0 CG B:ASP223 2.9 51.2 1.0 O B:HOH451 4.0 44.5 1.0 NE2 B:HIS122 4.1 36.5 1.0 CG C:GLU227 4.2 56.7 1.0 CG B:GLU152 4.2 35.5 1.0 NE2 C:HIS228 4.3 55.5 1.0 CB B:ASP223 4.4 52.0 1.0 CE1 C:HIS228 4.4 54.8 1.0 O B:HOH423 4.7 40.4 1.0 CD2 B:HIS122 4.7 31.2 1.0 CD G:DAR1002 4.8 66.4 1.0 O C:HOH449 4.9 34.4 1.0

Zinc binding site 7 out of 12 in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1G


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1G within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:61.0 occ:1.00 OE2 B:GLU227 2.2 61.8 1.0 O C:HOH460 2.4 47.7 1.0 OD2 C:ASP223 2.5 68.6 1.0 OE2 C:GLU152 2.6 53.4 1.0 OE1 B:GLU227 2.7 70.9 1.0 CD B:GLU227 2.7 64.3 1.0 OE1 C:GLU152 2.8 58.6 1.0 CD C:GLU152 3.0 57.8 1.0 CG C:ASP223 3.2 71.7 1.0 OD1 C:ASP223 3.3 70.8 1.0 NE2 C:HIS122 4.0 41.6 1.0 CD H:DAR1002 4.2 72.9 1.0 CG B:GLU227 4.2 55.9 1.0 O C:HOH442 4.4 48.8 1.0 NE2 B:HIS228 4.5 50.4 1.0 CG C:GLU152 4.6 57.7 1.0 CE1 B:HIS228 4.6 50.7 1.0 CG H:DAR1002 4.6 68.9 1.0 CD2 C:HIS122 4.6 39.8 1.0 CB C:ASP223 4.7 62.1 1.0 O B:HOH432 4.8 51.6 1.0 CB B:GLU227 5.0 49.5 1.0

Zinc binding site 8 out of 12 in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1G


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1G within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:42.4 occ:1.00 NE2 C:HIS189 2.0 45.8 1.0 NE2 C:HIS120 2.1 36.1 1.0 ND1 C:HIS122 2.2 35.7 1.0 SG H:DCY1004 2.4 54.3 1.0 CD2 C:HIS189 2.8 43.0 1.0 CE1 C:HIS120 3.0 35.1 1.0 CD2 C:HIS120 3.1 40.3 1.0 CE1 C:HIS122 3.1 35.1 1.0 CG C:HIS122 3.2 39.5 1.0 CE1 C:HIS189 3.2 40.4 1.0 CB H:DCY1004 3.3 61.1 1.0 CB C:HIS122 3.5 39.2 1.0 ZN C:ZN302 3.9 38.8 1.0 CG C:HIS189 4.0 40.6 1.0 ND1 C:HIS120 4.1 37.5 1.0 SG C:CYS208 4.1 40.7 1.0 CG C:HIS120 4.1 37.0 1.0 CB C:CYS208 4.1 45.9 1.0 ND1 C:HIS189 4.2 39.3 1.0 OD1 C:ASP124 4.2 42.0 1.0 NE2 C:HIS122 4.2 41.6 1.0 CD2 C:HIS122 4.3 39.8 1.0 CG2 C:THR190 4.5 37.3 1.0 OD2 C:ASP124 4.6 49.4 1.0 CA H:DCY1004 4.7 60.7 1.0 CG C:ASP124 4.8 48.8 1.0 O H:DCY1004 5.0 70.4 1.0 C H:DCY1004 5.0 67.1 1.0 CA C:HIS122 5.0 39.9 1.0

Zinc binding site 9 out of 12 in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1G


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1G within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:38.8 occ:1.00 OD2 C:ASP124 1.8 49.4 1.0 NE2 C:HIS250 2.1 59.3 1.0 SG C:CYS208 2.3 40.7 1.0 SG H:DCY1004 2.3 54.3 1.0 CG C:ASP124 3.0 48.8 1.0 CE1 C:HIS250 3.0 56.3 1.0 CD2 C:HIS250 3.2 58.1 1.0 CB C:CYS208 3.5 45.9 1.0 OD1 C:ASP124 3.5 42.0 1.0 CB H:DCY1004 3.5 61.1 1.0 ZN C:ZN301 3.9 42.4 1.0 CA H:DCY1004 4.0 60.7 1.0 ND1 C:HIS250 4.1 53.2 1.0 CB C:SER249 4.2 50.3 1.0 CB C:ASP124 4.2 44.2 1.0 CD H:PRO1005 4.2 69.5 1.0 CG C:HIS250 4.3 54.8 1.0 OG C:SER249 4.5 45.5 1.0 NE2 C:HIS189 4.5 45.8 1.0 C H:DCY1004 4.5 67.1 1.0 N H:PRO1005 4.5 72.9 1.0 CE1 C:HIS120 4.5 35.1 1.0 CA C:CYS208 4.6 43.4 1.0 NE2 C:HIS120 4.6 36.1 1.0 CE C:LYS125 4.7 51.1 1.0 CE1 C:HIS189 4.8 40.4 1.0 CD C:LYS125 5.0 48.4 1.0

Zinc binding site 10 out of 12 in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1G


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1G within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:45.6 occ:1.00 NE2 D:HIS120 2.0 41.2 1.0 NE2 D:HIS189 2.1 37.8 1.0 ND1 D:HIS122 2.2 33.3 1.0 SG I:DCY1004 2.5 44.7 1.0 CD2 D:HIS189 2.8 38.3 1.0 CE1 D:HIS120 3.0 42.6 1.0 CD2 D:HIS120 3.0 35.1 1.0 CE1 D:HIS122 3.1 36.4 1.0 CG D:HIS122 3.2 37.4 1.0 CB I:DCY1004 3.3 57.1 1.0 CE1 D:HIS189 3.3 39.3 1.0 CB D:HIS122 3.4 38.8 1.0 ZN D:ZN302 3.8 37.8 1.0 ND1 D:HIS120 4.0 37.4 1.0 SG D:CYS208 4.1 41.2 1.0 OD1 D:ASP124 4.1 44.7 1.0 CG D:HIS189 4.1 40.3 1.0 CG D:HIS120 4.1 36.5 1.0 CB D:CYS208 4.1 42.3 1.0 NE2 D:HIS122 4.3 38.7 1.0 CD2 D:HIS122 4.3 37.8 1.0 ND1 D:HIS189 4.3 36.9 1.0 O D:HOH432 4.5 42.3 1.0 OD2 D:ASP124 4.5 41.8 1.0 CG2 D:THR190 4.5 39.2 1.0 CG D:ASP124 4.7 44.2 1.0 CA I:DCY1004 4.8 57.7 1.0 CA D:HIS122 4.9 44.7 1.0

V.K.Mulligan, S.Workman, T.Sun, S.Rettie, X.Li, L.J.Worrall, T.W.Craven, D.T.King, P.Hosseinzadeh, A.M.Watkins, P.D.Renfrew, S.Guffy, J.W.Labonte, R.Moretti, R.Bonneau, N.C.J.Strynadka, D.Baker. Computationally Designed Peptide Macrocycle Inhibitors of New Delhi Metallo-Beta-Lactamase 1. Proc.Natl.Acad.Sci.Usa V. 118 2021.
ISSN: ESSN 1091-6490
PubMed: 33723038
DOI: 10.1073/PNAS.2012800118