Zinc in PDB 6xbe: Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F

The structure of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F, PDB code: 6xbe 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)	46.76 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	42.699, 74.551, 77.31, 96.52, 103.11, 106.24
R / Rfree (%)	18.5 / 22.3

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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-1F (pdb code 6xbe). 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-1F, PDB code: 6xbe:
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-1F


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-1F within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:25.5 occ:1.00 ND1 A:HIS122 2.0 23.7 1.0 NE2 A:HIS189 2.1 28.6 1.0 NE2 A:HIS120 2.2 25.9 1.0 SG F:DCY1004 2.3 29.4 1.0 CE1 A:HIS122 3.0 24.9 1.0 CG A:HIS122 3.1 24.3 1.0 CD2 A:HIS189 3.1 25.6 1.0 CD2 A:HIS120 3.1 23.4 1.0 CE1 A:HIS189 3.1 24.7 1.0 CE1 A:HIS120 3.1 26.6 1.0 CB F:DCY1004 3.2 29.0 1.0 CB A:HIS122 3.4 24.1 1.0 ZN A:ZN302 3.8 20.8 1.0 OD1 A:ASP124 4.1 26.2 1.0 NE2 A:HIS122 4.1 25.2 1.0 SG A:CYS208 4.1 25.6 1.0 CD2 A:HIS122 4.2 23.7 1.0 ND1 A:HIS189 4.2 25.4 1.0 ND1 A:HIS120 4.2 24.1 1.0 CG A:HIS120 4.2 24.1 1.0 CG A:HIS189 4.2 25.4 1.0 CB A:CYS208 4.3 24.5 1.0 CG2 A:THR190 4.6 25.2 1.0 OD2 A:ASP124 4.6 33.5 1.0 CA F:DCY1004 4.7 28.3 1.0 CG A:ASP124 4.8 29.2 1.0 O A:HOH528 4.8 29.3 1.0 CA A:HIS122 4.8 23.1 1.0

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


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-1F within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:20.8 occ:1.00 OD2 A:ASP124 2.0 33.5 1.0 NE2 A:HIS250 2.2 27.7 1.0 SG F:DCY1004 2.3 29.4 1.0 SG A:CYS208 2.3 25.6 1.0 O A:HOH528 3.1 29.3 1.0 CG A:ASP124 3.1 29.2 1.0 CD2 A:HIS250 3.2 29.7 1.0 CE1 A:HIS250 3.2 26.3 1.0 CB A:CYS208 3.4 24.5 1.0 CB F:DCY1004 3.5 29.0 1.0 OD1 A:ASP124 3.6 26.2 1.0 ZN A:ZN301 3.8 25.5 1.0 CA F:DCY1004 4.0 28.3 1.0 CD F:PRO1005 4.1 35.0 1.0 ND1 A:HIS250 4.3 27.0 1.0 CB A:SER249 4.3 24.3 1.0 CG A:HIS250 4.3 30.1 1.0 CB A:ASP124 4.3 27.5 1.0 N F:PRO1005 4.4 34.2 1.0 NE2 A:HIS189 4.4 28.6 1.0 C F:DCY1004 4.4 33.7 1.0 CA A:CYS208 4.6 26.1 1.0 CE1 A:HIS189 4.6 24.7 1.0 CE1 A:HIS120 4.6 26.6 1.0 NE2 A:HIS120 4.6 25.9 1.0 OG A:SER249 4.7 28.0 1.0 O A:HOH407 4.9 44.1 1.0

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


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-1F within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:45.8 occ:1.00 O F:HOH1104 2.2 43.8 1.0 O A:HOH489 2.3 32.6 1.0 OE2 A:GLU152 2.6 40.4 1.0 OE1 A:GLU152 2.6 34.4 1.0 CD A:GLU152 3.0 36.5 1.0 NH2 F:DAR1002 3.8 52.0 1.0 NE F:DAR1002 3.9 54.4 1.0 NE2 A:HIS122 4.0 25.2 1.0 O A:HOH532 4.3 32.1 1.0 CZ F:DAR1002 4.3 56.8 1.0 CG A:GLU152 4.5 33.8 1.0 CD2 A:HIS122 4.6 23.7 1.0 O A:HOH417 4.8 41.5 1.0 CB A:ASP223 5.0 50.0 1.0

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


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-1F within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:28.9 occ:1.00 NE2 B:HIS189 2.0 27.5 1.0 ND1 B:HIS122 2.1 25.3 1.0 NE2 B:HIS120 2.1 25.1 1.0 SG G:DCY1004 2.3 35.9 1.0 CD2 B:HIS189 3.0 25.3 1.0 CE1 B:HIS122 3.0 27.6 1.0 CD2 B:HIS120 3.0 25.6 1.0 CE1 B:HIS189 3.1 27.2 1.0 CE1 B:HIS120 3.1 26.4 1.0 CG B:HIS122 3.1 25.1 1.0 CB G:DCY1004 3.3 38.7 1.0 CB B:HIS122 3.4 24.2 1.0 ZN B:ZN302 3.8 22.9 1.0 OD1 B:ASP124 4.1 26.7 1.0 SG B:CYS208 4.1 32.4 1.0 CG B:HIS189 4.1 26.8 1.0 ND1 B:HIS120 4.1 25.6 1.0 ND1 B:HIS189 4.2 28.0 1.0 CG B:HIS120 4.2 25.8 1.0 NE2 B:HIS122 4.2 27.2 1.0 CD2 B:HIS122 4.2 29.1 1.0 CB B:CYS208 4.2 30.3 1.0 O B:HOH498 4.4 32.6 1.0 CG2 B:THR190 4.6 27.6 1.0 OD2 B:ASP124 4.6 30.3 1.0 CA G:DCY1004 4.7 39.0 1.0 CG B:ASP124 4.8 31.6 1.0 CA B:HIS122 4.9 24.5 1.0 O B:HOH412 5.0 35.4 1.0

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


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-1F within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:22.9 occ:1.00 OD2 B:ASP124 2.0 30.3 1.0 NE2 B:HIS250 2.2 33.2 1.0 SG G:DCY1004 2.3 35.9 1.0 SG B:CYS208 2.3 32.4 1.0 O B:HOH498 2.5 32.6 1.0 CG B:ASP124 3.1 31.6 1.0 CD2 B:HIS250 3.1 30.3 1.0 CE1 B:HIS250 3.2 31.4 1.0 CB B:CYS208 3.4 30.3 1.0 CB G:DCY1004 3.5 38.7 1.0 OD1 B:ASP124 3.6 26.7 1.0 ZN B:ZN301 3.8 28.9 1.0 CA G:DCY1004 3.9 39.0 1.0 CD G:PRO1005 4.0 45.0 1.0 ND1 B:HIS250 4.3 33.0 1.0 CG B:HIS250 4.3 32.1 1.0 N G:PRO1005 4.3 43.1 1.0 CB B:SER249 4.3 27.7 1.0 C G:DCY1004 4.3 44.4 1.0 CB B:ASP124 4.4 30.3 1.0 NE2 B:HIS189 4.4 27.5 1.0 CA B:CYS208 4.5 29.2 1.0 CE1 B:HIS189 4.6 27.2 1.0 CE1 B:HIS120 4.6 26.4 1.0 NE2 B:HIS120 4.7 25.1 1.0 OG B:SER249 4.7 28.7 1.0

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


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-1F within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:21.1 occ:1.00 OD2 B:ASP223 2.2 37.9 1.0 OE2 C:GLU227 2.2 41.9 1.0 OE2 B:GLU152 2.3 26.1 1.0 O B:HOH508 2.3 23.3 1.0 OE1 B:GLU152 2.4 27.9 1.0 OE1 C:GLU227 2.4 38.6 1.0 CD C:GLU227 2.6 37.2 1.0 CD B:GLU152 2.7 24.1 1.0 OD1 B:ASP223 2.8 47.2 1.0 CG B:ASP223 2.8 41.6 1.0 O B:HOH463 4.1 33.9 1.0 CG C:GLU227 4.2 39.1 1.0 NE2 B:HIS122 4.2 27.2 1.0 CG B:GLU152 4.2 25.4 1.0 CB B:ASP223 4.3 39.8 1.0 NE2 C:HIS228 4.4 36.0 1.0 O B:HOH431 4.5 36.5 1.0 O G:HOH1102 4.5 52.4 1.0 CE1 C:HIS228 4.6 37.8 1.0 CD2 B:HIS122 4.7 29.1 1.0 O C:HOH457 4.8 38.0 1.0

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


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-1F within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:36.1 occ:1.00 OE2 B:GLU227 2.0 46.0 1.0 O C:HOH460 2.4 34.9 1.0 OD2 C:ASP223 2.4 49.4 1.0 OE2 C:GLU152 2.4 42.5 1.0 OE1 C:GLU152 2.5 45.8 1.0 OE1 B:GLU227 2.6 52.1 1.0 CD B:GLU227 2.6 49.3 1.0 CD C:GLU152 2.7 46.9 1.0 OD1 C:ASP223 2.9 51.1 1.0 CG C:ASP223 3.0 51.6 1.0 NE2 C:HIS122 4.0 30.5 1.0 CG B:GLU227 4.1 42.4 1.0 CG C:GLU152 4.3 42.2 1.0 O C:HOH429 4.3 36.5 1.0 NE2 B:HIS228 4.4 37.8 1.0 CE1 B:HIS228 4.5 38.2 1.0 CB C:ASP223 4.5 46.6 1.0 CD2 C:HIS122 4.6 32.3 1.0 CD H:DAR1002 4.8 49.5 1.0 O H:HOH1101 4.8 24.3 0.5 CB B:GLU227 4.9 37.8 1.0 O B:HOH475 4.9 43.4 1.0

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


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-1F within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:34.5 occ:1.00 ND1 C:HIS122 2.1 35.8 1.0 NE2 C:HIS189 2.1 31.2 1.0 NE2 C:HIS120 2.1 30.2 1.0 SG H:DCY1004 2.4 45.8 1.0 CD2 C:HIS189 3.0 30.9 1.0 CE1 C:HIS122 3.0 33.0 1.0 CD2 C:HIS120 3.0 35.5 1.0 CE1 C:HIS120 3.0 34.7 1.0 CG C:HIS122 3.1 33.8 1.0 CE1 C:HIS189 3.1 30.1 1.0 CB H:DCY1004 3.3 44.3 1.0 CB C:HIS122 3.4 34.7 1.0 ZN C:ZN302 3.8 30.5 1.0 OD1 C:ASP124 4.1 35.4 1.0 SG C:CYS208 4.1 30.4 1.0 O C:HOH447 4.1 53.6 1.0 ND1 C:HIS120 4.1 36.6 1.0 NE2 C:HIS122 4.1 30.5 1.0 CG C:HIS120 4.1 32.6 1.0 CG C:HIS189 4.2 28.9 1.0 CD2 C:HIS122 4.2 32.3 1.0 ND1 C:HIS189 4.2 28.6 1.0 CB C:CYS208 4.2 32.6 1.0 CG2 C:THR190 4.6 33.1 1.0 OD2 C:ASP124 4.6 32.2 1.0 CA H:DCY1004 4.7 44.3 1.0 CG C:ASP124 4.8 37.3 1.0 O C:HOH417 4.8 42.5 1.0 CA C:HIS122 4.9 34.4 1.0

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


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-1F within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:30.5 occ:1.00 OD2 C:ASP124 1.9 32.2 1.0 NE2 C:HIS250 2.1 37.4 1.0 SG C:CYS208 2.3 30.4 1.0 SG H:DCY1004 2.3 45.8 1.0 O C:HOH447 2.4 53.6 1.0 CG C:ASP124 3.0 37.3 1.0 CE1 C:HIS250 3.0 35.8 1.0 CD2 C:HIS250 3.1 37.9 1.0 CB C:CYS208 3.4 32.6 1.0 OD1 C:ASP124 3.5 35.4 1.0 CB H:DCY1004 3.5 44.3 1.0 ZN C:ZN301 3.8 34.5 1.0 CA H:DCY1004 4.0 44.3 1.0 CB C:SER249 4.1 37.7 1.0 ND1 C:HIS250 4.2 38.3 1.0 CD H:PRO1005 4.2 42.2 1.0 CG C:HIS250 4.2 38.2 1.0 CB C:ASP124 4.2 35.8 1.0 NE2 C:HIS189 4.5 31.2 1.0 CE1 C:HIS120 4.5 34.7 1.0 N H:PRO1005 4.5 40.3 1.0 OG C:SER249 4.5 37.5 1.0 C H:DCY1004 4.5 41.8 1.0 CA C:CYS208 4.6 30.0 1.0 NE2 C:HIS120 4.6 30.2 1.0 CE1 C:HIS189 4.8 30.1 1.0 CE C:LYS125 4.9 37.5 1.0

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


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-1F within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:33.3 occ:1.00 ND1 D:HIS122 2.0 25.8 1.0 NE2 D:HIS189 2.1 30.7 1.0 NE2 D:HIS120 2.1 26.6 1.0 SG I:DCY1004 2.5 47.7 1.0 CE1 D:HIS122 2.9 31.0 1.0 CG D:HIS122 3.0 28.6 1.0 CD2 D:HIS189 3.0 29.6 1.0 CD2 D:HIS120 3.0 26.4 1.0 CE1 D:HIS120 3.1 27.3 1.0 CE1 D:HIS189 3.2 31.0 1.0 CB D:HIS122 3.4 32.9 1.0 CB I:DCY1004 3.4 49.3 1.0 ZN D:ZN302 3.8 27.7 1.0 NE2 D:HIS122 4.0 31.4 1.0 CD2 D:HIS122 4.1 29.1 1.0 OD1 D:ASP124 4.1 39.2 1.0 CG D:HIS120 4.2 26.7 1.0 ND1 D:HIS120 4.2 26.7 1.0 SG D:CYS208 4.2 38.6 1.0 CG D:HIS189 4.2 29.1 1.0 ND1 D:HIS189 4.2 27.7 1.0 CB D:CYS208 4.3 31.2 1.0 CG2 D:THR190 4.5 29.3 1.0 OD2 D:ASP124 4.6 35.9 1.0 O D:HOH477 4.7 28.9 1.0 CG D:ASP124 4.8 37.8 1.0 CA D:HIS122 4.8 32.7 1.0 CA I:DCY1004 4.9 53.9 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